Epigenomics
Epigenomics
Program Publications
Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| The DNA methylome. | Pelizzola M, Ecker JR | FEBS letters | 21056564 | FEBS Lett | 2011 Jul 7 |
| Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. | Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF | Nature biotechnology | 20852635 | Nat Biotechnol | 2010 Oct |
| An assessment of histone-modification antibody quality. | Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD | Nature structural & molecular biology | 21131980 | Nat Struct Mol Biol | 2011 Jan |
| Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. | Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B | Cell | 22341451 | Cell | 2012 Feb 17 |
| DNA methylation data analysis and its application to cancer research. | Ma X, Wang YW, Zhang MQ, Gazdar AF | Epigenomics | 23750645 | Epigenomics | 2013 Jun |
| Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. | Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, He C | Nature communications | 23443545 | Nat Commun | 2013 |
| Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells. | Sawan C, Hernandez-Vargas H, Murr R, Lopez F, Vaissière T, Ghantous AY, Cuenin C, Imbert J, Wang ZQ, Ren B, Herceg Z | Stem cells (Dayton, Ohio) | 23362228 | Stem Cells | 2013 May |
| Updates to the RMAP short-read mapping software. | Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ | Bioinformatics (Oxford, England) | 19736251 | Bioinformatics | 2009 Nov 1 |
| Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity. | Wang SM, Zhang MQ | Journal of cellular physiology | 20143329 | J Cell Physiol | 2010 Jun |
| Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. | Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B | Cell stem cell | 20452322 | Cell Stem Cell | 2010 May 7 |
| DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. | Pavlovic M, Ray P, Pavlovic K, Kotamarti A, Chen M, Zhang MQ | Bioinformatics (Oxford, England) | 28505334 | Bioinformatics | 2017 Oct 1 |
| Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. | Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, Li Y, Szulwach KE, Jin P, Lorincz MC, Ren B | Proceedings of the National Academy of Sciences of the United States of America | 24757056 | Proc Natl Acad Sci U S A | 2014 May 6 |
| Mapping human epigenomes. | Rivera CM, Ren B | Cell | 24074860 | Cell | 2013 Sep 26 |
| Genetics: Closing the distance on obesity culprits. | Gorkin DU, Ren B | Nature | 24646989 | Nature | 2014 Mar 20 |
| Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. | Liu GH, Qu J, Suzuki K, Nivet E, Li M, Montserrat N, Yi F, Xu X, Ruiz S, Zhang W, Wagner U, Kim A, Ren B, Li Y, Goebl A, Kim J, Soligalla RD, Dubova I, Thompson J, Yates J 3rd, Esteban CR, Sancho-Martinez I, Izpisua Belmonte JC | Nature | 23075850 | Nature | 2012 Nov 22 |
| Thermal stability of fibroblast growth factor protein is a determinant factor in regulating self-renewal, differentiation, and reprogramming in human pluripotent stem cells. | Chen G, Gulbranson DR, Yu P, Hou Z, Thomson JA | Stem cells (Dayton, Ohio) | 22213113 | Stem Cells | 2012 Apr |
| Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells. | Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y, Wang W | Nucleic acids research | 22730289 | Nucleic Acids Res | 2012 Sep 1 |
| Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. | Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B | Nature genetics | 23995138 | Nat Genet | 2013 Oct |
| Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance. | Yousefi S, Deng R, Lanko K, Salsench EM, Nikoncuk A, van der Linde HC, Perenthaler E, van Ham TJ, Mulugeta E, Barakat TS | Genome medicine | 34663447 | Genome Med | 2021 Oct 19 |
| Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells. | Chen G, Hou Z, Gulbranson DR, Thomson JA | Cell stem cell | 20682449 | Cell Stem Cell | 2010 Aug 6 |
| Constructing 3D interaction maps from 1D epigenomes. | Zhu Y, Chen Z, Zhang K, Wang M, Medovoy D, Whitaker JW, Ding B, Li N, Zheng L, Wang W | Nature communications | 26960733 | Nat Commun | 2016 Mar 10 |
| Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. | Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R | Immunity | 23791644 | Immunity | 2013 Jun 27 |
| Comparative annotation of functional regions in the human genome using epigenomic data. | Won KJ, Zhang X, Wang T, Ding B, Raha D, Snyder M, Ren B, Wang W | Nucleic acids research | 23482391 | Nucleic Acids Res | 2013 Apr |
| The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. | May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA | Nature communications | 23900278 | Nat Commun | 2013 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie W, Ren B | Science (New York, N.Y.) | 23869010 | Science | 2013 Jul 19 |
| A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. | Xing H, Liao W, Mo Y, Zhang MQ | Journal of visualized experiments : JoVE | 23271069 | J Vis Exp | 2012 Dec 10 |
| A high-resolution map of the three-dimensional chromatin interactome in human cells. | Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B | Nature | 24141950 | Nature | 2013 Nov 14 |
| Predicting the human epigenome from DNA motifs. | Whitaker JW, Chen Z, Wang W | Nature methods | 25240437 | Nat Methods | 2015 Mar |
| Computational schemes for the prediction and annotation of enhancers from epigenomic assays. | Whitaker JW, Nguyen TT, Zhu Y, Wildberg A, Wang W | Methods (San Diego, Calif.) | 25461775 | Methods | 2015 Jan 15 |
| Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. | Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ | Nucleic acids research | 24343027 | Nucleic Acids Res | 2014 Mar |
| Aggregate culture of human embryonic stem cell-derived hepatocytes in suspension are an improved in vitro model for drug metabolism and toxicity testing. | Sengupta S, Johnson BP, Swanson SA, Stewart R, Bradfield CA, Thomson JA | Toxicological sciences : an official journal of the Society of Toxicology | 24752503 | Toxicol Sci | 2014 Jul |
| Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing. | Huo W, Adams HM, Zhang MQ, Palmer KL | Journal of bacteriology | 25825433 | J Bacteriol | 2015 Jun |
| Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates. | Wang A, Yue F, Li Y, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M | Cell stem cell | 25842977 | Cell Stem Cell | 2015 Apr 2 |
| Integrative analysis of 111 reference human epigenomes. | Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M | Nature | 25693563 | Nature | 2015 Feb 19 |
| Integrative analysis of haplotype-resolved epigenomes across human tissues. | Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B | Nature | 25693566 | Nature | 2015 Feb 19 |
| A common set of distinct features that characterize noncoding RNAs across multiple species. | Hu L, Di C, Kai M, Yang YC, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ | Nucleic acids research | 25505163 | Nucleic Acids Res | 2015 Jan |
| Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. | Pugacheva EM, Rivero-Hinojosa S, Espinoza CA, Méndez-Catalá CF, Kang S, Suzuki T, Kosaka-Suzuki N, Robinson S, Nagarajan V, Ye Z, Boukaba A, Rasko JE, Strunnikov AV, Loukinov D, Ren B, Lobanenkov VV | Genome biology | 26268681 | Genome Biol | 2015 Aug 14 |
| Human body epigenome maps reveal noncanonical DNA methylation variation. | Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR | Nature | 26030523 | Nature | 2015 Jul 9 |
| Passaging and colony expansion of human pluripotent stem cells by enzyme-free dissociation in chemically defined culture conditions. | Beers J, Gulbranson DR, George N, Siniscalchi LI, Jones J, Thomson JA, Chen G | Nature protocols | 23099485 | Nat Protoc | 2012 Nov |
| Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. | Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C | Nature protocols | 23196972 | Nat Protoc | 2012 Dec |
| Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. | Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR | Nature | 21289626 | Nature | 2011 Mar 3 |
| Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. | Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C | Cell | 22608086 | Cell | 2012 Jun 8 |
| STAR: an integrated solution to management and visualization of sequencing data. | Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W | Bioinformatics (Oxford, England) | 24078702 | Bioinformatics | 2013 Dec 15 |
| Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. | Gu J, Xuan Z | PloS one | 24278370 | PLoS One | 2013 |
| Genome organization and long-range regulation of gene expression by enhancers. | Smallwood A, Ren B | Current opinion in cell biology | 23465541 | Curr Opin Cell Biol | 2013 Jun |
| Epigenomic analysis of multilineage differentiation of human embryonic stem cells. | Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B | Cell | 23664764 | Cell | 2013 May 23 |
| RFECS: a random-forest based algorithm for enhancer identification from chromatin state. | Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B | PLoS computational biology | 23526891 | PLoS Comput Biol | 2013 |
| Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. | Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J | Frontiers in oncology | 23293768 | Front Oncol | 2012 |
| Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. | Lister R, Gregory BD, Ecker JR | Current opinion in plant biology | 19157957 | Curr Opin Plant Biol | 2009 Apr |
| Next-generation genomics: an integrative approach. | Hawkins RD, Hon GC, Ren B | Nature reviews. Genetics | 20531367 | Nat Rev Genet | 2010 Jul |
| Human DNA methylomes at base resolution show widespread epigenomic differences. | Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR | Nature | 19829295 | Nature | 2009 Nov 19 |
| 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. | Schultz MD, Schmitz RJ, Ecker JR | Trends in genetics : TIG | 23131467 | Trends Genet | 2012 Dec |
| The 3D genome in transcriptional regulation and pluripotency. | Gorkin DU, Leung D, Ren B | Cell stem cell | 24905166 | Cell Stem Cell | 2014 Jun 5 |
| CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. | Tam KW, Zhang W, Soh J, Stastny V, Chen M, Sun H, Thu K, Rios JJ, Yang C, Marconett CN, Selamat SA, Laird-Offringa IA, Taguchi A, Hanash S, Shames D, Ma X, Zhang MQ, Lam WL, Gazdar A | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 24077454 | J Thorac Oncol | 2013 Nov |
| Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. | Selvaraj S, R Dixon J, Bansal V, Ren B | Nature biotechnology | 24185094 | Nat Biotechnol | 2013 Dec |
| Chemically defined conditions for human iPSC derivation and culture. | Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, Probasco MD, Smuga-Otto K, Howden SE, Diol NR, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JM, Thomson JA | Nature methods | 21478862 | Nat Methods | 2011 May |
| Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. | Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B | G3 (Bethesda, Md.) | 25122670 | G3 (Bethesda) | 2014 Aug 12 |
| Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. | Hou Z, Meyer S, Propson NE, Nie J, Jiang P, Stewart R, Thomson JA | Cell research | 25591927 | Cell Res | 2015 Mar |
| Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. | Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B | Cell research | 21876557 | Cell Res | 2011 Oct |
| Population dynamics of cancer cells with cell state conversions. | Zhou D, Wu D, Li Z, Qian M, Zhang MQ | Quantitative biology (Beijing, China) | 26085954 | Quant Biol | 2013 Sep |
| Chromatin architecture reorganization during stem cell differentiation. | Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B | Nature | 25693564 | Nature | 2015 Feb 19 |
| methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. | Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M | BMC bioinformatics | 26415965 | BMC Bioinformatics | 2015 Sep 29 |
| Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer. | Casadei S, Norquist BM, Walsh T, Stray S, Mandell JB, Lee MK, Stamatoyannopoulos JA, King MC | Cancer research | 21285249 | Cancer Res | 2011 Mar 15 |
| Genomic discovery of potent chromatin insulators for human gene therapy. | Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G | Nature biotechnology | 25580597 | Nat Biotechnol | 2015 Feb |
| Role of DNA Methylation in Modulating Transcription Factor Occupancy. | Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA | Cell reports | 26257180 | Cell Rep | 2015 Aug 18 |
| Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. | Yen A, Kellis M | Nature communications | 26282110 | Nat Commun | 2015 Aug 18 |
| Cell-of-origin chromatin organization shapes the mutational landscape of cancer. | Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence M, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR | Nature | 25693567 | Nature | 2015 Feb 19 |
| Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. | Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA | Cell | 23953118 | Cell | 2013 Aug 15 |
| Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. | Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA | Nature genetics | 26502339 | Nat Genet | 2015 Dec |
| BEDOPS: high-performance genomic feature operations. | Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA | Bioinformatics (Oxford, England) | 22576172 | Bioinformatics | 2012 Jul 15 |
| Systematic localization of common disease-associated variation in regulatory DNA. | Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA | Science (New York, N.Y.) | 22955828 | Science | 2012 Sep 7 |
| Taking Stock of Regulatory Variation. | Maurano MT, Stamatoyannopoulos JA | Cell systems | 27135686 | Cell Syst | 2015 Jul 29 |
| Quantitative comparison of genome-wide DNA methylation mapping technologies. | Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A | Nature biotechnology | 20852634 | Nat Biotechnol | 2010 Oct |
| The simplest explanation: passive DNA demethylation in PGCs. | Smith ZD, Meissner A | The EMBO journal | 23299938 | EMBO J | 2013 Feb 6 |
| Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. | Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A | Nature methods | 20062050 | Nat Methods | 2010 Feb |
| Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. | Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ | Cancer cell | 25490447 | Cancer Cell | 2014 Dec 8 |
| A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research. | De Jager PL, Ma Y, McCabe C, Xu J, Vardarajan BN, Felsky D, Klein HU, White CC, Peters MA, Lodgson B, Nejad P, Tang A, Mangravite LM, Yu L, Gaiteri C, Mostafavi S, Schneider JA, Bennett DA | Scientific data | 30084846 | Sci Data | 2018 Aug 7 |
| An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. | Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H, Piccioni F, Silver SJ, Jain M, Pearson D, Kluk MJ, Ott CJ, Shultz LD, Brehm MA, Greiner DL, Gutierrez A, Stegmaier K, Kung AL, Root DE, Bradner JE, Aster JC, Kelliher MA, Bernstein BE | Nature genetics | 24584072 | Nat Genet | 2014 Apr |
| DNA methylation: roles in mammalian development. | Smith ZD, Meissner A | Nature reviews. Genetics | 23400093 | Nat Rev Genet | 2013 Mar |
| Genome-wide chromatin state transitions associated with developmental and environmental cues. | Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE | Cell | 23333102 | Cell | 2013 Jan 31 |
| Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. | Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG | Genome research | 22466170 | Genome Res | 2012 Jun |
| Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans. | Ma Y, Yu L, Olah M, Smith R, Oatman SR, Allen M, Pishva E, Zhang B, Menon V, Ertekin-Taner N, Lunnon K, Bennett DA, Klein HU, De Jager PL | Alzheimer's & dementia : the journal of the Alzheimer's Association | 34482628 | Alzheimers Dement | 2022 Apr |
| Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. | Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL | Nature communications | 34857756 | Nat Commun | 2021 Dec 2 |
| Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. | Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A | Nature protocols | 21412275 | Nat Protoc | 2011 Apr |
| Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. | Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A | Cell | 21295703 | Cell | 2011 Feb 4 |
| Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. | Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC | Proceedings of the National Academy of Sciences of the United States of America | 21737748 | Proc Natl Acad Sci U S A | 2011 Sep 6 |
| Uncovering the Role of the Methylome in Dementia and Neurodegeneration. | Klein HU, De Jager PL | Trends in molecular medicine | 27423266 | Trends Mol Med | 2016 Aug |
| Genetic and epigenetic fine mapping of causal autoimmune disease variants. | Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE | Nature | 25363779 | Nature | 2015 Feb 19 |
| Epigenetic obstacles encountered by transcription factors: reprogramming against all odds. | Gifford CA, Meissner A | Current opinion in genetics & development | 22922161 | Curr Opin Genet Dev | 2012 Oct |
| Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. | Hardison RC | The Journal of biological chemistry | 22952232 | J Biol Chem | 2012 Sep 7 |
| Transcription factor-mediated epigenetic reprogramming. | Sindhu C, Samavarchi-Tehrani P, Meissner A | The Journal of biological chemistry | 22952239 | J Biol Chem | 2012 Sep 7 |
| An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. | Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE | Cell reports | 23707066 | Cell Rep | 2013 May 30 |
| Epigenetic reprogramming in cancer. | Suvà ML, Riggi N, Bernstein BE | Science (New York, N.Y.) | 23539597 | Science | 2013 Mar 29 |
| Locus-specific editing of histone modifications at endogenous enhancers. | Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE | Nature biotechnology | 24013198 | Nat Biotechnol | 2013 Dec |
| Transcription factor binding dynamics during human ES cell differentiation. | Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A | Nature | 25693565 | Nature | 2015 Feb 19 |
| Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. | Zhan L, Li J, Jew B, Sul JH | PLoS genetics | 34516545 | PLoS Genet | 2021 Sep |
| Genetic and multi-omic risk assessment of Alzheimer's disease implicates core associated biological domains. | Cary GA, Wiley JC, Gockley J, Keegan S, Amirtha Ganesh SS, Heath L, Butler RR 3rd, Mangravite LM, Logsdon BA, Longo FM, Levey A, Greenwood AK, Carter GW | Alzheimer's & dementia (New York, N. Y.) | 38650747 | Alzheimers Dement (N Y) | 2024 Apr-Jun |
| Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease. | Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins J | medRxiv : the preprint server for health sciences | 38014121 | medRxiv | 2023 Nov 16 |
| Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. | Ziller MJ, Hansen KD, Meissner A, Aryee MJ | Nature methods | 25362363 | Nat Methods | 2015 Mar |
| Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. | De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA | Nature neuroscience | 25129075 | Nat Neurosci | 2014 Sep |
| RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. | Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W | Bioinformatics (Oxford, England) | 22155871 | Bioinformatics | 2012 Feb 1 |
| Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. | Adli M, Bernstein BE | Nature protocols | 21959244 | Nat Protoc | 2011 Sep 29 |
| Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. | Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC, Aster JC, Bernstein BE, Kieff E | Proceedings of the National Academy of Sciences of the United States of America | 21746931 | Proc Natl Acad Sci U S A | 2011 Sep 6 |
| Epigenetic modifications in pluripotent and differentiated cells. | Meissner A | Nature biotechnology | 20944600 | Nat Biotechnol | 2010 Oct |
| Mouse ooplasm confers context-specific reprogramming capacity. | Chan MM, Smith ZD, Egli D, Regev A, Meissner A | Nature genetics | 22902786 | Nat Genet | 2012 Sep |
| High-throughput bisulfite sequencing in mammalian genomes. | Smith ZD, Gu H, Bock C, Gnirke A, Meissner A | Methods (San Diego, Calif.) | 19442738 | Methods | 2009 Jul |
| Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. | Bove RM, Patrick E, Aubin CM, Srivastava G, Schneider JA, Bennett DA, De Jager PL, Chibnik LB | PloS one | 30052629 | PLoS One | 2018 |
| A unique regulatory phase of DNA methylation in the early mammalian embryo. | Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A | Nature | 22456710 | Nature | 2012 Mar 28 |
| Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. | Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A | Cell | 23664763 | Cell | 2013 May 23 |
| Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. | Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N | Stem cell reports | 24052944 | Stem Cell Reports | 2013 |
| Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology. | Smith RG, Hannon E, De Jager PL, Chibnik L, Lott SJ, Condliffe D, Smith AR, Haroutunian V, Troakes C, Al-Sarraj S, Bennett DA, Powell J, Lovestone S, Schalkwyk L, Mill J, Lunnon K | Alzheimer's & dementia : the journal of the Alzheimer's Association | 29550519 | Alzheimers Dement | 2018 Dec |
| An explainable graph neural network approach for effectively integrating multi-omics with prior knowledge to identify biomarkers from interacting biological domains. | Tripathy RK, Frohock Z, Wang H, Cary GA, Keegan S, Carter GW, Li Y | bioRxiv : the preprint server for biology | 39253523 | bioRxiv | 2024 Sep 26 |
| Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. | Karnik R, Meissner A | Cell stem cell | 23827707 | Cell Stem Cell | 2013 Jul 3 |
| Charting a dynamic DNA methylation landscape of the human genome. | Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A | Nature | 23925113 | Nature | 2013 Aug 22 |
| Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells. | Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE | BMC genomics | 23414147 | BMC Genomics | 2013 Feb 15 |
| Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. | Adli M, Zhu J, Bernstein BE | Nature methods | 20622861 | Nat Methods | 2010 Aug |
| Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. | Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A | Genome biology | 23034176 | Genome Biol | 2012 Oct 3 |
| Erosion of dosage compensation impacts human iPSC disease modeling. | Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, Eggan K | Cell stem cell | 22560080 | Cell Stem Cell | 2012 May 4 |
| DNA methylation dynamics of the human preimplantation embryo. | Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A | Nature | 25079558 | Nature | 2014 Jul 31 |
| Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. | Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A | PLoS genetics | 22174693 | PLoS Genet | 2011 Dec |
| Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer's disease. | Patrick E, Rajagopal S, Wong HA, McCabe C, Xu J, Tang A, Imboywa SH, Schneider JA, Pochet N, Krichevsky AM, Chibnik LB, Bennett DA, De Jager PL | Molecular neurodegeneration | 28668092 | Mol Neurodegener | 2017 Jul 1 |
| Dissecting neural differentiation regulatory networks through epigenetic footprinting. | Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A | Nature | 25533951 | Nature | 2015 Feb 19 |
| EPIGENOMIC FEATURES RELATED TO MICROGLIA ARE ASSOCIATED WITH ATTENUATED EFFECT OF APOE ε4 ON ALZHEIMER'S DISEASE RISK IN HUMANS. | Ma Y, Yu L, Olah M, Smith R, Oatman SR, Allen M, Pishva E, Zhang B, Menon V, Ertekin-Taner N, Lunnon K, Bennett DA, Klein HU, De Jager PL | Alzheimer's & dementia : the journal of the Alzheimer's Association | 34393677 | Alzheimers Dement | 2020 Dec |
| Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset. | Leung YY, Lee WP, Kuzma AB, Nicaretta H, Valladares O, Gangadharan P, Qu L, Zhao Y, Ren Y, Cheng PL, Kuksa PP, Wang H, White H, Katanic Z, Bass L, Saravanan N, Greenfest-Allen E, Kirsch M, Cantwell L, Iqbal T, Wheeler NR, Farrell JJ, Zhu C, Turner SL, Gunasekaran TI, Mena PR, Jin J, Carter L, Alzheimer’s Disease Sequencing Project, Zhang X, Vardarajan BN, Toga A, Cuccaro M, Hohman TJ, Bush WS, Naj AC, Martin E, Dalgard C, Kunkle BW, Farrer LA, Mayeux RP, Haines JL, Pericak-Vance MA, Schellenberg GD, Wang LS | medRxiv : the preprint server for health sciences | 39677464 | medRxiv | 2024 Dec 6 |
| The Role of X Chromosome in Alzheimer's Disease Genetics. | Belloy ME, Guen YL, Stewart I, Herz J, Sherva R, Zhang R, Merritt V, Panizzon MS, Hauger RL, VA Million Veteran Program, Gaziano JM, Logue M, Napolioni V, Greicius MD | medRxiv : the preprint server for health sciences | 38712163 | medRxiv | 2024 Apr 23 |
| Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer's disease. | Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins JE | Nature communications | 39875385 | Nat Commun | 2025 Jan 28 |
| The Human Epigenome Browser at Washington University. | Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T | Nature methods | 22127213 | Nat Methods | 2011 Nov 29 |
| Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. | Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, Xing X, Zhou J, Sundaram V, Elliott G, Gu J, Shi T, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Maire CL, Ligon KL, Madden PA, Tam A, Moore R, Hirst M, Marra MA, Zhang B, Costello JF, Wang T | Genome research | 23804400 | Genome Res | 2013 Sep |
| Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. | Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T | Genome research | 23804401 | Genome Res | 2013 Sep |
| Epigenetics of neurological cancers. | Fouse SD, Costello JF | Future oncology (London, England) | 20001799 | Future Oncol | 2009 Dec |
| Intermediate DNA methylation is a conserved signature of genome regulation. | Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF | Nature communications | 25691127 | Nat Commun | 2015 Feb 18 |
| Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. | Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, Farnham PJ | Genome biology | 25239471 | Genome Biol | 2014 Sep 20 |
| RADIA: RNA and DNA integrated analysis for somatic mutation detection. | Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D | PloS one | 25405470 | PLoS One | 2014 |
| Functional annotation of colon cancer risk SNPs. | Yao L, Tak YG, Berman BP, Farnham PJ | Nature communications | 25268989 | Nat Commun | 2014 Sep 30 |
| Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. | Li D, Zhang B, Xing X, Wang T | Methods (San Diego, Calif.) | 25448294 | Methods | 2015 Jan 15 |
| Recurrent epimutations activate gene body promoters in primary glioblastoma. | Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF | Genome research | 24709822 | Genome Res | 2014 May |
| Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing X, Zhang B, Li D, Wang T | Methods in molecular biology (Clifton, N.J.) | 29224147 | Methods Mol Biol | 2018 |
| The transcription factor encyclopedia. | Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW | Genome biology | 22458515 | Genome Biol | 2012 |
| The UCSC genome browser and associated tools. | Kuhn RM, Haussler D, Kent WJ | Briefings in bioinformatics | 22908213 | Brief Bioinform | 2013 Mar |
| Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ | Developmental cell | 33891899 | Dev Cell | 2021 May 3 |
| The UCSC Genome Browser database: extensions and updates 2011. | Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Pohl A, Malladi VS, Li CH, Learned K, Kirkup V, Hsu F, Harte RA, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, James Kent W | Nucleic acids research | 22086951 | Nucleic Acids Res | 2012 Jan |
| The UCSC Genome Browser database: update 2011. | Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ | Nucleic acids research | 20959295 | Nucleic Acids Res | 2011 Jan |
| Using ChIP-seq technology to generate high-resolution profiles of histone modifications. | O'Geen H, Echipare L, Farnham PJ | Methods in molecular biology (Clifton, N.J.) | 21913086 | Methods Mol Biol | 2011 |
| Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. | Yao L, Berman BP, Farnham PJ | Critical reviews in biochemistry and molecular biology | 26446758 | Crit Rev Biochem Mol Biol | 2015 |
| DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. | Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T | Nature genetics | 23708189 | Nat Genet | 2013 Jul |
| Rare somatic cells from human breast tissue exhibit extensive lineage plasticity. | Roy S, Gascard P, Dumont N, Zhao J, Pan D, Petrie S, Margeta M, Tlsty TD | Proceedings of the National Academy of Sciences of the United States of America | 23487770 | Proc Natl Acad Sci U S A | 2013 Mar 19 |
| Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. | Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T | Nature biotechnology | 25690851 | Nat Biotechnol | 2015 Apr |
| Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. | Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ | Bioinformatics (Oxford, England) | 24227676 | Bioinformatics | 2014 Apr 1 |
| Recombinant antibodies to histone post-translational modifications. | Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S | Nature methods | 23955773 | Nat Methods | 2013 Oct |
| Widespread contribution of transposable elements to the innovation of gene regulatory networks. | Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T | Genome research | 25319995 | Genome Res | 2014 Dec |
| Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. | Lowdon RF, Zhang B, Bilenky M, Mauro T, Li D, Gascard P, Sigaroudinia M, Farnham PJ, Bastian BC, Tlsty TD, Marra MA, Hirst M, Costello JF, Wang T, Cheng JB | Nature communications | 25421844 | Nat Commun | 2014 Nov 25 |
| Conserved role of intragenic DNA methylation in regulating alternative promoters. | Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF | Nature | 20613842 | Nature | 2010 Jul 8 |
| Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. | Yao L, Shen H, Laird PW, Farnham PJ, Berman BP | Genome biology | 25994056 | Genome Biol | 2015 May 21 |
| Spark: a navigational paradigm for genomic data exploration. | Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ | Genome research | 22960372 | Genome Res | 2012 Nov |
| Epigenomic programming in early fetal brain development. | Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJ, Marra MA, Ligon KL, Costello JF, Hirst M | Epigenomics | 32677466 | Epigenomics | 2020 Jun |
| Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. | Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ | PloS one | 21347206 | PLoS One | 2011 Feb 15 |
| SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73. | Pan D, Roy S, Gascard P, Zhao J, Chen-Tanyolac C, Tlsty TD | Cellular signalling | 27705752 | Cell Signal | 2016 Dec |
| Exploring long-range genome interactions using the WashU Epigenome Browser. | Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T | Nature methods | 23629413 | Nat Methods | 2013 May |
| Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. | Hangauer MJ, Vaughn IW, McManus MT | PLoS genetics | 23818866 | PLoS Genet | 2013 Jun |
| Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. | Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D | Cancer research | 23940299 | Cancer Res | 2013 Oct 1 |
| Using the Wash U Epigenome Browser to examine genome-wide sequencing data. | Zhou X, Wang T | Current protocols in bioinformatics | 23255151 | Curr Protoc Bioinformatics | 2012 Dec |
| The UCSC Genome Browser database: extensions and updates 2013. | Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ | Nucleic acids research | 23155063 | Nucleic Acids Res | 2013 Jan |
| Epigenomics: sequencing the methylome. | Hirst M | Methods in molecular biology (Clifton, N.J.) | 23412782 | Methods Mol Biol | 2013 |
| The clonal and mutational evolution spectrum of primary triple-negative breast cancers. | Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S | Nature | 22495314 | Nature | 2012 Apr 4 |
| Comparative epigenomic annotation of regulatory DNA. | Xiao S, Xie D, Cao X, Yu P, Xing X, Chen CC, Musselman M, Xie M, West FD, Lewin HA, Wang T, Zhong S | Cell | 22682255 | Cell | 2012 Jun 8 |
| methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. | Zhou X, Li D, Lowdon RF, Costello JF, Wang T | Bioinformatics (Oxford, England) | 24728854 | Bioinformatics | 2014 Aug 1 |
| Next generation sequencing based approaches to epigenomics. | Hirst M, Marra MA | Briefings in functional genomics | 21266347 | Brief Funct Genomics | 2010 Dec |
| Epigenetic and transcriptional determinants of the human breast. | Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M | Nature communications | 25690954 | Nat Commun | 2015 Feb 18 |
| Involvement of dopamine and acetylcholine in the interaction between amygdala and nucleus accumbens: chronic microdialysis in rats. | Hajnal A, Mark GP, Keys AS, Lénárd L | Neurobiology (Budapest, Hungary) | 9778654 | Neurobiology (Bp) | 1998 |
| Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools. | Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A | BMC bioinformatics | 25080362 | BMC Bioinformatics | 2014 |
| Recommendations for the design and analysis of epigenome-wide association studies. | Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA | Nature methods | 24076989 | Nat Methods | 2013 Oct |
| NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. | Kuo AJ, Cheung P, Chen K, Zee BM, Kioi M, Lauring J, Xi Y, Park BH, Shi X, Garcia BA, Li W, Gozani O | Molecular cell | 22099308 | Mol Cell | 2011 Nov 18 |
| BSMAP: whole genome bisulfite sequence MAPping program. | Xi Y, Li W | BMC bioinformatics | 19635165 | BMC Bioinformatics | 2009 Jul 27 |
| Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). | Fawcett GL, Raveendran M, Deiros DR, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs R, Rogers J | BMC genomics | 21668978 | BMC Genomics | 2011 Jun 13 |
| Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation. | Xi Y, Yao J, Chen R, Li W, He X | Genome research | 21363969 | Genome Res | 2011 May |
| Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. | Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA | Nucleic acids research | 24391148 | Nucleic Acids Res | 2014 Apr |
| CpG methylation differences between neurons and glia are highly conserved from mouse to human. | Kessler NJ, Van Baak TE, Baker MS, Laritsky E, Coarfa C, Waterland RA | Human molecular genetics | 26566671 | Hum Mol Genet | 2016 Jan 15 |
| Corrigendum: High-throughput discovery of novel developmental phenotypes. | Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, International Mouse Phenotyping Consortium, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA | Nature | 29144450 | Nature | 2017 Nov 16 |
| Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types. | Onuchic V, Hartmaier RJ, Boone DN, Samuels ML, Patel RY, White WM, Garovic VD, Oesterreich S, Roth ME, Lee AV, Milosavljevic A | Cell reports | 27851969 | Cell Rep | 2016 Nov 15 |
| Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. | Amin V, Harris RA, Onuchic V, Jackson AR, Charnecki T, Paithankar S, Lakshmi Subramanian S, Riehle K, Coarfa C, Milosavljevic A | Nature communications | 25691256 | Nat Commun | 2015 Feb 18 |
| Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. | Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A | Science (New York, N.Y.) | 30139913 | Science | 2018 Sep 28 |
| Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. | Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A | PLoS genetics | 22615578 | PLoS Genet | 2012 |
| SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. | Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF | Nature | 22722849 | Nature | 2012 Jul 5 |
| Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. | Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A | BMC bioinformatics | 21092284 | BMC Bioinformatics | 2010 Nov 23 |
| Putting epigenome comparison into practice. | Milosavljevic A | Nature biotechnology | 20944597 | Nat Biotechnol | 2010 Oct |
| ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. | Miller CA, Hampton O, Coarfa C, Milosavljevic A | PloS one | 21305028 | PLoS One | 2011 Jan 31 |
| Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. | Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A | PLoS genetics | 23468659 | PLoS Genet | 2013 |
| Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. | Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J | Genome biology | 22703893 | Genome Biol | 2012 Jun 15 |
| Atlas2 Cloud: a framework for personal genome analysis in the cloud. | Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F | BMC genomics | 23134663 | BMC Genomics | 2012 |
| An integrative variant analysis suite for whole exome next-generation sequencing data. | Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F | BMC bioinformatics | 22239737 | BMC Bioinformatics | 2012 Jan 12 |
| Emerging patterns of epigenomic variation. | Milosavljevic A | Trends in genetics : TIG | 21507501 | Trends Genet | 2011 Jun |
| A case study in cross-talk: the histone lysine methyltransferases G9a and GLP. | Collins R, Cheng X | Nucleic acids research | 20159995 | Nucleic Acids Res | 2010 Jun |
| The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. | Dhayalan A, Tamas R, Bock I, Tattermusch A, Dimitrova E, Kudithipudi S, Ragozin S, Jeltsch A | Human molecular genetics | 21421568 | Hum Mol Genet | 2011 Jun 1 |
| Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. | Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X | Nature structural & molecular biology | 20023638 | Nat Struct Mol Biol | 2010 Jan |
| Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. | Chang Y, Ganesh T, Horton JR, Spannhoff A, Liu J, Sun A, Zhang X, Bedford MT, Shinkai Y, Snyder JP, Cheng X | Journal of molecular biology | 20434463 | J Mol Biol | 2010 Jul 2 |
| The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding. | Gao T, Collins RE, Horton JR, Zhang X, Zhang R, Dhayalan A, Tamas R, Jeltsch A, Cheng X | Proteins | 19434754 | Proteins | 2009 Aug 15 |
| Dynamics of histone lysine methylation: structures of methyl writers and erasers. | Upadhyay AK, Cheng X | Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques | 21141727 | Prog Drug Res | 2011 |
| The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. | Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S, Jeltsch A | The Journal of biological chemistry | 20547484 | J Biol Chem | 2010 Aug 20 |
| Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. | Cheng X, Blumenthal RM | Biochemistry | 20210320 | Biochemistry | 2010 Apr 13 |
| Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae. | Baker SP, Phillips J, Anderson S, Qiu Q, Shabanowitz J, Smith MM, Yates JR 3rd, Hunt DF, Grant PA | Nature cell biology | 20139971 | Nat Cell Biol | 2010 Mar |
| Identification of lysine 37 of histone H2B as a novel site of methylation. | Gardner KE, Zhou L, Parra MA, Chen X, Strahl BD | PloS one | 21249157 | PLoS One | 2011 Jan 13 |
| Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells. | He YF, Bao HM, Xiao XF, Zuo S, Du RY, Tang SW, Yang PY, Chen X | Proteomics | 19834888 | Proteomics | 2009 Dec |
| Proteomic dissection of cell type-specific H2AX-interacting protein complex associated with hepatocellular carcinoma. | Yang X, Zou P, Yao J, Yun D, Bao H, Du R, Long J, Chen X | Journal of proteome research | 20000738 | J Proteome Res | 2010 Mar 5 |
| BCLAF1 is a radiation-induced H2AX-interacting partner involved in γH2AX-mediated regulation of apoptosis and DNA repair. | Lee YY, Yu YB, Gunawardena HP, Xie L, Chen X | Cell death & disease | 22833098 | Cell Death Dis | 2012 Jul 26 |
| Sites of acetylation on newly synthesized histone H4 are required for chromatin assembly and DNA damage response signaling. | Ge Z, Nair D, Guan X, Rastogi N, Freitas MA, Parthun MR | Molecular and cellular biology | 23775118 | Mol Cell Biol | 2013 Aug |
| Discovery of histone modification crosstalk networks by stable isotope labeling of amino acids in cell culture mass spectrometry (SILAC MS). | Guan X, Rastogi N, Parthun MR, Freitas MA | Molecular & cellular proteomics : MCP | 23592332 | Mol Cell Proteomics | 2013 Aug |
| H1 histones: current perspectives and challenges. | Harshman SW, Young NL, Parthun MR, Freitas MA | Nucleic acids research | 23945933 | Nucleic Acids Res | 2013 Nov |
| SILAC peptide ratio calculator: a tool for SILAC quantitation of peptides and post-translational modifications. | Guan X, Rastogi N, Parthun MR, Freitas MA | Journal of proteome research | 24328097 | J Proteome Res | 2014 Feb 7 |
| A 96-well plate assay for high-throughput analysis of holocarboxylase synthetase activity. | Rios-Avila L, Prince SA, Wijeratne SS, Zempleni J | Clinica chimica acta; international journal of clinical chemistry | 21195703 | Clin Chim Acta | 2011 Apr 11 |
| Biotin. | Zempleni J, Kuroishi T | Advances in nutrition (Bethesda, Md.) | 22516729 | Adv Nutr | 2012 Mar 1 |
| Human holocarboxylase synthetase with a start site at methionine-58 is the predominant nuclear variant of this protein and has catalytic activity. | Bao B, Wijeratne SS, Rodriguez-Melendez R, Zempleni J | Biochemical and biophysical research communications | 21802411 | Biochem Biophys Res Commun | 2011 Aug 19 |
| Effects of single-nucleotide polymorphisms in the human holocarboxylase synthetase gene on enzyme catalysis. | Esaki S, Malkaram SA, Zempleni J | European journal of human genetics : EJHG | 22027809 | Eur J Hum Genet | 2012 Apr |
| Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells. | Bao B, Rodriguez-Melendez R, Zempleni J | The Journal of nutritional biochemistry | 21764280 | J Nutr Biochem | 2012 Jun |
| The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation. | Hassan YI, Moriyama H, Zempleni J | Archives of biochemistry and biophysics | 20026029 | Arch Biochem Biophys | 2010 Mar 1 |
| Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18. | Bao B, Pestinger V, Hassan YI, Borgstahl GE, Kolar C, Zempleni J | The Journal of nutritional biochemistry | 20688500 | J Nutr Biochem | 2011 May |
| K16-biotinylated histone H4 is overrepresented in repeat regions and participates in the repression of transcriptionally competent genes in human Jurkat lymphoid cells. | Rios-Avila L, Pestinger V, Zempleni J | The Journal of nutritional biochemistry | 22192339 | J Nutr Biochem | 2012 Dec |
| Biotin requirements for DNA damage prevention. | Zempleni J, Teixeira DC, Kuroishi T, Cordonier EL, Baier S | Mutation research | 21871906 | Mutat Res | 2012 May 1 |
| The role of holocarboxylase synthetase in genome stability is mediated partly by epigenomic synergies between methylation and biotinylation events. | Zempleni J, Li Y, Xue J, Cordonier EL | Epigenetics | 21555910 | Epigenetics | 2011 Jul |
| Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes. | Pestinger V, Wijeratne SS, Rodriguez-Melendez R, Zempleni J | The Journal of nutritional biochemistry | 20691578 | J Nutr Biochem | 2011 Apr |
| Holocarboxylase synthetase interacts physically with euchromatic histone-lysine N-methyltransferase, linking histone biotinylation with methylation events. | Li Y, Hassan YI, Moriyama H, Zempleni J | The Journal of nutritional biochemistry | 23337344 | J Nutr Biochem | 2013 Aug |
| Enrichment of meiotic recombination hotspot sequences by avidin capture technology. | Camara Teixeira D, Malkaram SA, Zempleni J | Gene | 23270922 | Gene | 2013 Mar 1 |
| Identification and assessment of markers of biotin status in healthy adults. | Eng WK, Giraud D, Schlegel VL, Wang D, Lee BH, Zempleni J | The British journal of nutrition | 23302490 | Br J Nutr | 2013 Jul 28 |
| Biotin regulates the expression of holocarboxylase synthetase in the miR-539 pathway in HEK-293 cells. | Bao B, Rodriguez-Melendez R, Wijeratne SS, Zempleni J | The Journal of nutrition | 20592104 | J Nutr | 2010 Sep |
| K12-biotinylated histone H4 is enriched in telomeric repeats from human lung IMR-90 fibroblasts. | Wijeratne SS, Camporeale G, Zempleni J | The Journal of nutritional biochemistry | 19369050 | J Nutr Biochem | 2010 Apr |
| Repression of transposable elements by histone biotinylation. | Zempleni J, Chew YC, Bao B, Pestinger V, Wijeratne SS | The Journal of nutrition | 19812216 | J Nutr | 2009 Dec |
| Online tools for bioinformatics analyses in nutrition sciences. | Malkaram SA, Hassan YI, Zempleni J | Advances in nutrition (Bethesda, Md.) | 22983844 | Adv Nutr | 2012 Sep 1 |
| Development of an internet based system for modeling biotin metabolism using Bayesian networks. | Zhou J, Wang D, Schlegel V, Zempleni J | Computer methods and programs in biomedicine | 21356565 | Comput Methods Programs Biomed | 2011 Nov |
| Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DNA adenine methyltransferase identification technology. | Singh D, Pannier AK, Zempleni J | Analytical biochemistry | 21303649 | Anal Biochem | 2011 Jun 1 |
| The role of histone H4 biotinylation in the structure of nucleosomes. | Filenko NA, Kolar C, West JT, Smith SA, Hassan YI, Borgstahl GE, Zempleni J, Lyubchenko YL | PloS one | 21298003 | PLoS One | 2011 Jan 27 |
| Biotinylation is a natural, albeit rare, modification of human histones. | Kuroishi T, Rios-Avila L, Pestinger V, Wijeratne SS, Zempleni J | Molecular genetics and metabolism | 21930408 | Mol Genet Metab | 2011 Dec |
| Biotin requirements are lower in human Jurkat lymphoid cells but homeostatic mechanisms are similar to those of HepG2 liver cells. | Mall GK, Chew YC, Zempleni J | The Journal of nutrition | 20357078 | J Nutr | 2010 Jun |
| A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics. | Quinn AM, Bedford MT, Espejo A, Spannhoff A, Austin CP, Oppermann U, Simeonov A | Nucleic acids research | 19897549 | Nucleic Acids Res | 2010 Jan |
| Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks. | Bua DJ, Kuo AJ, Cheung P, Liu CL, Migliori V, Espejo A, Casadio F, Bassi C, Amati B, Bedford MT, Guccione E, Gozani O | PloS one | 19956676 | PLoS One | 2009 Aug 26 |
| Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling. | Chang Y, Levy D, Horton JR, Peng J, Zhang X, Gozani O, Cheng X | Nucleic acids research | 21515635 | Nucleic Acids Res | 2011 Aug |
| Borrelidin modulates the alternative splicing of VEGF in favour of anti-angiogenic isoforms. | Woolard J, Vousden W, Moss SJ, Krishnakumar A, Gammons MV, Nowak DG, Dixon N, Micklefield J, Spannhoff A, Bedford MT, Gregory MA, Martin CJ, Leadlay PF, Zhang MQ, Harper SJ, Bates DO, Wilkinson B | Chemical science | 22822423 | Chem Sci | 2011 Feb 1 |
| Methylation by Set9 modulates FoxO3 stability and transcriptional activity. | Calnan DR, Webb AE, White JL, Stowe TR, Goswami T, Shi X, Espejo A, Bedford MT, Gozani O, Gygi SP, Brunet A | Aging | 22820736 | Aging (Albany NY) | 2012 Jul |
| Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. | Levy D, Kuo AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S, Tennen RI, Kuo AY, Tanjing S, Cheung R, Chua KF, Utz PJ, Shi X, Prinjha RK, Lee K, Garcia BA, Bedford MT, Tarakhovsky A, Cheng X, Gozani O | Nature immunology | 21131967 | Nat Immunol | 2011 Jan |
| Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. | Deal RB, Henikoff JG, Henikoff S | Science (New York, N.Y.) | 20508129 | Science | 2010 May 28 |
| Capturing the dynamic epigenome. | Deal RB, Henikoff S | Genome biology | 20959022 | Genome Biol | 2010 |
| Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. | Yang YY, Grammel M, Raghavan AS, Charron G, Hang HC | Chemistry & biology | 21095571 | Chem Biol | 2010 Nov 24 |
| Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters. | Rangan KJ, Yang YY, Charron G, Hang HC | Journal of the American Chemical Society | 20230003 | J Am Chem Soc | 2010 Aug 11 |
| Bioorthogonal chemical reporters for monitoring protein acetylation. | Yang YY, Ascano JM, Hang HC | Journal of the American Chemical Society | 20192265 | J Am Chem Soc | 2010 Mar 24 |
| Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. | Yount JS, Moltedo B, Yang YY, Charron G, Moran TM, López CB, Hang HC | Nature chemical biology | 20601941 | Nat Chem Biol | 2010 Aug |
| Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants. | Wilson JP, Raghavan AS, Yang YY, Charron G, Hang HC | Molecular & cellular proteomics : MCP | 21076176 | Mol Cell Proteomics | 2011 Mar |
| A peptide tag system for facile purification and single-molecule immobilization. | Huang J, Nagy SS, Koide A, Rock RS, Koide S | Biochemistry | 19928925 | Biochemistry | 2009 Dec 22 |
| The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. | Koide S, Sidhu SS | ACS chemical biology | 19298050 | ACS Chem Biol | 2009 May 15 |
| Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. | Koide S | Current opinion in biotechnology | 19700302 | Curr Opin Biotechnol | 2009 Aug |
| Engineering of recombinant crystallization chaperones. | Koide S | Current opinion in structural biology | 19477632 | Curr Opin Struct Biol | 2009 Aug |
| Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. | Nishikori S, Hattori T, Fuchs SM, Yasui N, Wojcik J, Koide A, Strahl BD, Koide S | Journal of molecular biology | 23041298 | J Mol Biol | 2012 Dec 14 |
| Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. | Huang J, Makabe K, Biancalana M, Koide A, Koide S | Journal of molecular biology | 19646997 | J Mol Biol | 2009 Oct 9 |
| Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. | Huang J, Koide S | ACS chemical biology | 20143785 | ACS Chem Biol | 2010 Mar 19 |
| Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. | Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S | Proceedings of the National Academy of Sciences of the United States of America | 26862167 | Proc Natl Acad Sci U S A | 2016 Feb 23 |
| Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. | Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD | Molecular & cellular proteomics : MCP | 22442256 | Mol Cell Proteomics | 2012 May |
| Next-generation characterization of the Cancer Cell Line Encyclopedia. | Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Vazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, Sellers WR | Nature | 31068700 | Nature | 2019 May |
| Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. | Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH | Genome research | 21177972 | Genome Res | 2011 Feb |
| Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. | Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD | Methods (San Diego, Calif.) | 25448295 | Methods | 2015 Jan 15 |
| Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions. | Wang H, Liu R | Expert review of proteomics | 21679115 | Expert Rev Proteomics | 2011 Jun |
| Selection of proteins with desired properties from natural proteome libraries using mRNA display. | Cotten SW, Zou J, Valencia CA, Liu R | Nature protocols | 21799486 | Nat Protoc | 2011 Jul 21 |
| Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS. | Gagliano SA, Ptak C, Mak DYF, Shamsi M, Oh G, Knight J, Boutros PC, Petronis A | American journal of human genetics | 27087318 | Am J Hum Genet | 2016 May 5 |
| Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. | Li P, Marshall L, Oh G, Jakubowski JL, Groot D, He Y, Wang T, Petronis A, Labrie V | Nature communications | 31113950 | Nat Commun | 2019 May 21 |
| Epigenetic approaches to psychiatric disorders. | Ptak C, Petronis A | Dialogues in clinical neuroscience | 20373664 | Dialogues Clin Neurosci | 2010 |
| Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. | Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupčinskas L, Brudno M, Petronis A | Nature structural & molecular biology | 27159559 | Nat Struct Mol Biol | 2016 Jun |
| A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. | Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J | Nature chemical biology | 21743462 | Nat Chem Biol | 2011 Jul 10 |
| 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. | Khare T, Pai S, Koncevicius K, Pal M, Kriukiene E, Liutkeviciute Z, Irimia M, Jia P, Ptak C, Xia M, Tice R, Tochigi M, Moréra S, Nazarians A, Belsham D, Wong AH, Blencowe BJ, Wang SC, Kapranov P, Kustra R, Labrie V, Klimasauskas S, Petronis A | Nature structural & molecular biology | 22961382 | Nat Struct Mol Biol | 2012 Oct |
| DNA unmethylome profiling by covalent capture of CpG sites. | Kriukienė E, Labrie V, Khare T, Urbanavičiūtė G, Lapinaitė A, Koncevičius K, Li D, Wang T, Pai S, Ptak C, Gordevičius J, Wang SC, Petronis A, Klimašauskas S | Nature communications | 23877302 | Nat Commun | 2013 |
| DNA modification study of major depressive disorder: beyond locus-by-locus comparisons. | Oh G, Wang SC, Pal M, Chen ZF, Khare T, Tochigi M, Ng C, Yang YA, Kwan A, Kaminsky ZA, Mill J, Gunasinghe C, Tackett JL, Gottesman II, Willemsen G, de Geus EJC, Vink JM, Slagboom PE, Wray NR, Heath AC, Montgomery GW, Turecki G, Martin NG, Boomsma DI, McGuffin P, Kustra R, Petronis A | Biological psychiatry | 25108803 | Biol Psychiatry | 2015 Feb 1 |
| Epigenetics as a unifying principle in the aetiology of complex traits and diseases. | Petronis A | Nature | 20535201 | Nature | 2010 Jun 10 |
| Epigenetics of major psychosis: progress, problems and perspectives. | Labrie V, Pai S, Petronis A | Trends in genetics : TIG | 22622229 | Trends Genet | 2012 Sep |
| Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. | Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, Jia P, Assadzadeh A, Flanagan J, Schumacher A, Wang SC, Petronis A | American journal of human genetics | 18319075 | Am J Hum Genet | 2008 Mar |
| Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome. | Oh E, Jeremian R, Oh G, Groot D, Susic M, Lee K, Foy K, Laird PW, Petronis A, Labrie V | Scientific reports | 28139744 | Sci Rep | 2017 Jan 31 |
| Epigenetic assimilation in the aging human brain. | Oh G, Ebrahimi S, Wang SC, Cortese R, Kaminsky ZA, Gottesman II, Burke JR, Plassman BL, Petronis A | Genome biology | 27122015 | Genome Biol | 2016 Apr 28 |
| A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. | Kaminsky Z, Tochigi M, Jia P, Pal M, Mill J, Kwan A, Ioshikhes I, Vincent JB, Kennedy JL, Strauss J, Pai S, Wang SC, Petronis A | Molecular psychiatry | 21647149 | Mol Psychiatry | 2012 Jul |
| High Precision DNA Modification Analysis of HCG9 in Major Psychosis. | Pal M, Ebrahimi S, Oh G, Khare T, Zhang A, Kaminsky ZA, Wang SC, Petronis A | Schizophrenia bulletin | 26078387 | Schizophr Bull | 2016 Jan |
| In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome. | Eyring KR, Pedersen BS, Yang IV, Schwartz DA | PloS one | 26642056 | PLoS One | 2015 |
| Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. | Pedersen BS, Schwartz DA, Yang IV, Kechris KJ | Bioinformatics (Oxford, England) | 22954632 | Bioinformatics | 2012 Nov 15 |
| The environment, epigenome, and asthma. | Yang IV, Lozupone CA, Schwartz DA | The Journal of allergy and clinical immunology | 28673400 | J Allergy Clin Immunol | 2017 Jul |
| Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group. | Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N, LaSalle JM, Schmidt R, Yousefi P, Perera F, Joubert BR, Wiemels J, Taylor M, Yang IV, Chen R, Hew KM, Freeland DM, Miller R, Murphy SK | Environmental health perspectives | 28362264 | Environ Health Perspect | 2017 Apr |
| DNA methylation and childhood asthma in the inner city. | Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA | The Journal of allergy and clinical immunology | 25769910 | J Allergy Clin Immunol | 2015 Jul |
| Epigenetic control of gene expression in the lung. | Yang IV, Schwartz DA | American journal of respiratory and critical care medicine | 21596832 | Am J Respir Crit Care Med | 2011 May 15 |
| An epigenome-wide association study of total serum immunoglobulin E concentration. | Liang L, Willis-Owen SAG, Laprise C, Wong KCC, Davies GA, Hudson TJ, Binia A, Hopkin JM, Yang IV, Grundberg E, Busche S, Hudson M, Rönnblom L, Pastinen TM, Schwartz DA, Lathrop GM, Moffatt MF, Cookson WOCM | Nature | 25707804 | Nature | 2015 Apr 30 |
| Epigenetic mechanisms and the development of asthma. | Yang IV, Schwartz DA | The Journal of allergy and clinical immunology | 23026498 | J Allergy Clin Immunol | 2012 Dec |
| Role of macrophage receptor with collagenous structure in innate immune tolerance. | Jing J, Yang IV, Hui L, Patel JA, Evans CM, Prikeris R, Kobzik L, O'Connor BP, Schwartz DA | Journal of immunology (Baltimore, Md. : 1950) | 23667110 | J Immunol | 2013 Jun 15 |
| The nasal methylome and childhood atopic asthma. | Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA | The Journal of allergy and clinical immunology | 27745942 | J Allergy Clin Immunol | 2017 May |
| The Nasal Methylome: A Key to Understanding Allergic Asthma. | Yang IV, Richards A, Davidson EJ, Stevens AD, Kolakowski CA, Martin RJ, Schwartz DA | American journal of respiratory and critical care medicine | 28294656 | Am J Respir Crit Care Med | 2017 Mar 15 |
| Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. | Liang L, Cookson WO | Human molecular genetics | 24927738 | Hum Mol Genet | 2014 Sep 15 |
| Methylene-tetrahydrofolate reductase contributes to allergic airway disease. | Eyring KR, Pedersen BS, Maclean KN, Stabler SP, Yang IV, Schwartz DA | PloS one | 29329322 | PLoS One | 2018 |
| Role of epigenetics in the development of childhood asthma. | Davidson EJ, Yang IV | Current opinion in allergy and clinical immunology | 29389731 | Curr Opin Allergy Clin Immunol | 2018 Apr |
| Epigenetic Signatures of Cigarette Smoking. | Joehanes R, Just AC, Marioni RE, Pilling LC, Reynolds LM, Mandaviya PR, Guan W, Xu T, Elks CE, Aslibekyan S, Moreno-Macias H, Smith JA, Brody JA, Dhingra R, Yousefi P, Pankow JS, Kunze S, Shah SH, McRae AF, Lohman K, Sha J, Absher DM, Ferrucci L, Zhao W, Demerath EW, Bressler J, Grove ML, Huan T, Liu C, Mendelson MM, Yao C, Kiel DP, Peters A, Wang-Sattler R, Visscher PM, Wray NR, Starr JM, Ding J, Rodriguez CJ, Wareham NJ, Irvin MR, Zhi D, Barrdahl M, Vineis P, Ambatipudi S, Uitterlinden AG, Hofman A, Schwartz J, Colicino E, Hou L, Vokonas PS, Hernandez DG, Singleton AB, Bandinelli S, Turner ST, Ware EB, Smith AK, Klengel T, Binder EB, Psaty BM, Taylor KD, Gharib SA, Swenson BR, Liang L, DeMeo DL, O'Connor GT, Herceg Z, Ressler KJ, Conneely KN, Sotoodehnia N, Kardia SL, Melzer D, Baccarelli AA, van Meurs JB, Romieu I, Arnett DK, Ong KK, Liu Y, Waldenberger M, Deary IJ, Fornage M, Levy D, London SJ | Circulation. Cardiovascular genetics | 27651444 | Circ Cardiovasc Genet | 2016 Oct |
| Penalized multimarker vs. single-marker regression methods for genome-wide association studies of quantitative traits. | Yi H, Breheny P, Imam N, Liu Y, Hoeschele I | Genetics | 25354699 | Genetics | 2015 Jan |
| Expression of socially sensitive genes: The multi-ethnic study of atherosclerosis. | Brown KM, Diez-Roux AV, Smith JA, Needham BL, Mukherjee B, Ware EB, Liu Y, Cole SW, Seeman TE, Kardia SLR | PloS one | 30973896 | PLoS One | 2019 |
| Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. | Ding J, Reynolds LM, Zeller T, Müller C, Lohman K, Nicklas BJ, Kritchevsky SB, Huang Z, de la Fuente A, Soranzo N, Settlage RE, Chuang CC, Howard T, Xu N, Goodarzi MO, Chen YD, Rotter JI, Siscovick DS, Parks JS, Murphy S, Jacobs DR Jr, Post W, Tracy RP, Wild PS, Blankenberg S, Hoeschele I, Herrington D, McCall CE, Liu Y | Diabetes | 26153245 | Diabetes | 2015 Oct |
| The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study. | Schmitz LL, Zhao W, Ratliff SM, Goodwin J, Miao J, Lu Q, Guo X, Taylor KD, Ding J, Liu Y, Levine M, Smith JA | Epigenetics | 34227900 | Epigenetics | 2022 Jun |
| Epidemiologic Features of Recovery From SARS-CoV-2 Infection. | Oelsner EC, Sun Y, Balte PP, Allen NB, Andrews H, Carson A, Cole SA, Coresh J, Couper D, Cushman M, Daviglus M, Demmer RT, Elkind MSV, Gallo LC, Gutierrez JD, Howard VJ, Isasi CR, Judd SE, Kanaya AM, Kandula NR, Kaplan RC, Kinney GL, Kucharska-Newton AM, Lackland DT, Lee JS, Make BJ, Min YI, Murabito JM, Norwood AF, Ortega VE, Pettee Gabriel K, Psaty BM, Regan EA, Sotres-Alvarez D, Schwartz D, Shikany JM, Thyagarajan B, Tracy RP, Umans JG, Vasan RS, Wenzel SE, Woodruff PG, Xanthakis V, Zhang Y, Post WS | JAMA network open | 38884994 | JAMA Netw Open | 2024 Jun 3 |
| Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. | Wen J, Xie M, Rowland B, Rosen JD, Sun Q, Chen J, Tapia AL, Qian H, Kowalski MH, Shan Y, Young KL, Graff M, Argos M, Avery CL, Bien SA, Buyske S, Yin J, Choquet H, Fornage M, Hodonsky CJ, Jorgenson E, Kooperberg C, Loos RJF, Liu Y, Moon JY, North KE, Rich SS, Rotter JI, Smith JA, Zhao W, Shang L, Wang T, Zhou X, Reiner AP, Raffield LM, Li Y | Genes | 34356065 | Genes (Basel) | 2021 Jul 8 |
| Multivariate adaptive shrinkage improves cross-population transcriptome prediction for transcriptome-wide association studies in underrepresented populations. | Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Im HK, Manichaikul A, Wheeler HE | bioRxiv : the preprint server for biology | 36798214 | bioRxiv | 2023 May 20 |
| Genetic architecture of gene expression traits across diverse populations. | Mogil LS, Andaleon A, Badalamenti A, Dickinson SP, Guo X, Rotter JI, Johnson WC, Im HK, Liu Y, Wheeler HE | PLoS genetics | 30096133 | PLoS Genet | 2018 Aug |
| AtheroSpectrum Reveals Novel Macrophage Foam Cell Gene Signatures Associated With Atherosclerotic Cardiovascular Disease Risk. | Li C, Qu L, Matz AJ, Murphy PA, Liu Y, Manichaikul AW, Aguiar D, Rich SS, Herrington DM, Vu D, Johnson WC, Rotter JI, Post WS, Vella AT, Rodriguez-Oquendo A, Zhou B | Circulation | 34913723 | Circulation | 2022 Jan 18 |
| Age-related variations in the methylome associated with gene expression in human monocytes and T cells. | Reynolds LM, Taylor JR, Ding J, Lohman K, Johnson C, Siscovick D, Burke G, Post W, Shea S, Jacobs DR Jr, Stunnenberg H, Kritchevsky SB, Hoeschele I, McCall CE, Herrington D, Tracy RP, Liu Y | Nature communications | 25404168 | Nat Commun | 2014 Nov 18 |
| Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. | Wan M, Bennett BD, Pittman GS, Campbell MR, Reynolds LM, Porter DK, Crowl CL, Wang X, Su D, Englert NA, Thompson IJ, Liu Y, Bell DA | Environmental health perspectives | 29706059 | Environ Health Perspect | 2018 Apr 27 |
| Differentially conserved transcriptomic response to adversity related to self-rated health in the multi-ethnic study of atherosclerosis. | Riestra P, Gebreab SY, Liu Y, Diez Roux AV, Khan RR, Gaye A, Xu R, Davis SK | Experimental biology and medicine (Maywood, N.J.) | 28927291 | Exp Biol Med (Maywood) | 2017 Dec |
| Transcriptomic profiles of aging in naïve and memory CD4(+) cells from mice. | Taylor J, Reynolds L, Hou L, Lohman K, Cui W, Kritchevsky S, McCall C, Liu Y | Immunity & ageing : I & A | 28642803 | Immun Ageing | 2017 |
| Transcriptome-Wide Analysis Identifies Novel Associations With Blood Pressure. | Zeller T, Schurmann C, Schramm K, Müller C, Kwon S, Wild PS, Teumer A, Herrington D, Schillert A, Iacoviello L, Kratzer A, Jagodzinski A, Karakas M, Ding J, Neumann JT, Kuulasmaa K, Gieger C, Kacprowski T, Schnabel RB, Roden M, Wahl S, Rotter JI, Ojeda F, Carstensen-Kirberg M, Tregouet DA, Dörr M, Meitinger T, Lackner KJ, Wolf P, Felix SB, Landmesser U, Costanzo S, Ziegler A, Liu Y, Völker U, Palmas W, Prokisch H, Guo X, Herder C, Blankenberg S, Homuth G | Hypertension (Dallas, Tex. : 1979) | 28784648 | Hypertension | 2017 Oct |
| A Peripheral Blood DNA Methylation Signature of Hepatic Fat Reveals a Potential Causal Pathway for Nonalcoholic Fatty Liver Disease. | Ma J, Nano J, Ding J, Zheng Y, Hennein R, Liu C, Speliotes EK, Huan T, Song C, Mendelson MM, Joehanes R, Long MT, Liang L, Smith JA, Reynolds LM, Ghanbari M, Muka T, van Meurs JBJ, Alferink LJM, Franco OH, Dehghan A, Ratliff S, Zhao W, Bielak L, Kardia SLR, Peyser PA, Ning H, VanWagner LB, Lloyd-Jones DM, Carr JJ, Greenland P, Lichtenstein AH, Hu FB, Liu Y, Hou L, Darwish Murad S, Levy D | Diabetes | 30936141 | Diabetes | 2019 May |
| DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical Atherosclerosis. | Reynolds LM, Wan M, Ding J, Taylor JR, Lohman K, Su D, Bennett BD, Porter DK, Gimple R, Pittman GS, Wang X, Howard TD, Siscovick D, Psaty BM, Shea S, Burke GL, Jacobs DR Jr, Rich SS, Hixson JE, Stein JH, Stunnenberg H, Barr RG, Kaufman JD, Post WS, Hoeschele I, Herrington DM, Bell DA, Liu Y | Circulation. Cardiovascular genetics | 26307030 | Circ Cardiovasc Genet | 2015 Oct |
| Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium. | Ma Y, Follis JL, Smith CE, Tanaka T, Manichaikul AW, Chu AY, Samieri C, Zhou X, Guan W, Wang L, Biggs ML, Chen YD, Hernandez DG, Borecki I, Chasman DI, Rich SS, Ferrucci L, Irvin MR, Aslibekyan S, Zhi D, Tiwari HK, Claas SA, Sha J, Kabagambe EK, Lai CQ, Parnell LD, Lee YC, Amouyel P, Lambert JC, Psaty BM, King IB, Mozaffarian D, McKnight B, Bandinelli S, Tsai MY, Ridker PM, Ding J, Mstat KL, Liu Y, Sotoodehnia N, Barberger-Gateau P, Steffen LM, Siscovick DS, Absher D, Arnett DK, Ordovás JM, Lemaitre RN | The American journal of clinical nutrition | 26791180 | Am J Clin Nutr | 2016 Feb |
| Bayesian Sparse Mediation Analysis with Targeted Penalization of Natural Indirect Effects. | Song Y, Zhou X, Kang J, Aung MT, Zhang M, Zhao W, Needham BL, Kardia SLR, Liu Y, Meeker JD, Smith JA, Mukherjee B | Journal of the Royal Statistical Society. Series C, Applied statistics | 34887595 | J R Stat Soc Ser C Appl Stat | 2021 Nov |
| Bayesian hierarchical models for high-dimensional mediation analysis with coordinated selection of correlated mediators. | Song Y, Zhou X, Kang J, Aung MT, Zhang M, Zhao W, Needham BL, Kardia SLR, Liu Y, Meeker JD, Smith JA, Mukherjee B | Statistics in medicine | 34404112 | Stat Med | 2021 Nov 30 |
| Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy. | Sofer T, Li R, Joehanes R, Lin H, Gower AC, Wang H, Kurniansyah N, Cade BE, Lee J, Williams S, Mehra R, Patel SR, Quan SF, Liu Y, Rotter JI, Rich SS, Spira A, Levy D, Gharib SA, Redline S, Gottlieb DJ | EBioMedicine | 32512511 | EBioMedicine | 2020 Jun |
| Whole Blood DNA Methylation Signatures of Diet Are Associated With Cardiovascular Disease Risk Factors and All-Cause Mortality. | Ma J, Rebholz CM, Braun KVE, Reynolds LM, Aslibekyan S, Xia R, Biligowda NG, Huan T, Liu C, Mendelson MM, Joehanes R, Hu EA, Vitolins MZ, Wood AC, Lohman K, Ochoa-Rosales C, van Meurs J, Uitterlinden A, Liu Y, Elhadad MA, Heier M, Waldenberger M, Peters A, Colicino E, Whitsel EA, Baldassari A, Gharib SA, Sotoodehnia N, Brody JA, Sitlani CM, Tanaka T, Hill WD, Corley J, Deary IJ, Zhang Y, Schöttker B, Brenner H, Walker ME, Ye S, Nguyen S, Pankow J, Demerath EW, Zheng Y, Hou L, Liang L, Lichtenstein AH, Hu FB, Fornage M, Voortman T, Levy D | Circulation. Genomic and precision medicine | 32525743 | Circ Genom Precis Med | 2020 Aug |
| Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis. | Brown KM, Diez-Roux AV, Smith JA, Needham BL, Mukherjee B, Ware EB, Liu Y, Cole SW, Seeman TE, Kardia SLR | Psychoneuroendocrinology | 32387875 | Psychoneuroendocrinology | 2020 Jul |
| Methods for large-scale single mediator hypothesis testing: Possible choices and comparisons. | Du J, Zhou X, Clark-Boucher D, Hao W, Liu Y, Smith JA, Mukherjee B | Genetic epidemiology | 36465006 | Genet Epidemiol | 2023 Mar |
| LXR signaling pathways link cholesterol metabolism with risk for prediabetes and diabetes. | Ding J, Nguyen AT, Lohman K, Hensley MT, Parker D, Hou L, Taylor J, Voora D, Sawyer JK, Boudyguina E, Bancks MP, Bertoni A, Pankow JS, Rotter JI, Goodarzi MO, Tracy RP, Murdoch DM, Duprez A, Rich SS, Psaty BM, Siscovick D, Newgard B, Herrington D, Hoeschele I, Shea S, Stein JH, Patel M, Post W, Jacobs D Jr, Parks JS, Liu Y | The Journal of clinical investigation | 38747290 | J Clin Invest | 2024 May 15 |
| Epigenetic aging & embodying injustice: US My Body My Story and Multi-Ethnic Atherosclerosis Study. | Krieger N, Testa C, Chen JT, Johnson N, Watkins SH, Suderman M, Simpkin AJ, Tilling K, Waterman PD, Coull BA, De Vivo I, Smith GD, Roux AVD, Relton C | medRxiv : the preprint server for health sciences | 38168159 | medRxiv | 2023 Dec 14 |
| An epigenome-wide analysis of DNA methylation, racialized and economic inequities, and air pollution. | Watkins SH, Testa C, Simpkin AJ, Smith GD, Coull B, De Vivo I, Tilling K, Waterman PD, Chen JT, Diez-Roux AV, Krieger N, Suderman M, Relton C | bioRxiv : the preprint server for biology | 38105971 | bioRxiv | 2023 Dec 8 |
| Classifying COVID-19 hospitalizations in epidemiology cohort studies: The C4R study. | Oelsner EC, Krishnaswamy A, Rustamov R, Balte PP, Ali T, Allen NB, Andrews HF, Anugu P, Arynchyn A, Bateman LA, Cai J, Chang H, Chen L, Elkind MSV, Floyd JS, Gabriel KP, Gharib SA, Gutierrez JD, Stukovsky KH, Howard VJ, Isasi CR, Jager L, Jin L, Judd SE, Kanaya AM, Kandula NR, Kelly MR, Khan SS, Kucharska-Newton A, Lee JS, Levitan EB, Lewis CE, Make BJ, Malloy K, Manly JJ, Mauger D, Min YI, Murabito JM, Murphy CG, Norwood AF, O'Connor GT, Ortega VE, Patel AA, Pirzada A, Regan EA, Ring KB, Rosamond WD, Schwartz DA, Shikany JM, Sotres-Alvarez D, Tarlton C, Tse J, Meneses EMU, Vankineni M, Wenzel SE, Woodruff PG, Xanthakis V, Yang JH, Zakai NA, Zhang Y, Post WS | PloS one | 39928595 | PLoS One | 2025 |
| Transcriptomic profiles of aging in purified human immune cells. | Reynolds LM, Ding J, Taylor JR, Lohman K, Soranzo N, de la Fuente A, Liu TF, Johnson C, Barr RG, Register TC, Donohue KM, Talor MV, Cihakova D, Gu C, Divers J, Siscovick D, Burke G, Post W, Shea S, Jacobs DR Jr, Hoeschele I, McCall CE, Kritchevsky SB, Herrington D, Tracy RP, Liu Y | BMC genomics | 25898983 | BMC Genomics | 2015 Apr 22 |
| Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. | Liu Y, Reynolds LM, Ding J, Hou L, Lohman K, Young T, Cui W, Huang Z, Grenier C, Wan M, Stunnenberg HG, Siscovick D, Hou L, Psaty BM, Rich SS, Rotter JI, Kaufman JD, Burke GL, Murphy S, Jacobs DR Jr, Post W, Hoeschele I, Bell DA, Herrington D, Parks JS, Tracy RP, McCall CE, Stein JH | Nature communications | 28855511 | Nat Commun | 2017 Aug 30 |
| Transcriptome prediction performance across machine learning models and diverse ancestries. | Okoro PC, Schubert R, Guo X, Johnson WC, Rotter JI, Hoeschele I, Liu Y, Im HK, Luke A, Dugas LR, Wheeler HE | HGG advances | 33937878 | HGG Adv | 2021 Apr 8 |
| Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome. | Zeng Y, Amador C, Gao C, Walker RM, Morris SW, Campbell A, Frkatović A, Madden RA, Adams MJ, He S, Bretherick AD, Hayward C, Porteous DJ, Wilson JF, Evans KL, McIntosh AM, Navarro P, Haley CS | EBioMedicine | 34883445 | EBioMedicine | 2021 Dec |
| A DNA methylation biomarker of alcohol consumption. | Liu C, Marioni RE, Hedman ÅK, Pfeiffer L, Tsai PC, Reynolds LM, Just AC, Duan Q, Boer CG, Tanaka T, Elks CE, Aslibekyan S, Brody JA, Kühnel B, Herder C, Almli LM, Zhi D, Wang Y, Huan T, Yao C, Mendelson MM, Joehanes R, Liang L, Love SA, Guan W, Shah S, McRae AF, Kretschmer A, Prokisch H, Strauch K, Peters A, Visscher PM, Wray NR, Guo X, Wiggins KL, Smith AK, Binder EB, Ressler KJ, Irvin MR, Absher DM, Hernandez D, Ferrucci L, Bandinelli S, Lohman K, Ding J, Trevisi L, Gustafsson S, Sandling JH, Stolk L, Uitterlinden AG, Yet I, Castillo-Fernandez JE, Spector TD, Schwartz JD, Vokonas P, Lind L, Li Y, Fornage M, Arnett DK, Wareham NJ, Sotoodehnia N, Ong KK, van Meurs JBJ, Conneely KN, Baccarelli AA, Deary IJ, Bell JT, North KE, Liu Y, Waldenberger M, London SJ, Ingelsson E, Levy D | Molecular psychiatry | 27843151 | Mol Psychiatry | 2018 Feb |
| Secondhand Tobacco Smoke Exposure Associations With DNA Methylation of the Aryl Hydrocarbon Receptor Repressor. | Reynolds LM, Magid HS, Chi GC, Lohman K, Barr RG, Kaufman JD, Hoeschele I, Blaha MJ, Navas-Acien A, Liu Y | Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco | 27613907 | Nicotine Tob Res | 2017 Apr 1 |
| Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis. | Smith JA, Zhao W, Wang X, Ratliff SM, Mukherjee B, Kardia SLR, Liu Y, Roux AVD, Needham BL | Epigenetics | 28678593 | Epigenetics | 2017 Aug |
| Associations of Early-Life Adversity With Later-Life Epigenetic Aging Profiles in the Multi-Ethnic Study of Atherosclerosis. | Schmitz LL, Duffie E, Zhao W, Ratliff SM, Ding J, Liu Y, Merkin SS, Smith JA, Seeman T | American journal of epidemiology | 37579321 | Am J Epidemiol | 2023 Nov 10 |
| Methylomics of gene expression in human monocytes. | Liu Y, Ding J, Reynolds LM, Lohman K, Register TC, De La Fuente A, Howard TD, Hawkins GA, Cui W, Morris J, Smith SG, Barr RG, Kaufman JD, Burke GL, Post W, Shea S, McCall CE, Siscovick D, Jacobs DR Jr, Tracy RP, Herrington DM, Hoeschele I | Human molecular genetics | 23900078 | Hum Mol Genet | 2013 Dec 15 |
| Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. | Chi GC, Liu Y, MacDonald JW, Reynolds LM, Enquobahrie DA, Fitzpatrick AL, Kerr KF, Budoff MJ, Lee SI, Siscovick D, Kaufman JD | Epigenetics | 33818294 | Epigenetics | 2022 Mar |
| An epigenetic biomarker of aging for lifespan and healthspan. | Levine ME, Lu AT, Quach A, Chen BH, Assimes TL, Bandinelli S, Hou L, Baccarelli AA, Stewart JD, Li Y, Whitsel EA, Wilson JG, Reiner AP, Aviv A, Lohman K, Liu Y, Ferrucci L, Horvath S | Aging | 29676998 | Aging (Albany NY) | 2018 Apr 18 |
| Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the Multi-Ethnic Study of Atherosclerosis (MESA). | Reynolds LM, Lohman K, Pittman GS, Barr RG, Chi GC, Kaufman J, Wan M, Bell DA, Blaha MJ, Rodriguez CJ, Liu Y | Epigenetics | 29166816 | Epigenetics | 2017 |
| Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American-specific associations. | Barfield R, Wang H, Liu Y, Brody JA, Swenson B, Li R, Bartz TM, Sotoodehnia N, Chen YI, Cade BE, Chen H, Patel SR, Zhu X, Gharib SA, Johnson WC, Rotter JI, Saxena R, Purcell S, Lin X, Redline S, Sofer T | Sleep | 31139831 | Sleep | 2019 Aug 1 |
| Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis. | Needham BL, Smith JA, Zhao W, Wang X, Mukherjee B, Kardia SL, Shively CA, Seeman TE, Liu Y, Diez Roux AV | Epigenetics | 26295359 | Epigenetics | 2015 |
| Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). | Chi GC, Liu Y, MacDonald JW, Barr RG, Donohue KM, Hensley MD, Hou L, McCall CE, Reynolds LM, Siscovick DS, Kaufman JD | Environmental health : a global access science source | 27903268 | Environ Health | 2016 Dec 1 |
| Racial and Ethnic Residential Segregation and Monocyte DNA Methylation Age Acceleration. | Hicken MT, Dou J, Kershaw KN, Liu Y, Hajat A, Bakulski KM | JAMA network open | 38019517 | JAMA Netw Open | 2023 Nov 1 |
| Multivariate adaptive shrinkage improves cross-population transcriptome prediction and association studies in underrepresented populations. | Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, NHLBI TOPMed Consortium, Im HK, Manichaikul A, Wheeler HE | HGG advances | 37869564 | HGG Adv | 2023 Oct 12 |
| Methods for mediation analysis with high-dimensional DNA methylation data: Possible choices and comparisons. | Clark-Boucher D, Zhou X, Du J, Liu Y, Needham BL, Smith JA, Mukherjee B | PLoS genetics | 37934796 | PLoS Genet | 2023 Nov |
| The association between aging-related monocyte transcriptional networks and comorbidity burden: the Multi-Ethnic Study of Atherosclerosis (MESA). | Ding J, Lohman K, Molina A, Delbono O, Bertoni A, Shea S, Post W, Guo X, Barr RG, Manichaikul AW, Pankow JS, Rotter JI, Hoeschele I, Kritchevsky SB, Liu Y | GeroScience | 35737188 | Geroscience | 2023 Feb |
| Methods for Mediation Analysis with High-Dimensional DNA Methylation Data: Possible Choices and Comparison. | Clark-Boucher D, Zhou X, Du J, Liu Y, Needham BL, Smith JA, Mukherjee B | medRxiv : the preprint server for health sciences | 36824903 | medRxiv | 2023 Feb 14 |
| Epigenetic Aging and Racialized, Economic, and Environmental Injustice: NIMHD Social Epigenomics Program. | Krieger N, Testa C, Chen JT, Johnson N, Watkins SH, Suderman M, Simpkin AJ, Tilling K, Waterman PD, Coull BA, De Vivo I, Smith GD, Diez Roux AV, Relton C | JAMA network open | 39073820 | JAMA Netw Open | 2024 Jul 1 |
| Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. | Cherepanova OA, Gomez D, Shankman LS, Swiatlowska P, Williams J, Sarmento OF, Alencar GF, Hess DL, Bevard MH, Greene ES, Murgai M, Turner SD, Geng YJ, Bekiranov S, Connelly JJ, Tomilin A, Owens GK | Nature medicine | 27183216 | Nat Med | 2016 Jun |
| Multigenerational effects of maternal undernutrition. | Einstein FH | Cell metabolism | 24896533 | Cell Metab | 2014 Jun 3 |
| Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth. | Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM, Einstein FH | Nature communications | 25300954 | Nat Commun | 2014 Oct 10 |
| Challenges of linking early-life conditions and disease susceptibility. | Einstein FH | Diabetes | 22517650 | Diabetes | 2012 May |
| Epigenetic and Transcriptomic Programming of HSC Quiescence Signaling in Large for Gestational Age Neonates. | Pelletier A, Carrier A, Zhao Y, Canouil M, Derhourhi M, Durand E, Berberian-Ferrato L, Greally J, Hughes F, Froguel P, Bonnefond A, Delahaye F | International journal of molecular sciences | 35806330 | Int J Mol Sci | 2022 Jun 30 |
| Pregnancy complicated by obesity induces global transcript expression alterations in visceral and subcutaneous fat. | Bashiri A, Heo HJ, Ben-Avraham D, Mazor M, Budagov T, Einstein FH, Atzmon G | Molecular genetics and genomics : MGG | 24696292 | Mol Genet Genomics | 2014 Aug |
| Perinephric and epididymal fat affect hepatic metabolism in rats. | Ben-Shlomo S, Einstein FH, Zvibel I, Atias D, Shlomai A, Halpern Z, Barzilai N, Fishman S | Obesity (Silver Spring, Md.) | 21818154 | Obesity (Silver Spring) | 2012 Jan |
| Diabetes in pregnancy: glycemia control guidelines and rationale. | Karakash SD, Einstein FH | Current opinion in endocrinology, diabetes, and obesity | 21330917 | Curr Opin Endocrinol Diabetes Obes | 2011 Apr |
| RAD51 mutants cause replication defects and chromosomal instability. | Kim TM, Ko JH, Hu L, Kim SA, Bishop AJ, Vijg J, Montagna C, Hasty P | Molecular and cellular biology | 22778135 | Mol Cell Biol | 2012 Sep |
| Minireview: Epigenetics of obesity and diabetes in humans. | Slomko H, Heo HJ, Einstein FH | Endocrinology | 22253427 | Endocrinology | 2012 Mar |
| The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. | Wijetunga NA, Delahaye F, Zhao YM, Golden A, Mar JC, Einstein FH, Greally JM | Nature communications | 25327398 | Nat Commun | 2014 Oct 20 |
| Effect of arachidonic acid on normal and dystrophic retinal pigment epithelium in tissue culture. | Tripathi BJ, Tripathi RC | Investigative ophthalmology & visual science | 7216671 | Invest Ophthalmol Vis Sci | 1981 Apr |
| Differential DNA methylation identified in the blood and retina of AMD patients. | Oliver VF, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL | Epigenetics | 26067391 | Epigenetics | 2015 |
| Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation. | Hackler L Jr, Masuda T, Oliver VF, Merbs SL, Zack DJ | Methods in molecular biology (Clifton, N.J.) | 22688715 | Methods Mol Biol | 2012 |
| Hypomethylation of the IL17RC promoter in peripheral blood leukocytes is not a hallmark of age-related macular degeneration. | Oliver VF, Franchina M, Jaffe AE, Branham KE, Othman M, Heckenlively JR, Swaroop A, Campochiaro B, Vote BJ, Craig JE, Saffery R, Mackey DA, Qian J, Zack DJ, Hewitt AW, Merbs SL | Cell reports | 24373284 | Cell Rep | 2013 Dec 26 |
| Measuring the reproducibility and quality of Hi-C data. | Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS | Genome biology | 30890172 | Genome Biol | 2019 Mar 19 |
| Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila. | Sparvoli D, Richardson E, Osakada H, Lan X, Iwamoto M, Bowman GR, Kontur C, Bourland WA, Lynn DH, Pritchard JK, Haraguchi T, Dacks JB, Turkewitz AP | Current biology : CB | 29478853 | Curr Biol | 2018 Mar 5 |
| Denoising genome-wide histone ChIP-seq with convolutional neural networks. | Koh PW, Pierson E, Kundaje A | Bioinformatics (Oxford, England) | 28881977 | Bioinformatics | 2017 Jul 15 |
| Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. | Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M | Cell | 26300125 | Cell | 2015 Aug 27 |
| Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila. | Kontur C, Kumar S, Lan X, Pritchard JK, Turkewitz AP | G3 (Bethesda, Md.) | 27317773 | G3 (Bethesda) | 2016 Aug 9 |
| Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. | Lan X, Pritchard JK | Science (New York, N.Y.) | 27199432 | Science | 2016 May 20 |
| Detection of human adaptation during the past 2000 years. | Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK | Science (New York, N.Y.) | 27738015 | Science | 2016 Nov 11 |
| Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. | Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH | Genome medicine | 28446242 | Genome Med | 2017 Apr 26 |
| Alternative empirical Bayes models for adjusting for batch effects in genomic studies. | Zhang Y, Jenkins DF, Manimaran S, Johnson WE | BMC bioinformatics | 30001694 | BMC Bioinformatics | 2018 Jul 13 |
| Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. | Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR | Bioinformatics (Oxford, England) | 26209429 | Bioinformatics | 2015 Nov 15 |
| BatchQC: interactive software for evaluating sample and batch effects in genomic data. | Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE | Bioinformatics (Oxford, England) | 27540268 | Bioinformatics | 2016 Dec 15 |
| Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. | Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M | Nature biotechnology | 27701403 | Nat Biotechnol | 2016 Nov |
| Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. | Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K | Cell reports | 28445736 | Cell Rep | 2017 Apr 25 |
| Cooperative Binding of Transcription Factors Orchestrates Reprogramming. | Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K | Cell | 28111071 | Cell | 2017 Jan 26 |
| rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. | Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y | Proceedings of the National Academy of Sciences of the United States of America | 25480548 | Proc Natl Acad Sci U S A | 2014 Dec 23 |
| Systematic discovery of conservation states for single-nucleotide annotation of the human genome. | Arneson A, Ernst J | Communications biology | 31286065 | Commun Biol | 2019 |
| Leveraging allelic imbalance to refine fine-mapping for eQTL studies. | Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E | PLoS genetics | 31834882 | PLoS Genet | 2019 Dec |
| Dual Roles of RNF2 in Melanoma Progression. | Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar AJ, Ernst J, Chin L | Cancer discovery | 26450788 | Cancer Discov | 2015 Dec |
| An integrative approach for fine-mapping chromatin interactions. | Jaroszewicz A, Ernst J | Bioinformatics (Oxford, England) | 31742318 | Bioinformatics | 2020 Mar 1 |
| Chromosome conformation elucidates regulatory relationships in developing human brain. | Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH | Nature | 27760116 | Nature | 2016 Oct 27 |
| Using genomic annotations increases statistical power to detect eGenes. | Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E | Bioinformatics (Oxford, England) | 27307612 | Bioinformatics | 2016 Jun 15 |
| Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. | Davis-Turak J, Johnson TL, Hoffmann A | Nucleic acids research | 30272246 | Nucleic Acids Res | 2018 Nov 16 |
| ChromTime: modeling spatio-temporal dynamics of chromatin marks. | Fiziev P, Ernst J | Genome biology | 30097049 | Genome Biol | 2018 Aug 10 |
| Chromatin-state discovery and genome annotation with ChromHMM. | Ernst J, Kellis M | Nature protocols | 29120462 | Nat Protoc | 2017 Dec |
| Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. | Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A | Nucleic acids research | 25541195 | Nucleic Acids Res | 2015 Jan |
| ChromGene: gene-based modeling of epigenomic data. | Jaroszewicz A, Ernst J | Genome biology | 37679846 | Genome Biol | 2023 Sep 7 |
| Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. | Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J | Nature communications | 33268804 | Nat Commun | 2020 Dec 2 |
| DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. | Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C | Nature genetics | 28604729 | Nat Genet | 2017 Jul |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon RF, Jang HS, Wang T | Trends in genetics : TIG | 27080453 | Trends Genet | 2016 May |
| Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. | Lee HJ, Lowdon RF, Maricque B, Zhang B, Stevens M, Li D, Johnson SL, Wang T | Nature communications | 25697895 | Nat Commun | 2015 Feb 20 |
| Co-opted transposons help perpetuate conserved higher-order chromosomal structures. | Choudhary MN, Friedman RZ, Wang JT, Jang HS, Zhuo X, Wang T | Genome biology | 31973766 | Genome Biol | 2020 Jan 24 |
| Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. | Pan Y, Daito T, Sasaki Y, Chung YH, Xing X, Pondugula S, Swamidass SJ, Wang T, Kim AH, Yano H | Scientific reports | 27516062 | Sci Rep | 2016 Aug 12 |
| Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults. | Hochner H, Allard C, Granot-Hershkovitz E, Chen J, Sitlani CM, Sazdovska S, Lumley T, McKnight B, Rice K, Enquobahrie DA, Meigs JB, Kwok P, Hivert MF, Borecki IB, Gomez F, Wang T, van Duijn C, Amin N, Rotter JI, Stamatoyannopoulos J, Meiner V, Manor O, Dupuis J, Friedlander Y, Siscovick DS | PLoS genetics | 26451733 | PLoS Genet | 2015 Oct |
| Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. | Cheng C, Deng PY, Ikeuchi Y, Yuede C, Li D, Rensing N, Huang J, Baldridge D, Maloney SE, Dougherty JD, Constantino J, Jahani-Asl A, Wong M, Wozniak DF, Wang T, Klyachko VA, Bonni A | Cell reports | 30403997 | Cell Rep | 2018 Nov 6 |
| Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. | Zhu L, Yan F, Wang Z, Dong H, Bian C, Wang T, Yu E, Li J | International journal of cancer | 30183087 | Int J Cancer | 2018 Nov 15 |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal A, Chou YL, Carey CE, Baranger DAA, Zhang B, Sherva R, Wetherill L, Kapoor M, Wang JC, Bertelsen S, Anokhin AP, Hesselbrock V, Kramer J, Lynskey MT, Meyers JL, Nurnberger JI, Rice JP, Tischfield J, Bierut LJ, Degenhardt L, Farrer LA, Gelernter J, Hariri AR, Heath AC, Kranzler HR, Madden PAF, Martin NG, Montgomery GW, Porjesz B, Wang T, Whitfield JB, Edenberg HJ, Foroud T, Goate AM, Bogdan R, Nelson EC | Molecular psychiatry | 29112194 | Mol Psychiatry | 2018 May |
| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model. | Sundaram V, Wang T | BioEssays : news and reviews in molecular, cellular and developmental biology | 29206283 | Bioessays | 2018 Jan |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T | G3 (Bethesda, Md.) | 26888867 | G3 (Bethesda) | 2016 Apr 7 |
| A comparative encyclopedia of DNA elements in the mouse genome. | Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium | Nature | 25409824 | Nature | 2014 Nov 20 |
| Perinatal deiodinase 2 expression in hepatocytes defines epigenetic susceptibility to liver steatosis and obesity. | Fonseca TL, Fernandes GW, McAninch EA, Bocco BM, Abdalla SM, Ribeiro MO, Mohácsik P, Fekete C, Li D, Xing X, Wang T, Gereben B, Bianco AC | Proceedings of the National Academy of Sciences of the United States of America | 26508642 | Proc Natl Acad Sci U S A | 2015 Nov 10 |
| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou J, Sears RL, Xing X, Zhang B, Li D, Rockweiler NB, Jang HS, Choudhary MNK, Lee HJ, Lowdon RF, Arand J, Tabers B, Gu CC, Cicero TJ, Wang T | BMC genomics | 28899353 | BMC Genomics | 2017 Sep 12 |
| EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He Y, Wang T | Bioinformatics (Oxford, England) | 28605501 | Bioinformatics | 2017 Oct 15 |
| Transposable elements drive widespread expression of oncogenes in human cancers. | Jang HS, Shah NM, Du AY, Dailey ZZ, Pehrsson EC, Godoy PM, Zhang D, Li D, Xing X, Kim S, O'Donnell D, Gordon JI, Wang T | Nature genetics | 30926969 | Nat Genet | 2019 Apr |
| The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. | Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M, Hardison R, Wang T, Yue F | Genome biology | 30286773 | Genome Biol | 2018 Oct 4 |
| WashU Epigenome Browser update 2019. | Li D, Hsu S, Purushotham D, Sears RL, Wang T | Nucleic acids research | 31165883 | Nucleic Acids Res | 2019 Jul 2 |
| The epigenomic landscape of transposable elements across normal human development and anatomy. | Pehrsson EC, Choudhary MNK, Sundaram V, Wang T | Nature communications | 31822674 | Nat Commun | 2019 Dec 10 |
| A map of cis-regulatory elements and 3D genome structures in zebrafish. | Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F | Nature | 33239788 | Nature | 2020 Dec |
| Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow JA, Miao B, Xing X, Wang T, Zhang B | Communications biology | 34021236 | Commun Biol | 2021 May 21 |
| Regulatory transposable elements in the encyclopedia of DNA elements. | Du AY, Chobirko JD, Zhuo X, Feschotte C, Wang T | Nature communications | 39217141 | Nat Commun | 2024 Aug 31 |
| Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2. | Liu F, Li D, Yu YY, Kang I, Cha MJ, Kim JY, Park C, Watson DK, Wang T, Choi K | EMBO reports | 25802403 | EMBO Rep | 2015 May |
| Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis. | Carey CE, Agrawal A, Zhang B, Conley ED, Degenhardt L, Heath AC, Li D, Lynskey MT, Martin NG, Montgomery GW, Wang T, Bierut LJ, Hariri AR, Nelson EC, Bogdan R | Journal of abnormal psychology | 26595473 | J Abnorm Psychol | 2015 Nov |
| A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. | Keleher MR, Zaidi R, Hicks L, Shah S, Xing X, Li D, Wang T, Cheverud JM | BMC genomics | 30526554 | BMC Genomics | 2018 Dec 7 |
| Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. | Jiang K, Wong L, Chen Y, Xing X, Li D, Wang T, Jarvis JN | Journal of reproductive immunology | 29800761 | J Reprod Immunol | 2018 Aug |
| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang B, Madden P, Gu J, Xing X, Sankar S, Flynn J, Kroll K, Wang T | BMC genomics | 28583088 | BMC Genomics | 2017 Jun 5 |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy DG, Kim WK, McCoy MJ, Lake AM, Ouwenga R, Lee SW, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS | Cell stem cell | 28886366 | Cell Stem Cell | 2017 Sep 7 |
| DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. | Shen J, Wang C, Li D, Xu T, Myers J, Ashton JM, Wang T, Zuscik MJ, McAlinden A, O'Keefe RJ | JCI insight | 28614801 | JCI Insight | 2017 Jun 15 |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu CX, Lee TJ, Sakurai N, Krchma K, Liu F, Li D, Wang T, Choi K | The Journal of experimental medicine | 28461595 | J Exp Med | 2017 Jun 5 |
| The NIEHS TaRGET II Consortium and environmental epigenomics. | Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZT, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA, TaRGET II Consortium, Bartolomei MS, Walker CL, Tyson FL | Nature biotechnology | 29509741 | Nat Biotechnol | 2018 Mar 6 |
| Functional characterization of enhancer activity during a long terminal repeat's evolution. | Du AY, Zhuo X, Sundaram V, Jensen NO, Chaudhari HG, Saccone NL, Cohen BA, Wang T | Genome research | 36192170 | Genome Res | 2022 Oct |
| Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. | Karlow JA, Devarakonda S, Xing X, Jang HS, Govindan R, Watson M, Wang T | Cancer research | 35706127 | Cancer Res | 2022 Aug 3 |
| DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods. | He Y, Jang HS, Xing X, Li D, Vasek MJ, Dougherty JD, Wang T | Science advances | 32937429 | Sci Adv | 2020 Jul |
| Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. | Karlow JA, Pehrsson EC, Xing X, Watson M, Devarakonda S, Govindan R, Wang T | Genomics, proteomics & bioinformatics | 37742993 | Genomics Proteomics Bioinformatics | 2023 Oct |
| Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. | Li J, Xing X, Li D, Zhang B, Mutch DG, Hagemann IS, Wang T | Neoplasia (New York, N.Y.) | 28088687 | Neoplasia | 2017 Feb |
| Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-β Signaling. | Zhang C, Lee HJ, Shrivastava A, Wang R, McQuiston TJ, Challberg SS, Pollok BA, Wang T | Cell reports | 30332641 | Cell Rep | 2018 Oct 16 |
| A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. | Dai X, Lin N, Li D, Wang T | Biometrics | 30387496 | Biometrics | 2019 Jun |
| Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. | Zhang B, Xing X, Li J, Lowdon RF, Zhou Y, Lin N, Zhang B, Sundaram V, Chiappinelli KB, Hagemann IS, Mutch DG, Goodfellow PJ, Wang T | BMC genomics | 25286960 | BMC Genomics | 2014 Oct 6 |
| Principles of regulatory information conservation between mouse and human. | Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP | Nature | 25409826 | Nature | 2014 Nov 20 |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram V, Choudhary MN, Pehrsson E, Xing X, Fiore C, Pandey M, Maricque B, Udawatta M, Ngo D, Chen Y, Paguntalan A, Ray T, Hughes A, Cohen BA, Wang T | Nature communications | 28348391 | Nat Commun | 2017 Mar 28 |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon RF, Wang T | PloS one | 28333948 | PLoS One | 2017 |
| Evidence of CNIH3 involvement in opioid dependence. | Nelson EC, Agrawal A, Heath AC, Bogdan R, Sherva R, Zhang B, Al-Hasani R, Bruchas MR, Chou YL, Demers CH, Carey CE, Conley ED, Fakira AK, Farrer LA, Goate A, Gordon S, Henders AK, Hesselbrock V, Kapoor M, Lynskey MT, Madden PA, Moron JA, Rice JP, Saccone NL, Schwab SG, Shand FL, Todorov AA, Wallace L, Wang T, Wray NR, Zhou X, Degenhardt L, Martin NG, Hariri AR, Kranzler HR, Gelernter J, Bierut LJ, Clark DJ, Montgomery GW | Molecular psychiatry | 26239289 | Mol Psychiatry | 2016 May |
| Heat shock factor 1 induces cancer stem cell phenotype in breast cancer cell lines. | Wang B, Lee CW, Witt A, Thakkar A, Ince TA | Breast cancer research and treatment | 26223813 | Breast Cancer Res Treat | 2015 Aug |
| Breast cancers from black women exhibit higher numbers of immunosuppressive macrophages with proliferative activity and of crown-like structures associated with lower survival compared to non-black Latinas and Caucasians. | Koru-Sengul T, Santander AM, Miao F, Sanchez LG, Jorda M, Glück S, Ince TA, Nadji M, Chen Z, Penichet ML, Cleary MP, Torroella-Kouri M | Breast cancer research and treatment | 27283835 | Breast Cancer Res Treat | 2016 Jul |
| Normal cell-type epigenetics and breast cancer classification: a case study of cell mixture-adjusted analysis of DNA methylation data from tumors. | Houseman EA, Ince TA | Cancer informatics | 25574126 | Cancer Inform | 2014 |
| Interactions between Adipocytes and Breast Cancer Cells Stimulate Cytokine Production and Drive Src/Sox2/miR-302b-Mediated Malignant Progression. | Picon-Ruiz M, Pan C, Drews-Elger K, Jang K, Besser AH, Zhao D, Morata-Tarifa C, Kim M, Ince TA, Azzam DJ, Wander SA, Wang B, Ergonul B, Datar RH, Cote RJ, Howard GA, El-Ashry D, Torné-Poyatos P, Marchal JA, Slingerland JM | Cancer research | 26744520 | Cancer Res | 2016 Jan 15 |
| Vitamin D and androgen receptor-targeted therapy for triple-negative breast cancer. | Thakkar A, Wang B, Picon-Ruiz M, Buchwald P, Ince TA | Breast cancer research and treatment | 27120467 | Breast Cancer Res Treat | 2016 May |
| Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. | Houseman EA, Kile ML, Christiani DC, Ince TA, Kelsey KT, Marsit CJ | BMC bioinformatics | 27358049 | BMC Bioinformatics | 2016 Jun 29 |
| Correlation between DNA methylation and gene expression in the brains of patients with bipolar disorder and schizophrenia. | Chen C, Zhang C, Cheng L, Reilly JL, Bishop JR, Sweeney JA, Chen HY, Gershon ES, Liu C | Bipolar disorders | 25243493 | Bipolar Disord | 2014 Dec |
| Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders. | Liu C, Chung M | Neuroscience bulletin | 25652815 | Neurosci Bull | 2015 Feb |
| DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data. | Jiang Y, Giase G, Grennan K, Shieh AW, Xia Y, Han L, Wang Q, Wei Q, Chen R, Liu S, White KP, Chen C, Li B, Liu C | PLoS computational biology | 32282793 | PLoS Comput Biol | 2020 Apr |
| Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders. | Xia Y, Dai R, Wang K, Jiao C, Zhang C, Xu Y, Li H, Jing X, Chen Y, Jiang Y, Kopp RF, Giase G, Chen C, Liu C | Molecular psychiatry | 30976086 | Mol Psychiatry | 2021 Mar |
| Detection of Sources in Non-Negative Blind Source Separation by Minimum Description Length Criterion. | Lin CH, Chi CY, Chen L, Miller DJ, Wang Y | IEEE transactions on neural networks and learning systems | 28981430 | IEEE Trans Neural Netw Learn Syst | 2018 Sep |
| Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues. | Wang N, Hoffman EP, Chen L, Chen L, Zhang Z, Liu C, Yu G, Herrington DM, Clarke R, Wang Y | Scientific reports | 26739359 | Sci Rep | 2016 Jan 7 |
| BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor. | Fu Y, Yu G, Levine DA, Wang N, Shih IeM, Zhang Z, Clarke R, Wang Y | Scientific reports | 26350498 | Sci Rep | 2015 Sep 9 |
| A decade in psychiatric GWAS research. | Horwitz T, Lam K, Chen Y, Xia Y, Liu C | Molecular psychiatry | 29942042 | Mol Psychiatry | 2019 Mar |
| Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance. | Li M, Luo XJ, Landén M, Bergen SE, Hultman CM, Li X, Zhang W, Yao YG, Zhang C, Liu J, Mattheisen M, Cichon S, Mühleisen TW, Degenhardt FA, Nöthen MM, Schulze TG, Grigoroiu-Serbanescu M, Li H, Fuller CK, Chen C, Dong Q, Chen C, Jamain S, Leboyer M, Bellivier F, Etain B, Kahn JP, Henry C, Preisig M, Kutalik Z, Castelao E, Wright A, Mitchell PB, Fullerton JM, Schofield PR, Montgomery GW, Medland SE, Gordon SD, Martin NG, MooDS Consortium, Swedish Bipolar Study Group, Rietschel M, Liu C, Kleinman JE, Hyde TM, Weinberger DR, Su B | The British journal of psychiatry : the journal of mental science | 26338991 | Br J Psychiatry | 2016 Feb |
| Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database. | Li J, Cai T, Jiang Y, Chen H, He X, Chen C, Li X, Shao Q, Ran X, Li Z, Xia K, Liu C, Sun ZS, Wu J | Molecular psychiatry | 25849321 | Mol Psychiatry | 2016 Feb |
| BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. | Jiao C, Yan P, Xia C, Shen Z, Tan Z, Tan Y, Wang K, Jiang Y, Huang L, Dai R, Wei Y, Xia Y, Meng Q, Ouyang Y, Yi L, Duan F, Dai J, Zhao S, Liu C, Chen C | Bioinformatics (Oxford, England) | 29985970 | Bioinformatics | 2019 Jan 1 |
| The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders. | Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, Cheng L, Gunaratne P, Gibbs RA, Min S, Coarfa C, Reid JG, Zhang C, Jiao C, Jiang Y, Giase G, Thomas A, Fitzgerald D, Brunetti T, Shieh A, Xia C, Wang Y, Wang Y, Badner JA, Gershon ES, White KP, Liu C | Science translational medicine | 30545964 | Sci Transl Med | 2018 Dec 19 |
| The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes. | Meng Q, Wang K, Brunetti T, Xia Y, Jiao C, Dai R, Fitzgerald D, Thomas A, Jay L, Eckart H, Grennan K, Imamura-Kawasawa Y, Li M, Sestan N, White KP, Chen C, Liu C | Science translational medicine | 30545965 | Sci Transl Med | 2018 Dec 19 |
| Molecular network analysis enhances understanding of the biology of mental disorders. | Grennan KS, Chen C, Gershon ES, Liu C | BioEssays : news and reviews in molecular, cellular and developmental biology | 24733456 | Bioessays | 2014 Jun |
| Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. | Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, Schork AJ, Appadurai V, Buil A, Werge TM, Liu C, White KP, CommonMind Consortium, PsychENCODE Consortium, iPSYCH-BROAD Working Group, Horvath S, Geschwind DH | Science (New York, N.Y.) | 29439242 | Science | 2018 Feb 9 |
| Positional effects revealed in Illumina methylation array and the impact on analysis. | Jiao C, Zhang C, Dai R, Xia Y, Wang K, Giase G, Chen C, Liu C | Epigenomics | 29469594 | Epigenomics | 2018 May |
| Psychiatric genetics in China: achievements and challenges. | Liu C, Saffen D, Schulze TG, Burmeister M, Sham PC, Yao YG, Kuo PH, Chen C, An Y, Dai J, Yue W, Li MX, Xue H, Su B, Chen L, Shi Y, Qiao M, Liu T, Xia K, Chan RCK | Molecular psychiatry | 26481319 | Mol Psychiatry | 2016 Jan |
| Integrative analyses prioritize GNL3 as a risk gene for bipolar disorder. | Meng Q, Wang L, Dai R, Wang J, Ren Z, Liu S, Xia Y, Jiang Y, Duan F, Wang K, Liu C, Chen C | Molecular psychiatry | 32826963 | Mol Psychiatry | 2020 Nov |
| Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders. | Chen Y, Dai J, Tang L, Mikhailova T, Liang Q, Li M, Zhou J, Kopp RF, Weickert C, Chen C, Liu C | Molecular psychiatry | 36424395 | Mol Psychiatry | 2023 Feb |
| Risperidone-induced changes in DNA methylation in peripheral blood from first-episode schizophrenia patients parallel changes in neuroimaging and cognitive phenotypes. | Hu M, Xia Y, Zong X, Sweeney JA, Bishop JR, Liao Y, Giase G, Li B, Rubin LH, Wang Y, Li Z, He Y, Chen X, Liu C, Chen C, Tang J | Psychiatry research | 36075150 | Psychiatry Res | 2022 Nov |
| Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. | Selvaraj S, Schmitt AD, Dixon JR, Ren B | BMC genomics | 26541200 | BMC Genomics | 2015 Nov 5 |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt AD, Hu M, Ren B | Nature reviews. Molecular cell biology | 27580841 | Nat Rev Mol Cell Biol | 2016 Dec |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu M, Ren B | Annual review of cell and developmental biology | 28783961 | Annu Rev Cell Dev Biol | 2017 Oct 6 |
| A compendium of promoter-centered long-range chromatin interactions in the human genome. | Jung I, Schmitt A, Diao Y, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr CL, Li B, Kuan S, Kim D, Ren B | Nature genetics | 31501517 | Nat Genet | 2019 Oct |
| A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. | Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B | Cell reports | 27851967 | Cell Rep | 2016 Nov 15 |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon JR, Gorkin DU, Ren B | Molecular cell | 27259200 | Mol Cell | 2016 Jun 2 |
| MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility. | Peck BC, Weiser M, Lee SE, Gipson GR, Iyer VB, Sartor RB, Herfarth HH, Long MD, Hansen JJ, Isaacs KL, Trembath DG, Rahbar R, Sadiq TS, Furey TS, Sethupathy P, Sheikh SZ | Inflammatory bowel diseases | 26164662 | Inflamm Bowel Dis | 2015 Sep |
| Colonic epithelial miR-31 associates with the development of Crohn's phenotypes. | Keith BP, Barrow JB, Toyonaga T, Kazgan N, O'Connor MH, Shah ND, Schaner MS, Wolber EA, Trad OK, Gipson GR, Pitman WA, Kanke M, Saxena SJ, Chaumont N, Sadiq TS, Koruda MJ, Cotney PA, Allbritton N, Trembath DG, Sylvester F, Furey TS, Sethupathy P, Sheikh SZ | JCI insight | 30282822 | JCI Insight | 2018 Oct 4 |
| Molecular classification of Crohn's disease reveals two clinically relevant subtypes. | Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DPB, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, Sheikh SZ | Gut | 27742763 | Gut | 2018 Jan |
| Correcting nucleotide-specific biases in high-throughput sequencing data. | Wang JR, Quach B, Furey TS | BMC bioinformatics | 28764645 | BMC Bioinformatics | 2017 Aug 1 |
| DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. | Quach B, Furey TS | Bioinformatics (Oxford, England) | 27993786 | Bioinformatics | 2017 Apr 1 |
| Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses. | Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, Sheikh SZ | European journal of immunology | 27159132 | Eur J Immunol | 2016 Aug |
| Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. | Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE | Skeletal muscle | 35971133 | Skelet Muscle | 2022 Aug 15 |
| Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors. | Bar-Nur O, Gerli MFM, Di Stefano B, Almada AE, Galvin A, Coffey A, Huebner AJ, Feige P, Verheul C, Cheung P, Payzin-Dogru D, Paisant S, Anselmo A, Sadreyev RI, Ott HC, Tajbakhsh S, Rudnicki MA, Wagers AJ, Hochedlinger K | Stem cell reports | 29742392 | Stem Cell Reports | 2018 May 8 |
| FOS licenses early events in stem cell activation driving skeletal muscle regeneration. | Almada AE, Horwitz N, Price FD, Gonzalez AE, Ko M, Bolukbasi OV, Messemer KA, Chen S, Sinha M, Rubin LL, Wagers AJ | Cell reports | 33503437 | Cell Rep | 2021 Jan 26 |
| Molecular circuitry of stem cell fate in skeletal muscle regeneration, ageing and disease. | Almada AE, Wagers AJ | Nature reviews. Molecular cell biology | 26956195 | Nat Rev Mol Cell Biol | 2016 May |
| Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. | Libbrecht MW, Ay F, Hoffman MM, Gilbert DM, Bilmes JA, Noble WS | Genome research | 25677182 | Genome Res | 2015 Apr |
| PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. | Durham TJ, Libbrecht MW, Howbert JJ, Bilmes J, Noble WS | Nature communications | 29643364 | Nat Commun | 2018 Apr 11 |
| Entropic Graph-based Posterior Regularization. | Libbrecht MW, Hoffman MM, Bilmes JA, Noble WS | Proceedings of the ... International Conference on Machine Learning. International Conference on Machine Learning | 39483441 | Proc Int Conf Mach Learn | 2015 Jul |
| NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions. | Zheng D, Trynda J, Sun Z, Li Z | BMC genomics | 31266464 | BMC Genomics | 2019 Jul 2 |
| High-resolution digital profiling of the epigenome. | Zentner GE, Henikoff S | Nature reviews. Genetics | 25297728 | Nat Rev Genet | 2014 Dec |
| CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer. | Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE, Shaknovich R, Lobanenkov VV, Liggitt D, Shmulevich I, Melnick A, Filippova GN | Cell reports | 24794443 | Cell Rep | 2014 May 22 |
| ARF inhibits the growth and malignant progression of non-small-cell lung carcinoma. | Busch SE, Moser RD, Gurley KE, Kelly-Spratt KS, Liggitt HD, Kemp CJ | Oncogene | 23752194 | Oncogene | 2014 May 15 |
| A unique chromatin complex occupies young α-satellite arrays of human centromeres. | Henikoff JG, Thakur J, Kasinathan S, Henikoff S | Science advances | 25927077 | Sci Adv | 2015 Feb 12 |
| Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. | Teves SS, Henikoff S | Genes & development | 22085965 | Genes Dev | 2011 Nov 15 |
| ARF suppresses hepatic vascular neoplasia in a carcinogen-exposed murine model. | Busch SE, Gurley KE, Moser RD, Kemp CJ | The Journal of pathology | 22430984 | J Pathol | 2012 Jul |
| Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years. | Kemp CJ | Cold Spring Harbor protocols | 26430259 | Cold Spring Harb Protoc | 2015 Oct 1 |
| Anthracyclines induce double-strand DNA breaks at active gene promoters. | Yang F, Kemp CJ, Henikoff S | Mutation research | 25705119 | Mutat Res | 2015 Mar |
| ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. | Zentner GE, Kasinathan S, Xin B, Rohs R, Henikoff S | Nature communications | 26490019 | Nat Commun | 2015 Oct 22 |
| High-resolution mapping of transcription factor binding sites on native chromatin. | Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S | Nature methods | 24336359 | Nat Methods | 2014 Feb |
| Tumors induce coordinate growth of artery, vein, and lymphatic vessel triads. | Ruddell A, Croft A, Kelly-Spratt K, Furuya M, Kemp CJ | BMC cancer | 24886322 | BMC Cancer | 2014 May 21 |
| Functional kinomics identifies candidate therapeutic targets in head and neck cancer. | Moser R, Xu C, Kao M, Annis J, Lerma LA, Schaupp CM, Gurley KE, Jang IS, Biktasova A, Yarbrough WG, Margolin AA, Grandori C, Kemp CJ, Méndez E | Clinical cancer research : an official journal of the American Association for Cancer Research | 25125259 | Clin Cancer Res | 2014 Aug 15 |
| Doxorubicin enhances nucleosome turnover around promoters. | Yang F, Kemp CJ, Henikoff S | Current biology : CB | 23602475 | Curr Biol | 2013 May 6 |
| Mot1 redistributes TBP from TATA-containing to TATA-less promoters. | Zentner GE, Henikoff S | Molecular and cellular biology | 24144978 | Mol Cell Biol | 2013 Dec |
| Doxorubicin, DNA torsion, and chromatin dynamics. | Yang F, Teves SS, Kemp CJ, Henikoff S | Biochimica et biophysica acta | 24361676 | Biochim Biophys Acta | 2014 Jan |
| Regulation of nucleosome dynamics by histone modifications. | Zentner GE, Henikoff S | Nature structural & molecular biology | 23463310 | Nat Struct Mol Biol | 2013 Mar |
| ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. | Zentner GE, Tsukiyama T, Henikoff S | PLoS genetics | 23468649 | PLoS Genet | 2013 |
| Surveying the epigenomic landscape, one base at a time. | Zentner GE, Henikoff S | Genome biology | 23088423 | Genome Biol | 2012 Oct 22 |
| The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. | Skene PJ, Hernandez AE, Groudine M, Henikoff S | eLife | 24737864 | Elife | 2014 Apr 15 |
| Mechanisms of Nucleosome Dynamics In Vivo. | Henikoff S | Cold Spring Harbor perspectives in medicine | 27503998 | Cold Spring Harb Perspect Med | 2016 Sep 1 |
| Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort. | Feinberg JI, Bakulski KM, Jaffe AE, Tryggvadottir R, Brown SC, Goldman LR, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Fallin MD, Feinberg AP | International journal of epidemiology | 25878217 | Int J Epidemiol | 2015 Aug |
| Identification of differentially methylated loci using wavelet-based functional mixed models. | Lee W, Morris JS | Bioinformatics (Oxford, England) | 26559505 | Bioinformatics | 2016 Mar 1 |
| Prenatal Metal Exposures and Child Social Responsiveness Scale Scores in 2 Prospective Studies. | Yu EX, Dou JF, Volk HE, Bakulski KM, Benke K, Hertz-Picciotto I, Schmidt RJ, Newschaffer CJ, Feinberg JI, Daniels J, Fallin MD, Ladd-Acosta C, Hamra GB | Environmental health insights | 38317694 | Environ Health Insights | 2024 |
| Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort. | Feinberg JI, Schrott R, Ladd-Acosta C, Newschaffer CJ, Hertz-Picciotto I, Croen LA, Daniele Fallin M, Feinberg AP, Volk HE | Molecular psychiatry | 37100868 | Mol Psychiatry | 2024 Jan |
| Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. | Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA | International journal of epidemiology | 22422453 | Int J Epidemiol | 2012 Feb |
| Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". | Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD | Current behavioral neuroscience reports | 28093577 | Curr Behav Neurosci Rep | 2016 Sep |
| Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns. | Bakulski KM, Lee H, Feinberg JI, Wells EM, Brown S, Herbstman JB, Witter FR, Halden RU, Caldwell K, Mortensen ME, Jaffe AE, Moye J Jr, Caulfield LE, Pan Y, Goldman LR, Feinberg AP, Fallin MD | International journal of epidemiology | 25906783 | Int J Epidemiol | 2015 Aug |
| Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI). | Aung MT, M Bakulski K, Feinberg JI, F Dou J, D Meeker J, Mukherjee B, Loch-Caruso R, Ladd-Acosta C, Volk HE, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Fallin MD | Epigenetics | 33794742 | Epigenetics | 2022 Mar |
| Maternal age is related to offspring DNA methylation: A meta-analysis of results from the PACE consortium. | Yeung E, Biedrzycki RJ, Gómez Herrera LC, Issarapu P, Dou J, Marques IF, Mansuri SR, Page CM, Harbs J, Khodasevich D, Poisel E, Niu Z, Allard C, Casey E, Berstein FM, Mancano G, Elliott HR, Richmond R, He Y, Ronkainen J, Sebert S, Bell EM, Sharp G, Mumford SL, Schisterman EF, Chandak GR, Fall CHD, Sahariah SA, Silver MJ, Prentice AM, Bouchard L, Domellof M, West C, Holland N, Cardenas A, Eskenazi B, Zillich L, Witt SH, Send T, Breton C, Bakulski KM, Fallin MD, Schmidt RJ, Stein DJ, Zar HJ, Jaddoe VWV, Wright J, Grazuleviciene R, Gutzkow KB, Sunyer J, Huels A, Vrijheid M, Harlid S, London S, Hivert MF, Felix J, Bustamante M, Guan W | Aging cell | 38808605 | Aging Cell | 2024 Aug |
| DNA methylation signatures of prenatal socioeconomic position associated with 36-month language outcomes. | Rajaprakash M, Palmore M, Bakulski KM, Howerton E, Lyall K, Schmidt RJ, Newschaffer C, Croen LA, Hertz-Picciotto I, Volk H, Ladd-Acosta C, Fallin MD | Research in developmental disabilities | 39357175 | Res Dev Disabil | 2024 Nov |
| Epigenetic Signatures as Biomarkers of Exposure. | Ladd-Acosta C | Current environmental health reports | 26231361 | Curr Environ Health Rep | 2015 Jun |
| Epigenetic marks of prenatal air pollution exposure found in multiple tissues relevant for child health. | Ladd-Acosta C, Feinberg JI, Brown SC, Lurmann FW, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Fallin MD, Volk HE | Environment international | 30826615 | Environ Int | 2019 May |
| DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. | Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD | International journal of epidemiology | 22422452 | Int J Epidemiol | 2012 Feb |
| Epigenetic epidemiology: promises for public health research. | Bakulski KM, Fallin MD | Environmental and molecular mutagenesis | 24449392 | Environ Mol Mutagen | 2014 Apr |
| Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. | Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Arking DE, Ladd-Acosta C, Fallin MD | Nature communications | 29066808 | Nat Commun | 2017 Oct 24 |
| Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. | Andrews SV, Sheppard B, Windham GC, Schieve LA, Schendel DE, Croen LA, Chopra P, Alisch RS, Newschaffer CJ, Warren ST, Feinberg AP, Fallin MD, Ladd-Acosta C | Molecular autism | 29988321 | Mol Autism | 2018 |
| "Gap hunting" to characterize clustered probe signals in Illumina methylation array data. | Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD | Epigenetics & chromatin | 27980682 | Epigenetics Chromatin | 2016 |
| Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium. | Felix JF, Joubert BR, Baccarelli AA, Sharp GC, Almqvist C, Annesi-Maesano I, Arshad H, Baïz N, Bakermans-Kranenburg MJ, Bakulski KM, Binder EB, Bouchard L, Breton CV, Brunekreef B, Brunst KJ, Burchard EG, Bustamante M, Chatzi L, Cheng Munthe-Kaas M, Corpeleijn E, Czamara D, Dabelea D, Davey Smith G, De Boever P, Duijts L, Dwyer T, Eng C, Eskenazi B, Everson TM, Falahi F, Fallin MD, Farchi S, Fernandez MF, Gao L, Gaunt TR, Ghantous A, Gillman MW, Gonseth S, Grote V, Gruzieva O, Håberg SE, Herceg Z, Hivert MF, Holland N, Holloway JW, Hoyo C, Hu D, Huang RC, Huen K, Järvelin MR, Jima DD, Just AC, Karagas MR, Karlsson R, Karmaus W, Kechris KJ, Kere J, Kogevinas M, Koletzko B, Koppelman GH, Küpers LK, Ladd-Acosta C, Lahti J, Lambrechts N, Langie SAS, Lie RT, Liu AH, Magnus MC, Magnus P, Maguire RL, Marsit CJ, McArdle W, Melén E, Melton P, Murphy SK, Nawrot TS, Nisticò L, Nohr EA, Nordlund B, Nystad W, Oh SS, Oken E, Page CM, Perron P, Pershagen G, Pizzi C, Plusquin M, Raikkonen K, Reese SE, Reischl E, Richiardi L, Ring S, Roy RP, Rzehak P, Schoeters G, Schwartz DA, Sebert S, Snieder H, Sørensen TIA, Starling AP, Sunyer J, Taylor JA, Tiemeier H, Ullemar V, Vafeiadi M, Van Ijzendoorn MH, Vonk JM, Vriens A, Vrijheid M, Wang P, Wiemels JL, Wilcox AJ, Wright RJ, Xu CJ, Xu Z, Yang IV, Yousefi P, Zhang H, Zhang W, Zhao S, Agha G, Relton CL, Jaddoe VWV, London SJ | International journal of epidemiology | 29025028 | Int J Epidemiol | 2018 Feb 1 |
| DNA methylation signatures as biomarkers of prior environmental exposures. | Ladd-Acosta C, Fallin MD | Current epidemiology reports | 31032172 | Curr Epidemiol Rep | 2019 Mar |
| Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes. | Mordaunt CE, Jianu JM, Laufer BI, Zhu Y, Hwang H, Dunaway KW, Bakulski KM, Feinberg JI, Volk HE, Lyall K, Croen LA, Newschaffer CJ, Ozonoff S, Hertz-Picciotto I, Fallin MD, Schmidt RJ, LaSalle JM | Genome medicine | 33054850 | Genome Med | 2020 Oct 14 |
| Associations between accelerated parental biologic age, autism spectrum disorder, social traits, and developmental and cognitive outcomes in their children. | Song AY, Bakulski K, Feinberg JI, Newschaffer C, Croen LA, Hertz-Picciotto I, Schmidt RJ, Farzadegan H, Lyall K, Fallin MD, Volk HE, Ladd-Acosta C | Autism research : official journal of the International Society for Autism Research | 36189953 | Autism Res | 2022 Dec |
| Xenoestrogen-induced epigenetic repression of microRNA-9-3 in breast epithelial cells. | Hsu PY, Deatherage DE, Rodriguez BA, Liyanarachchi S, Weng YI, Zuo T, Liu J, Cheng AS, Huang TH | Cancer research | 19549897 | Cancer Res | 2009 Jul 15 |
| Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. | Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, Huang TH, Jin VX | BMC genomics | 23368971 | BMC Genomics | 2013 Jan 31 |
| Seed in soil, with an epigenetic view. | Lin HJ, Zuo T, Chao JR, Peng Z, Asamoto LK, Yamashita SS, Huang TH | Biochimica et biophysica acta | 19162126 | Biochim Biophys Acta | 2009 Sep |
| HRTBLDb: an informative data resource for hormone receptors target binding loci. | Kennedy BA, Gao W, Huang TH, Jin VX | Nucleic acids research | 19773424 | Nucleic Acids Res | 2010 Jan |
| Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells. | Weng YI, Hsu PY, Liyanarachchi S, Liu J, Deatherage DE, Huang YW, Zuo T, Rodriguez B, Lin CH, Cheng AL, Huang TH | Toxicology and applied pharmacology | 20678512 | Toxicol Appl Pharmacol | 2010 Oct 15 |
| Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. | Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, Heerema N, Hsiao TH, Chiu YC, Chen Y, Liu Y, Li L, Li R, Thompson IM, Nephew KP, Sharp ZD, Kirma NB, Jin VX, Huang TH | Cancer cell | 23948299 | Cancer Cell | 2013 Aug 12 |
| Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells. | Hsu PY, Hsu HK, Hsiao TH, Ye Z, Wang E, Profit AL, Jatoi I, Chen Y, Kirma NB, Jin VX, Sharp ZD, Huang TH | Oncogene | 26300005 | Oncogene | 2016 May 5 |
| Black raspberries protectively regulate methylation of Wnt pathway genes in precancerous colon tissue. | Wang LS, Kuo CT, Huang TH, Yearsley M, Oshima K, Stoner GD, Yu J, Lechner JF, Huang YW | Cancer prevention research (Philadelphia, Pa.) | 24129635 | Cancer Prev Res (Phila) | 2013 Dec |
| Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. | Weng YI, Huang TH, Yan PS | Methods in molecular biology (Clifton, N.J.) | 19763503 | Methods Mol Biol | 2009 |
| Methods in DNA methylation profiling. | Zuo T, Tycko B, Liu TM, Lin JJ, Huang TH | Epigenomics | 20526417 | Epigenomics | 2009 Dec |
| High-fat or ethinyl-oestradiol intake during pregnancy increases mammary cancer risk in several generations of offspring. | de Assis S, Warri A, Cruz MI, Laja O, Tian Y, Zhang B, Wang Y, Huang TH, Hilakivi-Clarke L | Nature communications | 22968699 | Nat Commun | 2012 |
| A modulator based regulatory network for ERα signaling pathway. | Wu HY, Zheng P, Jiang G, Liu Y, Nephew KP, Huang TH, Li L | BMC genomics | 23134758 | BMC Genomics | 2012 |
| A phase Ib study of the effects of black raspberries on rectal polyps in patients with familial adenomatous polyposis. | Wang LS, Burke CA, Hasson H, Kuo CT, Molmenti CL, Seguin C, Liu P, Huang TH, Frankel WL, Stoner GD | Cancer prevention research (Philadelphia, Pa.) | 24764585 | Cancer Prev Res (Phila) | 2014 Jul |
| Epigenetic deregulation of the anaplastic lymphoma kinase gene modulates mesenchymal characteristics of oral squamous cell carcinomas. | Huang TT, Gonzales CB, Gu F, Hsu YT, Jadhav RR, Wang CM, Redding SW, Tseng CE, Lee CC, Thompson IM, Chen HR, Huang TH, Kirma NB | Carcinogenesis | 23568951 | Carcinogenesis | 2013 Aug |
| Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. | Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC, Weng YI, Deatherage DE, Chen Z, Pereira JS, Lopez R, Russo J, Wang Q, Lamartiniere CA, Nephew KP, Huang TH | Genome research | 20442245 | Genome Res | 2010 Jun |
| Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. | Tang B, Hsu HK, Hsu PY, Bonneville R, Chen SS, Huang TH, Jin VX | Scientific reports | 23166858 | Sci Rep | 2012 |
| CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. | Gu F, Doderer MS, Huang YW, Roa JC, Goodfellow PJ, Kizer EL, Huang TH, Chen Y | PloS one | 23630576 | PLoS One | 2013 |
| Chromatin remodeling in mammary gland differentiation and breast tumorigenesis. | Huang TH, Esteller M | Cold Spring Harbor perspectives in biology | 20610549 | Cold Spring Harb Perspect Biol | 2010 Sep |
| Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment. | Dworkin AM, Huang TH, Toland AE | Seminars in cancer biology | 19429480 | Semin Cancer Biol | 2009 Jun |
| Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. | Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH | Cancer research | 21216892 | Cancer Res | 2011 Mar 1 |
| Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells. | Rodriguez BA, Weng YI, Liu TM, Zuo T, Hsu PY, Lin CH, Cheng AL, Cui H, Yan PS, Huang TH | Carcinogenesis | 21304052 | Carcinogenesis | 2011 Jun |
| Epithelial Notch signaling regulates interstitial fibrosis development in the kidneys of mice and humans. | Bielesz B, Sirin Y, Si H, Niranjan T, Gruenwald A, Ahn S, Kato H, Pullman J, Gessler M, Haase VH, Susztak K | The Journal of clinical investigation | 20978353 | J Clin Invest | 2010 Nov |
| Endocardial to myocardial notch-wnt-bmp axis regulates early heart valve development. | Wang Y, Wu B, Chamberlain AA, Lui W, Koirala P, Susztak K, Klein D, Taylor V, Zhou B | PloS one | 23560082 | PLoS One | 2013 |
| Epithelial-mesenchymal transition and podocyte loss in diabetic kidney disease. | Reidy K, Susztak K | American journal of kidney diseases : the official journal of the National Kidney Foundation | 19781451 | Am J Kidney Dis | 2009 Oct |
| Molecular mechanisms of diabetic kidney disease. | Reidy K, Kang HM, Hostetter T, Susztak K | The Journal of clinical investigation | 24892707 | J Clin Invest | 2014 Jun |
| Defective fatty acid oxidation in renal tubular epithelial cells has a key role in kidney fibrosis development. | Kang HM, Ahn SH, Choi P, Ko YA, Han SH, Chinga F, Park AS, Tao J, Sharma K, Pullman J, Bottinger EP, Goldberg IJ, Susztak K | Nature medicine | 25419705 | Nat Med | 2015 Jan |
| Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations. | Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox CS, Coresh J, Linda Kao WH | BMC genetics | 25007794 | BMC Genet | 2014 Jul 9 |
| Loss of ELK1 has differential effects on age-dependent organ fibrosis. | Cairns JT, Habgood A, Edwards-Pritchard RC, Joseph C, John AE, Wilkinson C, Stewart ID, Leslie J, Blaxall BC, Susztak K, Alberti S, Nordheim A, Oakley F, Jenkins G, Tatler AL | The international journal of biochemistry & cell biology | 31877385 | Int J Biochem Cell Biol | 2020 Mar |
| Understanding the kidney one cell at a time. | Park J, Liu CL, Kim J, Susztak K | Kidney international | 31492507 | Kidney Int | 2019 Oct |
| Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease. | Gluck C, Qiu C, Han SY, Palmer M, Park J, Ko YA, Guan Y, Sheng X, Hanson RL, Huang J, Chen Y, Park ASD, Izquierdo MC, Mantzaris I, Verma A, Pullman J, Li H, Susztak K | Nature communications | 31165727 | Nat Commun | 2019 Jun 5 |
| The interdependence of renal epithelial and endothelial metabolism and cell state. | Balzer MS, Susztak K | Science signaling | 32518144 | Sci Signal | 2020 Jun 9 |
| Repair problems in podocytes: Wnt, Notch, and glomerulosclerosis. | Kato H, Susztak K | Seminars in nephrology | 22958489 | Semin Nephrol | 2012 Jul |
| Diet-Induced Podocyte Dysfunction in Drosophila and Mammals. | Na J, Sweetwyne MT, Park AS, Susztak K, Cagan RL | Cell reports | 26190114 | Cell Rep | 2015 Jul 28 |
| Diabetic kidney disease. | Thomas MC, Brownlee M, Susztak K, Sharma K, Jandeleit-Dahm KA, Zoungas S, Rossing P, Groop PH, Cooper ME | Nature reviews. Disease primers | 27188921 | Nat Rev Dis Primers | 2015 Jul 30 |
| The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. | Lin J, Zhang X, Xue C, Zhang H, Shashaty MG, Gosai SJ, Meyer N, Grazioli A, Hinkle C, Caughey J, Li W, Susztak K, Gregory BD, Li M, Reilly MP | American journal of physiology. Renal physiology | 26400545 | Am J Physiol Renal Physiol | 2015 Dec 1 |
| The transcriptomic signature of the aging podocyte. | Mukhi D, Susztak K | Kidney international | 33126968 | Kidney Int | 2020 Nov |
| Genomic integration of ERRγ-HNF1β regulates renal bioenergetics and prevents chronic kidney disease. | Zhao J, Lupino K, Wilkins BJ, Qiu C, Liu J, Omura Y, Allred AL, McDonald C, Susztak K, Barish GD, Pei L | Proceedings of the National Academy of Sciences of the United States of America | 29735694 | Proc Natl Acad Sci U S A | 2018 May 22 |
| Transcriptome- and proteome-wide association studies identify genes associated with renal cell carcinoma. | Dutta D, Guo X, Winter TD, Jahagirdar O, Renal Cancer Genetics Consortium, Ha E, Susztak K, Machiela MJ, Chanock SJ, Purdue MP | American journal of human genetics | 39137781 | Am J Hum Genet | 2024 Sep 5 |
| HIV viral protein R induces loss of DCT1-type renal tubules. | Latt KZ, Yoshida T, Shrivastav S, Abedini A, Reece JM, Sun Z, Lee H, Okamoto K, Dagur P, Heymann J, Zhao Y, Chung JY, Hewitt S, Jose PA, Lee K, He JC, Winkler CA, Knepper MA, Kino T, Rosenberg AZ, Susztak K, Kopp JB | bioRxiv : the preprint server for biology | 36945458 | bioRxiv | 2023 Nov 13 |
| Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development. | Dhillon P, Mulholland KA, Hu H, Park J, Sheng X, Abedini A, Liu H, Vassalotti A, Wu J, Susztak K | Nature communications | 36732547 | Nat Commun | 2023 Feb 2 |
| PGC-1α Protects from Notch-Induced Kidney Fibrosis Development. | Han SH, Wu MY, Nam BY, Park JT, Yoo TH, Kang SW, Park J, Chinga F, Li SY, Susztak K | Journal of the American Society of Nephrology : JASN | 28751525 | J Am Soc Nephrol | 2017 Nov |
| Epigenetics and Epigenomics: Implications for Diabetes and Obesity. | Rosen ED, Kaestner KH, Natarajan R, Patti ME, Sallari R, Sander M, Susztak K | Diabetes | 30237160 | Diabetes | 2018 Oct |
| Epigenome-wide association studies identify DNA methylation associated with kidney function. | Chu AY, Tin A, Schlosser P, Ko YA, Qiu C, Yao C, Joehanes R, Grams ME, Liang L, Gluck CA, Liu C, Coresh J, Hwang SJ, Levy D, Boerwinkle E, Pankow JS, Yang Q, Fornage M, Fox CS, Susztak K, Köttgen A | Nature communications | 29097680 | Nat Commun | 2017 Nov 3 |
| Katalin Susztak. | Trends in molecular medicine | 29980480 | Trends Mol Med | 2018 Aug | |
| Introduction: Systems Biology of Kidney Disease. | Sharma K, Susztak K, Pennathur S | Seminars in nephrology | 29602402 | Semin Nephrol | 2018 Mar |
| Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. | Park J, Shrestha R, Qiu C, Kondo A, Huang S, Werth M, Li M, Barasch J, Suszták K | Science (New York, N.Y.) | 29622724 | Science | 2018 May 18 |
| Associations of Fenofibrate Therapy With Incidence and Progression of CKD in Patients With Type 2 Diabetes. | Frazier R, Mehta R, Cai X, Lee J, Napoli S, Craven T, Tuazon J, Safdi A, Scialla J, Susztak K, Isakova T | Kidney international reports | 30596172 | Kidney Int Rep | 2019 Jan |
| Genome-wide association studies identify the role of caspase-9 in kidney disease. | Doke T, Huang S, Qiu C, Sheng X, Seasock M, Liu H, Ma Z, Palmer M, Susztak K | Science advances | 34739325 | Sci Adv | 2021 Nov 5 |
| Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. | Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K | Nature communications | 33859189 | Nat Commun | 2021 Apr 15 |
| Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. | Balzer MS, Doke T, Yang YW, Aldridge DL, Hu H, Mai H, Mukhi D, Ma Z, Shrestha R, Palmer MB, Hunter CA, Susztak K | Nature communications | 35821371 | Nat Commun | 2022 Jul 11 |
| Antisense oligonucleotides ameliorate kidney dysfunction in podocyte-specific APOL1 risk variant mice. | Yang YW, Poudel B, Frederick J, Dhillon P, Shrestha R, Ma Z, Wu J, Okamoto K, Kopp JB, Booten SL, Gattis D, Watt AT, Palmer M, Aghajan M, Susztak K | Molecular therapy : the journal of the American Society of Gene Therapy | 35450819 | Mol Ther | 2022 Jul 6 |
| Fetal environment, epigenetics, and pediatric renal disease. | Woroniecki R, Gaikwad AB, Susztak K | Pediatric nephrology (Berlin, Germany) | 21174217 | Pediatr Nephrol | 2011 May |
| Transcriptome analysis of human diabetic kidney disease. | Woroniecka KI, Park AS, Mohtat D, Thomas DB, Pullman JM, Susztak K | Diabetes | 21752957 | Diabetes | 2011 Sep |
| Smad1 as a biomarker for diabetic nephropathy. | Kato H, Si H, Hostetter T, Susztak K | Diabetes | 18511448 | Diabetes | 2008 Jun |
| The next generation of therapeutics for chronic kidney disease. | Breyer MD, Susztak K | Nature reviews. Drug discovery | 27230798 | Nat Rev Drug Discov | 2016 Aug |
| The Role of Peroxisome Proliferator-Activated Receptor γ Coactivator 1α (PGC-1α) in Kidney Disease. | Li SY, Susztak K | Seminars in nephrology | 29602395 | Semin Nephrol | 2018 Mar |
| Human Kidney Tubule-Specific Gene Expression Based Dissection of Chronic Kidney Disease Traits. | Beckerman P, Qiu C, Park J, Ledo N, Ko YA, Park AD, Han SY, Choi P, Palmer M, Susztak K | EBioMedicine | 28970079 | EBioMedicine | 2017 Oct |
| Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions. | Shungin D, Deng WQ, Varga TV, Luan J, Mihailov E, Metspalu A, GIANT Consortium, Morris AP, Forouhi NG, Lindgren C, Magnusson PKE, Pedersen NL, Hallmans G, Chu AY, Justice AE, Graff M, Winkler TW, Rose LM, Langenberg C, Cupples LA, Ridker PM, Wareham NJ, Ong KK, Loos RJF, Chasman DI, Ingelsson E, Kilpeläinen TO, Scott RA, Mägi R, Paré G, Franks PW | PLoS genetics | 28614350 | PLoS Genet | 2017 Jun |
| Kidney triglyceride accumulation in the fasted mouse is dependent upon serum free fatty acids. | Scerbo D, Son NH, Sirwi A, Zeng L, Sas KM, Cifarelli V, Schoiswohl G, Huggins LA, Gumaste N, Hu Y, Pennathur S, Abumrad NA, Kershaw EE, Hussain MM, Susztak K, Goldberg IJ | Journal of lipid research | 28404638 | J Lipid Res | 2017 Jun |
| Transgenic expression of human APOL1 risk variants in podocytes induces kidney disease in mice. | Beckerman P, Bi-Karchin J, Park AS, Qiu C, Dummer PD, Soomro I, Boustany-Kari CM, Pullen SS, Miner JH, Hu CA, Rohacs T, Inoue K, Ishibe S, Saleem MA, Palmer MB, Cuervo AM, Kopp JB, Susztak K | Nature medicine | 28218918 | Nat Med | 2017 Apr |
| The long noncoding RNA Tug1 connects metabolic changes with kidney disease in podocytes. | Li SY, Susztak K | The Journal of clinical investigation | 27760046 | J Clin Invest | 2016 Nov 1 |
| Developing Treatments for Chronic Kidney Disease in the 21st Century. | Breyer MD, Susztak K | Seminars in nephrology | 27987541 | Semin Nephrol | 2016 Nov |
| Genome-Wide Association of Copy Number Polymorphisms and Kidney Function. | Li M, Carey J, Cristiano S, Susztak K, Coresh J, Boerwinkle E, Kao WH, Beaty TH, Köttgen A, Scharpf RB | PloS one | 28135296 | PLoS One | 2017 |
| Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue. | Gluck C, Ko YA, Susztak K | Current diabetes reports | 28364354 | Curr Diab Rep | 2017 May |
| Emerging role of autophagy in kidney function, diseases and aging. | Huber TB, Edelstein CL, Hartleben B, Inoki K, Jiang M, Koya D, Kume S, Lieberthal W, Pallet N, Quiroga A, Ravichandran K, Susztak K, Yoshida S, Dong Z | Autophagy | 22692002 | Autophagy | 2012 Jul 1 |
| Sweet debate: fructose versus glucose in diabetic kidney disease. | Beckerman P, Susztak K | Journal of the American Society of Nephrology : JASN | 24876119 | J Am Soc Nephrol | 2014 Nov |
| Functional genomic annotation of genetic risk loci highlights inflammation and epithelial biology networks in CKD. | Ledo N, Ko YA, Park AS, Kang HM, Han SY, Choi P, Susztak K | Journal of the American Society of Nephrology : JASN | 25231882 | J Am Soc Nephrol | 2015 Mar |
| Epigenomics: the science of no-longer-junk DNA. Why study it in chronic kidney disease? | Ko YA, Susztak K | Seminars in nephrology | 24011577 | Semin Nephrol | 2013 Jul |
| Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming. | Huang S, Park J, Qiu C, Chung KW, Li SY, Sirin Y, Han SH, Taylor V, Zimber-Strobl U, Susztak K | PLoS biology | 30226866 | PLoS Biol | 2018 Sep |
| Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. | Hu CY, Mohtat D, Yu Y, Ko YA, Shenoy N, Bhattacharya S, Izquierdo MC, Park AS, Giricz O, Vallumsetla N, Gundabolu K, Ware K, Bhagat TD, Suzuki M, Pullman J, Liu XS, Greally JM, Susztak K, Verma A | Clinical cancer research : an official journal of the American Association for Cancer Research | 24916699 | Clin Cancer Res | 2014 Aug 15 |
| Sox9-Positive Progenitor Cells Play a Key Role in Renal Tubule Epithelial Regeneration in Mice. | Kang HM, Huang S, Reidy K, Han SH, Chinga F, Susztak K | Cell reports | 26776520 | Cell Rep | 2016 Feb 2 |
| From mapping kidney function to mechanism and prediction. | Hirohama D, Susztak K | Nature reviews. Nephrology | 34819631 | Nat Rev Nephrol | 2022 Feb |
| The kidney transcriptome, from single cells to whole organs and back. | Huang S, Sheng X, Susztak K | Current opinion in nephrology and hypertension | 30844884 | Curr Opin Nephrol Hypertens | 2019 May |
| APOL1 risk variants in individuals of African genetic ancestry drive endothelial cell defects that exacerbate sepsis. | Wu J, Ma Z, Raman A, Beckerman P, Dhillon P, Mukhi D, Palmer M, Chen HC, Cohen CR, Dunn T, Reilly J, Meyer N, Shashaty M, Arany Z, Haskó G, Laudanski K, Hung A, Susztak K | Immunity | 34715018 | Immunity | 2021 Nov 9 |
| Longitudinal urinary biomarkers of immunological activation in covid-19 patients without clinically apparent kidney disease versus acute and chronic failure. | Laudanski K, Okeke T, Hajj J, Siddiq K, Rader DJ, Wu J, Susztak K | Scientific reports | 34608231 | Sci Rep | 2021 Oct 4 |
| Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes. | Mychaleckyj JC, Valo E, Ichimura T, Ahluwalia TS, Dina C, Miller RG, Shabalin IG, Gyorgy B, Cao J, Onengut-Gumuscu S, Satake E, Smiles AM, Haukka JK, Tregouet DA, Costacou T, O'Neil K, Paterson AD, Forsblom C, Keenan HA, Pezzolesi MG, Pragnell M, Galecki A, Rich SS, Sandholm N, Klein R, Klein BE, Susztak K, Orchard TJ, Korstanje R, King GL, Hadjadj S, Rossing P, Bonventre JV, Groop PH, Warram JH, Krolewski AS | Journal of the American Society of Nephrology : JASN | 34261756 | J Am Soc Nephrol | 2021 Oct |
| Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis. | Vujkovic M, Keaton JM, Lynch JA, Miller DR, Zhou J, Tcheandjieu C, Huffman JE, Assimes TL, Lorenz K, Zhu X, Hilliard AT, Judy RL, Huang J, Lee KM, Klarin D, Pyarajan S, Danesh J, Melander O, Rasheed A, Mallick NH, Hameed S, Qureshi IH, Afzal MN, Malik U, Jalal A, Abbas S, Sheng X, Gao L, Kaestner KH, Susztak K, Sun YV, DuVall SL, Cho K, Lee JS, Gaziano JM, Phillips LS, Meigs JB, Reaven PD, Wilson PW, Edwards TL, Rader DJ, Damrauer SM, O'Donnell CJ, Tsao PS, HPAP Consortium, Regeneron Genetics Center, VA Million Veteran Program, Chang KM, Voight BF, Saleheen D | Nature genetics | 32541925 | Nat Genet | 2020 Jul |
| It Takes Two to Tango: The Role of Dysregulated Metabolism and Inflammation in Kidney Disease Development. | Quinn GZ, Dhillon P, Susztak K | Seminars in nephrology | 32303282 | Semin Nephrol | 2020 Mar |
| ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing. | Fan J, Hu J, Xue C, Zhang H, Susztak K, Reilly MP, Xiao R, Li M | PLoS genetics | 32392242 | PLoS Genet | 2020 May |
| Phenome-wide association analysis suggests the APOL1 linked disease spectrum primarily drives kidney-specific pathways. | Bajaj A, Ihegword A, Qiu C, Small AM, Wei WQ, Bastarache L, Feng Q, Kember RL, Risman M, Bloom RD, Birtwell DL, Williams H, Shaffer CM, Chen J, Center RG, Denny JC, Rader DJ, Stein CM, Damrauer SM, Susztak K | Kidney international | 32247630 | Kidney Int | 2020 May |
| The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation. | Dhillon P, Park J, Hurtado Del Pozo C, Li L, Doke T, Huang S, Zhao J, Kang HM, Shrestra R, Balzer MS, Chatterjee S, Prado P, Han SY, Liu H, Sheng X, Dierickx P, Batmanov K, Romero JP, Prósper F, Li M, Pei L, Kim J, Montserrat N, Susztak K | Cell metabolism | 33301705 | Cell Metab | 2021 Feb 2 |
| Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney. | Abedini A, Zhu YO, Chatterjee S, Halasz G, Devalaraja-Narashimha K, Shrestha R, S Balzer M, Park J, Zhou T, Ma Z, Sullivan KM, Hu H, Sheng X, Liu H, Wei Y, Boustany-Kari CM, Patel U, Almaani S, Palmer M, Townsend R, Blady S, Hogan J, Morton L, Susztak K, TRIDENT Study Investigators | Journal of the American Society of Nephrology : JASN | 33531352 | J Am Soc Nephrol | 2021 Mar |
| Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis. | Miguel V, Tituaña J, Herrero JI, Herrero L, Serra D, Cuevas P, Barbas C, Puyol DR, Márquez-Expósito L, Ruiz-Ortega M, Castillo C, Sheng X, Susztak K, Ruiz-Canela M, Salas-Salvadó J, González MAM, Ortega S, Ramos R, Lamas S | The Journal of clinical investigation | 33465052 | J Clin Invest | 2021 Mar 1 |
| Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. | Sheng X, Guan Y, Ma Z, Wu J, Liu H, Qiu C, Vitale S, Miao Z, Seasock MJ, Palmer M, Shin MK, Duffin KL, Pullen SS, Edwards TL, Hellwege JN, Hung AM, Li M, Voight BF, Coffman TM, Brown CD, Susztak K | Nature genetics | 34385711 | Nat Genet | 2021 Sep |
| Unbiased Human Kidney Tissue Proteomics Identifies Matrix Metalloproteinase 7 as a Kidney Disease Biomarker. | Hirohama D, Abedini A, Moon S, Surapaneni A, Dillon ST, Vassalotti A, Liu H, Doke T, Martinez V, Md Dom Z, Karihaloo A, Palmer MB, Coresh J, Grams ME, Niewczas MA, Susztak K | Journal of the American Society of Nephrology : JASN | 37022120 | J Am Soc Nephrol | 2023 Jul 1 |
| DNA methylation markers for kidney function and progression of diabetic kidney disease. | Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, TRANSCEND Consortium, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW | Nature communications | 37188670 | Nat Commun | 2023 May 15 |
| Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment. | Liang X, Aranyi T, Zhou J, Guan Y, Hu H, Liu H, Susztak K | Journal of the American Society of Nephrology : JASN | 36522157 | J Am Soc Nephrol | 2023 Apr 1 |
| Immunological Signatures in Blood and Urine in 80 Individuals Hospitalized during the Initial Phase of COVID-19 Pandemic with Quantified Nicotine Exposure. | Laudanski K, Mahmoud MA, Ahmed AS, Susztak K, Mathew A, Chen J | International journal of molecular sciences | 38612525 | Int J Mol Sci | 2024 Mar 27 |
| The key role of altered tubule cell lipid metabolism in kidney disease development. | Lee LE, Doke T, Mukhi D, Susztak K | Kidney international | 38614389 | Kidney Int | 2024 Jul |
| Combing Genome-Wide Association Studies and Single-Cell Analysis to Elucidate the Mechanisms of Kidney Disease: Proceedings of the Henry Shavelle Professorship. | Levinsohn J, Li S, Ha E, Susztak K | Glomerular diseases | 38033715 | Glomerular Dis | 2023 Jan-Dec |
| Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression. | Abedini A, Levinsohn J, Klötzer KA, Dumoulin B, Ma Z, Frederick J, Dhillon P, Balzer MS, Shrestha R, Liu H, Vitale S, Bergeson AM, Devalaraja-Narashimha K, Grandi P, Bhattacharyya T, Hu E, Pullen SS, Boustany-Kari CM, Guarnieri P, Karihaloo A, Traum D, Yan H, Coleman K, Palmer M, Sarov-Blat L, Morton L, Hunter CA, Kaestner KH, Li M, Susztak K | Nature genetics | 39048792 | Nat Genet | 2024 Aug |
| Is IgA Class Switching Epigenetically Wired?: Untangling the Evidence. | Quinn GZ, Susztak K | Journal of the American Society of Nephrology : JASN | 39500311 | J Am Soc Nephrol | 2024 Dec 1 |
| TET2 germline variants promote kidney disease by impairing DNA repair and activating cytosolic nucleotide sensors. | Liang X, Liu H, Hu H, Ha E, Zhou J, Abedini A, Sanchez-Navarro A, Klötzer KA, Susztak K | Nature communications | 39511169 | Nat Commun | 2024 Nov 7 |
| Poly(ADP-ribose) polymerase inhibitors ameliorate nephropathy of type 2 diabetic Leprdb/db mice. | Szabó C, Biser A, Benko R, Böttinger E, Suszták K | Diabetes | 17065336 | Diabetes | 2006 Nov |
| The role of osteopontin in the development of albuminuria. | Lorenzen J, Shah R, Biser A, Staicu SA, Niranjan T, Garcia AM, Gruenwald A, Thomas DB, Shatat IF, Supe K, Woroniecki RP, Susztak K | Journal of the American Society of Nephrology : JASN | 18443355 | J Am Soc Nephrol | 2008 May |
| Tracing the footsteps of glomerular insulin signaling in diabetic kidney disease. | Chang GY, Park AS, Susztak K | Kidney international | 21451535 | Kidney Int | 2011 Apr |
| Deletion of Lkb1 in Renal Tubular Epithelial Cells Leads to CKD by Altering Metabolism. | Han SH, Malaga-Dieguez L, Chinga F, Kang HM, Tao J, Reidy K, Susztak K | Journal of the American Society of Nephrology : JASN | 26054542 | J Am Soc Nephrol | 2016 Feb |
| Notch1 and Notch2 in Podocytes Play Differential Roles During Diabetic Nephropathy Development. | Sweetwyne MT, Gruenwald A, Niranjan T, Nishinakamura R, Strobl LJ, Susztak K | Diabetes | 26293507 | Diabetes | 2015 Dec |
| Validation and genomic interrogation of the MET variant rs11762213 as a predictor of adverse outcomes in clear cell renal cell carcinoma. | Hakimi AA, Ostrovnaya I, Jacobsen A, Susztak K, Coleman JA, Russo P, Winer AG, Mano R, Sankin AI, Motzer RJ, Voss MH, Offit K, Purdue M, Pomerantz M, Freedman M, Choueiri TK, Hsieh JJ, Klein RJ | Cancer | 26505625 | Cancer | 2016 Feb 1 |
| Role of DNA methylation in renal cell carcinoma. | Shenoy N, Vallumsetla N, Zou Y, Galeas JN, Shrivastava M, Hu C, Susztak K, Verma A | Journal of hematology & oncology | 26198328 | J Hematol Oncol | 2015 Jul 22 |
| Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. | Pattaro C, Teumer A, Gorski M, Chu AY, Li M, Mijatovic V, Garnaas M, Tin A, Sorice R, Li Y, Taliun D, Olden M, Foster M, Yang Q, Chen MH, Pers TH, Johnson AD, Ko YA, Fuchsberger C, Tayo B, Nalls M, Feitosa MF, Isaacs A, Dehghan A, d'Adamo P, Adeyemo A, Dieffenbach AK, Zonderman AB, Nolte IM, van der Most PJ, Wright AF, Shuldiner AR, Morrison AC, Hofman A, Smith AV, Dreisbach AW, Franke A, Uitterlinden AG, Metspalu A, Tonjes A, Lupo A, Robino A, Johansson Å, Demirkan A, Kollerits B, Freedman BI, Ponte B, Oostra BA, Paulweber B, Krämer BK, Mitchell BD, Buckley BM, Peralta CA, Hayward C, Helmer C, Rotimi CN, Shaffer CM, Müller C, Sala C, van Duijn CM, Saint-Pierre A, Ackermann D, Shriner D, Ruggiero D, Toniolo D, Lu Y, Cusi D, Czamara D, Ellinghaus D, Siscovick DS, Ruderfer D, Gieger C, Grallert H, Rochtchina E, Atkinson EJ, Holliday EG, Boerwinkle E, Salvi E, Bottinger EP, Murgia F, Rivadeneira F, Ernst F, Kronenberg F, Hu FB, Navis GJ, Curhan GC, Ehret GB, Homuth G, Coassin S, Thun GA, Pistis G, Gambaro G, Malerba G, Montgomery GW, Eiriksdottir G, Jacobs G, Li G, Wichmann HE, Campbell H, Schmidt H, Wallaschofski H, Völzke H, Brenner H, Kroemer HK, Kramer H, Lin H, Leach IM, Ford I, Guessous I, Rudan I, Prokopenko I, Borecki I, Heid IM, Kolcic I, Persico I, Jukema JW, Wilson JF, Felix JF, Divers J, Lambert JC, Stafford JM, Gaspoz JM, Smith JA, Faul JD, Wang JJ, Ding J, Hirschhorn JN, Attia J, Whitfield JB, Chalmers J, Viikari J, Coresh J, Denny JC, Karjalainen J, Fernandes JK, Endlich K, Butterbach K, Keene KL, Lohman K, Portas L, Launer LJ, Lyytikäinen LP, Yengo L, Franke L, Ferrucci L, Rose LM, Kedenko L, Rao M, Struchalin M, Kleber ME, Cavalieri M, Haun M, Cornelis MC, Ciullo M, Pirastu M, de Andrade M, McEvoy MA, Woodward M, Adam M, Cocca M, Nauck M, Imboden M, Waldenberger M, Pruijm M, Metzger M, Stumvoll M, Evans MK, Sale MM, Kähönen M, Boban M, Bochud M, Rheinberger M, Verweij N, Bouatia-Naji N, Martin NG, Hastie N, Probst-Hensch N, Soranzo N, Devuyst O, Raitakari O, Gottesman O, Franco OH, Polasek O, Gasparini P, Munroe PB, Ridker PM, Mitchell P, Muntner P, Meisinger C, Smit JH, ICBP Consortium, AGEN Consortium, CARDIOGRAM, CHARGe-Heart Failure Group, ECHOGen Consortium, Kovacs P, Wild PS, Froguel P, Rettig R, Mägi R, Biffar R, Schmidt R, Middelberg RP, Carroll RJ, Penninx BW, Scott RJ, Katz R, Sedaghat S, Wild SH, Kardia SL, Ulivi S, Hwang SJ, Enroth S, Kloiber S, Trompet S, Stengel B, Hancock SJ, Turner ST, Rosas SE, Stracke S, Harris TB, Zeller T, Zemunik T, Lehtimäki T, Illig T, Aspelund T, Nikopensius T, Esko T, Tanaka T, Gyllensten U, Völker U, Emilsson V, Vitart V, Aalto V, Gudnason V, Chouraki V, Chen WM, Igl W, März W, Koenig W, Lieb W, Loos RJ, Liu Y, Snieder H, Pramstaller PP, Parsa A, O'Connell JR, Susztak K, Hamet P, Tremblay J, de Boer IH, Böger CA, Goessling W, Chasman DI, Köttgen A, Kao WH, Fox CS | Nature communications | 26831199 | Nat Commun | 2016 Jan 21 |
| Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease. | Ko YA, Yi H, Qiu C, Huang S, Park J, Ledo N, Köttgen A, Li H, Rader DJ, Pack MA, Brown CD, Susztak K | American journal of human genetics | 28575649 | Am J Hum Genet | 2017 Jun 1 |
| In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice. | Seki Y, Suzuki M, Guo X, Glenn AS, Vuguin PM, Fiallo A, Du Q, Ko YA, Yu Y, Susztak K, Zheng D, Greally JM, Katz EB, Charron MJ | Endocrinology | 28911167 | Endocrinology | 2017 Sep 1 |
| APOL1 and Cardiovascular Disease: A Story in Evolution. | Bajaj A, Susztak K, Damrauer SM | Arteriosclerosis, thrombosis, and vascular biology | 28835482 | Arterioscler Thromb Vasc Biol | 2017 Sep |
| Diabetic nephropathy: a national dialogue. | Breyer MD, Coffman TM, Flessner MF, Fried LF, Harris RC, Ketchum CJ, Kretzler M, Nelson RG, Sedor JR, Susztak K, Kidney Research National Dialogue (KRND) | Clinical journal of the American Society of Nephrology : CJASN | 23788618 | Clin J Am Soc Nephrol | 2013 Sep |
| Notch ties a knot on fistula maturation. | Dember LM, Susztak K | Journal of the American Society of Nephrology : JASN | 24480826 | J Am Soc Nephrol | 2014 Apr |
| Understanding the epigenetic syntax for the genetic alphabet in the kidney. | Susztak K | Journal of the American Society of Nephrology : JASN | 24179169 | J Am Soc Nephrol | 2014 Jan |
| Unbiased Analysis of Temporal Changes in Immune Serum Markers in Acute COVID-19 Infection With Emphasis on Organ Failure, Anti-Viral Treatment, and Demographic Characteristics. | Laudanski K, Jihane H, Antalosky B, Ghani D, Phan U, Hernandez R, Okeke T, Wu J, Rader D, Susztak K | Frontiers in immunology | 34177897 | Front Immunol | 2021 |
| The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development. | Doke T, Susztak K | Trends in cell biology | 35473814 | Trends Cell Biol | 2022 Oct |
| NAD(+) precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury. | Doke T, Mukherjee S, Mukhi D, Dhillon P, Abedini A, Davis JG, Chellappa K, Chen B, Baur JA, Susztak K | Nature metabolism | 36914909 | Nat Metab | 2023 Mar |
| Absence of miR-146a in Podocytes Increases Risk of Diabetic Glomerulopathy via Up-regulation of ErbB4 and Notch-1. | Lee HW, Khan SQ, Khaliqdina S, Altintas MM, Grahammer F, Zhao JL, Koh KH, Tardi NJ, Faridi MH, Geraghty T, Cimbaluk DJ, Susztak K, Moita LF, Baltimore D, Tharaux PL, Huber TB, Kretzler M, Bitzer M, Reiser J, Gupta V | The Journal of biological chemistry | 27913625 | J Biol Chem | 2017 Jan 13 |
| APOL1 at 10 years: progress and next steps. | Freedman BI, Kopp JB, Sampson MG, Susztak K | Kidney international | 33794228 | Kidney Int | 2021 Jun |
| Ascorbic acid-induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma. | Shenoy N, Bhagat TD, Cheville J, Lohse C, Bhattacharyya S, Tischer A, Machha V, Gordon-Mitchell S, Choudhary G, Wong LF, Gross L, Ressigue E, Leibovich B, Boorjian SA, Steidl U, Wu X, Pradhan K, Gartrell B, Agarwal B, Pagliaro L, Suzuki M, Greally JM, Rakheja D, Thompson RH, Susztak K, Witzig T, Zou Y, Verma A | The Journal of clinical investigation | 30702441 | J Clin Invest | 2019 Mar 4 |
| Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease. | Qiu C, Huang S, Park J, Park Y, Ko YA, Seasock MJ, Bryer JS, Xu XX, Song WC, Palmer M, Hill J, Guarnieri P, Hawkins J, Boustany-Kari CM, Pullen SS, Brown CD, Susztak K | Nature medicine | 30275566 | Nat Med | 2018 Nov |
| APOL1: The Balance Imposed by Infection, Selection, and Kidney Disease. | Beckerman P, Susztak K | Trends in molecular medicine | 29886044 | Trends Mol Med | 2018 Aug |
| A signature of circulating inflammatory proteins and development of end-stage renal disease in diabetes. | Niewczas MA, Pavkov ME, Skupien J, Smiles A, Md Dom ZI, Wilson JM, Park J, Nair V, Schlafly A, Saulnier PJ, Satake E, Simeone CA, Shah H, Qiu C, Looker HC, Fiorina P, Ware CF, Sun JK, Doria A, Kretzler M, Susztak K, Duffin KL, Nelson RG, Krolewski AS | Nature medicine | 31011203 | Nat Med | 2019 May |
| Going from acute to chronic kidney injury with FoxO3. | Gu X, Raman A, Susztak K | The Journal of clinical investigation | 31063992 | J Clin Invest | 2019 May 6 |
| Functional methylome analysis of human diabetic kidney disease. | Park J, Guan Y, Sheng X, Gluck C, Seasock MJ, Hakimi AA, Qiu C, Pullman J, Verma A, Li H, Palmer M, Susztak K | JCI insight | 31167971 | JCI Insight | 2019 Jun 6 |
| Diabetes mellitus-Progress and opportunities in the evolving epidemic. | Abel ED, Gloyn AL, Evans-Molina C, Joseph JJ, Misra S, Pajvani UB, Simcox J, Susztak K, Drucker DJ | Cell | 39059357 | Cell | 2024 Jul 25 |
| Cytosine methylation predicts renal function decline in American Indians. | Qiu C, Hanson RL, Fufaa G, Kobes S, Gluck C, Huang J, Chen Y, Raj D, Nelson RG, Knowler WC, Susztak K | Kidney international | 29709239 | Kidney Int | 2018 Jun |
| Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution. | Balzer MS, Pavkovic M, Frederick J, Abedini A, Freyberger A, Vienenkötter J, Mathar I, Siudak K, Eitner F, Sandner P, Grundmann M, Susztak K | Cell reports. Medicine | 37023747 | Cell Rep Med | 2023 Apr 18 |
| ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules. | Mukhi D, Li L, Liu H, Doke T, Kolligundla LP, Ha E, Kloetzer K, Abedini A, Mukherjee S, Wu J, Dhillon P, Hu H, Guan D, Funai K, Uehara K, Titchenell PM, Baur JA, Wellen KE, Susztak K | The Journal of clinical investigation | 38051585 | J Clin Invest | 2023 Dec 5 |
| Worsened Outcome in Patients with Membranous Nephropathy Carrying Apolipoprotein L1 High-Risk Genotype. | Susztak K | Clinical journal of the American Society of Nephrology : CJASN | 36764286 | Clin J Am Soc Nephrol | 2023 Mar 1 |
| Molecular pathways that drive diabetic kidney disease. | Mohandes S, Doke T, Hu H, Mukhi D, Dhillon P, Susztak K | The Journal of clinical investigation | 36787250 | J Clin Invest | 2023 Feb 15 |
| Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. | Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H, Susztak K | Nature communications | 38287030 | Nat Commun | 2024 Jan 29 |
| Fibrosis uncovered: ADAMTS12 cuts to the core of extracellular matrix drama. | Dumoulin B, Susztak K | The Journal of clinical investigation | 39286974 | J Clin Invest | 2024 Sep 17 |
| The critical role of endoplasmic reticulum stress and the stimulator of interferon genes (STING) pathway in kidney fibrosis. | Andrade-Silva M, Dhillon P, Sanchez-Navarro A, Mukhi D, Hu H, Kolligundla LP, Bergeson A, Abedini A, Levinsohn J, Dumoulin B, Câmara NOS, Miner JJ, Susztak K | Kidney international | 39566842 | Kidney Int | 2025 Feb |
| Human and murine kidneys show gender- and species-specific gene expression differences in response to injury. | Si H, Banga RS, Kapitsinou P, Ramaiah M, Lawrence J, Kambhampati G, Gruenwald A, Bottinger E, Glicklich D, Tellis V, Greenstein S, Thomas DB, Pullman J, Fazzari M, Susztak K | PloS one | 19277126 | PLoS One | 2009 |
| Fine tuning gene expression: the epigenome. | Mohtat D, Susztak K | Seminars in nephrology | 21044758 | Semin Nephrol | 2010 Sep |
| Epigenetics: a new way to look at kidney diseases. | Beckerman P, Ko YA, Susztak K | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 24675284 | Nephrol Dial Transplant | 2014 Oct |
| Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development. | Ko YA, Mohtat D, Suzuki M, Park AS, Izquierdo MC, Han SY, Kang HM, Si H, Hostetter T, Pullman JM, Fazzari M, Verma A, Zheng D, Greally JM, Susztak K | Genome biology | 24098934 | Genome Biol | 2013 |
| ADCK4 "reenergizes" nephrotic syndrome. | Malaga-Dieguez L, Susztak K | The Journal of clinical investigation | 24270414 | J Clin Invest | 2013 Dec |
| DNA methylation profile associated with rapid decline in kidney function: findings from the CRIC study. | Wing MR, Devaney JM, Joffe MM, Xie D, Feldman HI, Dominic EA, Guzman NJ, Ramezani A, Susztak K, Herman JG, Cope L, Harmon B, Kwabi-Addo B, Gordish-Dressman H, Go AS, He J, Lash JP, Kusek JW, Raj DS, Chronic Renal Insufficiency Cohort (CRIC) Study | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 24516231 | Nephrol Dial Transplant | 2014 Apr |
| Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer. | Bhagat TD, Zou Y, Huang S, Park J, Palmer MB, Hu C, Li W, Shenoy N, Giricz O, Choudhary G, Yu Y, Ko YA, Izquierdo MC, Park AS, Vallumsetla N, Laurence R, Lopez R, Suzuki M, Pullman J, Kaner J, Gartrell B, Hakimi AA, Greally JM, Patel B, Benhadji K, Pradhan K, Verma A, Susztak K | The Journal of biological chemistry | 27909050 | J Biol Chem | 2017 Jan 20 |
| Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. | Gu X, Yang H, Sheng X, Ko YA, Qiu C, Park J, Huang S, Kember R, Judy RL, Park J, Damrauer SM, Nadkarni G, Loos RJF, My VTH, Chaudhary K, Bottinger EP, Paranjpe I, Saha A, Brown C, Akilesh S, Hung AM, Palmer M, Baras A, Overton JD, Reid J, Ritchie M, Rader DJ, Susztak K | Science translational medicine | 33441424 | Sci Transl Med | 2021 Jan 13 |
| Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis. | Doke T, Huang S, Qiu C, Liu H, Guan Y, Hu H, Ma Z, Wu J, Miao Z, Sheng X, Zhou J, Cao A, Li J, Kaufman L, Hung A, Brown CD, Pestell R, Susztak K | The Journal of clinical investigation | 33998598 | J Clin Invest | 2021 May 17 |
| Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. | Wang X, Park J, Susztak K, Zhang NR, Li M | Nature communications | 30670690 | Nat Commun | 2019 Jan 22 |
| DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development. | Li SY, Park J, Guan Y, Chung K, Shrestha R, Palmer MB, Susztak K | Journal of the American Society of Nephrology : JASN | 30850438 | J Am Soc Nephrol | 2019 Apr |
| Increasing the level of peroxisome proliferator-activated receptor γ coactivator-1α in podocytes results in collapsing glomerulopathy. | Li SY, Park J, Qiu C, Han SH, Palmer MB, Arany Z, Susztak K | JCI insight | 28724797 | JCI Insight | 2017 Jul 20 |
| Benign and tumor parenchyma metabolomic profiles affect compensatory renal growth in renal cell carcinoma surgical patients. | Rosenzweig B, Rubinstein ND, Reznik E, Shingarev R, Juluru K, Akin O, Hsieh JJ, Jaimes EA, Russo P, Susztak K, Coleman JA, Hakimi AA | PloS one | 28727768 | PLoS One | 2017 |
| Mitochondrial Damage and Activation of the STING Pathway Lead to Renal Inflammation and Fibrosis. | Chung KW, Dhillon P, Huang S, Sheng X, Shrestha R, Qiu C, Kaufman BA, Park J, Pei L, Baur J, Palmer M, Susztak K | Cell metabolism | 31474566 | Cell Metab | 2019 Oct 1 |
| Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. | Giri A, Hellwege JN, Keaton JM, Park J, Qiu C, Warren HR, Torstenson ES, Kovesdy CP, Sun YV, Wilson OD, Robinson-Cohen C, Roumie CL, Chung CP, Birdwell KA, Damrauer SM, DuVall SL, Klarin D, Cho K, Wang Y, Evangelou E, Cabrera CP, Wain LV, Shrestha R, Mautz BS, Akwo EA, Sargurupremraj M, Debette S, Boehnke M, Scott LJ, Luan J, Zhao JH, Willems SM, Thériault S, Shah N, Oldmeadow C, Almgren P, Li-Gao R, Verweij N, Boutin TS, Mangino M, Ntalla I, Feofanova E, Surendran P, Cook JP, Karthikeyan S, Lahrouchi N, Liu C, Sepúlveda N, Richardson TG, Kraja A, Amouyel P, Farrall M, Poulter NR, Understanding Society Scientific Group, International Consortium for Blood Pressure, Blood Pressure-International Consortium of Exome Chip Studies, Laakso M, Zeggini E, Sever P, Scott RA, Langenberg C, Wareham NJ, Conen D, Palmer CNA, Attia J, Chasman DI, Ridker PM, Melander O, Mook-Kanamori DO, Harst PV, Cucca F, Schlessinger D, Hayward C, Spector TD, Jarvelin MR, Hennig BJ, Timpson NJ, Wei WQ, Smith JC, Xu Y, Matheny ME, Siew EE, Lindgren C, Herzig KH, Dedoussis G, Denny JC, Psaty BM, Howson JMM, Munroe PB, Newton-Cheh C, Caulfield MJ, Elliott P, Gaziano JM, Concato J, Wilson PWF, Tsao PS, Velez Edwards DR, Susztak K, Million Veteran Program, O'Donnell CJ, Hung AM, Edwards TL | Nature genetics | 30578418 | Nat Genet | 2019 Jan |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A | PLoS genetics | 30625149 | PLoS Genet | 2019 Jan |
| Unravelling the complex genetics of common kidney diseases: from variants to mechanisms. | Sullivan KM, Susztak K | Nature reviews. Nephrology | 32514149 | Nat Rev Nephrol | 2020 Nov |
| Loss of IL-27Rα Results in Enhanced Tubulointerstitial Fibrosis Associated with Elevated Th17 Responses. | Coppock GM, Aronson LR, Park J, Qiu C, Park J, DeLong JH, Radaelli E, Suszták K, Hunter CA | Journal of immunology (Baltimore, Md. : 1950) | 32522836 | J Immunol | 2020 Jul 15 |
| Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease. | Sheng X, Qiu C, Liu H, Gluck C, Hsu JY, He J, Hsu CY, Sha D, Weir MR, Isakova T, Raj D, Rincon-Choles H, Feldman HI, Townsend R, Li H, Susztak K | Proceedings of the National Academy of Sciences of the United States of America | 33144501 | Proc Natl Acad Sci U S A | 2020 Nov 17 |
| Podocytopathies. | Kopp JB, Anders HJ, Susztak K, Podestà MA, Remuzzi G, Hildebrandt F, Romagnani P | Nature reviews. Disease primers | 32792490 | Nat Rev Dis Primers | 2020 Aug 13 |
| Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. | Guan Y, Liu H, Ma Z, Li SY, Park J, Sheng X, Susztak K | Journal of the American Society of Nephrology : JASN | 32127410 | J Am Soc Nephrol | 2020 Apr |
| SORBS1 gene, a new candidate for diabetic nephropathy: results from a multi-stage genome-wide association study in patients with type 1 diabetes. | Germain M, Pezzolesi MG, Sandholm N, McKnight AJ, Susztak K, Lajer M, Forsblom C, Marre M, Parving HH, Rossing P, Toppila I, Skupien J, Roussel R, Ko YA, Ledo N, Folkersen L, Civelek M, Maxwell AP, Tregouet DA, Groop PH, Tarnow L, Hadjadj S | Diabetologia | 25476525 | Diabetologia | 2015 Mar |
| APOL1 Variants: From Parasites to Kidney Function to Cardiovascular Disease. | Reiner AP, Susztak K | Arteriosclerosis, thrombosis, and vascular biology | 26819463 | Arterioscler Thromb Vasc Biol | 2016 Feb |
| Podocytes: the Weakest Link in Diabetic Kidney Disease? | Lin JS, Susztak K | Current diabetes reports | 27053072 | Curr Diab Rep | 2016 May |
| The evolving understanding of the contribution of lipid metabolism to diabetic kidney disease. | Stadler K, Goldberg IJ, Susztak K | Current diabetes reports | 25957525 | Curr Diab Rep | 2015 Jul |
| Epithelial Plasticity versus EMT in Kidney Fibrosis. | Huang S, Susztak K | Trends in molecular medicine | 26700490 | Trends Mol Med | 2016 Jan |
| Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes. | Teumer A, Tin A, Sorice R, Gorski M, Yeo NC, Chu AY, Li M, Li Y, Mijatovic V, Ko YA, Taliun D, Luciani A, Chen MH, Yang Q, Foster MC, Olden M, Hiraki LT, Tayo BO, Fuchsberger C, Dieffenbach AK, Shuldiner AR, Smith AV, Zappa AM, Lupo A, Kollerits B, Ponte B, Stengel B, Krämer BK, Paulweber B, Mitchell BD, Hayward C, Helmer C, Meisinger C, Gieger C, Shaffer CM, Müller C, Langenberg C, Ackermann D, Siscovick D, DCCT/EDIC, Boerwinkle E, Kronenberg F, Ehret GB, Homuth G, Waeber G, Navis G, Gambaro G, Malerba G, Eiriksdottir G, Li G, Wichmann HE, Grallert H, Wallaschofski H, Völzke H, Brenner H, Kramer H, Mateo Leach I, Rudan I, Hillege HL, Beckmann JS, Lambert JC, Luan J, Zhao JH, Chalmers J, Coresh J, Denny JC, Butterbach K, Launer LJ, Ferrucci L, Kedenko L, Haun M, Metzger M, Woodward M, Hoffman MJ, Nauck M, Waldenberger M, Pruijm M, Bochud M, Rheinberger M, Verweij N, Wareham NJ, Endlich N, Soranzo N, Polasek O, van der Harst P, Pramstaller PP, Vollenweider P, Wild PS, Gansevoort RT, Rettig R, Biffar R, Carroll RJ, Katz R, Loos RJ, Hwang SJ, Coassin S, Bergmann S, Rosas SE, Stracke S, Harris TB, Corre T, Zeller T, Illig T, Aspelund T, Tanaka T, Lendeckel U, Völker U, Gudnason V, Chouraki V, Koenig W, Kutalik Z, O'Connell JR, Parsa A, Heid IM, Paterson AD, de Boer IH, Devuyst O, Lazar J, Endlich K, Susztak K, Tremblay J, Hamet P, Jacob HJ, Böger CA, Fox CS, Pattaro C, Köttgen A | Diabetes | 26631737 | Diabetes | 2016 Mar |
| Developmental signalling pathways in renal fibrosis: the roles of Notch, Wnt and Hedgehog. | Edeling M, Ragi G, Huang S, Pavenstädt H, Susztak K | Nature reviews. Nephrology | 27140856 | Nat Rev Nephrol | 2016 Jul |
| Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists. | Abedini A, Sánchez-Navaro A, Wu J, Klötzer KA, Ma Z, Poudel B, Doke T, Balzer MS, Frederick J, Cernecka H, Liu H, Liang X, Vitale S, Kolkhof P, Susztak K | The Journal of clinical investigation | 37906287 | J Clin Invest | 2024 Jan 2 |
| Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. | Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K | Nature genetics | 35710981 | Nat Genet | 2022 Jul |
| Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. | Quinn GZ, Abedini A, Liu H, Ma Z, Cucchiara A, Havasi A, Hill J, Palmer MB, Susztak K | Journal of the American Society of Nephrology : JASN | 34348909 | J Am Soc Nephrol | 2021 Nov |
| A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. | Guan Y, Liang X, Ma Z, Hu H, Liu H, Miao Z, Linkermann A, Hellwege JN, Voight BF, Susztak K | Nature communications | 34426578 | Nat Commun | 2021 Aug 23 |
| How Many Cell Types Are in the Kidney and What Do They Do? | Balzer MS, Rohacs T, Susztak K | Annual review of physiology | 34843404 | Annu Rev Physiol | 2022 Feb 10 |
| Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. | Doke T, Abedini A, Aldridge DL, Yang YW, Park J, Hernandez CM, Balzer MS, Shrestra R, Coppock G, Rico JMI, Han SY, Kim J, Xin S, Piliponsky AM, Angelozzi M, Lefebvre V, Siracusa MC, Hunter CA, Susztak K | Nature immunology | 35552540 | Nat Immunol | 2022 Jun |
| Unmasking the elusive erythropoietin-producing 'Norn' cell. | Abedini A, Klötzer KA, Susztak K | Nature medicine | 37130964 | Nat Med | 2023 May |
| The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. | Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L, Koesterer R, Gilbert C, Welch RP, Kudtarkar P, Hoang Q, Boughton AP, Singh P, Sun Y, Duby M, Moriondo A, Nguyen T, Smadbeck P, Alexander BR, Brandes M, Carmichael M, Dornbos P, Green T, Huellas-Bruskiewicz KC, Ji Y, Kluge A, McMahon AC, Mercader JM, Ruebenacker O, Sengupta S, Spalding D, Taliun D, AMP-T2D Consortium, Smith P, Thomas MK, Akolkar B, Brosnan MJ, Cherkas A, Chu AY, Fauman EB, Fox CS, Kamphaus TN, Miller MR, Nguyen L, Parsa A, Reilly DF, Ruetten H, Wholley D, Zaghloul NA, Abecasis GR, Altshuler D, Keane TM, McCarthy MI, Gaulton KJ, Florez JC, Boehnke M, Burtt NP, Flannick J | Cell metabolism | 36963395 | Cell Metab | 2023 Apr 4 |
| Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression. | Huang B, Song JH, Cheng Y, Abraham JM, Ibrahim S, Sun Z, Ke X, Meltzer SJ | Oncogene | 26876208 | Oncogene | 2016 Sep 15 |
| Long non-coding RNA HNF1A-AS1 regulates proliferation and migration in oesophageal adenocarcinoma cells. | Yang X, Song JH, Cheng Y, Wu W, Bhagat T, Yu Y, Abraham JM, Ibrahim S, Ravich W, Roland BC, Khashab M, Singh VK, Shin EJ, Yang X, Verma AK, Meltzer SJ, Mori Y | Gut | 24000294 | Gut | 2014 Jun |
| LARP7 is a potential tumor suppressor gene in gastric cancer. | Cheng Y, Jin Z, Agarwal R, Ma K, Yang J, Ibrahim S, Olaru AV, David S, Ashktorab H, Smoot DT, Duncan MD, Hutcheon DF, Abraham JM, Meltzer SJ, Mori Y | Laboratory investigation; a journal of technical methods and pathology | 22488152 | Lab Invest | 2012 Jul |
| Identification of the putative intestinal stem cell marker doublecortin and CaM kinase-like-1 in Barrett's esophagus and esophageal adenocarcinoma. | Vega KJ, May R, Sureban SM, Lightfoot SA, Qu D, Reed A, Weygant N, Ramanujam R, Souza R, Madhoun M, Whorton J, Anant S, Meltzer SJ, Houchen CW | Journal of gastroenterology and hepatology | 21916995 | J Gastroenterol Hepatol | 2012 Apr |
| Germline mutations in MSR1, ASCC1, and CTHRC1 in patients with Barrett esophagus and esophageal adenocarcinoma. | Orloff M, Peterson C, He X, Ganapathi S, Heald B, Yang YR, Bebek G, Romigh T, Song JH, Wu W, David S, Cheng Y, Meltzer SJ, Eng C | JAMA | 21791690 | JAMA | 2011 Jul 27 |
| Comparative genomic analysis of esophageal adenocarcinoma and squamous cell carcinoma. | Agrawal N, Jiao Y, Bettegowda C, Hutfless SM, Wang Y, David S, Cheng Y, Twaddell WS, Latt NL, Shin EJ, Wang LD, Wang L, Yang W, Velculescu VE, Vogelstein B, Papadopoulos N, Kinzler KW, Meltzer SJ | Cancer discovery | 22877736 | Cancer Discov | 2012 Oct |
| Methylation of the CpG sites only on the sense strand of the APC gene is specific for hepatocellular carcinoma. | Jain S, Chang TT, Hamilton JP, Lin SY, Lin YJ, Evans AA, Selaru FM, Lin PW, Chen SH, Block TM, Hu CT, Song W, Meltzer SJ, Su YH | PloS one | 22073196 | PLoS One | 2011 |
| TQ inhibits hepatocellular carcinoma growth in vitro and in vivo via repression of Notch signaling. | Ke X, Zhao Y, Lu X, Wang Z, Liu Y, Ren M, Lu G, Zhang D, Sun Z, Xu Z, Song JH, Cheng Y, Meltzer SJ, He S | Oncotarget | 26416455 | Oncotarget | 2015 Oct 20 |
| Epigenetic events in gastrointestinal cancer. | Selaru FM, David S, Meltzer SJ, Hamilton JP | The American journal of gastroenterology | 19661933 | Am J Gastroenterol | 2009 Aug |
| Chromosomal abnormalities and novel disease-related regions in progression from Barrett's esophagus to esophageal adenocarcinoma. | Akagi T, Ito T, Kato M, Jin Z, Cheng Y, Kan T, Yamamoto G, Olaru A, Kawamata N, Boult J, Soukiasian HJ, Miller CW, Ogawa S, Meltzer SJ, Koeffler HP | International journal of cancer | 19670330 | Int J Cancer | 2009 Nov 15 |
| Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis. | Alvarez H, Opalinska J, Zhou L, Sohal D, Fazzari MJ, Yu Y, Montagna C, Montgomery EA, Canto M, Dunbar KB, Wang J, Roa JC, Mo Y, Bhagat T, Ramesh KH, Cannizzaro L, Mollenhauer J, Thompson RF, Suzuki M, Meltzer SJ, Melnick A, Greally JM, Maitra A, Verma A | PLoS genetics | 21483804 | PLoS Genet | 2011 Mar |
| Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma. | Jain S, Chen S, Chang KC, Lin YJ, Hu CT, Boldbaatar B, Hamilton JP, Lin SY, Chang TT, Chen SH, Song W, Meltzer SJ, Block TM, Su YH | PloS one | 22536438 | PLoS One | 2012 |
| Effects of vitamin D3 stimulation of thioredoxin-interacting protein in hepatocellular carcinoma. | Hamilton JP, Potter JJ, Koganti L, Meltzer SJ, Mezey E | Hepatology research : the official journal of the Japan Society of Hepatology | 24451003 | Hepatol Res | 2014 Dec |
| The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. | Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ | Cancer | 28081303 | Cancer | 2017 May 1 |
| Evidence for enhanced telomerase activity in Barrett's esophagus with dysplasia and adenocarcinoma. | Merchant NB, Dutta SK, Girotra M, Arora M, Meltzer SJ | Asian Pacific journal of cancer prevention : APJCP | 23621218 | Asian Pac J Cancer Prev | 2013 |
| Endoglin promoter hypermethylation identifies a field defect in human primary esophageal cancer. | Jin Z, Zhao Z, Cheng Y, Dong M, Zhang X, Wang L, Fan X, Feng X, Mori Y, Meltzer SJ | Cancer | 23893879 | Cancer | 2013 Oct 15 |
| MAL hypermethylation is a tissue-specific event that correlates with MAL mRNA expression in esophageal carcinoma. | Jin Z, Wang L, Zhang Y, Cheng Y, Gao Y, Feng X, Dong M, Cao Z, Chen S, Yu H, Zhao Z, Zhang X, Liu J, Mori Y, Fan X, Meltzer SJ | Scientific reports | 24088706 | Sci Rep | 2013 Oct 3 |
| Integrated miRNA profiling and bioinformatics analyses reveal potential causative miRNAs in gastric adenocarcinoma. | Zhang X, Peng Y, Jin Z, Huang W, Cheng Y, Liu Y, Feng X, Yang M, Huang Y, Zhao Z, Wang L, Wei Y, Fan X, Zheng D, Meltzer SJ | Oncotarget | 26460735 | Oncotarget | 2015 Oct 20 |
| Aberrant methylation of the PTPRO gene in peripheral blood as a potential biomarker in esophageal squamous cell carcinoma patients. | You YJ, Chen YP, Zheng XX, Meltzer SJ, Zhang H | Cancer letters | 22099875 | Cancer Lett | 2012 Feb 28 |
| MicroRNA involvement in esophageal carcinogenesis. | David S, Meltzer SJ | Current opinion in pharmacology | 21992930 | Curr Opin Pharmacol | 2011 Dec |
| Phosphorus-32, a clinically available drug, inhibits cancer growth by inducing DNA double-strand breakage. | Cheng Y, Kiess AP, Herman JM, Pomper MG, Meltzer SJ, Abraham JM | PloS one | 26030880 | PLoS One | 2015 |
| Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma. | Wu W, Bhagat TD, Yang X, Song JH, Cheng Y, Agarwal R, Abraham JM, Ibrahim S, Bartenstein M, Hussain Z, Suzuki M, Yu Y, Chen W, Eng C, Greally J, Verma A, Meltzer SJ | Gastroenterology | 23333711 | Gastroenterology | 2013 May |
| A sequence variant in the phospholipase C epsilon C2 domain is associated with esophageal carcinoma and esophagitis. | Wang LD, Bi X, Song X, Pohl NM, Cheng Y, Zhou Y, Shears S, Ansong E, Xing M, Wang S, Xu XC, Huang P, Xu L, Wang L, Fan Z, Zhao X, Dong H, Meltzer SJ, Ding I, Yang W | Molecular carcinogenesis | 23390063 | Mol Carcinog | 2013 Nov |
| A multicenter, double-blinded validation study of methylation biomarkers for progression prediction in Barrett's esophagus. | Jin Z, Cheng Y, Gu W, Zheng Y, Sato F, Mori Y, Olaru AV, Paun BC, Yang J, Kan T, Ito T, Hamilton JP, Selaru FM, Agarwal R, David S, Abraham JM, Wolfsen HC, Wallace MB, Shaheen NJ, Washington K, Wang J, Canto MI, Bhattacharyya A, Nelson MA, Wagner PD, Romero Y, Wang KK, Feng Z, Sampliner RE, Meltzer SJ | Cancer research | 19435894 | Cancer Res | 2009 May 15 |
| MicroRNA-21 inhibits Serpini1, a gene with novel tumour suppressive effects in gastric cancer. | Yamanaka S, Olaru AV, An F, Luvsanjav D, Jin Z, Agarwal R, Tomuleasa C, Popescu I, Alexandrescu S, Dima S, Chivu-Economescu M, Montgomery EA, Torbenson M, Meltzer SJ, Selaru FM | Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver | 22464652 | Dig Liver Dis | 2012 Jul |
| Consensus statements for management of Barrett's dysplasia and early-stage esophageal adenocarcinoma, based on a Delphi process. | Bennett C, Vakil N, Bergman J, Harrison R, Odze R, Vieth M, Sanders S, Gay L, Pech O, Longcroft-Wheaton G, Romero Y, Inadomi J, Tack J, Corley DA, Manner H, Green S, Al Dulaimi D, Ali H, Allum B, Anderson M, Curtis H, Falk G, Fennerty MB, Fullarton G, Krishnadath K, Meltzer SJ, Armstrong D, Ganz R, Cengia G, Going JJ, Goldblum J, Gordon C, Grabsch H, Haigh C, Hongo M, Johnston D, Forbes-Young R, Kay E, Kaye P, Lerut T, Lovat LB, Lundell L, Mairs P, Shimoda T, Spechler S, Sontag S, Malfertheiner P, Murray I, Nanji M, Poller D, Ragunath K, Regula J, Cestari R, Shepherd N, Singh R, Stein HJ, Talley NJ, Galmiche JP, Tham TC, Watson P, Yerian L, Rugge M, Rice TW, Hart J, Gittens S, Hewin D, Hochberger J, Kahrilas P, Preston S, Sampliner R, Sharma P, Stuart R, Wang K, Waxman I, Abley C, Loft D, Penman I, Shaheen NJ, Chak A, Davies G, Dunn L, Falck-Ytter Y, Decaestecker J, Bhandari P, Ell C, Griffin SM, Attwood S, Barr H, Allen J, Ferguson MK, Moayyedi P, Jankowski JA | Gastroenterology | 22537613 | Gastroenterology | 2012 Aug |
| Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas. | Joseph CG, Hwang H, Jiao Y, Wood LD, Kinde I, Wu J, Mandahl N, Luo J, Hruban RH, Diaz LA Jr, He TC, Vogelstein B, Kinzler KW, Mertens F, Papadopoulos N | Genes, chromosomes & cancer | 24190505 | Genes Chromosomes Cancer | 2014 Jan |
| Aberrant methylation of the Ras-related associated with diabetes gene in human primary esophageal cancer. | Jin Z, Feng X, Jian Q, Cheng Y, Gao Y, Zhang X, Wang L, Zhang Y, Huang W, Fan X, Chen S, Yu H, Zhao Z, Dong M, Liu J, Mori Y, Meltzer SJ | Anticancer research | 24222170 | Anticancer Res | 2013 Nov |
| Paf15 expression correlates with rectal cancer prognosis, cell proliferation and radiation response. | Yan R, Zhu K, Dang C, Lan K, Wang H, Yuan D, Chen W, Meltzer SJ, Li K | Oncotarget | 27246972 | Oncotarget | 2016 Jun 21 |
| Epigenomic program of Barrett's-associated neoplastic progression reveals possible involvement of insulin signaling pathways. | Agarwal R, Jin Z, Yang J, Mori Y, Song JH, Kumar S, Sato M, Cheng Y, Olaru AV, Abraham JM, Verma A, Meltzer SJ | Endocrine-related cancer | 22194443 | Endocr Relat Cancer | 2012 Feb |
| Inhibition of the miR-192/215-Rab11-FIP2 axis suppresses human gastric cancer progression. | Zhang X, Peng Y, Huang Y, Deng S, Feng X, Hou G, Lin H, Wang J, Yan R, Zhao Y, Fan X, Meltzer SJ, Li S, Jin Z | Cell death & disease | 30006518 | Cell Death Dis | 2018 Jul 13 |
| SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling. | Zhang X, Peng Y, Huang Y, Yang M, Yan R, Zhao Y, Cheng Y, Liu X, Deng S, Feng X, Lin H, Yu H, Chen S, Zhao Z, Li S, Li K, Wang L, Wei Y, He Z, Fan X, Meltzer SJ, Li S, Jin Z | Cancer medicine | 29239144 | Cancer Med | 2018 Jan |
| SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. | Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A | Cancer biology & therapy | 20686364 | Cancer Biol Ther | 2010 Oct 15 |
| LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma. | Doucet-O'Hare TT, Rodić N, Sharma R, Darbari I, Abril G, Choi JA, Young Ahn J, Cheng Y, Anders RA, Burns KH, Meltzer SJ, Kazazian HH Jr | Proceedings of the National Academy of Sciences of the United States of America | 26283398 | Proc Natl Acad Sci U S A | 2015 Sep 1 |
| Klotho: a tumor suppressor and modulator of the Wnt/β-catenin pathway in human hepatocellular carcinoma. | Tang X, Wang Y, Fan Z, Ji G, Wang M, Lin J, Huang S, Meltzer SJ | Laboratory investigation; a journal of technical methods and pathology | 26237271 | Lab Invest | 2016 Feb |
| Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. | Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED | Nature cell biology | 25503565 | Nat Cell Biol | 2015 Jan |
| Creatine kinase B controls futile creatine cycling in thermogenic fat. | Rahbani JF, Roesler A, Hussain MF, Samborska B, Dykstra CB, Tsai L, Jedrychowski MP, Vergnes L, Reue K, Spiegelman BM, Kazak L | Nature | 33597756 | Nature | 2021 Feb |
| Isthmin-1 is an adipokine that promotes glucose uptake and improves glucose tolerance and hepatic steatosis. | Jiang Z, Zhao M, Voilquin L, Jung Y, Aikio MA, Sahai T, Dou FY, Roche AM, Carcamo-Orive I, Knowles JW, Wabitsch M, Appel EA, Maikawa CL, Camporez JP, Shulman GI, Tsai L, Rosen ED, Gardner CD, Spiegelman BM, Svensson KJ | Cell metabolism | 34348115 | Cell Metab | 2021 Sep 7 |
| Genetic variants in genes involved in creatine biosynthesis in patients with severe obesity or anorexia nervosa. | Rajcsanyi LS, Hoffmann A, Ghosh A, Matrisch-Dinkler B, Zheng Y, Peters T, Sun W, Dong H, Noé F, Wolfrum C, Herpertz-Dahlmann B, Seitz J, de Zwaan M, Herzog W, Ehrlich S, Zipfel S, Giel K, Egberts K, Burghardt R, Föcker M, Tsai LT, Müller TD, Blüher M, Hebebrand J, Hirtz R, Hinney A | Frontiers in genetics | 37101650 | Front Genet | 2023 |
| Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. | Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET | Cell | 36334589 | Cell | 2022 Nov 23 |
| Ablation of adipocyte creatine transport impairs thermogenesis and causes diet-induced obesity. | Kazak L, Rahbani JF, Samborska B, Lu GZ, Jedrychowski MP, Lajoie M, Zhang S, Ramsay L, Dou FY, Tenen D, Chouchani ET, Dzeja P, Watson IR, Tsai L, Rosen ED, Spiegelman BM | Nature metabolism | 31161155 | Nat Metab | 2019 |
| A smooth muscle-like origin for beige adipocytes. | Long JZ, Svensson KJ, Tsai L, Zeng X, Roh HC, Kong X, Rao RR, Lou J, Lokurkar I, Baur W, Castellot JJ Jr, Rosen ED, Spiegelman BM | Cell metabolism | 24709624 | Cell Metab | 2014 May 6 |
| A single-cell atlas of human and mouse white adipose tissue. | Emont MP, Jacobs C, Essene AL, Pant D, Tenen D, Colleluori G, Di Vincenzo A, Jørgensen AM, Dashti H, Stefek A, McGonagle E, Strobel S, Laber S, Agrawal S, Westcott GP, Kar A, Veregge ML, Gulko A, Srinivasan H, Kramer Z, De Filippis E, Merkel E, Ducie J, Boyd CG, Gourash W, Courcoulas A, Lin SJ, Lee BT, Morris D, Tobias A, Khera AV, Claussnitzer M, Pers TH, Giordano A, Ashenberg O, Regev A, Tsai LT, Rosen ED | Nature | 35296864 | Nature | 2022 Mar |
| Insulin-sensitizing effects of vitamin D repletion mediated by adipocyte vitamin D receptor: Studies in humans and mice. | Lontchi-Yimagou E, Kang S, Goyal A, Zhang K, You JY, Carey M, Jain S, Bhansali S, Kehlenbrink S, Guo P, Rosen ED, Kishore P, Hawkins M | Molecular metabolism | 33045433 | Mol Metab | 2020 Dec |
| Epigenomic and transcriptional control of insulin resistance. | Rosen ED | Journal of internal medicine | 27739225 | J Intern Med | 2016 Nov |
| What we talk about when we talk about fat. | Rosen ED, Spiegelman BM | Cell | 24439368 | Cell | 2014 Jan 16 |
| RAG: a recombinase diversified. | Matthews AG, Oettinger MA | Nature immunology | 19621044 | Nat Immunol | 2009 Aug |
| Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. | Yuan CC, Matthews AG, Jin Y, Chen CF, Chapman BA, Ohsumi TK, Glass KC, Kutateladze TG, Borowsky ML, Struhl K, Oettinger MA | Cell reports | 22720264 | Cell Rep | 2012 Feb 23 |
| Acetylation is indispensable for p53 activation. | Tang Y, Zhao W, Chen Y, Zhao Y, Gu W | Cell | 18485870 | Cell | 2008 May 16 |
| Lysine propionylation and butyrylation are novel post-translational modifications in histones. | Chen Y, Sprung R, Tang Y, Ball H, Sangras B, Kim SC, Falck JR, Peng J, Gu W, Zhao Y | Molecular & cellular proteomics : MCP | 17267393 | Mol Cell Proteomics | 2007 May |
| Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. | Zhang K, Chen Y, Zhang Z, Zhao Y | Journal of proteome research | 19113941 | J Proteome Res | 2009 Feb |
| The first global screening of protein substrates bearing protein-bound 3,4-Dihydroxyphenylalanine in Escherichia coli and human mitochondria. | Lee S, Chen Y, Luo H, Wu AA, Wilde M, Schumacker PT, Zhao Y | Journal of proteome research | 20818827 | J Proteome Res | 2010 Nov 5 |
| Quantitative proteomic analysis of histone modifications. | Huang H, Lin S, Garcia BA, Zhao Y | Chemical reviews | 25688442 | Chem Rev | 2015 Mar 25 |
| Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. | Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J | Cell | 20064375 | Cell | 2009 Dec 24 |
| Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. | Chen Y, Zhang J, Xing G, Zhao Y | Journal of proteome research | 19368407 | J Proteome Res | 2009 Jun |
| Unrestrictive identification of non-phosphorylation PTMs in yeast kinases by MS and PTMap. | Zhang K, Chen Y, Zhang Z, Tao S, Zhu H, Zhao Y | Proteomics | 20049863 | Proteomics | 2010 Mar |
| Lysine succinylation and lysine malonylation in histones. | Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, Boeke JD, Zhao Y | Molecular & cellular proteomics : MCP | 22389435 | Mol Cell Proteomics | 2012 May |
| CHD7 cooperates with PBAF to control multipotent neural crest formation. | Bajpai R, Chen DA, Rada-Iglesias A, Zhang J, Xiong Y, Helms J, Chang CP, Zhao Y, Swigut T, Wysocka J | Nature | 20130577 | Nature | 2010 Feb 18 |
| Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway. | Huang H, Luo Z, Qi S, Huang J, Xu P, Wang X, Gao L, Li F, Wang J, Zhao W, Gu W, Chen Z, Dai L, Dai J, Zhao Y | Cell research | 29192674 | Cell Res | 2018 Jan |
| MS/MS/MS reveals false positive identification of histone serine methylation. | Zhang J, Chen Y, Zhang Z, Xing G, Wysocka J, Zhao Y | Journal of proteome research | 19877717 | J Proteome Res | 2010 Jan |
| Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. | Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y | Cell | 21925322 | Cell | 2011 Sep 16 |
| Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. | Xie Z, Zhang D, Chung D, Tang Z, Huang H, Dai L, Qi S, Li J, Colak G, Chen Y, Xia C, Peng C, Ruan H, Kirkey M, Wang D, Jensen LM, Kwon OK, Lee S, Pletcher SD, Tan M, Lombard DB, White KP, Zhao H, Li J, Roeder RG, Yang X, Zhao Y | Molecular cell | 27105115 | Mol Cell | 2016 Apr 21 |
| Nuclear mobility and mitotic chromosome binding: similarities between pioneer transcription factor FoxA and linker histone H1. | Zaret KS, Caravaca JM, Tulin A, Sekiya T | Cold Spring Harbor symposia on quantitative biology | 21502411 | Cold Spring Harb Symp Quant Biol | 2010 |
| Bookmarking promoters in mitotic chromatin: poly(ADP-ribose)polymerase-1 as an epigenetic mark. | Lodhi N, Kossenkov AV, Tulin AV | Nucleic acids research | 24861619 | Nucleic Acids Res | 2014 Jun |
| Pioneer transcription factors: establishing competence for gene expression. | Zaret KS, Carroll JS | Genes & development | 22056668 | Genes Dev | 2011 Nov 1 |
| High-Throughput Colorimetric Assay for Identifying PARP-1 Inhibitors Using a Large Small-Molecule Collection. | Kotova E, Tulin AV | Methods in molecular biology (Clifton, N.J.) | 28695517 | Methods Mol Biol | 2017 |
| The roles of PARP1 in gene control and cell differentiation. | Ji Y, Tulin AV | Current opinion in genetics & development | 20591646 | Curr Opin Genet Dev | 2010 Oct |
| Minor grove binding ligands disrupt PARP-1 activation pathways. | Kirsanov KI, Kotova E, Makhov P, Golovine K, Lesovaya EA, Kolenko VM, Yakubovskaya MG, Tulin AV | Oncotarget | 24504413 | Oncotarget | 2014 Jan 30 |
| Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. | Thomas CJ, Kotova E, Andrake M, Adolf-Bryfogle J, Glaser R, Regnard C, Tulin AV | Molecular cell | 24508391 | Mol Cell | 2014 Mar 6 |
| Mitotic bookmarking: maintaining post-mitotic reprogramming of transcription reactivation. | Lodhi N, Ji Y, Tulin A | Current molecular biology reports | 27042400 | Curr Mol Biol Rep | 2016 Mar |
| PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq). | Lodhi N, Tulin AV | Methods in molecular biology (Clifton, N.J.) | 21870262 | Methods Mol Biol | 2011 |
| Small-molecule collection and high-throughput colorimetric assay to identify PARP1 inhibitors. | Kotova E, Pinnola AD, Tulin AV | Methods in molecular biology (Clifton, N.J.) | 21870279 | Methods Mol Biol | 2011 |
| Charon Mediates Immune Deficiency-Driven PARP-1-Dependent Immune Responses in Drosophila. | Ji Y, Thomas C, Tulin N, Lodhi N, Boamah E, Kolenko V, Tulin AV | Journal of immunology (Baltimore, Md. : 1950) | 27527593 | J Immunol | 2016 Sep 15 |
| Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. | Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS | Genes & development | 23355396 | Genes Dev | 2013 Feb 1 |
| Drosophila histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin. | Kotova E, Lodhi N, Jarnik M, Pinnola AD, Ji Y, Tulin AV | Proceedings of the National Academy of Sciences of the United States of America | 21444826 | Proc Natl Acad Sci U S A | 2011 Apr 12 |
| Human factors and pathways essential for mediating epigenetic gene silencing. | Poleshko A, Kossenkov AV, Shalginskikh N, Pecherskaya A, Einarson MB, Marie Skalka A, Katz RA | Epigenetics | 25147916 | Epigenetics | 2014 Sep |
| Inhibitor of DNA Binding 4 (ID4) is highly expressed in human melanoma tissues and may function to restrict normal differentiation of melanoma cells. | Peretz Y, Wu H, Patel S, Bellacosa A, Katz RA | PloS one | 25642713 | PLoS One | 2015 |
| Identification of a functional network of human epigenetic silencing factors. | Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD, Skalka AM, Katz RA | The Journal of biological chemistry | 19880521 | J Biol Chem | 2010 Jan 1 |
| The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. | Poleshko A, Mansfield KM, Burlingame CC, Andrake MD, Shah NR, Katz RA | Cell reports | 24209742 | Cell Rep | 2013 Oct 31 |
| Efficient iPS cell production with the MyoD transactivation domain in serum-free culture. | Hirai H, Katoku-Kikyo N, Karian P, Firpo M, Kikyo N | PloS one | 22479546 | PLoS One | 2012 |
| Radical acceleration of nuclear reprogramming by chromatin remodeling with the transactivation domain of MyoD. | Hirai H, Tani T, Katoku-Kikyo N, Kellner S, Karian P, Firpo M, Kikyo N | Stem cells (Dayton, Ohio) | 21732495 | Stem Cells | 2011 Sep |
| Regulation of embryonic stem cell self-renewal and pluripotency by leukaemia inhibitory factor. | Hirai H, Karian P, Kikyo N | The Biochemical journal | 21793804 | Biochem J | 2011 Aug 15 |
| Structure and functions of powerful transactivators: VP16, MyoD and FoxA. | Hirai H, Tani T, Kikyo N | The International journal of developmental biology | 21404180 | Int J Dev Biol | 2010 |
| Establishment of LIF-dependent human iPS cells closely related to basic FGF-dependent authentic iPS cells. | Hirai H, Firpo M, Kikyo N | PloS one | 22720020 | PLoS One | 2012 |
| RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations. | Yao S, Yuan P, Ouellette B, Zhou T, Mortrud M, Balaram P, Chatterjee S, Wang Y, Daigle TL, Tasic B, Kuang X, Gong H, Luo Q, Zeng S, Curtright A, Dhaka A, Kahan A, Gradinaru V, Chrapkiewicz R, Schnitzer M, Zeng H, Cetin A | Nature methods | 32203389 | Nat Methods | 2020 Apr |
| Comparative cellular analysis of motor cortex in human, marmoset and mouse. | Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES | Nature | 34616062 | Nature | 2021 Oct |
| Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. | Mich JK, Graybuck LT, Hess EE, Mahoney JT, Kojima Y, Ding Y, Somasundaram S, Miller JA, Kalmbach BE, Radaelli C, Gore BB, Weed N, Omstead V, Bishaw Y, Shapovalova NV, Martinez RA, Fong O, Yao S, Mortrud M, Chong P, Loftus L, Bertagnolli D, Goldy J, Casper T, Dee N, Opitz-Araya X, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Sunkin SM, Gradinaru V, Horwitz GD, Zeng H, Tasic B, Lein ES, Ting JT, Levi BP | Cell reports | 33789096 | Cell Rep | 2021 Mar 30 |
| Enhancer viruses for combinatorial cell-subclass-specific labeling. | Graybuck LT, Daigle TL, Sedeño-Cortés AE, Walker M, Kalmbach B, Lenz GH, Morin E, Nguyen TN, Garren E, Bendrick JL, Kim TK, Zhou T, Mortrud M, Yao S, Siverts LA, Larsen R, Gore BB, Szelenyi ER, Trader C, Balaram P, van Velthoven CTJ, Chiang M, Mich JK, Dee N, Goldy J, Cetin AH, Smith K, Way SW, Esposito L, Yao Z, Gradinaru V, Sunkin SM, Lein E, Levi BP, Ting JT, Zeng H, Tasic B | Neuron | 33789083 | Neuron | 2021 May 5 |
| A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. | Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H | Cell | 30007418 | Cell | 2018 Jul 12 |
| SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology. | Long B, Zhou Z, Cetin A, Ting J, Gwinn R, Tasic B, Daigle T, Lein E, Zeng H, Saggau P, Hawrylycz M, Peng H | Scientific reports | 28839271 | Sci Rep | 2017 Aug 24 |
| Local connectivity and synaptic dynamics in mouse and human neocortex. | Campagnola L, Seeman SC, Chartrand T, Kim L, Hoggarth A, Gamlin C, Ito S, Trinh J, Davoudian P, Radaelli C, Kim MH, Hage T, Braun T, Alfiler L, Andrade J, Bohn P, Dalley R, Henry A, Kebede S, Alice M, Sandman D, Williams G, Larsen R, Teeter C, Daigle TL, Berry K, Dotson N, Enstrom R, Gorham M, Hupp M, Dingman Lee S, Ngo K, Nicovich PR, Potekhina L, Ransford S, Gary A, Goldy J, McMillen D, Pham T, Tieu M, Siverts L, Walker M, Farrell C, Schroedter M, Slaughterbeck C, Cobb C, Ellenbogen R, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Carey D, Casper T, Crichton K, Clark M, Dee N, Ellingwood L, Gloe J, Kroll M, Sulc J, Tung H, Wadhwani K, Brouner K, Egdorf T, Maxwell M, McGraw M, Pom CA, Ruiz A, Bomben J, Feng D, Hejazinia N, Shi S, Szafer A, Wakeman W, Phillips J, Bernard A, Esposito L, D'Orazi FD, Sunkin S, Smith K, Tasic B, Arkhipov A, Sorensen S, Lein E, Koch C, Murphy G, Zeng H, Jarsky T | Science (New York, N.Y.) | 35271334 | Science | 2022 Mar 11 |
| Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. | Gray LT, Yao Z, Nguyen TN, Kim TK, Zeng H, Tasic B | eLife | 28112643 | Elife | 2017 Jan 23 |
| Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons. | Kalmbach BE, Hodge RD, Jorstad NL, Owen S, de Frates R, Yanny AM, Dalley R, Mallory M, Graybuck LT, Radaelli C, Keene CD, Gwinn RP, Silbergeld DL, Cobbs C, Ojemann JG, Ko AL, Patel AP, Ellenbogen RG, Bakken TE, Daigle TL, Dee N, Lee BR, McGraw M, Nicovich PR, Smith K, Sorensen SA, Tasic B, Zeng H, Koch C, Lein ES, Ting JT | Neuron | 34534454 | Neuron | 2021 Sep 15 |
| Epigenome engineering in cancer: fairytale or a realistic path to the clinic? | Falahi F, Sgro A, Blancafort P | Frontiers in oncology | 25705610 | Front Oncol | 2015 |
| Hallmarks of cancer: The CRISPR generation. | Moses C, Garcia-Bloj B, Harvey AR, Blancafort P | European journal of cancer (Oxford, England : 1990) | 29433054 | Eur J Cancer | 2018 Apr |
| Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system. | Garcia-Bloj B, Moses C, Sgro A, Plani-Lam J, Arooj M, Duffy C, Thiruvengadam S, Sorolla A, Rashwan R, Mancera RL, Leisewitz A, Swift-Scanlan T, Corvalan AH, Blancafort P | Oncotarget | 27528034 | Oncotarget | 2016 Sep 13 |
| Activating PTEN Tumor Suppressor Expression with the CRISPR/dCas9 System. | Moses C, Nugent F, Waryah CB, Garcia-Bloj B, Harvey AR, Blancafort P | Molecular therapy. Nucleic acids | 30654190 | Mol Ther Nucleic Acids | 2019 Mar 1 |
| Tumor penetrating peptides inhibiting MYC as a potent targeted therapeutic strategy for triple-negative breast cancers. | Wang E, Sorolla A, Cunningham PT, Bogdawa HM, Beck S, Golden E, Dewhurst RE, Florez L, Cruickshank MN, Hoffmann K, Hopkins RM, Kim J, Woo AJ, Watt PM, Blancafort P | Oncogene | 30076412 | Oncogene | 2019 Jan |
| Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity. | Alves E, McLeish E, Blancafort P, Coudert JD, Gaudieri S | Frontiers in immunology | 34456921 | Front Immunol | 2021 |
| Reprogramming the anti-tumor immune response via CRISPR genetic and epigenetic editing. | Alves E, Taifour S, Dolcetti R, Chee J, Nowak AK, Gaudieri S, Blancafort P | Molecular therapy. Methods & clinical development | 34095343 | Mol Ther Methods Clin Dev | 2021 Jun 11 |
| Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). | Gandhi NS, Blancafort P, Mancera RL | Oncotarget | 29854286 | Oncotarget | 2018 Apr 27 |
| A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. | Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R | Genome research | 29907613 | Genome Res | 2018 Aug |
| Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. | Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ | Nucleic acids research | 25122745 | Nucleic Acids Res | 2014 |
| The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer. | Golden E, Rashwan R, Woodward EA, Sgro A, Wang E, Sorolla A, Waryah C, Tie WJ, Cuyàs E, Ratajska M, Kardaś I, Kozlowski P, Johnstone EKM, See HB, Duffy C, Parry J, Lagerborg KA, Czapiewski P, Menendez JA, Gorczyński A, Wasag B, Pfleger KDG, Curtis C, Lee BK, Kim J, Cursons J, Pavlos NJ, Biernat W, Jain M, Woo AJ, Redfern A, Blancafort P | Nature communications | 33772001 | Nat Commun | 2021 Mar 26 |
| Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. | Waryah CB, Moses C, Arooj M, Blancafort P | Methods in molecular biology (Clifton, N.J.) | 29524128 | Methods Mol Biol | 2018 |
| Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing. | Moses C, Hodgetts SI, Nugent F, Ben-Ary G, Park KK, Blancafort P, Harvey AR | Scientific reports | 32647121 | Sci Rep | 2020 Jul 9 |
| Epigenome engineering: new technologies for precision medicine. | Sgro A, Blancafort P | Nucleic acids research | 33196851 | Nucleic Acids Res | 2020 Dec 16 |
| Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer. | Stolzenburg S, Beltran AS, Swift-Scanlan T, Rivenbark AG, Rashwan R, Blancafort P | Oncogene | 25684141 | Oncogene | 2015 Oct |
| The CRISPR road: from bench to bedside on an RNA-guided path. | Garcia-Bloj B, Moses C, Blancafort P | Annals of translational medicine | 26366391 | Ann Transl Med | 2015 Aug |
| Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. | de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R | Genome biology | 35883107 | Genome Biol | 2022 Jul 26 |
| Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. | Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A | Nature | 28959968 | Nature | 2017 Sep 28 |
| (Epi)genomics approaches and their applications. | Meissner A | Methods (San Diego, Calif.) | 25597875 | Methods | 2015 Jan 15 |
| Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. | Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ | Cell | 29656892 | Cell | 2018 Apr 19 |
| Global delay in nascent strand DNA methylation. | Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A | Nature structural & molecular biology | 29531288 | Nat Struct Mol Biol | 2018 Apr |
| Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome. | Shea JM, Serra RW, Carone BR, Shulha HP, Kucukural A, Ziller MJ, Vallaster MP, Gu H, Tapper AR, Gardner PD, Meissner A, Garber M, Rando OJ | Developmental cell | 26702833 | Dev Cell | 2015 Dec 21 |
| Genome-wide tracking of dCas9-methyltransferase footprints. | Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schöler HR, Gnirke A, Ziller MJ, Meissner A | Nature communications | 29426832 | Nat Commun | 2018 Feb 9 |
| Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons. | Ichida JK, Staats KA, Davis-Dusenbery BN, Clement K, Galloway KE, Babos KN, Shi Y, Son EY, Kiskinis E, Atwater N, Gu H, Gnirke A, Meissner A, Eggan K | Development (Cambridge, England) | 30337375 | Development | 2018 Nov 21 |
| Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain. | Janssens S, Schotsaert M, Karnik R, Balasubramaniam V, Dejosez M, Meissner A, García-Sastre A, Zwaka TP | mSystems | 29435496 | mSystems | 2018 Jan-Feb |
| Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. | Ziller MJ, Ortega JA, Quinlan KA, Santos DP, Gu H, Martin EJ, Galonska C, Pop R, Maidl S, Di Pardo A, Huang M, Meltzer HY, Gnirke A, Heckman CJ, Meissner A, Kiskinis E | Cell stem cell | 29551301 | Cell Stem Cell | 2018 Apr 5 |
| Targets and genomic constraints of ectopic Dnmt3b expression. | Zhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A | eLife | 30468428 | Elife | 2018 Nov 23 |
| Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. | Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A | Nature genetics | 25822089 | Nat Genet | 2015 May |
| Genome stress response in early development. | Marzluff WF, Duronio RJ | Developmental cell | 24871944 | Dev Cell | 2014 May 27 |
| Interrogating the function of metazoan histones using engineered gene clusters. | McKay DJ, Klusza S, Penke TJ, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG | Developmental cell | 25669886 | Dev Cell | 2015 Feb 9 |
| Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. | Meers MP, Henriques T, Lavender CA, McKay DJ, Strahl BD, Duronio RJ, Adelman K, Matera AG | eLife | 28346137 | Elife | 2017 Mar 27 |
| Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. | Meers MP, Adelman K, Duronio RJ, Strahl BD, McKay DJ, Matera AG | BMC genomics | 29466941 | BMC Genomics | 2018 Feb 21 |
| Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation. | Leatham-Jensen M, Uyehara CM, Strahl BD, Matera AG, Duronio RJ, McKay DJ | PLoS genetics | 30699116 | PLoS Genet | 2019 Jan |
| Functional Redundancy of Variant and Canonical Histone H3 Lysine 9 Modification in Drosophila. | Penke TJR, McKay DJ, Strahl BD, Matera AG, Duronio RJ | Genetics | 29133298 | Genetics | 2018 Jan |
| Fate mapping during regeneration: Cells that undergo compensatory proliferation in damaged Drosophila eye imaginal discs differentiate into multiple retinal accessory cell types. | Meserve JH, Duronio RJ | Developmental biology | 30347187 | Dev Biol | 2018 Dec 15 |
| Direct interrogation of the role of H3K9 in metazoan heterochromatin function. | Penke TJ, McKay DJ, Strahl BD, Matera AG, Duronio RJ | Genes & development | 27566777 | Genes Dev | 2016 Aug 15 |
| Interpreting the language of histone and DNA modifications. | Rothbart SB, Strahl BD | Biochimica et biophysica acta | 24631868 | Biochim Biophys Acta | 2014 Aug |
| An Animal Model for Genetic Analysis of Multi-Gene Families: Cloning and Transgenesis of Large Tandemly Repeated Histone Gene Clusters. | Meers MP, Leatham-Jensen M, Penke TJR, McKay DJ, Duronio RJ, Matera AG | Methods in molecular biology (Clifton, N.J.) | 30073535 | Methods Mol Biol | 2018 |
| Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila. | Li Y, Armstrong RL, Duronio RJ, MacAlpine DM | Nucleic acids research | 27131378 | Nucleic Acids Res | 2016 Sep 6 |
| Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. | Crain AT, Klusza S, Armstrong RL, Santa Rosa P, Temple BRS, Strahl BD, McKay DJ, Matera AG, Duronio RJ | Genetics | 35404465 | Genetics | 2022 May 31 |
| A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders. | Carrette LLG, Wang CY, Wei C, Press W, Ma W, Kelleher RJ 3rd, Lee JT | Proceedings of the National Academy of Sciences of the United States of America | 29282321 | Proc Natl Acad Sci U S A | 2018 Jan 23 |
| A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation. | Lessing D, Dial TO, Wei C, Payer B, Carrette LL, Kesner B, Szanto A, Jadhav A, Maloney DJ, Simeonov A, Theriault J, Hasaka T, Bedalov A, Bartolomei MS, Lee JT | Proceedings of the National Academy of Sciences of the United States of America | 28182563 | Proc Natl Acad Sci U S A | 2016 Dec 13 |
| Female mice lacking Xist RNA show partial dosage compensation and survive to term. | Yang L, Kirby JE, Sunwoo H, Lee JT | Genes & development | 27542829 | Genes Dev | 2016 Aug 1 |
| Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. | Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT | Molecular & cellular proteomics : MCP | 25680957 | Mol Cell Proteomics | 2015 Jun |
| Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. | Minajigi A, Froberg J, Wei C, Sunwoo H, Kesner B, Colognori D, Lessing D, Payer B, Boukhali M, Haas W, Lee JT | Science (New York, N.Y.) | 26089354 | Science | 2015 Jul 17 |
| Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. | Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT | Nature structural & molecular biology | 30664740 | Nat Struct Mol Biol | 2019 Feb |
| Tsix-Mecp2 female mouse model for Rett syndrome reveals that low-level MECP2 expression extends life and improves neuromotor function. | Carrette LLG, Blum R, Ma W, Kelleher RJ 3rd, Lee JT | Proceedings of the National Academy of Sciences of the United States of America | 30038001 | Proc Natl Acad Sci U S A | 2018 Aug 7 |
| Nuclear architecture as an epigenetic regulator of neural development and function. | Alexander JM, Lomvardas S | Neuroscience | 24486963 | Neuroscience | 2014 Apr 4 |
| Chemosensory receptor specificity and regulation. | Dalton RP, Lomvardas S | Annual review of neuroscience | 25938729 | Annu Rev Neurosci | 2015 Jul 8 |
| Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice. | Mukai J, Cannavò E, Crabtree GW, Sun Z, Diamantopoulou A, Thakur P, Chang CY, Cai Y, Lomvardas S, Takata A, Xu B, Gogos JA | Neuron | 31606247 | Neuron | 2019 Nov 6 |
| Enhancer interaction networks as a means for singular olfactory receptor expression. | Markenscoff-Papadimitriou E, Allen WE, Colquitt BM, Goh T, Murphy KK, Monahan K, Mosley CP, Ahituv N, Lomvardas S | Cell | 25417106 | Cell | 2014 Oct 23 |
| Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan K, Schieren I, Cheung J, Mumbey-Wafula A, Monuki ES, Lomvardas S | eLife | 28933695 | Elife | 2017 Sep 21 |
| Monobodies and other synthetic binding proteins for expanding protein science. | Sha F, Salzman G, Gupta A, Koide S | Protein science : a publication of the Protein Society | 28249355 | Protein Sci | 2017 May |
| ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. | Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J | eLife | 26523391 | Elife | 2015 Nov 2 |
| Facile target validation in an animal model with intracellularly expressed monobodies. | Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S | Nature chemical biology | 30013062 | Nat Chem Biol | 2018 Sep |
| Next-generation antibodies for post-translational modifications. | Hattori T, Koide S | Current opinion in structural biology | 29753204 | Curr Opin Struct Biol | 2018 Aug |
| sNASP and ASF1A function through both competitive and compatible modes of histone binding. | Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG | Nucleic acids research | 28123037 | Nucleic Acids Res | 2017 Jan 25 |
| Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide. | Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B | ACS synthetic biology | 26474029 | ACS Synth Biol | 2016 Jan 15 |
| Engineering and Application of LOV2-Based Photoswitches. | Zimmerman SP, Kuhlman B, Yumerefendi H | Methods in enzymology | 27586333 | Methods Enzymol | 2016 |
| Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker. | Adikes RC, Hallett RA, Saway BF, Kuhlman B, Slep KC | The Journal of cell biology | 29259096 | J Cell Biol | 2018 Feb 5 |
| Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation. | Yumerefendi H, Dickinson DJ, Wang H, Zimmerman SP, Bear JE, Goldstein B, Hahn K, Kuhlman B | PloS one | 26083500 | PLoS One | 2015 |
| Go in! Go out! Inducible control of nuclear localization. | Di Ventura B, Kuhlman B | Current opinion in chemical biology | 27372352 | Curr Opin Chem Biol | 2016 Oct |
| Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. | Zimmerman SP, Hallett RA, Bourke AM, Bear JE, Kennedy MJ, Kuhlman B | Biochemistry | 27529180 | Biochemistry | 2016 Sep 20 |
| LOVTRAP: an optogenetic system for photoinduced protein dissociation. | Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM | Nature methods | 27427858 | Nat Methods | 2016 Sep |
| Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. | Yumerefendi H, Lerner AM, Zimmerman SP, Hahn K, Bear JE, Strahl BD, Kuhlman B | Nature chemical biology | 27089030 | Nat Chem Biol | 2016 Jun |
| Cells lay their own tracks - optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration. | Zimmerman SP, Asokan SB, Kuhlman B, Bear JE | Journal of cell science | 28754687 | J Cell Sci | 2017 Sep 15 |
| LOVTRAP: A Versatile Method to Control Protein Function with Light. | Wang H, Hahn KM | Current protocols in cell biology | 27906450 | Curr Protoc Cell Biol | 2016 Dec 1 |
| Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution. | Lerner AM, Yumerefendi H, Goudy OJ, Strahl BD, Kuhlman B | ACS synthetic biology | 30441907 | ACS Synth Biol | 2018 Dec 21 |
| Lamellipodia are crucial for haptotactic sensing and response. | King SJ, Asokan SB, Haynes EM, Zimmerman SP, Rotty JD, Alb JG Jr, Tagliatela A, Blake DR, Lebedeva IP, Marston D, Johnson HE, Parsons M, Sharpless NE, Kuhlman B, Haugh JM, Bear JE | Journal of cell science | 27173494 | J Cell Sci | 2016 Jun 15 |
| An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation. | Lerner AM, Hepperla AJ, Keele GR, Meriesh HA, Yumerefendi H, Restrepo D, Zimmerman S, Bear JE, Kuhlman B, Davis IJ, Strahl BD | Genome research | 33020206 | Genome Res | 2020 Nov |
| Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. | Yumerefendi H, Wang H, Dickinson DJ, Lerner AM, Malkus P, Goldstein B, Hahn K, Kuhlman B | Chembiochem : a European journal of chemical biology | 29446199 | Chembiochem | 2018 Jun 18 |
| Race/ethnicity, gender, and monitoring socioeconomic gradients in health: a comparison of area-based socioeconomic measures--the public health disparities geocoding project. | Krieger N, Chen JT, Waterman PD, Rehkopf DH, Subramanian SV | American journal of public health | 14534218 | Am J Public Health | 2003 Oct |
| CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. | Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA | Nature biotechnology | 28369033 | Nat Biotechnol | 2017 Jun |
| Genetic engineering: Chemical control for CRISPR editing. | Hilton IB, Gersbach CA | Nature chemical biology | 27820804 | Nat Chem Biol | 2017 Jan |
| Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2. | Pathak GP, Spiltoir JI, Höglund C, Polstein LR, Heine-Koskinen S, Gersbach CA, Rossi J, Tucker CL | Nucleic acids research | 28431041 | Nucleic Acids Res | 2017 Nov 16 |
| Genome engineering: the next genomic revolution. | Gersbach CA | Nature methods | 25264777 | Nat Methods | 2014 Oct |
| A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. | Polstein LR, Gersbach CA | Nature chemical biology | 25664691 | Nat Chem Biol | 2015 Mar |
| Synthetic transcription factors for cell fate reprogramming. | Black JB, Gersbach CA | Current opinion in genetics & development | 29803990 | Curr Opin Genet Dev | 2018 Oct |
| The Development of TALE Nucleases for Biotechnology. | Ousterout DG, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 26443211 | Methods Mol Biol | 2016 |
| Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. | Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA | Nature biotechnology | 25849900 | Nat Biotechnol | 2015 May |
| Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage. | Josephs EA, Kocak DD, Fitzgibbon CJ, McMenemy J, Gersbach CA, Marszalek PE | Nucleic acids research | 26384421 | Nucleic Acids Res | 2015 Oct 15 |
| An Engineered Optogenetic Switch for Spatiotemporal Control of Gene Expression, Cell Differentiation, and Tissue Morphogenesis. | Polstein LR, Juhas M, Hanna G, Bursac N, Gersbach CA | ACS synthetic biology | 28793186 | ACS Synth Biol | 2017 Nov 17 |
| Step-Wise Chondrogenesis of Human Induced Pluripotent Stem Cells and Purification Via a Reporter Allele Generated by CRISPR-Cas9 Genome Editing. | Adkar SS, Wu CL, Willard VP, Dicks A, Ettyreddy A, Steward N, Bhutani N, Gersbach CA, Guilak F | Stem cells (Dayton, Ohio) | 30378731 | Stem Cells | 2019 Jan |
| AP-1 subunits converge promiscuously at enhancers to potentiate transcription. | Seo J, Koçak DD, Bartelt LC, Williams CA, Barrera A, Gersbach CA, Reddy TE | Genome research | 33674350 | Genome Res | 2021 Apr |
| Zip code caveat: bias due to spatiotemporal mismatches between zip codes and US census-defined geographic areas--the Public Health Disparities Geocoding Project. | Krieger N, Waterman P, Chen JT, Soobader MJ, Subramanian SV, Carson R | American journal of public health | 12084688 | Am J Public Health | 2002 Jul |
| Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors. | Thakore PI, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 26443215 | Methods Mol Biol | 2016 |
| Mammalian Synthetic Biology: Engineering Biological Systems. | Black JB, Perez-Pinera P, Gersbach CA | Annual review of biomedical engineering | 28633563 | Annu Rev Biomed Eng | 2017 Jun 21 |
| RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. | Thakore PI, Kwon JB, Nelson CE, Rouse DC, Gemberling MP, Oliver ML, Gersbach CA | Nature communications | 29700298 | Nat Commun | 2018 Apr 26 |
| Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. | Kabadi AM, Ousterout DG, Hilton IB, Gersbach CA | Nucleic acids research | 25122746 | Nucleic Acids Res | 2014 Oct 29 |
| A CRISPR/Cas9-based system for reprogramming cell lineage specification. | Chakraborty S, Ji H, Kabadi AM, Gersbach CA, Christoforou N, Leong KW | Stem cell reports | 25448066 | Stem Cell Reports | 2014 Dec 9 |
| The next generation of CRISPR-Cas technologies and applications. | Pickar-Oliver A, Gersbach CA | Nature reviews. Molecular cell biology | 31147612 | Nat Rev Mol Cell Biol | 2019 Aug |
| Editing the epigenome: technologies for programmable transcription and epigenetic modulation. | Thakore PI, Black JB, Hilton IB, Gersbach CA | Nature methods | 26820547 | Nat Methods | 2016 Feb |
| Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. | Fufa TD, Harris ML, Watkins-Chow DE, Levy D, Gorkin DU, Gildea DE, Song L, Safi A, Crawford GE, Sviderskaya EV, Bennett DC, Mccallion AS, Loftus SK, Pavan WJ | Human molecular genetics | 26206884 | Hum Mol Genet | 2015 Oct 1 |
| Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. | D'Ippolito AM, McDowell IC, Barrera A, Hong LK, Leichter SM, Bartelt LC, Vockley CM, Majoros WH, Safi A, Song L, Gersbach CA, Crawford GE, Reddy TE | Cell systems | 30031775 | Cell Syst | 2018 Aug 22 |
| Increasing the specificity of CRISPR systems with engineered RNA secondary structures. | Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA | Nature biotechnology | 30988504 | Nat Biotechnol | 2019 Jun |
| Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. | Carullo NVN, Phillips Iii RA, Simon RC, Soto SAR, Hinds JE, Salisbury AJ, Revanna JS, Bunner KD, Ianov L, Sultan FA, Savell KE, Gersbach CA, Day JJ | Nucleic acids research | 32810208 | Nucleic Acids Res | 2020 Sep 25 |
| Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens. | Black JB, McCutcheon SR, Dube S, Barrera A, Klann TS, Rice GA, Adkar SS, Soderling SH, Reddy TE, Gersbach CA | Cell reports | 33264623 | Cell Rep | 2020 Dec 1 |
| Transgenic mice for in vivo epigenome editing with CRISPR-based systems. | Gemberling MP, Siklenka K, Rodriguez E, Tonn-Eisinger KR, Barrera A, Liu F, Kantor A, Li L, Cigliola V, Hazlett MF, Williams CA, Bartelt LC, Madigan VJ, Bodle JC, Daniels H, Rouse DC, Hilton IB, Asokan A, Ciofani M, Poss KD, Reddy TE, West AE, Gersbach CA | Nature methods | 34341582 | Nat Methods | 2021 Aug |
| Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies. | Gersbach CA, Gaj T, Barbas CF 3rd | Accounts of chemical research | 24877793 | Acc Chem Res | 2014 Aug 19 |
| Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine. | Gersbach CA, Perez-Pinera P | Expert opinion on therapeutic targets | 24917359 | Expert Opin Ther Targets | 2014 Aug |
| Painting a truer picture of US socioeconomic and racial/ethnic health inequalities: the Public Health Disparities Geocoding Project. | Krieger N, Chen JT, Waterman PD, Rehkopf DH, Subramanian SV | American journal of public health | 15671470 | Am J Public Health | 2005 Feb |
| Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. | Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA | Genome research | 26025803 | Genome Res | 2015 Aug |
| Genome Engineering for Personalized Arthritis Therapeutics. | Adkar SS, Brunger JM, Willard VP, Wu CL, Gersbach CA, Guilak F | Trends in molecular medicine | 28887050 | Trends Mol Med | 2017 Oct |
| Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells. | Black JB, Adler AF, Wang HG, D'Ippolito AM, Hutchinson HA, Reddy TE, Pitt GS, Leong KW, Gersbach CA | Cell stem cell | 27524438 | Cell Stem Cell | 2016 Sep 1 |
| Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. | Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DY, Seydoux G, Mohr SE, Zuber J, Perrimon N | Nature reviews. Genetics | 27795562 | Nat Rev Genet | 2017 Jan |
| Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes. | Chen LF, Lin YT, Gallegos DA, Hazlett MF, Gómez-Schiavon M, Yang MG, Kalmeta B, Zhou AS, Holtzman L, Gersbach CA, Grandl J, Buchler NE, West AE | Cell reports | 30699347 | Cell Rep | 2019 Jan 29 |
| Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. | Klann TS, Crawford GE, Reddy TE, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 29524151 | Methods Mol Biol | 2018 |
| Pulling the genome in opposite directions to dissect gene networks. | Gersbach CA, Barrangou R | Genome biology | 29580291 | Genome Biol | 2018 Mar 26 |
| CRISPR-based methods for high-throughput annotation of regulatory DNA. | Klann TS, Black JB, Gersbach CA | Current opinion in biotechnology | 29500989 | Curr Opin Biotechnol | 2018 Aug |
| Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing. | Rohm D, Black JB, McCutcheon SR, Barrera A, Berry SS, Morone DJ, Nuttle X, de Esch CE, Tai DJC, Talkowski ME, Iglesias N, Gersbach CA | Cell genomics | 39947136 | Cell Genom | 2025 Feb 12 |
| Light-inducible gene regulation with engineered zinc finger proteins. | Polstein LR, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 24718797 | Methods Mol Biol | 2014 |
| Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. | Kabadi AM, Gersbach CA | Methods (San Diego, Calif.) | 25010559 | Methods | 2014 Sep |
| Special issue on engineered DNA-binding proteins. | Kabadi AM, Gersbach CA | ACS synthetic biology | 25324185 | ACS Synth Biol | 2014 Oct 17 |
| Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. | Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA | Nature methods | 26501517 | Nat Methods | 2015 Dec |
| (*) CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments. | Farhang N, Brunger JM, Stover JD, Thakore PI, Lawrence B, Guilak F, Gersbach CA, Setton LA, Bowles RD | Tissue engineering. Part A | 28095751 | Tissue Eng Part A | 2017 Aug |
| Editing the Epigenome: Reshaping the Genomic Landscape. | Holtzman L, Gersbach CA | Annual review of genomics and human genetics | 29852072 | Annu Rev Genomics Hum Genet | 2018 Aug 31 |
| Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. | McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE | Genome research | 30097539 | Genome Res | 2018 Sep |
| Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. | Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA | Nature biotechnology | 31548729 | Nat Biotechnol | 2019 Dec |
| Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. | Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA | ACS synthetic biology | 25494287 | ACS Synth Biol | 2015 Jun 19 |
| Enabling functional genomics with genome engineering. | Hilton IB, Gersbach CA | Genome research | 26430154 | Genome Res | 2015 Oct |
| Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. | Frank CL, Liu F, Wijayatunge R, Song L, Biegler MT, Yang MG, Vockley CM, Safi A, Gersbach CA, Crawford GE, West AE | Nature neuroscience | 25849986 | Nat Neurosci | 2015 May |
| Genome editing: the end of the beginning. | Doudna JA, Gersbach CA | Genome biology | 26700220 | Genome Biol | 2015 Dec 23 |
| Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing. | Rohm D, Black JB, McCutcheon SR, Barrera A, Morone DJ, Nuttle X, de Esch CE, Tai DJC, Talkowski ME, Iglesias N, Gersbach CA | bioRxiv : the preprint server for biology | 38496583 | bioRxiv | 2024 Mar 4 |
| Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei Y, Shah S, Harvey S, Qi LS, Cai L | Biophysical journal | 28427715 | Biophys J | 2017 May 9 |
| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ | Nature methods | 28481362 | Nat Methods | 2017 Jun |
| CRISPR/Cas9 for Human Genome Engineering and Disease Research. | Xiong X, Chen M, Lim WA, Zhao D, Qi LS | Annual review of genomics and human genetics | 27216776 | Annu Rev Genomics Hum Genet | 2016 Aug 31 |
| Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. | Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS | Cell | 25307932 | Cell | 2014 Oct 23 |
| Inference of single-cell phylogenies from lineage tracing data using Cassiopeia. | Jones MG, Khodaverdian A, Quinn JJ, Chan MM, Hussmann JA, Wang R, Xu C, Weissman JS, Yosef N | Genome biology | 32290857 | Genome Biol | 2020 Apr 14 |
| CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. | Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA | Science (New York, N.Y.) | 27980086 | Science | 2017 Jan 6 |
| CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. | Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS | Bioinformatics (Oxford, England) | 26209430 | Bioinformatics | 2015 Nov 15 |
| Synthetic biology approaches to engineer T cells. | Wu CY, Rupp LJ, Roybal KT, Lim WA | Current opinion in immunology | 26218616 | Curr Opin Immunol | 2015 Aug |
| Mapping the Genetic Landscape of Human Cells. | Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA | Cell | 30033366 | Cell | 2018 Aug 9 |
| A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. | Xu X, Qi LS | Journal of molecular biology | 29958882 | J Mol Biol | 2019 Jan 4 |
| Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. | Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, Bivona TG, Weissman JS | Science (New York, N.Y.) | 33479121 | Science | 2021 Feb 26 |
| Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. | Dominguez AA, Lim WA, Qi LS | Nature reviews. Molecular cell biology | 26670017 | Nat Rev Mol Cell Biol | 2016 Jan |
| Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. | Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA | Nature communications | 27363581 | Nat Commun | 2016 Jul 1 |
| A protein-tagging system for signal amplification in gene expression and fluorescence imaging. | Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD | Cell | 25307933 | Cell | 2014 Oct 23 |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA | Cell | 27238023 | Cell | 2016 Jun 2 |
| A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription. | Zhou XX, Zou X, Chung HK, Gao Y, Liu Y, Qi LS, Lin MZ | ACS chemical biology | 28938067 | ACS Chem Biol | 2018 Feb 16 |
| CRISPR interference (CRISPRi) for sequence-specific control of gene expression. | Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS | Nature protocols | 24136345 | Nat Protoc | 2013 Nov |
| Small molecules enhance CRISPR genome editing in pluripotent stem cells. | Yu C, Liu Y, Ma T, Liu K, Xu S, Zhang Y, Liu H, La Russa M, Xie M, Ding S, Qi LS | Cell stem cell | 25658371 | Cell Stem Cell | 2015 Feb 5 |
| CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. | Daley TP, Lin Z, Lin X, Liu Y, Wong WH, Qi LS | Genome biology | 30296940 | Genome Biol | 2018 Oct 8 |
| Nucleosomes impede Cas9 access to DNA in vivo and in vitro. | Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS | eLife | 26987018 | Elife | 2016 Mar 17 |
| Versatile protein tagging in cells with split fluorescent protein. | Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B | Nature communications | 26988139 | Nat Commun | 2016 Mar 18 |
| Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. | Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK | Nature methods | 29083402 | Nat Methods | 2017 Dec |
| Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. | Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R | eLife | 27130520 | Elife | 2016 Apr 28 |
| Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes. | Horlbeck MA, Liu SJ, Chang HY, Lim DA, Weissman JS | Nature biotechnology | 32094656 | Nat Biotechnol | 2020 May |
| Specific gene repression by CRISPRi system transferred through bacterial conjugation. | Ji W, Lee D, Wong E, Dadlani P, Dinh D, Huang V, Kearns K, Teng S, Chen S, Haliburton J, Heimberg G, Heineike B, Ramasubramanian A, Stevens T, Helmke KJ, Zepeda V, Qi LS, Lim WA | ACS synthetic biology | 25409531 | ACS Synth Biol | 2014 Dec 19 |
| Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. | Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA | Cell | 25533786 | Cell | 2015 Jan 15 |
| The New State of the Art: Cas9 for Gene Activation and Repression. | La Russa MF, Qi LS | Molecular and cellular biology | 26370509 | Mol Cell Biol | 2015 Nov |
| Ribosome profiling reveals the what, when, where and how of protein synthesis. | Brar GA, Weissman JS | Nature reviews. Molecular cell biology | 26465719 | Nat Rev Mol Cell Biol | 2015 Nov |
| A versatile framework for microbial engineering using synthetic non-coding RNAs. | Qi LS, Arkin AP | Nature reviews. Microbiology | 24736794 | Nat Rev Microbiol | 2014 May |
| A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. | Mendelsohn BA, Bennett NK, Darch MA, Yu K, Nguyen MK, Pucciarelli D, Nelson M, Horlbeck MA, Gilbert LA, Hyun W, Kampmann M, Nakamura JL, Nakamura K | PLoS biology | 30148842 | PLoS Biol | 2018 Aug |
| CRISPR Approaches to Small Molecule Target Identification. | Jost M, Weissman JS | ACS chemical biology | 29261286 | ACS Chem Biol | 2018 Feb 16 |
| Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. | Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY | Cell | 29731168 | Cell | 2018 May 31 |
| Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. | Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B | Nucleic acids research | 26740581 | Nucleic Acids Res | 2016 May 5 |
| Repurposing CRISPR System for Transcriptional Activation. | Chen M, Qi LS | Advances in experimental medicine and biology | 28639197 | Adv Exp Med Biol | 2017 |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS | Nature methods | 27776111 | Nat Methods | 2016 Dec |
| Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. | Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A | Cell | 27984732 | Cell | 2016 Dec 15 |
| Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. | Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P | Nature methods | 28319113 | Nat Methods | 2017 Jun |
| Cellular response to small molecules that selectively stall protein synthesis by the ribosome. | Liaud N, Horlbeck MA, Gilbert LA, Gjoni K, Weissman JS, Cate JHD | PLoS genetics | 30875366 | PLoS Genet | 2019 Mar |
| Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. | Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B | Cell | 24360272 | Cell | 2013 Dec 19 |
| Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. | Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS | eLife | 27661255 | Elife | 2016 Sep 23 |
| A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. | Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS | Cell | 27984733 | Cell | 2016 Dec 15 |
| Pharmaceutical-Grade Rigosertib Is a Microtubule-Destabilizing Agent. | Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS | Molecular cell | 32619469 | Mol Cell | 2020 Jul 2 |
| Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform. | Wangensteen KJ, Wang YJ, Dou Z, Wang AW, Mosleh-Shirazi E, Horlbeck MA, Gilbert LA, Weissman JS, Berger SL, Kaestner KH | Hepatology (Baltimore, Md.) | 29091290 | Hepatology | 2018 Aug |
| Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. | Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS | Molecular cell | 28985505 | Mol Cell | 2017 Oct 5 |
| Genetic and epigenetic control of gene expression by CRISPR-Cas systems. | Lo A, Qi L | F1000Research | 28649363 | F1000Res | 2017 |
| Molecular recording of mammalian embryogenesis. | Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS | Nature | 31086336 | Nature | 2019 Jun |
| Exploring genetic interaction manifolds constructed from rich single-cell phenotypes. | Norman TM, Horlbeck MA, Replogle JM, Ge AY, Xu A, Jost M, Gilbert LA, Weissman JS | Science (New York, N.Y.) | 31395745 | Science | 2019 Aug 23 |
| Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis. | Hawkins JS, Silvis MR, Koo BM, Peters JM, Osadnik H, Jost M, Hearne CC, Weissman JS, Todor H, Gross CA | Cell systems | 33080209 | Cell Syst | 2020 Nov 18 |
| Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. | Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B | Nature biotechnology | 32231336 | Nat Biotechnol | 2020 Aug |
| Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi). | Hawkins JS, Wong S, Peters JM, Almeida R, Qi LS | Methods in molecular biology (Clifton, N.J.) | 25981485 | Methods Mol Biol | 2015 |
| Bacterial CRISPR: accomplishments and prospects. | Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA, Qi LS | Current opinion in microbiology | 26363124 | Curr Opin Microbiol | 2015 Oct |
| YAP Induces Human Naive Pluripotency. | Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song JS, Ramalho-Santos M | Cell reports | 26947063 | Cell Rep | 2016 Mar 15 |
| CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. | Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR | Cell stem cell | 26971820 | Cell Stem Cell | 2016 Apr 7 |
| Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system. | Kipniss NH, Dingal PCDP, Abbott TR, Gao Y, Wang H, Dominguez AA, Labanieh L, Qi LS | Nature communications | 29263378 | Nat Commun | 2017 Dec 20 |
| Visualization of the Drosophila dKeap1-CncC interaction on chromatin illumines cooperative, xenobiotic-specific gene activation. | Deng H, Kerppola TK | Development (Cambridge, England) | 25063457 | Development | 2014 Aug |
| Visualization by BiFC of different C/EBPβ dimers and their interaction with HP1α reveals a differential subnuclear distribution of complexes in living cells. | Susperreguy S, Prendes LP, Desbats MA, Charó NL, Brown K, MacDougald OA, Kerppola T, Schwartz J, Piwien-Pilipuk G | Experimental cell research | 21122806 | Exp Cell Res | 2011 Apr 1 |
| Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation. | Ren X, Vincenz C, Kerppola TK | Molecular and cellular biology | 18316406 | Mol Cell Biol | 2008 May |
| Multiple roles of Nrf2-Keap1 signaling: regulation of development and xenobiotic response using distinct mechanisms. | Deng H | Fly | 24406335 | Fly (Austin) | 2014 |
| Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. | Deng H, Kerppola TK | Methods in enzymology | 28336073 | Methods Enzymol | 2017 |
| KAP1 represses differentiation-inducible genes in embryonic stem cells through cooperative binding with PRC1 and derepresses pluripotency-associated genes. | Cheng B, Ren X, Kerppola TK | Molecular and cellular biology | 24687849 | Mol Cell Biol | 2014 Jun |
| ATR-101 disrupts mitochondrial functions in adrenocortical carcinoma cells and in vivo. | Cheng Y, Kerppola RE, Kerppola TK | Endocrine-related cancer | 26843528 | Endocr Relat Cancer | 2016 Apr |
| Virus Infection Induces Keap1 Binding to Cytokine Genes, Which Recruits NF-κB p50 and G9a-GLP and Represses Cytokine Transcription. | Burns VE, Kerppola TK | Journal of immunology (Baltimore, Md. : 1950) | 34400522 | J Immunol | 2021 Sep 1 |
| Regulation of Drosophila metamorphosis by xenobiotic response regulators. | Deng H, Kerppola TK | PLoS genetics | 23408904 | PLoS Genet | 2013 |
| REST interacts with Cbx proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements. | Ren X, Kerppola TK | Molecular and cellular biology | 21402785 | Mol Cell Biol | 2011 May |
| ATR-101 inhibits cholesterol efflux and cortisol secretion by ATP-binding cassette transporters, causing cytotoxic cholesterol accumulation in adrenocortical carcinoma cells. | Burns VE, Kerppola TK | British journal of pharmacology | 28710789 | Br J Pharmacol | 2017 Oct |
| Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in live cells. | Kerppola TK | Cold Spring Harbor protocols | 23906917 | Cold Spring Harb Protoc | 2013 Aug 1 |
| Opposite orientations of a transcription factor heterodimer bind DNA cooperatively with interaction partners but have different effects on interferon-β gene transcription. | Burns V, Kerppola TK | The Journal of biological chemistry | 22843696 | J Biol Chem | 2012 Sep 14 |
| Opposing roles of FoxP1 and Nfat3 in transcriptional control of cardiomyocyte hypertrophy. | Bai S, Kerppola TK | Molecular and cellular biology | 21606195 | Mol Cell Biol | 2011 Jul |
| Keap1 moderates the transcription of virus induced genes through G9a-GLP and NFκB p50 recruitment. | Burns VE, Kerppola TK | Immunology | 35751391 | Immunology | 2022 Sep |
| A Novel Substrate Radiotracer for Molecular Imaging of SIRT2 Expression and Activity with Positron Emission Tomography. | Bonomi RE, Laws M, Popov V, Kamal S, Potukutchi S, Shavrin A, Lu X, Turkman N, Liu RS, Mangner T, Gelovani JG | Molecular imaging and biology | 29423902 | Mol Imaging Biol | 2018 Aug |
| An improved synthesis of 1'-[18F]fluoroethyl-β-D-lactose ([18F]-FEL) for positron emission tomography imaging of pancreatic cancer. | Turkman N, Gelovani JG, Alauddin MM | Journal of labelled compounds & radiopharmaceuticals | 24285438 | J Labelled Comp Radiopharm | 2013 Jun 15 |
| Molecular imaging HDACs class IIa expression-activity and pharmacologic inhibition in intracerebral glioma models in rats using PET/CT/(MRI) with [(18)F]TFAHA. | Laws MT, Bonomi RE, Kamal S, Gelovani DJ, Llaniguez J, Potukutchi S, Lu X, Mangner T, Gelovani JG | Scientific reports | 30837601 | Sci Rep | 2019 Mar 5 |
| Molecular Imaging of Sirtuin1 Expression-Activity in Rat Brain Using Positron-Emission Tomography-Magnetic-Resonance Imaging with [(18)F]-2-Fluorobenzoylaminohexanoicanilide. | Bonomi R, Popov V, Laws MT, Gelovani D, Majhi A, Shavrin A, Lu X, Muzik O, Turkman N, Liu R, Mangner T, Gelovani JG | Journal of medicinal chemistry | 30052441 | J Med Chem | 2018 Aug 23 |
| Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics. | Aguilar CA, Craighead HG | Nature nanotechnology | 24091454 | Nat Nanotechnol | 2013 Oct |
| Multiplexed microcolumn-based process for efficient selection of RNA aptamers. | Latulippe DR, Szeto K, Ozer A, Duarte FM, Kelly CV, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | Analytical chemistry | 23398198 | Anal Chem | 2013 Mar 19 |
| Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling. | Ozer A, Tome JM, Friedman RC, Gheba D, Schroth GP, Lis JT | Nature protocols | 26182240 | Nat Protoc | 2015 Aug |
| High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. | Szeto K, Reinholt SJ, Duarte FM, Pagano JM, Ozer A, Yao L, Lis JT, Craighead HG | Analytical and bioanalytical chemistry | 24553662 | Anal Bioanal Chem | 2014 Apr |
| Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits. | Yeh JW, Szeto K | Biomicrofluidics | 28794818 | Biomicrofluidics | 2017 Jul |
| Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. | Reinholt SJ, Ozer A, Lis JT, Craighead HG | Scientific reports | 27432610 | Sci Rep | 2016 Jul 19 |
| Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. | Ozer A, White BS, Lis JT, Shalloway D | Nucleic acids research | 23737446 | Nucleic Acids Res | 2013 Aug |
| Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. | Tome JM, Ozer A, Pagano JM, Gheba D, Schroth GP, Lis JT | Nature methods | 24809628 | Nat Methods | 2014 Jun |
| New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. | Ozer A, Pagano JM, Lis JT | Molecular therapy. Nucleic acids | 25093707 | Mol Ther Nucleic Acids | 2014 Aug 5 |
| RAPID-SELEX for RNA aptamers. | Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | PloS one | 24376564 | PLoS One | 2013 |
| RNA aptamers that functionally interact with green fluorescent protein and its derivatives. | Shui B, Ozer A, Zipfel W, Sahu N, Singh A, Lis JT, Shi H, Kotlikoff MI | Nucleic acids research | 22189104 | Nucleic Acids Res | 2012 Mar |
| Stoichiometric analysis of protein complexes by cell fusion and single molecule imaging. | Singh A, Van Slyke AL, Sirenko M, Song A, Kammermeier PJ, Zipfel WR | Scientific reports | 32913201 | Sci Rep | 2020 Sep 10 |
| In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression. | Vander Schaaf NA, Oghamian S, Park JA, Kang L, Laird PW, Lee KH | Journal of visualized experiments : JoVE | 30985765 | J Vis Exp | 2019 Mar 29 |
| The REMOTE-control system: a system for reversible and tunable control of endogenous gene expression in mice. | Lee KH, Oghamian S, Park JA, Kang L, Laird PW | Nucleic acids research | 28981717 | Nucleic Acids Res | 2017 Dec 1 |
| All Things in Moderation: Prevention of Intestinal Adenomas by DNA Hypomethylation. | Lee KH, Laird PW | Cancer prevention research (Philadelphia, Pa.) | 27190044 | Cancer Prev Res (Phila) | 2016 Jul |
| Relaxin is essential for renal vasodilation during pregnancy in conscious rats. | Novak J, Danielson LA, Kerchner LJ, Sherwood OD, Ramirez RJ, Moalli PA, Conrad KP | The Journal of clinical investigation | 11390429 | J Clin Invest | 2001 Jun |
| Interplay between the cancer genome and epigenome. | Shen H, Laird PW | Cell | 23540689 | Cell | 2013 Mar 28 |
| Emerging role of relaxin in the maternal adaptations to normal pregnancy: implications for preeclampsia. | Conrad KP | Seminars in nephrology | 21266262 | Semin Nephrol | 2011 Jan |
| Unveiling the vasodilatory actions and mechanisms of relaxin. | Conrad KP | Hypertension (Dallas, Tex. : 1979) | 20497994 | Hypertension | 2010 Jul |
| Class I HDAC imaging using [ (3)H]CI-994 autoradiography. | Wang Y, Zhang YL, Hennig K, Gale JP, Hong Y, Cha A, Riley M, Wagner F, Haggarty SJ, Holson E, Hooker J | Epigenetics | 23803584 | Epigenetics | 2013 Jul |
| Histone deacetylase inhibitor, MS-275, exhibits poor brain penetration: PK studies of [C]MS-275 using Positron Emission Tomography. | Hooker JM, Kim SW, Alexoff D, Xu Y, Shea C, Reid A, Volkow N, Fowler JS | ACS chemical neuroscience | 20657706 | ACS Chem Neurosci | 2010 |
| Expression of HDAC2 but Not HDAC1 Transcript Is Reduced in Dorsolateral Prefrontal Cortex of Patients with Schizophrenia. | Schroeder FA, Gilbert TM, Feng N, Taillon BD, Volkow ND, Innis RB, Hooker JM, Lipska BK | ACS chemical neuroscience | 27959513 | ACS Chem Neurosci | 2017 Mar 15 |
| A chemical strategy for the cell-based detection of HDAC activity. | Diyabalanage HV, Van de Bittner GC, Ricq EL, Hooker JM | ACS chemical biology | 25056147 | ACS Chem Biol | 2014 Jun 20 |
| In vivo imaging of histone deacetylases (HDACs) in the central nervous system and major peripheral organs. | Wang C, Schroeder FA, Wey HY, Borra R, Wagner FF, Reis S, Kim SW, Holson EB, Haggarty SJ, Hooker JM | Journal of medicinal chemistry | 25203558 | J Med Chem | 2014 Oct 9 |
| Crebinostat: a novel cognitive enhancer that inhibits histone deacetylase activity and modulates chromatin-mediated neuroplasticity. | Fass DM, Reis SA, Ghosh B, Hennig KM, Joseph NF, Zhao WN, Nieland TJ, Guan JS, Kuhnle CE, Tang W, Barker DD, Mazitschek R, Schreiber SL, Tsai LH, Haggarty SJ | Neuropharmacology | 22771460 | Neuropharmacology | 2013 Jan |
| Insights into neuroepigenetics through human histone deacetylase PET imaging. | Wey HY, Gilbert TM, Zürcher NR, She A, Bhanot A, Taillon BD, Schroeder FA, Wang C, Haggarty SJ, Hooker JM | Science translational medicine | 27510902 | Sci Transl Med | 2016 Aug 10 |
| Visualizing epigenetics: current advances and advantages in HDAC PET imaging techniques. | Wang C, Schroeder FA, Hooker JM | Neuroscience | 24051365 | Neuroscience | 2014 Apr 4 |
| Development of a Fluorinated Class-I HDAC Radiotracer Reveals Key Chemical Determinants of Brain Penetrance. | Strebl MG, Wang C, Schroeder FA, Placzek MS, Wey HY, Van de Bittner GC, Neelamegam R, Hooker JM | ACS chemical neuroscience | 26675505 | ACS Chem Neurosci | 2016 May 18 |
| A philosophy for CNS radiotracer design. | Van de Bittner GC, Ricq EL, Hooker JM | Accounts of chemical research | 25272291 | Acc Chem Res | 2014 Oct 21 |
| FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors. | Schroeder FA, Chonde DB, Riley MM, Moseley CK, Granda ML, Wilson CM, Wagner FF, Zhang YL, Gale J, Holson EB, Haggarty SJ, Hooker JM | Neuroscience letters | 23810801 | Neurosci Lett | 2013 Aug 29 |
| Whole-body pharmacokinetics of HDAC inhibitor drugs, butyric acid, valproic acid and 4-phenylbutyric acid measured with carbon-11 labeled analogs by PET. | Kim SW, Hooker JM, Otto N, Win K, Muench L, Shea C, Carter P, King P, Reid AE, Volkow ND, Fowler JS | Nuclear medicine and biology | 23906667 | Nucl Med Biol | 2013 Oct |
| Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain. | Seo YJ, Muench L, Reid A, Chen J, Kang Y, Hooker JM, Volkow ND, Fowler JS, Kim SW | Bioorganic & medicinal chemistry letters | 24210501 | Bioorg Med Chem Lett | 2013 Dec 15 |
| Dissecting structure-activity-relationships of crebinostat: Brain penetrant HDAC inhibitors for neuroepigenetic regulation. | Ghosh B, Zhao WN, Reis SA, Patnaik D, Fass DM, Tsai LH, Mazitschek R, Haggarty SJ | Bioorganic & medicinal chemistry letters | 26804233 | Bioorg Med Chem Lett | 2016 Feb 15 |
| Translation of HDAC6 PET Imaging Using [(18)F]EKZ-001-cGMP Production and Measurement of HDAC6 Target Occupancy in Nonhuman Primates. | Celen S, Rokka J, Gilbert TM, Koole M, Vermeulen I, Serdons K, Schroeder FA, Wagner FF, Bleeser T, Hightower BG, Hu J, Rahal D, Beyzavi H, Vanduffel W, Van Laere K, Kranz JE, Hooker JM, Bormans G, Cawthorne CJ | ACS chemical neuroscience | 32159328 | ACS Chem Neurosci | 2020 Apr 1 |
| [(11)C]Martinostat PET analysis reveals reduced HDAC I availability in Alzheimer's disease. | Pascoal TA, Chamoun M, Lax E, Wey HY, Shin M, Ng KP, Kang MS, Mathotaarachchi S, Benedet AL, Therriault J, Lussier FZ, Schroeder FA, DuBois JM, Hightower BG, Gilbert TM, Zürcher NR, Wang C, Hopewell R, Chakravarty M, Savard M, Thomas E, Mohaddes S, Farzin S, Salaciak A, Tullo S, Cuello AC, Soucy JP, Massarweh G, Hwang H, Kobayashi E, Hyman BT, Dickerson BC, Guiot MC, Szyf M, Gauthier S, Hooker JM, Rosa-Neto P | Nature communications | 35853847 | Nat Commun | 2022 Jul 19 |
| Image-guided synthesis reveals potent blood-brain barrier permeable histone deacetylase inhibitors. | Seo YJ, Kang Y, Muench L, Reid A, Caesar S, Jean L, Wagner F, Holson E, Haggarty SJ, Weiss P, King P, Carter P, Volkow ND, Fowler JS, Hooker JM, Kim SW | ACS chemical neuroscience | 24780082 | ACS Chem Neurosci | 2014 Jul 16 |
| Design, synthesis, and evaluation of hydroxamic acid-based molecular probes for in vivo imaging of histone deacetylase (HDAC) in brain. | Wang C, Eessalu TE, Barth VN, Mitch CH, Wagner FF, Hong Y, Neelamegam R, Schroeder FA, Holson EB, Haggarty SJ, Hooker JM | American journal of nuclear medicine and molecular imaging | 24380043 | Am J Nucl Med Mol Imaging | 2013 |
| Probing the role of HDACs and mechanisms of chromatin-mediated neuroplasticity. | Haggarty SJ, Tsai LH | Neurobiology of learning and memory | 21545841 | Neurobiol Learn Mem | 2011 Jul |
| Kinetic Analysis and Quantification of [¹¹C]Martinostat for in Vivo HDAC Imaging of the Brain. | Wey HY, Wang C, Schroeder FA, Logan J, Price JC, Hooker JM | ACS chemical neuroscience | 25768025 | ACS Chem Neurosci | 2015 May 20 |
| Clinical validation of the novel HDAC6 radiotracer [(18)F]EKZ-001 in the human brain. | Koole M, Van Weehaeghe D, Serdons K, Herbots M, Cawthorne C, Celen S, Schroeder FA, Hooker JM, Bormans G, de Hoon J, Kranz JE, Van Laere K, Gilbert TM | European journal of nuclear medicine and molecular imaging | 32638097 | Eur J Nucl Med Mol Imaging | 2021 Feb |
| A selective HDAC 1/2 inhibitor modulates chromatin and gene expression in brain and alters mouse behavior in two mood-related tests. | Schroeder FA, Lewis MC, Fass DM, Wagner FF, Zhang YL, Hennig KM, Gale J, Zhao WN, Reis S, Barker DD, Berry-Scott E, Kim SW, Clore EL, Hooker JM, Holson EB, Haggarty SJ, Petryshen TL | PloS one | 23967191 | PLoS One | 2013 |
| Combination therapy: histone deacetylase inhibitors and platinum-based chemotherapeutics for cancer. | Diyabalanage HV, Granda ML, Hooker JM | Cancer letters | 23032720 | Cancer Lett | 2013 Feb 1 |
| PET imaging demonstrates histone deacetylase target engagement and clarifies brain penetrance of known and novel small molecule inhibitors in rat. | Schroeder FA, Wang C, Van de Bittner GC, Neelamegam R, Takakura WR, Karunakaran A, Wey HY, Reis SA, Gale J, Zhang YL, Holson EB, Haggarty SJ, Hooker JM | ACS chemical neuroscience | 25188794 | ACS Chem Neurosci | 2014 Oct 15 |
| Class I Histone Deacetylase Inhibition by Tianeptinaline Modulates Neuroplasticity and Enhances Memory. | Zhao WN, Ghosh B, Tyler M, Lalonde J, Joseph NF, Kosaric N, Fass DM, Tsai LH, Mazitschek R, Haggarty SJ | ACS chemical neuroscience | 29932631 | ACS Chem Neurosci | 2018 Sep 19 |
| Neuroepigenetic signatures of age and sex in the living human brain. | Gilbert TM, Zürcher NR, Catanese MC, Tseng CJ, Di Biase MA, Lyall AE, Hightower BG, Parmar AJ, Bhanot A, Wu CJ, Hibert ML, Kim M, Mahmood U, Stufflebeam SM, Schroeder FA, Wang C, Roffman JL, Holt DJ, Greve DN, Pasternak O, Kubicki M, Wey HY, Hooker JM | Nature communications | 31270332 | Nat Commun | 2019 Jul 3 |
| PET Neurochemical Imaging Modes. | Placzek MS, Zhao W, Wey HY, Morin TM, Hooker JM | Seminars in nuclear medicine | 26687854 | Semin Nucl Med | 2016 Jan |
| An epigenetic trap stabilizes singular olfactory receptor expression. | Lyons DB, Allen WE, Goh T, Tsai L, Barnea G, Lomvardas S | Cell | 23870122 | Cell | 2013 Jul 18 |
| Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. | Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA | Cell reports | 27851973 | Cell Rep | 2016 Nov 15 |
| An epigenetic signature for monoallelic olfactory receptor expression. | Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, Barnea G, Kellis M, Lomvardas S | Cell | 21529909 | Cell | 2011 May 13 |
| Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons. | Lyons DB, Magklara A, Goh T, Sampath SC, Schaefer A, Schotta G, Lomvardas S | Cell reports | 25437545 | Cell Rep | 2014 Nov 6 |
| Visualizing cell architecture and molecular location using soft x-ray tomography and correlated cryo-light microscopy. | McDermott G, Le Gros MA, Larabell CA | Annual review of physical chemistry | 22242730 | Annu Rev Phys Chem | 2012 |
| Stochastic gene expression in mammals: lessons from olfaction. | Magklara A, Lomvardas S | Trends in cell biology | 23689023 | Trends Cell Biol | 2013 Sep |
| Nuclear aggregation of olfactory receptor genes governs their monogenic expression. | Clowney EJ, LeGros MA, Mosley CP, Clowney FG, Markenskoff-Papadimitriou EC, Myllys M, Barnea G, Larabell CA, Lomvardas S | Cell | 23141535 | Cell | 2012 Nov 9 |
| Population Epigenetics. | Greally JM | Current opinion in systems biology | 28367533 | Curr Opin Syst Biol | 2017 Feb |
| Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry. | Sato H, Singer RH, Greally JM | Bio-protocol | 33043098 | Bio Protoc | 2020 Sep 5 |
| Pediatric Obesity-Related Asthma: The Role of Metabolic Dysregulation. | Vijayakanthi N, Greally JM, Rastogi D | Pediatrics | 27244776 | Pediatrics | 2016 May |
| Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. | Sato H, Wu B, Delahaye F, Singer RH, Greally JM | The Journal of cell biology | 31110057 | J Cell Biol | 2019 Jun 3 |
| Current status and future prospects for epigenetic psychopharmacology. | Boks MP, de Jong NM, Kas MJ, Vinkers CH, Fernandes C, Kahn RS, Mill J, Ophoff RA | Epigenetics | 22207355 | Epigenetics | 2012 Jan 1 |
| Meta-analysis of epigenetic aging in schizophrenia reveals multifaceted relationships with age, sex, illness duration, and polygenic risk. | Ori APS, Olde Loohuis LM, Guintivano J, Hannon E, Dempster E, St Clair D, Bass NJ, McQuillin A, Mill J, Sullivan PF, Kahn RS, Horvath S, Ophoff RA | Clinical epigenetics | 38589929 | Clin Epigenetics | 2024 Apr 8 |
| Seasonal changes in gene expression represent cell-type composition in whole blood. | De Jong S, Neeleman M, Luykx JJ, ten Berg MJ, Strengman E, Den Breeijen HH, Stijvers LC, Buizer-Voskamp JE, Bakker SC, Kahn RS, Horvath S, Van Solinge WW, Ophoff RA | Human molecular genetics | 24399446 | Hum Mol Genet | 2014 May 15 |
| Characterization of genome-methylome interactions in 22 nuclear pedigrees. | Plongthongkum N, van Eijk KR, de Jong S, Wang T, Sul JH, Boks MP, Kahn RS, Fung HL, Ophoff RA, Zhang K | PloS one | 25019935 | PLoS One | 2014 |
| Identification of schizophrenia-associated loci by combining DNA methylation and gene expression data from whole blood. | van Eijk KR, de Jong S, Strengman E, Buizer-Voskamp JE, Kahn RS, Boks MP, Horvath S, Ophoff RA | European journal of human genetics : EJHG | 25424713 | Eur J Hum Genet | 2015 Aug |
| Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. | van Eijk KR, de Jong S, Boks MP, Langeveld T, Colas F, Veldink JH, de Kovel CG, Janson E, Strengman E, Langfelder P, Kahn RS, van den Berg LH, Horvath S, Ophoff RA | BMC genomics | 23157493 | BMC Genomics | 2012 Nov 17 |
| Aging effects on DNA methylation modules in human brain and blood tissue. | Horvath S, Zhang Y, Langfelder P, Kahn RS, Boks MP, van Eijk K, van den Berg LH, Ophoff RA | Genome biology | 23034122 | Genome Biol | 2012 Oct 3 |
| Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. | Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, Min J, Nicholson T, Chen T, Xu G, Shi Y, Zhang K, Shi YG | Molecular cell | 21514197 | Mol Cell | 2011 May 20 |
| Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. | Choi JH, Li Y, Guo J, Pei L, Rauch TA, Kramer RS, Macmil SL, Wiley GB, Bennett LB, Schnabel JL, Taylor KH, Kim S, Xu D, Sreekumar A, Pfeifer GP, Roe BA, Caldwell CW, Bhalla KN, Shi H | PloS one | 20927367 | PLoS One | 2010 Sep 29 |
| Sequencing the cancer methylome. | Shull AY, Noonepalle SK, Lee EJ, Choi JH, Shi H | Methods in molecular biology (Clifton, N.J.) | 25421684 | Methods Mol Biol | 2015 |
| PRIMEGENSw3: a web-based tool for high-throughput primer and probe design. | Kushwaha G, Srivastava GP, Xu D | Methods in molecular biology (Clifton, N.J.) | 25697661 | Methods Mol Biol | 2015 |
| Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. | Pei L, Choi JH, Liu J, Lee EJ, McCarthy B, Wilson JM, Speir E, Awan F, Tae H, Arthur G, Schnabel JL, Taylor KH, Wang X, Xu D, Ding HF, Munn DH, Caldwell C, Shi H | Epigenetics | 22534504 | Epigenetics | 2012 Jun 1 |
| A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. | Wang H, He C, Kushwaha G, Xu D, Qiu J | BMC bioinformatics | 26818685 | BMC Bioinformatics | 2016 Jan 11 |
| Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells. | Lee EJ, Rath P, Liu J, Ryu D, Pei L, Noonepalle SK, Shull AY, Feng Q, Litofsky NS, Miller DC, Anthony DC, Kirk MD, Laterra J, Deng L, Xin HB, Wang X, Choi JH, Shi H | Journal of genetics and genomics = Yi chuan xue bao | 26233891 | J Genet Genomics | 2015 Jul 20 |
| Neuronal activity modifies the DNA methylation landscape in the adult brain. | Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H | Nature neuroscience | 21874013 | Nat Neurosci | 2011 Aug 28 |
| Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. | Shoemaker R, Deng J, Wang W, Zhang K | Genome research | 20418490 | Genome Res | 2010 Jul |
| Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. | Lee EJ, Pei L, Srivastava G, Joshi T, Kushwaha G, Choi JH, Robertson KD, Wang X, Colbourne JK, Zhang L, Schroth GP, Xu D, Zhang K, Shi H | Nucleic acids research | 21785137 | Nucleic Acids Res | 2011 Oct |
| Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. | Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K | Nature biotechnology | 19330000 | Nat Biotechnol | 2009 Apr |
| Analyzing the cancer methylome through targeted bisulfite sequencing. | Lee EJ, Luo J, Wilson JM, Shi H | Cancer letters | 23200671 | Cancer Lett | 2013 Nov 1 |
| Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. | Liu GH, Barkho BZ, Ruiz S, Diep D, Qu J, Yang SL, Panopoulos AD, Suzuki K, Kurian L, Walsh C, Thompson J, Boue S, Fung HL, Sancho-Martinez I, Zhang K, Yates J 3rd, Izpisua Belmonte JC | Nature | 21346760 | Nature | 2011 Apr 14 |
| Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. | Liu GH, Suzuki K, Qu J, Sancho-Martinez I, Yi F, Li M, Kumar S, Nivet E, Kim J, Soligalla RD, Dubova I, Goebl A, Plongthongkum N, Fung HL, Zhang K, Loring JF, Laurent LC, Izpisua Belmonte JC | Cell stem cell | 21596650 | Cell Stem Cell | 2011 Jun 3 |
| Library-free methylation sequencing with bisulfite padlock probes. | Diep D, Plongthongkum N, Gore A, Fung HL, Shoemaker R, Zhang K | Nature methods | 22306810 | Nat Methods | 2012 Feb 5 |
| Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. | Kushwaha G, Dozmorov M, Wren JD, Qiu J, Shi H, Xu D | Human genomics | 27461342 | Hum Genomics | 2016 Jul 25 |
| Increased methylation variation in epigenetic domains across cancer types. | Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP | Nature genetics | 21706001 | Nat Genet | 2011 Jun 26 |
| Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. | Ramanagoudr-Bhojappa R, Blair LP, Tackett AJ, Raney KD | Nucleic acids research | 23175612 | Nucleic Acids Res | 2013 Jan |
| Misregulation of Rad50 expression in melanoma cells. | Avaritt NL, Owens R, Larson SK, Reynolds M, Byrum S, Hiatt KM, Smoller BR, Tackett AJ, Cheung WL | Journal of cutaneous pathology | 22725639 | J Cutan Pathol | 2012 Jul |
| Proteomics and melanoma: a current perspective. | Shields BD, Tackett AJ, Shalin SC | Global dermatology | 30214824 | Glob Dermatol | 2016 Aug |
| Quantitative analysis of histone exchange for transcriptionally active chromatin. | Byrum SD, Taverna SD, Tackett AJ | Journal of clinical bioinformatics | 21884633 | J Clin Bioinforma | 2011 Jul 7 |
| Application of MassSQUIRM for quantitative measurements of lysine demethylase activity. | Blair LP, Avaritt NL, Tackett AJ | Journal of visualized experiments : JoVE | 22433969 | J Vis Exp | 2012 Mar 11 |
| Analysis of Histone Exchange during Chromatin Purification. | Byrum S, Mackintosh SG, Edmondson RD, Cheung WL, Taverna SD, Tackett AJ | Journal of integrated OMICS | 21709819 | J Integr OMICS | 2011 Feb 1 |
| Microscopes and Mass Spectrometers. | Shields B, Shalin SC, Tackett AJ | Journal of proteomics & bioinformatics | 29910559 | J Proteomics Bioinform | 2016 |
| Myogenin recruits the histone chaperone facilitates chromatin transcription (FACT) to promote nucleosome disassembly at muscle-specific genes. | Lolis AA, Londhe P, Beggs BC, Byrum SD, Tackett AJ, Davie JK | The Journal of biological chemistry | 23364797 | J Biol Chem | 2013 Mar 15 |
| A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. | Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD, Tackett AJ | Molecular and cellular biology | 19581291 | Mol Cell Biol | 2009 Sep |
| A quantitative proteomic analysis of FFPE melanoma. | Byrum S, Avaritt NL, Mackintosh SG, Munkberg JM, Badgwell BD, Cheung WL, Tackett AJ | Journal of cutaneous pathology | 21883366 | J Cutan Pathol | 2011 Nov |
| Identification of small molecule inhibitors of Jumonji AT-rich interactive domain 1B (JARID1B) histone demethylase by a sensitive high throughput screen. | Sayegh J, Cao J, Zou MR, Morales A, Blair LP, Norcia M, Hoyer D, Tackett AJ, Merkel JS, Yan Q | The Journal of biological chemistry | 23408432 | J Biol Chem | 2013 Mar 29 |
| sarA-mediated repression of protease production plays a key role in the pathogenesis of Staphylococcus aureus USA300 isolates. | Zielinska AK, Beenken KE, Mrak LN, Spencer HJ, Post GR, Skinner RA, Tackett AJ, Horswill AR, Smeltzer MS | Molecular microbiology | 23075270 | Mol Microbiol | 2012 Dec |
| Drug discovery: Reader's block. | Taverna SD, Cole PA | Nature | 21179160 | Nature | 2010 Dec 23 |
| MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity. | Blair LP, Avaritt NL, Huang R, Cole PA, Taverna SD, Tackett AJ | Epigenetics | 21273814 | Epigenetics | 2011 Apr |
| ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. | Byrum SD, Raman A, Taverna SD, Tackett AJ | Cell reports | 22840409 | Cell Rep | 2012 Jul 26 |
| Proteomic technologies for the study of osteosarcoma. | Byrum SD, Washam CL, Montgomery CO, Tackett AJ, Suva LJ | Sarcoma | 22550414 | Sarcoma | 2012 |
| Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma. | Byrum SD, Larson SK, Avaritt NL, Moreland LE, Mackintosh SG, Cheung WL, Tackett AJ | Journal of proteomics & bioinformatics | 23976835 | J Proteomics Bioinform | 2013 Mar 1 |
| Separation and purification of multiply acetylated proteins using cation-exchange chromatography. | Papazyan R, Taverna SD | Methods in molecular biology (Clifton, N.J.) | 23381856 | Methods Mol Biol | 2013 |
| Mapping the local protein interactome of the NuA3 histone acetyltransferase. | Smart SK, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ | Protein science : a publication of the Protein Society | 19621382 | Protein Sci | 2009 Sep |
| A maternal high-fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates. | Suter MA, Chen A, Burdine MS, Choudhury M, Harris RA, Lane RH, Friedman JE, Grove KL, Tackett AJ, Aagaard KM | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22982377 | FASEB J | 2012 Dec |
| A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. | Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BC, Wade H, Tackett AJ, Strahl BD, Taverna SD | Molecular & cellular proteomics : MCP | 25104842 | Mol Cell Proteomics | 2014 Nov |
| TBX2 blocks myogenesis and promotes proliferation in rhabdomyosarcoma cells. | Zhu B, Zhang M, Byrum SD, Tackett AJ, Davie JK | International journal of cancer | 24470334 | Int J Cancer | 2014 Aug 15 |
| Analysis of stable and transient protein-protein interactions. | Byrum S, Smart SK, Larson S, Tackett AJ | Methods in molecular biology (Clifton, N.J.) | 22183593 | Methods Mol Biol | 2012 |
| The bromodomain of Gcn5 regulates site specificity of lysine acetylation on histone H3. | Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD | Molecular & cellular proteomics : MCP | 25106422 | Mol Cell Proteomics | 2014 Nov |
| Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. | Udensi UK, Tackett AJ, Byrum S, Avaritt NL, Sengupta D, Moreland LW, Tchounwou PB, Isokpehi RD | Journal of proteomics & bioinformatics | 25419056 | J Proteomics Bioinform | 2014 Jul |
| Nanogel surface coatings for improved single-molecule imaging substrates. | Tessler LA, Donahoe CD, Garcia DJ, Jun YS, Elbert DL, Mitra RD | Journal of the Royal Society, Interface | 21325313 | J R Soc Interface | 2011 Oct 7 |
| Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. | Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD | Nucleic acids research | 19494183 | Nucleic Acids Res | 2009 Aug |
| Sensitive single-molecule protein quantification and protein complex detection in a microarray format. | Tessler LA, Mitra RD | Proteomics | 22038904 | Proteomics | 2011 Dec |
| Retrotransposon profiling of RNA polymerase III initiation sites. | Qi X, Daily K, Nguyen K, Wang H, Mayhew D, Rigor P, Forouzan S, Johnston M, Mitra RD, Baldi P, Sandmeyer S | Genome research | 22287102 | Genome Res | 2012 Apr |
| Nested Patch PCR for highly multiplexed amplification of genomic loci. | Varley KE, Mitra RD | Cold Spring Harbor protocols | 20147217 | Cold Spring Harb Protoc | 2009 Jul |
| Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. | Varley KE, Mitra RD | Genome research | 20627893 | Genome Res | 2010 Sep |
| GATA factors in endocrine neoplasia. | Pihlajoki M, Färkkilä A, Soini T, Heikinheimo M, Wilson DB | Molecular and cellular endocrinology | 26027919 | Mol Cell Endocrinol | 2016 Feb 5 |
| Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. | Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, Craig NL | Proceedings of the National Academy of Sciences of the United States of America | 23248290 | Proc Natl Acad Sci U S A | 2013 Jan 2 |
| Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue. | Röhrig T, Pihlajoki M, Ziegler R, Cochran RS, Schrade A, Schillebeeckx M, Mitra RD, Heikinheimo M, Wilson DB | Molecular and cellular endocrinology | 25498963 | Mol Cell Endocrinol | 2015 Jun 15 |
| Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret. | Schillebeeckx M, Pihlajoki M, Gretzinger E, Yang W, Thol F, Hiller T, Löbs AK, Röhrig T, Schrade A, Cochran R, Jay PY, Heikinheimo M, Mitra RD, Wilson DB | Molecular and cellular endocrinology | 25289806 | Mol Cell Endocrinol | 2015 Jan 5 |
| Transcription factor regulation and chromosome dynamics during pseudohyphal growth. | Mayhew D, Mitra RD | Molecular biology of the cell | 25009286 | Mol Biol Cell | 2014 Sep 1 |
| IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. | Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P | BMC genomics | 22703188 | BMC Genomics | 2012 Jun 15 |
| Origin and consequences of the relationship between protein mean and variance. | Vallania FL, Sherman M, Goodwin Z, Mogno I, Cohen BA, Mitra RD | PloS one | 25062021 | PLoS One | 2014 |
| Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. | Schillebeeckx M, Schrade A, Löbs AK, Pihlajoki M, Wilson DB, Mitra RD | Nucleic acids research | 23589626 | Nucleic Acids Res | 2013 Jun |
| High-throughput discovery of rare insertions and deletions in large cohorts. | Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD | Genome research | 21041413 | Genome Res | 2010 Dec |
| Detection of rare genomic variants from pooled sequencing using SPLINTER. | Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE | Journal of visualized experiments : JoVE | 22760212 | J Vis Exp | 2012 Jun 23 |
| Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins. | Wang H, Mayhew D, Chen X, Johnston M, Mitra RD | Genome research | 21471402 | Genome Res | 2011 May |
| "Calling cards" for DNA-binding proteins in mammalian cells. | Wang H, Mayhew D, Chen X, Johnston M, Mitra RD | Genetics | 22214611 | Genetics | 2012 Mar |
| The qBED track: a novel genome browser visualization for point processes. | Moudgil A, Li D, Hsu S, Purushotham D, Wang T, Mitra RD | Bioinformatics (Oxford, England) | 32941613 | Bioinformatics | 2021 May 23 |
| Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. | Murphy PJ, Cipriany BR, Wallin CB, Ju CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD | Proceedings of the National Academy of Sciences of the United States of America | 23610441 | Proc Natl Acad Sci U S A | 2013 May 7 |
| Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells. | Benítez JJ, Topolancik J, Tian HC, Wallin CB, Latulippe DR, Szeto K, Murphy PJ, Cipriany BR, Levy SL, Soloway PD, Craighead HG | Lab on a chip | 23018789 | Lab Chip | 2012 Nov 21 |
| Nanoscale resolution, multicomponent biomolecular arrays generated by aligned printing with parylene peel-off. | Tan CP, Cipriany BR, Lin DM, Craighead HG | Nano letters | 20088589 | Nano Lett | 2010 Feb 10 |
| Single DNA molecule patterning for high-throughput epigenetic mapping. | Cerf A, Cipriany BR, Benítez JJ, Craighead HG | Analytical chemistry | 21981444 | Anal Chem | 2011 Nov 1 |
| Transfer-printing of single DNA molecule arrays on graphene for high-resolution electron imaging and analysis. | Cerf A, Alava T, Barton RA, Craighead HG | Nano letters | 21919532 | Nano Lett | 2011 Oct 12 |
| Successful computational prediction of novel imprinted genes from epigenomic features. | Brideau CM, Eilertson KE, Hagarman JA, Bustamante CD, Soloway PD | Molecular and cellular biology | 20421412 | Mol Cell Biol | 2010 Jul |
| Ordered arrays of native chromatin molecules for high-resolution imaging and analysis. | Cerf A, Tian HC, Craighead HG | ACS nano | 22816516 | ACS Nano | 2012 Sep 25 |
| Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. | Cipriany BR, Murphy PJ, Hagarman JA, Cerf A, Latulippe D, Levy SL, Benítez JJ, Tan CP, Topolancik J, Soloway PD, Craighead HG | Proceedings of the National Academy of Sciences of the United States of America | 22586076 | Proc Natl Acad Sci U S A | 2012 May 29 |
| Single molecule epigenetic analysis in a nanofluidic channel. | Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD | Analytical chemistry | 20184350 | Anal Chem | 2010 Mar 15 |
| Identification of a cancer stem cell-specific function for the histone deacetylases, HDAC1 and HDAC7, in breast and ovarian cancer. | Witt AE, Lee CW, Lee TI, Azzam DJ, Wang B, Caslini C, Petrocca F, Grosso J, Jones M, Cohick EB, Gropper AB, Wahlestedt C, Richardson AL, Shiekhattar R, Young RA, Ince TA | Oncogene | 27694895 | Oncogene | 2017 Mar 23 |
| MYC and transcription elongation. | Rahl PB, Young RA | Cold Spring Harbor perspectives in medicine | 24384817 | Cold Spring Harb Perspect Med | 2014 Jan 1 |
| Tubal and ovarian pathways to pelvic epithelial cancer: a pathological perspective. | Jarboe EA, Folkins AK, Drapkin R, Ince TA, Agoston ES, Crum CP | Histopathology | 19912369 | Histopathology | 2009 Nov |
| c-Myc regulates transcriptional pause release. | Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA | Cell | 20434984 | Cell | 2010 Apr 30 |
| Defined, serum-free conditions for in vitro culture of primary human T-ALL blasts. | Yost AJ, Shevchuk OO, Gooch R, Gusscott S, You MJ, Ince TA, Aster JC, Weng AP | Leukemia | 23246990 | Leukemia | 2013 Jun |
| Master transcription factors and mediator establish super-enhancers at key cell identity genes. | Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA | Cell | 23582322 | Cell | 2013 Apr 11 |
| Selective inhibition of tumor oncogenes by disruption of super-enhancers. | Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA | Cell | 23582323 | Cell | 2013 Apr 11 |
| Transcriptional regulation and its misregulation in disease. | Lee TI, Young RA | Cell | 23498934 | Cell | 2013 Mar 14 |
| Super-enhancers in the control of cell identity and disease. | Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA | Cell | 24119843 | Cell | 2013 Nov 7 |
| Revisiting global gene expression analysis. | Lovén J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA | Cell | 23101621 | Cell | 2012 Oct 26 |
| Transcriptional amplification in tumor cells with elevated c-Myc. | Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA | Cell | 23021215 | Cell | 2012 Sep 28 |
| A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity. | D'Alessio AC, Fan ZP, Wert KJ, Baranov P, Cohen MA, Saini JS, Cohick E, Charniga C, Dadon D, Hannett NM, Young MJ, Temple S, Jaenisch R, Lee TI, Young RA | Stem cell reports | 26603904 | Stem Cell Reports | 2015 Nov 10 |
| The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. | Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI | Nature | 21430779 | Nature | 2011 Mar 24 |
| Poised chromatin at the ZEB1 promoter enables breast cancer cell plasticity and enhances tumorigenicity. | Chaffer CL, Marjanovic ND, Lee T, Bell G, Kleer CG, Reinhardt F, D'Alessio AC, Young RA, Weinberg RA | Cell | 23827675 | Cell | 2013 Jul 3 |
| CpG island structure and trithorax/polycomb chromatin domains in human cells. | Orlando DA, Guenther MG, Frampton GM, Young RA | Genomics | 22819920 | Genomics | 2012 Nov |
| Taxonomy of breast cancer based on normal cell phenotype predicts outcome. | Santagata S, Thakkar A, Ergonul A, Wang B, Woo T, Hu R, Harrell JC, McNamara G, Schwede M, Culhane AC, Kindelberger D, Rodig S, Richardson A, Schnitt SJ, Tamimi RM, Ince TA | The Journal of clinical investigation | 24463450 | J Clin Invest | 2014 Feb |
| A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. | Petrocca F, Altschuler G, Tan SM, Mendillo ML, Yan H, Jerry DJ, Kung AL, Hide W, Ince TA, Lieberman J | Cancer cell | 23948298 | Cancer Cell | 2013 Aug 12 |
| Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. | Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, Young RA | Cell stem cell | 20682450 | Cell Stem Cell | 2010 Aug 6 |
| HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers. | Mendillo ML, Santagata S, Koeva M, Bell GW, Hu R, Tamimi RM, Fraenkel E, Ince TA, Whitesell L, Lindquist S | Cell | 22863008 | Cell | 2012 Aug 3 |
| Tubal and ovarian pathways to pelvic epithelial cancer: a pathological perspective. | Jarboe EA, Folkins AK, Drapkin R, Ince TA, Agoston ES, Crum CP | Histopathology | 18298580 | Histopathology | 2008 Aug |
| Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes. | Merritt MA, Bentink S, Schwede M, Iwanicki MP, Quackenbush J, Woo T, Agoston ES, Reinhardt F, Crum CP, Berkowitz RS, Mok SC, Witt AE, Jones MA, Wang B, Ince TA | PloS one | 24303006 | PLoS One | 2013 |
| Genome-wide localization of small molecules. | Anders L, Guenther MG, Qi J, Fan ZP, Marineau JJ, Rahl PB, Lovén J, Sigova AA, Smith WB, Lee TI, Bradner JE, Young RA | Nature biotechnology | 24336317 | Nat Biotechnol | 2014 Jan |
| High levels of nuclear heat-shock factor 1 (HSF1) are associated with poor prognosis in breast cancer. | Santagata S, Hu R, Lin NU, Mendillo ML, Collins LC, Hankinson SE, Schnitt SJ, Whitesell L, Tamimi RM, Lindquist S, Ince TA | Proceedings of the National Academy of Sciences of the United States of America | 22042860 | Proc Natl Acad Sci U S A | 2011 Nov 8 |
| Normal cell phenotypes of breast epithelial cells provide the foundation of a breast cancer taxonomy. | Santagata S, Ince TA | Expert review of anticancer therapy | 25263303 | Expert Rev Anticancer Ther | 2014 Dec |
| Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours. | Ince TA, Sousa AD, Jones MA, Harrell JC, Agoston ES, Krohn M, Selfors LM, Liu W, Chen K, Yong M, Buchwald P, Wang B, Hale KS, Cohick E, Sergent P, Witt A, Kozhekbaeva Z, Gao S, Agoston AT, Merritt MA, Foster R, Rueda BR, Crum CP, Brugge JS, Mills GB | Nature communications | 26080861 | Nat Commun | 2015 Jun 17 |
| Genome organizing function of SATB1 in tumor progression. | Kohwi-Shigematsu T, Poterlowicz K, Ordinario E, Han HJ, Botchkarev VA, Kohwi Y | Seminars in cancer biology | 22771615 | Semin Cancer Biol | 2013 Apr |
| SATB1-mediated functional packaging of chromatin into loops. | Kohwi-Shigematsu T, Kohwi Y, Takahashi K, Richards HW, Ayers SD, Han HJ, Cai S | Methods (San Diego, Calif.) | 22782115 | Methods | 2012 Nov |
| Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. | Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR Jr, Calof AL, Lander AD, Groudine MT, Yokomori K | The Journal of biological chemistry | 21454523 | J Biol Chem | 2011 May 20 |
| HP1: heterochromatin binding proteins working the genome. | Zeng W, Ball AR Jr, Yokomori K | Epigenetics | 20421743 | Epigenetics | 2010 May 16 |
| Cohesin: a critical chromatin organizer in mammalian gene regulation. | Chien R, Zeng W, Ball AR, Yokomori K | Biochemistry and cell biology = Biochimie et biologie cellulaire | 21851156 | Biochem Cell Biol | 2011 Oct |
| Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. | Ball AR Jr, Chen YY, Yokomori K | Biochimica et biophysica acta | 24269489 | Biochim Biophys Acta | 2014 Mar |
| Genetic and epigenetic characteristics of FSHD-associated 4q and 10q D4Z4 that are distinct from non-4q/10q D4Z4 homologs. | Zeng W, Chen YY, Newkirk DA, Wu B, Balog J, Kong X, Ball AR Jr, Zanotti S, Tawil R, Hashimoto N, Mortazavi A, van der Maarel SM, Yokomori K | Human mutation | 24838473 | Hum Mutat | 2014 Aug |
| Dynamic regulation of the PR-Set7 histone methyltransferase is required for normal cell cycle progression. | Wu S, Wang W, Kong X, Congdon LM, Yokomori K, Kirschner MW, Rice JC | Genes & development | 20966048 | Genes Dev | 2010 Nov 15 |
| Monocyte polarization: the relationship of genome-wide changes in H4 acetylation with polarization. | Zhang Z, Song L, Maurer K, Bagashev A, Sullivan KE | Genes and immunity | 21451557 | Genes Immun | 2011 Sep |
| Cytokine-induced monocyte characteristics in SLE. | Zhang Z, Maurer K, Perin JC, Song L, Sullivan KE | Journal of biomedicine & biotechnology | 20625490 | J Biomed Biotechnol | 2010 |
| SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs. | Shii L, Song L, Maurer K, Zhang Z, Sullivan KE | Molecular immunology | 28578223 | Mol Immunol | 2017 Aug |
| Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes. | Shi L, Perin JC, Leipzig J, Zhang Z, Sullivan KE | Gene | 21803131 | Gene | 2011 Nov 1 |
| The Role of MicroRNAs and Human Epidermal Growth Factor Receptor 2 in Proliferative Lupus Nephritis. | Costa-Reis P, Russo PA, Zhang Z, Colonna L, Maurer K, Gallucci S, Schulz SW, Kiani AN, Petri M, Sullivan KE | Arthritis & rheumatology (Hoboken, N.J.) | 26016809 | Arthritis Rheumatol | 2015 Sep |
| Global H4 acetylation analysis by ChIP-chip in systemic lupus erythematosus monocytes. | Zhang Z, Song L, Maurer K, Petri MA, Sullivan KE | Genes and immunity | 19710693 | Genes Immun | 2010 Mar |
| Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90. | Kelly M, Lihua S, Zhe Z, Li S, Yoselin P, Michelle P, Sullivan Kathleen E | Clinical immunology (Orlando, Fla.) | 30149120 | Clin Immunol | 2018 Dec |
| Noncoding RNAs and LRRFIP1 regulate TNF expression. | Shi L, Song L, Fitzgerald M, Maurer K, Bagashev A, Sullivan KE | Journal of immunology (Baltimore, Md. : 1950) | 24567534 | J Immunol | 2014 Apr 1 |
| H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus. | Zhang Z, Shi L, Dawany N, Kelsen J, Petri MA, Sullivan KE | Clinical epigenetics | 26839600 | Clin Epigenetics | 2016 |
| Interferon regulatory factor 1 marks activated genes and can induce target gene expression in systemic lupus erythematosus. | Zhang Z, Shi L, Song L, Ephrem E, Petri M, Sullivan KE | Arthritis & rheumatology (Hoboken, N.J.) | 25418955 | Arthritis Rheumatol | 2015 Mar |
| Endotoxin tolerance in monocytes can be mitigated by α2-interferon. | Shi L, Song L, Maurer K, Sharp J, Zhang Z, Sullivan KE | Journal of leukocyte biology | 26206900 | J Leukoc Biol | 2015 Oct |
| Monocyte enhancers are highly altered in systemic lupus erythematosus. | Shi L, Zhang Z, Song L, Leung YT, Petri MA, Sullivan KE | Epigenomics | 26442457 | Epigenomics | 2015 |
| IL-1 Transcriptional Responses to Lipopolysaccharides Are Regulated by a Complex of RNA Binding Proteins. | Shi L, Song L, Maurer K, Dou Y, Patel VR, Su C, Leonard ME, Lu S, Hodge KM, Torres A, Chesi A, Grant SFA, Wells AD, Zhang Z, Petri MA, Sullivan KE | Journal of immunology (Baltimore, Md. : 1950) | 31953354 | J Immunol | 2020 Mar 1 |
| New insights into the immunopathogenesis of systemic lupus erythematosus. | Tsokos GC, Lo MS, Costa Reis P, Sullivan KE | Nature reviews. Rheumatology | 27872476 | Nat Rev Rheumatol | 2016 Nov 22 |
| Enhancer RNA and NFκB-dependent P300 regulation of ADAMDEC1. | Shi L, Li S, Maurer K, Zhang Z, Petri M, Sullivan KE | Molecular immunology | 30352365 | Mol Immunol | 2018 Nov |
| Aberrant regulation of the integrin very late antigen-4 in systemic lupus erythematosus. | Rahimi H, Maurer K, Song L, Akhter E, Petri M, Sullivan KE | Lupus | 23439470 | Lupus | 2013 Mar |
| The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs. | Shi L, Zhang Z, Yu AM, Wang W, Wei Z, Akhter E, Maurer K, Costa Reis P, Song L, Petri M, Sullivan KE | PloS one | 24796678 | PLoS One | 2014 |
| Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies. | Sullivan KE, Bassiri H, Bousfiha AA, Costa-Carvalho BT, Freeman AF, Hagin D, Lau YL, Lionakis MS, Moreira I, Pinto JA, de Moraes-Pinto MI, Rawat A, Reda SM, Reyes SOL, Seppänen M, Tang MLK | Journal of clinical immunology | 28786026 | J Clin Immunol | 2017 Oct |
| Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus. | Leung YT, Shi L, Maurer K, Song L, Zhang Z, Petri M, Sullivan KE | Epigenetics | 25611806 | Epigenetics | 2015 |
| Epigenetic mechanisms in Alzheimer's disease. | Mastroeni D, Grover A, Delvaux E, Whiteside C, Coleman PD, Rogers J | Neurobiology of aging | 21482442 | Neurobiol Aging | 2011 Jul |
| Nuclear but not mitochondrial-encoded oxidative phosphorylation genes are altered in aging, mild cognitive impairment, and Alzheimer's disease. | Mastroeni D, Khdour OM, Delvaux E, Nolz J, Olsen G, Berchtold N, Cotman C, Hecht SM, Coleman PD | Alzheimer's & dementia : the journal of the Alzheimer's Association | 27793643 | Alzheimers Dement | 2017 May |
| Novel antioxidants protect mitochondria from the effects of oligomeric amyloid beta and contribute to the maintenance of epigenome function. | Mastroeni D, Khdour OM, Arce PM, Hecht SM, Coleman PD | ACS chemical neuroscience | 25668062 | ACS Chem Neurosci | 2015 Apr 15 |
| Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells. | Delvaux E, Mastroeni D, Nolz J, Coleman PD | Neuroepigenetics | 27158594 | Neuroepigenetics | 2016 Jun |
| An evaluation of processing methods for HumanMethylation450 BeadChip data. | Liu J, Siegmund KD | BMC genomics | 27334613 | BMC Genomics | 2016 Jun 22 |
| Aberrant intracellular localization of H3k4me3 demonstrates an early epigenetic phenomenon in Alzheimer's disease. | Mastroeni D, Delvaux E, Nolz J, Tan Y, Grover A, Oddo S, Coleman PD | Neurobiology of aging | 26553823 | Neurobiol Aging | 2015 Dec |
| A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. | Smith RG, Pishva E, Shireby G, Smith AR, Roubroeks JAY, Hannon E, Wheildon G, Mastroeni D, Gasparoni G, Riemenschneider M, Giese A, Sharp AJ, Schalkwyk L, Haroutunian V, Viechtbauer W, van den Hove DLA, Weedon M, Brokaw D, Francis PT, Thomas AJ, Love S, Morgan K, Walter J, Coleman PD, Bennett DA, De Jager PL, Mill J, Lunnon K | Nature communications | 34112773 | Nat Commun | 2021 Jun 10 |
| Massive changes in gene expression and their cause(s) can be a unifying principle in the pathobiology of Alzheimer's disease. | Coleman PD, Delvaux E, Kordower JH, Boehringer A, Huseby CJ | Alzheimer's & dementia : the journal of the Alzheimer's Association | 39912452 | Alzheimers Dement | 2025 Feb |
| Predicting conversion from mild cognitive impairment to Alzheimer's disease using neuropsychological tests and multivariate methods. | Chapman RM, Mapstone M, McCrary JW, Gardner MN, Porsteinsson A, Sandoval TC, Guillily MD, Degrush E, Reilly LA | Journal of clinical and experimental neuropsychology | 20711906 | J Clin Exp Neuropsychol | 2011 Feb |
| Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer's disease. | Mastroeni D, McKee A, Grover A, Rogers J, Coleman PD | PloS one | 19672297 | PLoS One | 2009 Aug 12 |
| Epigenetic changes in Alzheimer's disease: decrements in DNA methylation. | Mastroeni D, Grover A, Delvaux E, Whiteside C, Coleman PD, Rogers J | Neurobiology of aging | 19117641 | Neurobiol Aging | 2010 Dec |
| The epigenetics of Alzheimer's disease--additional considerations. | Rogers J, Mastroeni D, Grover A, Delvaux E, Whiteside C, Coleman PD | Neurobiology of aging | 21497949 | Neurobiol Aging | 2011 Jul |
| Cell death and survival pathways in Alzheimer's disease: an integrative hypothesis testing approach utilizing -omic data sets. | Brokaw DL, Piras IS, Mastroeni D, Weisenberger DJ, Nolz J, Delvaux E, Serrano GE, Beach TG, Huentelman MJ, Coleman PD | Neurobiology of aging | 32745806 | Neurobiol Aging | 2020 Nov |
| Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer's Disease. | Piras IS, Brokaw D, Kong Y, Weisenberger DJ, Krate J, Delvaux E, Mahurkar S, Blattler A, Siegmund KD, Sue L, Serrano GE, Beach TG, Laird PW, Huentelman MJ, Coleman PD | Cellular and molecular neurobiology | 36596913 | Cell Mol Neurobiol | 2023 Jul |
| Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients. | Chouliaras L, Mastroeni D, Delvaux E, Grover A, Kenis G, Hof PR, Steinbusch HW, Coleman PD, Rutten BP, van den Hove DL | Neurobiology of aging | 23582657 | Neurobiol Aging | 2013 Sep |
| Reduced RAN expression and disrupted transport between cytoplasm and nucleus; a key event in Alzheimer's disease pathophysiology. | Mastroeni D, Chouliaras L, Grover A, Liang WS, Hauns K, Rogers J, Coleman PD | PloS one | 23308199 | PLoS One | 2013 |
| Synaptic genes are extensively downregulated across multiple brain regions in normal human aging and Alzheimer's disease. | Berchtold NC, Coleman PD, Cribbs DH, Rogers J, Gillen DL, Cotman CW | Neurobiology of aging | 23273601 | Neurobiol Aging | 2013 Jun |
| Differential processing of amyloid precursor protein in brain and in peripheral blood leukocytes. | Delvaux E, Bentley K, Stubbs V, Sabbagh M, Coleman PD | Neurobiology of aging | 23298733 | Neurobiol Aging | 2013 Jun |
| Association of genetic variants in the receptor for advanced glycation end products gene with diabetic retinopathy: A meta-analysis. | Yu W, Yang J, Sui W, Qu B, Huang P, Chen Y | Medicine | 27684793 | Medicine (Baltimore) | 2016 Sep |
| Diurnal and seasonal molecular rhythms in human neocortex and their relation to Alzheimer's disease. | Lim AS, Klein HU, Yu L, Chibnik LB, Ali S, Xu J, Bennett DA, De Jager PL | Nature communications | 28368004 | Nat Commun | 2017 Apr 3 |
| Occupational cognitive requirements and late-life cognitive aging. | Pool LR, Weuve J, Wilson RS, Bültmann U, Evans DA, Mendes de Leon CF | Neurology | 26984944 | Neurology | 2016 Apr 12 |
| Circadian alterations during early stages of Alzheimer's disease are associated with aberrant cycles of DNA methylation in BMAL1. | Cronin P, McCarthy MJ, Lim ASP, Salmon DP, Galasko D, Masliah E, De Jager PL, Bennett DA, Desplats P | Alzheimer's & dementia : the journal of the Alzheimer's Association | 27883893 | Alzheimers Dement | 2017 Jun |
| Epigenomics of Alzheimer's disease. | Bennett DA, Yu L, Yang J, Srivastava GP, Aubin C, De Jager PL | Translational research : the journal of laboratory and clinical medicine | 24905038 | Transl Res | 2015 Jan |
| cindr, the Drosophila Homolog of the CD2AP Alzheimer's Disease Risk Gene, Is Required for Synaptic Transmission and Proteostasis. | Ojelade SA, Lee TV, Giagtzoglou N, Yu L, Ugur B, Li Y, Duraine L, Zuo Z, Petyuk V, De Jager PL, Bennett DA, Arenkiel BR, Bellen HJ, Shulman JM | Cell reports | 31412248 | Cell Rep | 2019 Aug 13 |
| Novel methods for integration and visualization of genomics and genetics data in Alzheimer's disease. | Bihlmeyer NA, Merrill E, Lambert Y, Srivastava GP, Clark TW, Hyman BT, Das S | Alzheimer's & dementia : the journal of the Alzheimer's Association | 30935898 | Alzheimers Dement | 2019 Jun |
| Prioritizing Parkinson's disease genes using population-scale transcriptomic data. | Li YI, Wong G, Humphrey J, Raj T | Nature communications | 30824768 | Nat Commun | 2019 Mar 1 |
| Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristics. | Gaiteri C, Dawe R, Mostafavi S, Blizinsky KD, Tasaki S, Komashko V, Yu L, Wang Y, Schneider JA, Arfanakis K, De Jager PL, Bennett DA | Brain imaging and behavior | 29934819 | Brain Imaging Behav | 2019 Aug |
| The association between apolipoprotein E and gallstone disease: an updated meta-analysis. | Li L, Qiao X, Wang X, Liu D, Xue Q, Han L, Dai F, Ma G, Yang Z, Zhang T, Yang S, Cai S, Gao M, Yang J | BMC medical genetics | 31200656 | BMC Med Genet | 2019 Jun 14 |
| Sex difference in daily rhythms of clock gene expression in the aged human cerebral cortex. | Lim AS, Myers AJ, Yu L, Buchman AS, Duffy JF, De Jager PL, Bennett DA | Journal of biological rhythms | 23606611 | J Biol Rhythms | 2013 Apr |
| Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline. | Yu L, Dawe RJ, Boyle PA, Gaiteri C, Yang J, Buchman AS, Schneider JA, Arfanakis K, De Jager PL, Bennett DA | JAMA neurology | 29084334 | JAMA Neurol | 2017 Dec 1 |
| Down-Regulated Phosphoglycerate Kinase 1 Expression Is Associated With Poor Prognosis in Patients With Gallbladder Cancer. | Lu W, Gao J, Yang J, Cao Y, Jiang L, Li M, Zhang Y, Zhou J, Liu Y | Medicine | 26656369 | Medicine (Baltimore) | 2015 Dec |
| Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer's disease related cognitive functioning. | Levine ME, Lu AT, Bennett DA, Horvath S | Aging | 26684672 | Aging (Albany NY) | 2015 Dec |
| Deciphering cellular transcriptional alterations in Alzheimer's disease brains. | Wang X, Allen M, Li S, Quicksall ZS, Patel TA, Carnwath TP, Reddy JS, Carrasquillo MM, Lincoln SJ, Nguyen TT, Malphrus KG, Dickson DW, Crook JE, Asmann YW, Ertekin-Taner N | Molecular neurodegeneration | 32660529 | Mol Neurodegener | 2020 Jul 13 |
| Exploring the role of the epigenome in multiple sclerosis: a window onto cell-specific transcriptional potential. | Kaliszewska A, De Jager PL | Journal of neuroimmunology | 22297167 | J Neuroimmunol | 2012 Jul 15 |
| Alzheimer's loci: epigenetic associations and interaction with genetic factors. | Chibnik LB, Yu L, Eaton ML, Srivastava G, Schneider JA, Kellis M, Bennett DA, De Jager PL | Annals of clinical and translational neurology | 26125039 | Ann Clin Transl Neurol | 2015 Jun |
| Irregular 24-hour activity rhythms and the metabolic syndrome in older adults. | Sohail S, Yu L, Bennett DA, Buchman AS, Lim AS | Chronobiology international | 26061588 | Chronobiol Int | 2015 |
| Total daily activity declines more rapidly with increasing age in older adults. | Buchman AS, Wilson RS, Yu L, James BD, Boyle PA, Bennett DA | Archives of gerontology and geriatrics | 24007938 | Arch Gerontol Geriatr | 2014 Jan-Feb |
| Metabolomics profiling reveals distinct, sex-specific signatures in serum and brain metabolomes in mouse models of Alzheimer's disease. | Pandey RS, Arnold M, Batra R, Krumsiek J, Kotredes KP, Garceau D, Williams H, Sasner M, Howell GR, Kaddurah-Daouk R, Carter GW | Alzheimer's & dementia : the journal of the Alzheimer's Association | 38676929 | Alzheimers Dement | 2024 Jun |
| Multi-transcriptomic analysis points to early organelle dysfunction in human astrocytes in Alzheimer's disease. | Galea E, Weinstock LD, Larramona-Arcas R, Pybus AF, Giménez-Llort L, Escartin C, Wood LB | Neurobiology of disease | 35143967 | Neurobiol Dis | 2022 May |
| Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics. | Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ | Science advances | 38781333 | Sci Adv | 2024 May 24 |
| Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins. | Oatman SR, Reddy JS, Quicksall Z, Carrasquillo MM, Wang X, Liu CC, Yamazaki Y, Nguyen TT, Malphrus K, Heckman M, Biswas K, Nho K, Baker M, Martens YA, Zhao N, Kim JP, Risacher SL, Rademakers R, Saykin AJ, DeTure M, Murray ME, Kanekiyo T, Alzheimer’s Disease Neuroimaging Initiative, Dickson DW, Bu G, Allen M, Ertekin-Taner N | Molecular neurodegeneration | 36609403 | Mol Neurodegener | 2023 Jan 7 |
| Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers. | Brase L, You SF, D'Oliveira Albanus R, Del-Aguila JL, Dai Y, Novotny BC, Soriano-Tarraga C, Dykstra T, Fernandez MV, Budde JP, Bergmann K, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Goate AM, Farlow M, Dominantly Inherited Alzheimer Network (DIAN), Sutherland GT, Kipnis J, Karch CM, Benitez BA, Harari O | Nature communications | 37085492 | Nat Commun | 2023 Apr 21 |
| Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain. | Barbash S, Simchovitz A, Buchman AS, Bennett DA, Shifman S, Soreq H | Translational psychiatry | 28786976 | Transl Psychiatry | 2017 Aug 8 |
| Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients. | Ma D, Yang J, Wang Y, Huang X, Du G, Zhou L | American journal of medical genetics. Part A | 28742274 | Am J Med Genet A | 2017 Oct |
| Deconstructing and targeting the genomic architecture of human neurodegeneration. | De Jager PL, Yang HS, Bennett DA | Nature neuroscience | 30258235 | Nat Neurosci | 2018 Oct |
| Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. | Tasaki S, Gaiteri C, Mostafavi S, Yu L, Wang Y, De Jager PL, Bennett DA | Frontiers in genetics | 30140277 | Front Genet | 2018 |
| Pan-primate studies of age and sex. | Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW | GeroScience | 37493860 | Geroscience | 2023 Dec |
| Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment. | Chiou KL, DeCasien AR, Rees KP, Testard C, Spurrell CH, Gogate AA, Pliner HA, Tremblay S, Mercer A, Whalen CJ, Negrón-Del Valle JE, Janiak MC, Bauman Surratt SE, González O, Compo NR, Stock MK, Ruiz-Lambides AV, Martínez MI, Cayo Biobank Research Unit, Wilson MA, Melin AD, Antón SC, Walker CS, Sallet J, Newbern JM, Starita LM, Shendure J, Higham JP, Brent LJN, Montague MJ, Platt ML, Snyder-Mackler N | Nature neuroscience | 36424430 | Nat Neurosci | 2022 Dec |
| Association between DNA methylation levels in brain tissue and late-life depression in community-based participants. | Hüls A, Robins C, Conneely KN, De Jager PL, Bennett DA, Epstein MP, Wingo TS, Wingo AP | Translational psychiatry | 32733030 | Transl Psychiatry | 2020 Jul 30 |
| Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. | Lam S, Hartmann N, Benfeitas R, Zhang C, Arif M, Turkez H, Uhlén M, Englert C, Knight R, Mardinoglu A | Biomedicines | 34680427 | Biomedicines | 2021 Sep 24 |
| NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. | He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM | Communications biology | 34040149 | Commun Biol | 2021 May 26 |
| Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease. | Serrano-Pozo A, Li Z, Noori A, Nguyen HN, Mezlini A, Li L, Hudry E, Jackson RJ, Hyman BT, Das S | Nature aging | 36199750 | Nat Aging | 2021 Oct |
| Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218. | Jurkiewicz M, Moser D, Koller A, Yu L, Chen EI, Bennett DA, Canli T | Translational psychiatry | 32839459 | Transl Psychiatry | 2020 Aug 24 |
| Cross-Species Analyses Identify Dlgap2 as a Regulator of Age-Related Cognitive Decline and Alzheimer's Dementia. | Ouellette AR, Neuner SM, Dumitrescu L, Anderson LC, Gatti DM, Mahoney ER, Bubier JA, Churchill G, Peters L, Huentelman MJ, Herskowitz JH, Yang HS, Smith AN, Reitz C, Kunkle BW, White CC, De Jager PL, Schneider JA, Bennett DA, Seyfried NT, Alzheimer’s Disease Genetics Consortium, Chesler EJ, Hadad N, Hohman TJ, Kaczorowski CC | Cell reports | 32877673 | Cell Rep | 2020 Sep 1 |
| Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data. | Wang J, Roeder K, Devlin B | Genome research | 33837133 | Genome Res | 2021 Oct |
| RNASE6 is a novel modifier of APOE-ε4 effects on cognition. | Seto M, Weiner RL, Dumitrescu L, Mahoney ER, Hansen SL, Janve V, Khan OA, Liu D, Wang Y, Menon V, De Jager PL, Schneider JA, Bennett DA, Gifford KA, Jefferson AL, Hohman TJ | Neurobiology of aging | 35896049 | Neurobiol Aging | 2022 Oct |
| Chromosome X-wide association study in case control studies of pathologically confirmed Alzheimer's disease in a European population. | Simmonds E, Leonenko G, Yaman U, Bellou E, Myers A, Morgan K, Brookes K, Hardy J, Salih D, Escott-Price V | Translational psychiatry | 39231932 | Transl Psychiatry | 2024 Sep 4 |
| 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. | Lim AS, Srivastava GP, Yu L, Chibnik LB, Xu J, Buchman AS, Schneider JA, Myers AJ, Bennett DA, De Jager PL | PLoS genetics | 25375876 | PLoS Genet | 2014 Nov |
| Long-term clinical outcomes of laparoscopy-assisted distal gastrectomy versus open distal gastrectomy for early gastric cancer: A comprehensive systematic review and meta-analysis of randomized control trials. | Lu W, Gao J, Yang J, Zhang Y, Lv W, Mu J, Dong P, Liu Y | Medicine | 27399073 | Medicine (Baltimore) | 2016 Jul |
| Loneliness 5 years ante-mortem is associated with disease-related differential gene expression in postmortem dorsolateral prefrontal cortex. | Canli T, Yu L, Yu X, Zhao H, Fleischman D, Wilson RS, De Jager PL, Bennett DA | Translational psychiatry | 29317593 | Transl Psychiatry | 2018 Jan 10 |
| Rescue of Early bace-1 and Global DNA Demethylation by S-Adenosylmethionine Reduces Amyloid Pathology and Improves Cognition in an Alzheimer's Model. | Do Carmo S, Hanzel CE, Jacobs ML, Machnes Z, Iulita MF, Yang J, Yu L, Ducatenzeiler A, Danik M, Breuillaud LS, Bennett DA, Szyf M, Cuello AC | Scientific reports | 27681803 | Sci Rep | 2016 Sep 29 |
| An inflection point in gene discovery efforts for neurodegenerative diseases: from syndromic diagnoses toward endophenotypes and the epigenome. | De Jager PL, Bennett DA | JAMA neurology | 23571780 | JAMA Neurol | 2013 Jun |
| CD33 Alzheimer's disease locus: altered monocyte function and amyloid biology. | Bradshaw EM, Chibnik LB, Keenan BT, Ottoboni L, Raj T, Tang A, Rosenkrantz LL, Imboywa S, Lee M, Von Korff A, Alzheimer Disease Neuroimaging Initiative, Morris MC, Evans DA, Johnson K, Sperling RA, Schneider JA, Bennett DA, De Jager PL | Nature neuroscience | 23708142 | Nat Neurosci | 2013 Jul |
| Alternative Approaches in Gene Discovery and Characterization in Alzheimer's Disease. | Ertekin-Taner N, De Jager PL, Yu L, Bennett DA | Current genetic medicine reports | 23482655 | Curr Genet Med Rep | 2013 Mar |
| Relation of DASH- and Mediterranean-like dietary patterns to cognitive decline in older persons. | Tangney CC, Li H, Wang Y, Barnes L, Schneider JA, Bennett DA, Morris MC | Neurology | 25230996 | Neurology | 2014 Oct 14 |
| The TMEM106B locus and TDP-43 pathology in older persons without FTLD. | Yu L, De Jager PL, Yang J, Trojanowski JQ, Bennett DA, Schneider JA | Neurology | 25653292 | Neurology | 2015 Mar 3 |
| Contribution of Alzheimer disease to mortality in the United States. | James BD, Leurgans SE, Hebert LE, Scherr PA, Yaffe K, Bennett DA | Neurology | 24598707 | Neurology | 2014 Mar 25 |
| A random change point model for cognitive decline in Alzheimer's disease and mild cognitive impairment. | Yu L, Boyle P, Wilson RS, Segawa E, Leurgans S, De Jager PL, Bennett DA | Neuroepidemiology | 22814083 | Neuroepidemiology | 2012 |
| Piezoelectric Versus Conventional Rotary Techniques for Impacted Third Molar Extraction: A Meta-analysis of Randomized Controlled Trials. | Jiang Q, Qiu Y, Yang C, Yang J, Chen M, Zhang Z | Medicine | 26469902 | Medicine (Baltimore) | 2015 Oct |
| Association of Bone Metabolic Markers With Diabetic Retinopathy and Diabetic Macular Edema in Elderly Chinese Individuals With Type 2 Diabetes Mellitus. | Zhang X, Yang J, Zhong Y, Xu L, Wang O, Huang P, Li C, Qu B, Wang J, Zheng C, Niu M, Yu W | The American journal of the medical sciences | 29078839 | Am J Med Sci | 2017 Oct |
| The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. | Grodstein F, Lemos B, Yu L, Klein HU, Iatrou A, Buchman AS, Shireby GL, Mill J, Schneider JA, De Jager PL, Bennett DA | Neurobiology of disease | 34153464 | Neurobiol Dis | 2021 Sep |
| SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration. | Moon S, Hwang J, Lee H | Journal of computational biology : a journal of computational molecular cell biology | 35951002 | J Comput Biol | 2022 Aug |
| Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning. | Lahti J, Tuominen S, Yang Q, Pergola G, Ahmad S, Amin N, Armstrong NJ, Beiser A, Bey K, Bis JC, Boerwinkle E, Bressler J, Campbell A, Campbell H, Chen Q, Corley J, Cox SR, Davies G, De Jager PL, Derks EM, Faul JD, Fitzpatrick AL, Fohner AE, Ford I, Fornage M, Gerring Z, Grabe HJ, Grodstein F, Gudnason V, Simonsick E, Holliday EG, Joshi PK, Kajantie E, Kaprio J, Karell P, Kleineidam L, Knol MJ, Kochan NA, Kwok JB, Leber M, Lam M, Lee T, Li S, Loukola A, Luck T, Marioni RE, Mather KA, Medland S, Mirza SS, Nalls MA, Nho K, O'Donnell A, Oldmeadow C, Painter J, Pattie A, Reppermund S, Risacher SL, Rose RJ, Sadashivaiah V, Scholz M, Satizabal CL, Schofield PW, Schraut KE, Scott RJ, Simino J, Smith AV, Smith JA, Stott DJ, Surakka I, Teumer A, Thalamuthu A, Trompet S, Turner ST, van der Lee SJ, Villringer A, Völker U, Wilson RS, Wittfeld K, Vuoksimaa E, Xia R, Yaffe K, Yu L, Zare H, Zhao W, Ames D, Attia J, Bennett DA, Brodaty H, Chasman DI, Goldman AL, Hayward C, Ikram MA, Jukema JW, Kardia SLR, Lencz T, Loeffler M, Mattay VS, Palotie A, Psaty BM, Ramirez A, Ridker PM, Riedel-Heller SG, Sachdev PS, Saykin AJ, Scherer M, Schofield PR, Sidney S, Starr JM, Trollor J, Ulrich W, Wagner M, Weir DR, Wilson JF, Wright MJ, Weinberger DR, Debette S, Eriksson JG, Mosley TH Jr, Launer LJ, van Duijn CM, Deary IJ, Seshadri S, Räikkönen K | Molecular psychiatry | 35974141 | Mol Psychiatry | 2022 Nov |
| Underlying features of epigenetic aging clocks in vivo and in vitro. | Liu Z, Leung D, Thrush K, Zhao W, Ratliff S, Tanaka T, Schmitz LL, Smith JA, Ferrucci L, Levine ME | Aging cell | 32930491 | Aging Cell | 2020 Oct |
| Epigenetic signatures of methylated DNA cytosine in Alzheimer's disease. | Fetahu IS, Ma D, Rabidou K, Argueta C, Smith M, Liu H, Wu F, Shi YG | Science advances | 31489368 | Sci Adv | 2019 Aug |
| Mendelian randomization integrating GWAS and mQTL data identified novel pleiotropic DNA methylation loci for neuropathology of Alzheimer's disease. | Liu D, Wang Y, Jing H, Meng Q, Yang J | Neurobiology of aging | 33120085 | Neurobiol Aging | 2021 Jan |
| Genetic control of the human brain proteome. | Robins C, Liu Y, Fan W, Duong DM, Meigs J, Harerimana NV, Gerasimov ES, Dammer EB, Cutler DJ, Beach TG, Reiman EM, De Jager PL, Bennett DA, Lah JJ, Wingo AP, Levey AI, Seyfried NT, Wingo TS | American journal of human genetics | 33571421 | Am J Hum Genet | 2021 Mar 4 |
| Monitoring Recessions: A Bayesian Sequential Quickest Detection Method. | Li H, Sheng XS, Yang J | International journal of forecasting | 33716367 | Int J Forecast | 2021 Apr-Jun |
| Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. | Reddy JS, Allen M, Ho CCG, Oatman SR, İş Ö, Quicksall ZS, Wang X, Jin J, Patel TA, Carnwath TP, Nguyen TT, Malphrus KG, Lincoln SJ, Carrasquillo MM, Crook JE, Kanekiyo T, Murray ME, Bu G, Dickson DW, Ertekin-Taner N | Acta neuropathologica communications | 34020725 | Acta Neuropathol Commun | 2021 May 21 |
| Aging the brain: multi-region methylation principal component based clock in the context of Alzheimer's disease. | Thrush KL, Bennett DA, Gaiteri C, Horvath S, Dyck CHV, Higgins-Chen AT, Levine ME | Aging | 35907208 | Aging (Albany NY) | 2022 Jul 30 |
| Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline. | Hüls A, Robins C, Conneely KN, Edgar R, De Jager PL, Bennett DA, Wingo AP, Epstein MP, Wingo TS | Biological psychiatry | 33838873 | Biol Psychiatry | 2022 Feb 15 |
| Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer's disease etiopathogenesis. | Madrid L, Moreno-Grau S, Ahmad S, González-Pérez A, de Rojas I, Xia R, Martino Adami PV, García-González P, Kleineidam L, Yang Q, Damotte V, Bis JC, Noguera-Perea F, Bellenguez C, Jian X, Marín-Muñoz J, Grenier-Boley B, Orellana A, Ikram MA, Amouyel P, Satizabal CL, Alzheimer’s Disease Neuroimaging Initiative (ADNI)*, EADI consortium, CHARGE consortium, GERAD consortium, GR@ACE/DEGESCO consortium, Real LM, Antúnez-Almagro C, DeStefano A, Cabrera-Socorro A, Sims R, Van Duijn CM, Boerwinkle E, Ramírez A, Fornage M, Lambert JC, Williams J, Seshadri S, ADAPTED consortium, Ried JS, Ruiz A, Saez ME | Aging | 33846280 | Aging (Albany NY) | 2021 Apr 12 |
| Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer's disease among women. | Chung J, Das A, Sun X, Sobreira DR, Leung YY, Igartua C, Mozaffari S, Chou YF, Thiagalingam S, Mez J, Zhang X, Jun GR, Stein TD, Kunkle BW, Martin ER, Pericak-Vance MA, Mayeux R, Haines JL, Schellenberg GD, Nobrega MA, Lunetta KL, Pinto JM, Wang LS, Ober C, Farrer LA | Alzheimer's & dementia : the journal of the Alzheimer's Association | 35770850 | Alzheimers Dement | 2023 Mar |
| New insights into the genetic etiology of Alzheimer's disease and related dementias. | Bellenguez C, Küçükali F, Jansen IE, Kleineidam L, Moreno-Grau S, Amin N, Naj AC, Campos-Martin R, Grenier-Boley B, Andrade V, Holmans PA, Boland A, Damotte V, van der Lee SJ, Costa MR, Kuulasmaa T, Yang Q, de Rojas I, Bis JC, Yaqub A, Prokic I, Chapuis J, Ahmad S, Giedraitis V, Aarsland D, Garcia-Gonzalez P, Abdelnour C, Alarcón-Martín E, Alcolea D, Alegret M, Alvarez I, Álvarez V, Armstrong NJ, Tsolaki A, Antúnez C, Appollonio I, Arcaro M, Archetti S, Pastor AA, Arosio B, Athanasiu L, Bailly H, Banaj N, Baquero M, Barral S, Beiser A, Pastor AB, Below JE, Benchek P, Benussi L, Berr C, Besse C, Bessi V, Binetti G, Bizarro A, Blesa R, Boada M, Boerwinkle E, Borroni B, Boschi S, Bossù P, Bråthen G, Bressler J, Bresner C, Brodaty H, Brookes KJ, Brusco LI, Buiza-Rueda D, Bûrger K, Burholt V, Bush WS, Calero M, Cantwell LB, Chene G, Chung J, Cuccaro ML, Carracedo Á, Cecchetti R, Cervera-Carles L, Charbonnier C, Chen HH, Chillotti C, Ciccone S, Claassen JAHR, Clark C, Conti E, Corma-Gómez A, Costantini E, Custodero C, Daian D, Dalmasso MC, Daniele A, Dardiotis E, Dartigues JF, de Deyn PP, de Paiva Lopes K, de Witte LD, Debette S, Deckert J, Del Ser T, Denning N, DeStefano A, Dichgans M, Diehl-Schmid J, Diez-Fairen M, Rossi PD, Djurovic S, Duron E, Düzel E, Dufouil C, Eiriksdottir G, Engelborghs S, Escott-Price V, Espinosa A, Ewers M, Faber KM, Fabrizio T, Nielsen SF, Fardo DW, Farotti L, Fenoglio C, Fernández-Fuertes M, Ferrari R, Ferreira CB, Ferri E, Fin B, Fischer P, Fladby T, Fließbach K, Fongang B, Fornage M, Fortea J, Foroud TM, Fostinelli S, Fox NC, Franco-Macías E, Bullido MJ, Frank-García A, Froelich L, Fulton-Howard B, Galimberti D, García-Alberca JM, García-González P, Garcia-Madrona S, Garcia-Ribas G, Ghidoni R, Giegling I, Giorgio G, Goate AM, Goldhardt O, Gomez-Fonseca D, González-Pérez A, Graff C, Grande G, Green E, Grimmer T, Grünblatt E, Grunin M, Gudnason V, Guetta-Baranes T, Haapasalo A, Hadjigeorgiou G, Haines JL, Hamilton-Nelson KL, Hampel H, Hanon O, Hardy J, Hartmann AM, Hausner L, Harwood J, Heilmann-Heimbach S, Helisalmi S, Heneka MT, Hernández I, Herrmann MJ, Hoffmann P, Holmes C, Holstege H, Vilas RH, Hulsman M, Humphrey J, Biessels GJ, Jian X, Johansson C, Jun GR, Kastumata Y, Kauwe J, Kehoe PG, Kilander L, Ståhlbom AK, Kivipelto M, Koivisto A, Kornhuber J, Kosmidis MH, Kukull WA, Kuksa PP, Kunkle BW, Kuzma AB, Lage C, Laukka EJ, Launer L, Lauria A, Lee CY, Lehtisalo J, Lerch O, Lleó A, Longstreth W Jr, Lopez O, de Munain AL, Love S, Löwemark M, Luckcuck L, Lunetta KL, Ma Y, Macías J, MacLeod CA, Maier W, Mangialasche F, Spallazzi M, Marquié M, Marshall R, Martin ER, Montes AM, Rodríguez CM, Masullo C, Mayeux R, Mead S, Mecocci P, Medina M, Meggy A, Mehrabian S, Mendoza S, Menéndez-González M, Mir P, Moebus S, Mol M, Molina-Porcel L, Montrreal L, Morelli L, Moreno F, Morgan K, Mosley T, Nöthen MM, Muchnik C, Mukherjee S, Nacmias B, Ngandu T, Nicolas G, Nordestgaard BG, Olaso R, Orellana A, Orsini M, Ortega G, Padovani A, Paolo C, Papenberg G, Parnetti L, Pasquier F, Pastor P, Peloso G, Pérez-Cordón A, Pérez-Tur J, Pericard P, Peters O, Pijnenburg YAL, Pineda JA, Piñol-Ripoll G, Pisanu C, Polak T, Popp J, Posthuma D, Priller J, Puerta R, Quenez O, Quintela I, Thomassen JQ, Rábano A, Rainero I, Rajabli F, Ramakers I, Real LM, Reinders MJT, Reitz C, Reyes-Dumeyer D, Ridge P, Riedel-Heller S, Riederer P, Roberto N, Rodriguez-Rodriguez E, Rongve A, Allende IR, Rosende-Roca M, Royo JL, Rubino E, Rujescu D, Sáez ME, Sakka P, Saltvedt I, Sanabria Á, Sánchez-Arjona MB, Sanchez-Garcia F, Juan PS, Sánchez-Valle R, Sando SB, Sarnowski C, Satizabal CL, Scamosci M, Scarmeas N, Scarpini E, Scheltens P, Scherbaum N, Scherer M, Schmid M, Schneider A, Schott JM, Selbæk G, Seripa D, Serrano M, Sha J, Shadrin AA, Skrobot O, Slifer S, Snijders GJL, Soininen H, Solfrizzi V, Solomon A, Song Y, Sorbi S, Sotolongo-Grau O, Spalletta G, Spottke A, Squassina A, Stordal E, Tartan JP, Tárraga L, Tesí N, Thalamuthu A, Thomas T, Tosto G, Traykov L, Tremolizzo L, Tybjærg-Hansen A, Uitterlinden A, Ullgren A, Ulstein I, Valero S, Valladares O, Broeckhoven CV, Vance J, Vardarajan BN, van der Lugt A, Dongen JV, van Rooij J, van Swieten J, Vandenberghe R, Verhey F, Vidal JS, Vogelgsang J, Vyhnalek M, Wagner M, Wallon D, Wang LS, Wang R, Weinhold L, Wiltfang J, Windle G, Woods B, Yannakoulia M, Zare H, Zhao Y, Zhang X, Zhu C, Zulaica M, EADB, GR@ACE, DEGESCO, EADI, GERAD, Demgene, FinnGen, ADGC, CHARGE, Farrer LA, Psaty BM, Ghanbari M, Raj T, Sachdev P, Mather K, Jessen F, Ikram MA, de Mendonça A, Hort J, Tsolaki M, Pericak-Vance MA, Amouyel P, Williams J, Frikke-Schmidt R, Clarimon J, Deleuze JF, Rossi G, Seshadri S, Andreassen OA, Ingelsson M, Hiltunen M, Sleegers K, Schellenberg GD, van Duijn CM, Sims R, van der Flier WM, Ruiz A, Ramirez A, Lambert JC | Nature genetics | 35379992 | Nat Genet | 2022 Apr |
| Exploring genes for immunoglobulin A nephropathy: a summary data-based mendelian randomization and FUMA analysis. | Zhang Q, Zhang K, Zhu Y, Yuan G, Yang J, Zhang M | BMC medical genomics | 36709307 | BMC Med Genomics | 2023 Jan 29 |
| Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure. | Yang Z, Zhang Z, Zhu Y, Yuan G, Yang J, Yu W | Genes | 37239387 | Genes (Basel) | 2023 Apr 30 |
| Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G. | Smullen M, Olson MN, Murray LF, Suresh M, Yan G, Dawes P, Barton NJ, Mason JN, Zhang Y, Fernandez-Fontaine AA, Church GM, Mastroeni D, Wang Q, Lim ET, Chan Y, Readhead B | Scientific reports | 37369829 | Sci Rep | 2023 Jun 27 |
| Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. | Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Alzheimer's Disease Genetics Consortium, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C | Alzheimer's & dementia : the journal of the Alzheimer's Association | 38958117 | Alzheimers Dement | 2024 Aug |
| Longitudinal change in memory performance as a strong endophenotype for Alzheimer's disease. | Archer DB, Eissman JM, Mukherjee S, Lee ML, Choi SE, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Alzheimer's Disease Neuroimaging Initiative (ADNI), Alzheimer's Disease Genetics Consortium (ADGC), Alzheimer's Disease Sequencing Project (ADSP), Cuccaro ML, Pericak-Vance MA, Farrer LA, Wang LS, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Dumitrescu L, Hohman TJ | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37985223 | Alzheimers Dement | 2024 Feb |
| Comparative gene regulatory networks modulating APOE expression in microglia and astrocytes. | Brase L, Yu Y, McDade E, Dominantly Inherited Alzheimer Network (DIAN), Harari O, Benitez BA | medRxiv : the preprint server for health sciences | 38699303 | medRxiv | 2024 Apr 22 |
| BLEND: Probabilistic Cellular Deconvolution with Automated Reference Selection. | Huang P, Cai M, McKennan C, Wang J | bioRxiv : the preprint server for biology | 39149243 | bioRxiv | 2024 Aug 6 |
| Targeted co-expression networks for the study of traits. | Gómez-Pascual A, Rocamora-Pérez G, Ibanez L, Botía JA | Scientific reports | 39030261 | Sci Rep | 2024 Jul 19 |
| Integrated multimodal cell atlas of Alzheimer's disease. | Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES | Nature neuroscience | 39402379 | Nat Neurosci | 2024 Dec |
| AutoFocus: a hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction. | Schweickart A, Chetnik K, Batra R, Kaddurah-Daouk R, Suhre K, Halama A, Krumsiek J | Communications biology | 39237774 | Commun Biol | 2024 Sep 6 |
| Cognitive resilience to Alzheimer's disease characterized by cell-type abundance. | O'Neill N, Stein TD, Olayinka OA, Empawi JA, Hu J, Tong T, Zhang X, Farrer LA | Alzheimer's & dementia : the journal of the Alzheimer's Association | 39262221 | Alzheimers Dement | 2024 Oct |
| Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease. | Arnold M, Buyukozkan M, Doraiswamy PM, Nho K, Wu T, Gudnason V, Launer LJ, Wang-Sattler R, Adamski J, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s Disease Metabolomics Consortium, De Jager PL, Ertekin-Taner N, Bennett DA, Saykin AJ, Peters A, Suhre K, Kaddurah-Daouk R, Kastenmüller G, Krumsiek J | Nature communications | 39994231 | Nat Commun | 2025 Feb 24 |
| Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance. | Seto M, Clifton M, Gomez ML, Coughlan G, Gifford KA, Jefferson AL, De Jager PL, Bennett DA, Wang Y, Barnes LL, Schneider JA, Hohman TJ, Buckley RF, Dumitrescu L | bioRxiv : the preprint server for biology | 39803447 | bioRxiv | 2025 Jan 2 |
| Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease. | Yu L, Chibnik LB, Srivastava GP, Pochet N, Yang J, Xu J, Kozubek J, Obholzer N, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA | JAMA neurology | 25365775 | JAMA Neurol | 2015 Jan |
| Effect of breastfeeding on childhood BMI and obesity: the China Family Panel Studies. | Jing H, Xu H, Wan J, Yang Y, Ding H, Chen M, Li L, Lv P, Hu J, Yang J | Medicine | 25170931 | Medicine (Baltimore) | 2014 Aug |
| Change in risk of Alzheimer disease over time. | Hebert LE, Bienias JL, Aggarwal NT, Wilson RS, Bennett DA, Shah RC, Evans DA | Neurology | 20805524 | Neurology | 2010 Aug 31 |
| Cognitive aging in older Black and White persons. | Wilson RS, Capuano AW, Sytsma J, Bennett DA, Barnes LL | Psychology and aging | 25961876 | Psychol Aging | 2015 Jun |
| Physical activity, motor function, and white matter hyperintensity burden in healthy older adults. | Fleischman DA, Yang J, Arfanakis K, Arvanitakis Z, Leurgans SE, Turner AD, Barnes LL, Bennett DA, Buchman AS | Neurology | 25762710 | Neurology | 2015 Mar 31 |
| Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease. | Bennett DA, Yu L, De Jager PL | Biochemical pharmacology | 24508835 | Biochem Pharmacol | 2014 Apr 15 |
| Efficacy of conbercept combined with panretinal photocoagulation in the treatment of proliferative diabetic retinopathy. | He F, Yang J, Zhang X, Yu W | Scientific reports | 32472048 | Sci Rep | 2020 May 29 |
| The association between genetic variants in lactotransferrin and dental caries: a meta- and gene-based analysis. | Li X, Su Y, Liu D, Yang J | BMC medical genetics | 32460726 | BMC Med Genet | 2020 May 27 |
| Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. | Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL | Nature neuroscience | 30559478 | Nat Neurosci | 2019 Jan |
| The Association Between Genetic Variants in the Dopaminergic System and Posttraumatic Stress Disorder: A Meta-Analysis. | Li L, Bao Y, He S, Wang G, Guan Y, Ma D, Wang P, Huang X, Tao S, Zhang D, Liu Q, Wang Y, Yang J | Medicine | 26986136 | Medicine (Baltimore) | 2016 Mar |
| Association of genetic variants in and promoter hypermethylation of CDH1 with gastric cancer: a meta-analysis. | Jing H, Dai F, Zhao C, Yang J, Li L, Kota P, Mao L, Xiang K, Zheng C, Yang J | Medicine | 25340495 | Medicine (Baltimore) | 2014 Oct |
| Seasonal plasticity of cognition and related biological measures in adults with and without Alzheimer disease: Analysis of multiple cohorts. | Lim ASP, Gaiteri C, Yu L, Sohail S, Swardfager W, Tasaki S, Schneider JA, Paquet C, Stuss DT, Masellis M, Black SE, Hugon J, Buchman AS, Barnes LL, Bennett DA, De Jager PL | PLoS medicine | 30180184 | PLoS Med | 2018 Sep |
| Religious Orders Study and Rush Memory and Aging Project. | Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, Schneider JA | Journal of Alzheimer's disease : JAD | 29865057 | J Alzheimers Dis | 2018 |
| The Association Between Genetic Polymorphism rs703842 in CYP27B1 and Multiple Sclerosis: A Meta-Analysis. | Jiang T, Li L, Wang Y, Zhao C, Yang J, Ma D, Guan Y, Zhao D, Bao Y, Wang Y, Yang J | Medicine | 27175669 | Medicine (Baltimore) | 2016 May |
| Neuroprotective effects respond to cerebral ischemia without susceptibility to HB-tumorigenesis in VHL heterozygous knockout mice. | Wang Y, Yang J, Du G, Ma D, Zhou L | Molecular carcinogenesis | 28574654 | Mol Carcinog | 2017 Oct |
| Genome-wide association study of brain arteriolosclerosis. | Shade LM, Katsumata Y, Hohman TJ, Nho K, Saykin AJ, Mukherjee S, Boehme KL, Kauwe JS, Farrer LA, Schellenberg GD, Haines JL, Mayeux RP, Schneider JA, Nelson PT, Fardo DW | Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism | 35156446 | J Cereb Blood Flow Metab | 2022 Aug |
| MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification. | Moon S, Lee H | Bioinformatics (Oxford, England) | 35157023 | Bioinformatics | 2022 Apr 12 |
| High PSQI score is associated with the development of dyskinesia in Parkinson's disease. | Tang X, Yang J, Zhu Y, Gong H, Sun H, Chen F, Guan Q, Yu L, Wang W, Zhang Z, Li L, Ma G, Wang X | NPJ Parkinson's disease | 36175559 | NPJ Parkinsons Dis | 2022 Sep 29 |
| Metabolomic and lipidomic signatures in autosomal dominant and late-onset Alzheimer's disease brains. | Novotny BC, Fernandez MV, Wang C, Budde JP, Bergmann K, Eteleeb AM, Bradley J, Webster C, Ebl C, Norton J, Gentsch J, Dube U, Wang F, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Chhatwal J, Dominantly Inherited Alzheimer Network (DIAN) Study Group, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's Disease Metabolomics Consortium (ADMC), Goate A, Farlow M, Schofield P, Chui H, Karch CM, Cruchaga C, Benitez BA, Harari O | Alzheimer's & dementia : the journal of the Alzheimer's Association | 36251323 | Alzheimers Dement | 2023 May |
| Differential Gene Expression and DNA Methylation in the Risk of Depression in LOAD Patients. | Upadhya S, Gingerich D, Lutz MW, Chiba-Falek O | Biomolecules | 36421693 | Biomolecules | 2022 Nov 12 |
| Multi-omic characterization of brain changes in the vascular endothelial growth factor family during aging and Alzheimer's disease. | Seto M, Dumitrescu L, Mahoney ER, Sclafani AM, De Jager PL, Menon V, Koran MEI, Robinson RA, Ruderfer DM, Cox NJ, Seyfried NT, Jefferson AL, Schneider JA, Bennett DA, Petyuk VA, Hohman TJ | Neurobiology of aging | 36905877 | Neurobiol Aging | 2023 Jun |
| Mendelian randomization analysis identified genes pleiotropically associated with the risk and prognosis of COVID-19. | Liu D, Yang J, Feng B, Lu W, Zhao C, Li L | The Journal of infection | 33259846 | J Infect | 2021 Jan |
| Progress of artificial intelligence in diabetic retinopathy screening. | Wang YL, Yang JY, Yang JY, Zhao XY, Chen YX, Yu WH | Diabetes/metabolism research and reviews | 33010796 | Diabetes Metab Res Rev | 2021 Jul |
| Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19. | Piras IS, Huentelman MJ, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Suszczewicz KE, Borja CL, Desforges M, Deture M, Dickson DW, Beach TG, Serrano GE | medRxiv : the preprint server for health sciences | 34545375 | medRxiv | 2021 Sep 15 |
| Brain microRNAs are associated with variation in cognitive trajectory in advanced age. | Wingo AP, Wang M, Liu J, Breen MS, Yang HS, Tang B, Schneider JA, Seyfried NT, Lah JJ, Levey AI, Bennett DA, Jin P, De Jager PL, Wingo TS | Translational psychiatry | 35105862 | Transl Psychiatry | 2022 Feb 1 |
| Mendelian randomization analysis identified genes potentially pleiotropically associated with periodontitis. | Wang F, Liu D, Zhuang Y, Feng B, Lu W, Yang J, Zhuang G | Saudi journal of biological sciences | 34220266 | Saudi J Biol Sci | 2021 Jul |
| Differential transcriptome expression in human nucleus accumbens as a function of loneliness. | Canli T, Wen R, Wang X, Mikhailik A, Yu L, Fleischman D, Wilson RS, Bennett DA | Molecular psychiatry | 27801889 | Mol Psychiatry | 2017 Jul |
| Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology. | Yu L, Chibnik LB, Yang J, McCabe C, Xu J, Schneider JA, De Jager PL, Bennett DA | Alzheimer's & dementia : the journal of the Alzheimer's Association | 27016692 | Alzheimers Dement | 2016 Sep |
| Mendelian randomization integrating GWAS and eQTL data revealed genes pleiotropically associated with major depressive disorder. | Yang H, Liu D, Zhao C, Feng B, Lu W, Yang X, Xu M, Zhou W, Jing H, Yang J | Translational psychiatry | 33866329 | Transl Psychiatry | 2021 Apr 17 |
| The Molecular and Neuropathological Consequences of Genetic Risk for Alzheimer's Dementia. | Tasaki S, Gaiteri C, Mostafavi S, De Jager PL, Bennett DA | Frontiers in neuroscience | 30349450 | Front Neurosci | 2018 |
| Age and the association of dementia-related pathology with trajectories of cognitive decline. | Jansen WJ, Wilson RS, Visser PJ, Nag S, Schneider JA, James BD, Leurgans SE, Capuano AW, Bennett DA, Boyle PA | Neurobiology of aging | 29078129 | Neurobiol Aging | 2018 Jan |
| "iNETgrate": integrating DNA methylation and gene expression data in a single gene network. | Sajedi S, Ebrahimi G, Roudi R, Mehta I, Samimi H, Kazempour S, Zainulabadeen A, Docking TR, Arora SP, Cigarroa F, Seshadri S, Karsan A, Zare H | Research square | 37645739 | Res Sq | 2023 Aug 18 |
| Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease. | Kim JP, Kim BH, Bice PJ, Seo SW, Bennett DA, Saykin AJ, Nho K | Biological psychiatry | 36150909 | Biol Psychiatry | 2023 May 1 |
| Downregulation of Dickkopf-3, a Wnt antagonist elevated in Alzheimer's disease, restores synapse integrity and memory in a disease mouse model. | Martin Flores N, Podpolny M, McLeod F, Workman I, Crawford K, Ivanov D, Leonenko G, Escott-Price V, Salinas PC | eLife | 38285009 | Elife | 2024 Jan 29 |
| A deep neural network to de-noise single-cell RNA sequencing data. | Sharifitabar M, Kazempour S, Razavian J, Sajedi S, Solhjoo S, Zare H | bioRxiv : the preprint server for biology | 39605470 | bioRxiv | 2024 Nov 21 |
| GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia. | Shade LMP, Katsumata Y, Abner EL, Aung KZ, Claas SA, Qiao Q, Heberle BA, Brandon JA, Page ML, Hohman TJ, Mukherjee S, Mayeux RP, Farrer LA, Schellenberg GD, Haines JL, Kukull WA, Nho K, Saykin AJ, Bennett DA, Schneider JA, National Alzheimer’s Coordinating Center, Ebbert MTW, Nelson PT, Fardo DW | Nature genetics | 39379761 | Nat Genet | 2024 Nov |
| Association of genetic variants in GNβ3 with functional dyspepsia: a meta-analysis. | Dai F, Liu Y, Shi H, Ge S, Song J, Dong L, Yang J | Digestive diseases and sciences | 24557575 | Dig Dis Sci | 2014 Aug |
| Cognitive decline following incident and preexisting diabetes mellitus in a population sample. | Rajan KB, Arvanitakis Z, Lynch EB, McAninch EA, Wilson RS, Weuve J, Barnes LL, Bianco AC, Evans DA | Neurology | 27655734 | Neurology | 2016 Oct 18 |
| Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. | Qiu Y, Wang J, Lei J, Roeder K | Bioinformatics (Oxford, England) | 33904573 | Bioinformatics | 2021 Oct 11 |
| Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer's disease. | He L, Loika Y, Park Y, Genotype Tissue Expression (GTEx) consortium, Bennett DA, Kellis M, Kulminski AM, Alzheimer’s Disease Neuroimaging Initiative | Translational psychiatry | 33637690 | Transl Psychiatry | 2021 Feb 26 |
| Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes. | Cheng Y, Saville L, Gollen B, Veronesi AA, Mohajerani M, Joseph JT, Zovoilis A | EMBO reports | 33645898 | EMBO Rep | 2021 May 5 |
| Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men. | Grodstein F, Lemos B, Yu L, Iatrou A, De Jager PL, Bennett DA | Frontiers in neuroscience | 33488342 | Front Neurosci | 2020 |
| Tau Activates Transposable Elements in Alzheimer's Disease. | Guo C, Jeong HH, Hsieh YC, Klein HU, Bennett DA, De Jager PL, Liu Z, Shulman JM | Cell reports | 29874575 | Cell Rep | 2018 Jun 5 |
| DNA methylation variability in Alzheimer's disease. | Huo Z, Zhu Y, Yu L, Yang J, De Jager P, Bennett DA, Zhao J | Neurobiology of aging | 30660039 | Neurobiol Aging | 2019 Apr |
| Aberrantly expressed mRNAs and long non-coding RNAs in patients with invasive ductal breast carcinoma: a pilot study. | Chen X, Yang J, Qian L, Cao T | Molecular medicine reports | 25411894 | Mol Med Rep | 2015 Mar |
| Incident parkinsonism in older adults without Parkinson disease. | Buchman AS, Leurgans SE, Yu L, Wilson RS, Lim AS, James BD, Shulman JM, Bennett DA | Neurology | 27488597 | Neurology | 2016 Sep 6 |
| An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. | Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL | Genome biology | 27511193 | Genome Biol | 2016 Aug 11 |
| Genetic variants in Alzheimer disease - molecular and brain network approaches. | Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA | Nature reviews. Neurology | 27282653 | Nat Rev Neurol | 2016 Jul |
| Susceptibility to neurofibrillary tangles: role of the PTPRD locus and limited pleiotropy with other neuropathologies. | Chibnik LB, White CC, Mukherjee S, Raj T, Yu L, Larson EB, Montine TJ, Keene CD, Sonnen J, Schneider JA, Crane PK, Shulman JM, Bennett DA, De Jager PL | Molecular psychiatry | 28322283 | Mol Psychiatry | 2018 Jun |
| CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease. | Ma Y, Jun GR, Chung J, Zhang X, Kunkle BW, Naj AC, White CC, Bennett DA, De Jager PL, Alzheimer’s Disease Genetics Consortium, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Farrer LA, Lunetta KL | Aging cell | 31144443 | Aging Cell | 2019 Aug |
| Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain. | Ng B, Casazza W, Patrick E, Tasaki S, Novakovsky G, Felsky D, Ma Y, Bennett DA, Gaiteri C, De Jager PL, Mostafavi S | American journal of human genetics | 31447098 | Am J Hum Genet | 2019 Sep 5 |
| Shared Causal Paths underlying Alzheimer's dementia and Type 2 Diabetes. | Hu Z, Jiao R, Wang P, Zhu Y, Zhao J, De Jager P, Bennett DA, Jin L, Xiong M | Scientific reports | 32139775 | Sci Rep | 2020 Mar 5 |
| Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies. | Yang J, Yu L, Gaiteri C, Srivastava GP, Chibnik LB, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA | The international journal of biochemistry & cell biology | 26003740 | Int J Biochem Cell Biol | 2015 Oct |
| Epigenomics in translational research. | Replogle JM, De Jager PL | Translational research : the journal of laboratory and clinical medicine | 25445204 | Transl Res | 2015 Jan |
| The Association Between Apolipoprotein E and Functional Outcome After Traumatic Brain Injury: A Meta-Analysis. | Li L, Bao Y, He S, Wang G, Guan Y, Ma D, Wu R, Wang P, Huang X, Tao S, Liu Q, Wang Y, Yang J | Medicine | 26579811 | Medicine (Baltimore) | 2015 Nov |
| Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia. | Wingo TS, Yang J, Fan W, Min Canon S, Gerasimov ES, Lori A, Logsdon B, Yao B, Seyfried NT, Lah JJ, Levey AI, Boyle PA, Schneider JA, De Jager PL, Bennett DA, Wingo AP | NPJ genomic medicine | 32047652 | NPJ Genom Med | 2020 |
| Genetic architecture of epigenetic and neuronal ageing rates in human brain regions. | Lu AT, Hannon E, Levine ME, Crimmins EM, Lunnon K, Mill J, Geschwind DH, Horvath S | Nature communications | 28516910 | Nat Commun | 2017 May 18 |
| Nerve growth factor receptor (Ngfr) induces neurogenic plasticity by suppressing reactive astroglial Lcn2/Slc22a17 signaling in Alzheimer's disease. | Siddiqui T, Cosacak MI, Popova S, Bhattarai P, Yilmaz E, Lee AJ, Min Y, Wang X, Allen M, İş Ö, Atasavum ZT, Rodriguez-Muela N, Vardarajan BN, Flaherty D, Teich AF, Santa-Maria I, Freudenberg U, Werner C, Tosto G, Mayeux R, Ertekin-Taner N, Kizil C | NPJ Regenerative medicine | 37429840 | NPJ Regen Med | 2023 Jul 10 |
| APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response. | Panitch R, Sahelijo N, Hu J, Nho K, Bennett DA, Lunetta KL, Au R, Stein TD, Farrer LA, Jun GR | Translational psychiatry | 38424036 | Transl Psychiatry | 2024 Feb 29 |
| The impact of blood MCP-1 levels on Alzheimer's disease with genetic variation of UNC5C and NAV3 loci. | Huang J, Wang Y, Stein TD, Ang TFA, Zhu Y, Tao Q, Lunetta KL, Mez J, Au R, Farrer LA, Qiu WQ, Zhang X | Research square | 37841863 | Res Sq | 2023 Sep 28 |
| Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package. | Sajedi S, Ebrahimi G, Roudi R, Mehta I, Heshmat A, Samimi H, Kazempour S, Zainulabadeen A, Docking TR, Arora SP, Cigarroa F, Seshadri S, Karsan A, Zare H | Scientific reports | 38066050 | Sci Rep | 2023 Dec 8 |
| Sex-specific genetic architecture of late-life memory performance. | Eissman JM, Archer DB, Mukherjee S, Lee ML, Choi SE, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Alzheimer's Disease Neuroimaging Initiative (ADNI) | Alzheimer's Disease Genetics Consortium (ADGC) | The Alzheimer's Disease Sequencing Project (ADSP), Cuccaro ML, Cruchaga C, Pericak-Vance MA, Farrer LA, Wang LS, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37984853 | Alzheimers Dement | 2024 Feb |
| Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease. | Arnold M, Buyukozkan M, Doraiswamy PM, Nho K, Wu T, Gudnason V, Launer LJ, Wang-Sattler R, Adamski J, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s Disease Metabolomics Consortium, De Jager PL, Ertekin-Taner N, Bennett DA, Saykin AJ, Peters A, Suhre K, Kaddurah-Daouk R, Kastenmüller G, Krumsiek J | medRxiv : the preprint server for health sciences | 38313266 | medRxiv | 2024 Jan 24 |
| Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. | Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N, Dufort C, Walker AC, Lucca LE, Kozareva V, Vanderburg C, Hong S, Bulstrode H, Hutchinson PJ, Gaffney DJ, Hafler DA, Franklin RJM, Macosko EZ, Stevens B | Nature neuroscience | 35260865 | Nat Neurosci | 2022 Mar |
| Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways. | Ibanez KR, McFarland KN, Phillips J, Allen M, Lessard CB, Zobel L, De La Cruz EG, Shah S, Vo Q, Wang X, Quicksall Z, Ryu D, Funk C, Ertekin-Taner N, Prokop S, Golde TE, Chakrabarty P | Alzheimer's research & therapy | 35897046 | Alzheimers Res Ther | 2022 Jul 27 |
| A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease. | Huang Y, Sun X, Jiang H, Yu S, Robins C, Armstrong MJ, Li R, Mei Z, Shi X, Gerasimov ES, De Jager PL, Bennett DA, Wingo AP, Jin P, Wingo TS, Qin ZS | Nature communications | 34294691 | Nat Commun | 2021 Jul 22 |
| Transcriptional landscape of human microglia implicates age, sex, and APOE-related immunometabolic pathway perturbations. | Patel T, Carnwath TP, Wang X, Allen M, Lincoln SJ, Lewis-Tuffin LJ, Quicksall ZS, Lin S, Tutor-New FQ, Ho CCG, Min Y, Malphrus KG, Nguyen TT, Martin E, Garcia CA, Alkharboosh RM, Grewal S, Chaichana K, Wharen R, Guerrero-Cazares H, Quinones-Hinojosa A, Ertekin-Taner N | Aging cell | 35388616 | Aging Cell | 2022 May |
| Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer's dementia: a network Mendelian randomization analysis. | Liu D, Wang Y, Jing H, Meng Q, Yang J | Epigenetics | 34461811 | Epigenetics | 2022 Jun-Jul |
| Integrated Genomic, Transcriptomic and Proteomic Analysis for Identifying Markers of Alzheimer's Disease. | Madrid L, Labrador SC, González-Pérez A, Sáez ME, The Alzheimer's Disease Neuroimaging Initiative Adni | Diagnostics (Basel, Switzerland) | 34943540 | Diagnostics (Basel) | 2021 Dec 8 |
| MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state. | You SF, Brase L, Filipello F, Iyer AK, Del-Aguila J, He J, D'Oliveira Albanus R, Budde J, Norton J, Gentsch J, Dräger NM, Sattler SM, Kampmann M, Piccio L, Morris JC, Perrin RJ, McDade E, Dominantly Inherited Alzheimer Network, Paul SM, Cashikar AG, Benitez BA, Harari O, Karch CM | medRxiv : the preprint server for health sciences | 36798226 | medRxiv | 2023 Feb 8 |
| Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci. | Grodstein F, Lemos B, Yang J, de Paiva Lopes K, Vialle RA, Seyfried N, Wang Y, Shireby G, Hannon E, Thomas A, Brookes K, Mill J, De Jager PL, Bennett DA | Epigenetics | 39169872 | Epigenetics | 2024 Dec |
| Metabolomics profiling reveals distinct, sex-specific signatures in the serum and brain metabolomes in the mouse models of Alzheimer's disease. | Pandey RS, Arnold M, Batra R, Krumsiek J, Kotredes KP, Garceau D, Williams H, Sasner M, Howell GR, Kaddurah-Daouk R, Carter GW | bioRxiv : the preprint server for biology | 38187571 | bioRxiv | 2023 Dec 22 |
| Integrative Network Analysis Reveals Novel Moderators of Aβ-Tau Interaction in Alzheimer's Disease. | Kitani A, Matsui Y | bioRxiv : the preprint server for biology | 39554095 | bioRxiv | 2024 Oct 28 |
| Whole-genome sequencing study in Koreans identifies novel loci for Alzheimer's disease. | Kang M, Farrell JJ, Zhu C, Park H, Kang S, Seo EH, Choi KY, Jun GR, Won S, Gim J, Lee KH, Farrer LA | Alzheimer's & dementia : the journal of the Alzheimer's Association | 39428694 | Alzheimers Dement | 2024 Dec |
| Deciphering novel mitochondrial signatures: multi-omics analysis uncovers cross-disease markers and oligodendrocyte pathways in Alzheimer's disease and glioblastoma. | Xu X, Wang J, Chen T, Wang S, Wang F, He J, Meng XY, Shen Y | Frontiers in aging neuroscience | 40018519 | Front Aging Neurosci | 2025 |
| Differential Transcriptional Programs Reveal Modular Network Rearrangements Associated with Late-Onset Alzheimer's Disease. | Pérez-González AP, Anda-Jáuregui G, Hernández-Lemus E | International journal of molecular sciences | 40076979 | Int J Mol Sci | 2025 Mar 6 |
| Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. | Hahn MA, Wu X, Li AX, Hahn T, Pfeifer GP | PloS one | 21526191 | PLoS One | 2011 Apr 19 |
| DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). | Rauch TA, Pfeifer GP | Methods (San Diego, Calif.) | 20304072 | Methods | 2010 Nov |
| MIRA-seq for DNA methylation analysis of CpG islands. | Jung M, Kadam S, Xiong W, Rauch TA, Jin SG, Pfeifer GP | Epigenomics | 25881900 | Epigenomics | 2015 Aug |
| Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. | Iqbal K, Jin SG, Pfeifer GP, Szabó PE | Proceedings of the National Academy of Sciences of the United States of America | 21321204 | Proc Natl Acad Sci U S A | 2011 Mar 1 |
| MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation. | Lee DH, Tran DA, Singh P, Oates N, Rivas GE, Larson GP, Pfeifer GP, Szabó PE | Epigenetics | 20948294 | Epigenetics | 2011 Feb |
| 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. | Jin SG, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, Krex D, Lu Q, Pfeifer GP | Cancer research | 22052461 | Cancer Res | 2011 Dec 15 |
| Genomic mapping of 5-hydroxymethylcytosine in the human brain. | Jin SG, Wu X, Li AX, Pfeifer GP | Nucleic acids research | 21378125 | Nucleic Acids Res | 2011 Jul |
| Aging and DNA methylation. | Jung M, Pfeifer GP | BMC biology | 25637097 | BMC Biol | 2015 Jan 31 |
| Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. | Jung M, Jin SG, Zhang X, Xiong W, Gogoshin G, Rodin AS, Pfeifer GP | Nucleic acids research | 25977295 | Nucleic Acids Res | 2015 Sep 3 |
| Allele-specific DNA methylation: beyond imprinting. | Tycko B | Human molecular genetics | 20855472 | Hum Mol Genet | 2010 Oct 15 |
| Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. | Reitz C, Jun G, Naj A, Rajbhandary R, Vardarajan BN, Wang LS, Valladares O, Lin CF, Larson EB, Graff-Radford NR, Evans D, De Jager PL, Crane PK, Buxbaum JD, Murrell JR, Raj T, Ertekin-Taner N, Logue M, Baldwin CT, Green RC, Barnes LL, Cantwell LB, Fallin MD, Go RC, Griffith P, Obisesan TO, Manly JJ, Lunetta KL, Kamboh MI, Lopez OL, Bennett DA, Hendrie H, Hall KS, Goate AM, Byrd GS, Kukull WA, Foroud TM, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Mayeux R, Alzheimer Disease Genetics Consortium | JAMA | 23571587 | JAMA | 2013 Apr 10 |
| Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. | Do C, Xing Z, Yu YE, Tycko B | Epigenomics | 27911079 | Epigenomics | 2017 Feb |
| Hormonal influences on cognition and risk for Alzheimer's disease. | Janicki SC, Schupf N | Current neurology and neuroscience reports | 20535591 | Curr Neurol Neurosci Rep | 2010 Sep |
| Age-at-onset linkage analysis in Caribbean Hispanics with familial late-onset Alzheimer's disease. | Lee JH, Barral S, Cheng R, Chacon I, Santana V, Williamson J, Lantigua R, Medrano M, Jimenez-Velazquez IZ, Stern Y, Tycko B, Rogaeva E, Wakutani Y, Kawarai T, St George-Hyslop P, Mayeux R | Neurogenetics | 17940814 | Neurogenetics | 2008 Feb |
| Genotype patterns at PICALM, CR1, BIN1, CLU, and APOE genes are associated with episodic memory. | Barral S, Bird T, Goate A, Farlow MR, Diaz-Arrastia R, Bennett DA, Graff-Radford N, Boeve BF, Sweet RA, Stern Y, Wilson RS, Foroud T, Ott J, Mayeux R, National Institute on Aging Late-Onset Alzheimer's Disease Genetics Study | Neurology | 22539578 | Neurology | 2012 May 8 |
| Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. | Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B | Genome biology | 28629478 | Genome Biol | 2017 Jun 19 |
| Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. | Mendioroz M, Do C, Jiang X, Liu C, Darbary HK, Lang CF, Lin J, Thomas A, Abu-Amero S, Stanier P, Temkin A, Yale A, Liu MM, Li Y, Salas M, Kerkel K, Capone G, Silverman W, Yu YE, Moore G, Wegiel J, Tycko B | Genome biology | 26607552 | Genome Biol | 2015 Nov 25 |
| Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. | Do C, Lang CF, Lin J, Darbary H, Krupska I, Gaba A, Petukhova L, Vonsattel JP, Gallagher MP, Goland RS, Clynes RA, Dwork A, Kral JG, Monk C, Christiano AM, Tycko B | American journal of human genetics | 27153397 | Am J Hum Genet | 2016 May 5 |
| Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. | Paliwal A, Temkin AM, Kerkel K, Yale A, Yotova I, Drost N, Lax S, Nhan-Chang CL, Powell C, Borczuk A, Aviv A, Wapner R, Chen X, Nagy PL, Schork N, Do C, Torkamani A, Tycko B | PLoS genetics | 24009515 | PLoS Genet | 2013 Aug |
| Epigenomic insights into common disease. | Revill K, Tycko B | Genome medicine | 22085423 | Genome Med | 2011 Nov 23 |
| Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals. | Lee JH, Cheng R, Barral S, Reitz C, Medrano M, Lantigua R, Jiménez-Velazquez IZ, Rogaeva E, St George-Hyslop PH, Mayeux R | Archives of neurology | 21059989 | Arch Neurol | 2011 Mar |
| An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. | Hannon E, Dempster E, Viana J, Burrage J, Smith AR, Macdonald R, St Clair D, Mustard C, Breen G, Therman S, Kaprio J, Toulopoulou T, Hulshoff Pol HE, Bohlken MM, Kahn RS, Nenadic I, Hultman CM, Murray RM, Collier DA, Bass N, Gurling H, McQuillin A, Schalkwyk L, Mill J | Genome biology | 27572077 | Genome Biol | 2016 Aug 30 |
| Tissue-specific patterns of allelically-skewed DNA methylation. | Marzi SJ, Meaburn EL, Dempster EL, Lunnon K, Paya-Cano JL, Smith RG, Volta M, Troakes C, Schalkwyk LC, Mill J | Epigenetics | 26786711 | Epigenetics | 2016 |
| Commentary: The seven plagues of epigenetic epidemiology. | Heijmans BT, Mill J | International journal of epidemiology | 22269254 | Int J Epidemiol | 2012 Feb |
| Epigenetic and genetic variation at the IGF2/H19 imprinting control region on 11p15.5 is associated with cerebellum weight. | Pidsley R, Dempster E, Troakes C, Al-Sarraj S, Mill J | Epigenetics | 22395465 | Epigenetics | 2012 Feb |
| Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain. | Smith AR, Smith RG, Condliffe D, Hannon E, Schalkwyk L, Mill J, Lunnon K | Neurobiology of aging | 27522519 | Neurobiol Aging | 2016 Nov |
| Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. | Hannon E, Lunnon K, Schalkwyk L, Mill J | Epigenetics | 26457534 | Epigenetics | 2015 |
| Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms. | Fisher HL, Murphy TM, Arseneault L, Caspi A, Moffitt TE, Viana J, Hannon E, Pidsley R, Burrage J, Dempster EL, Wong CC, Pariante CM, Mill J | Epigenetics | 26479702 | Epigenetics | 2015 |
| Toward an integrated genetic and epigenetic approach to Alzheimer's disease. | Mill J | Neurobiology of aging | 21497948 | Neurobiol Aging | 2011 Jul |
| Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. | Pidsley R, Viana J, Hannon E, Spiers H, Troakes C, Al-Saraj S, Mechawar N, Turecki G, Schalkwyk LC, Bray NJ, Mill J | Genome biology | 25347937 | Genome Biol | 2014 |
| Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. | Devall M, Roubroeks J, Mill J, Weedon M, Lunnon K | Neuroscience letters | 26876477 | Neurosci Lett | 2016 Jun 20 |
| The mitochondrial epigenome: a role in Alzheimer's disease? | Devall M, Mill J, Lunnon K | Epigenomics | 25531259 | Epigenomics | 2014 |
| Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. | Hannon E, Spiers H, Viana J, Pidsley R, Burrage J, Murphy TM, Troakes C, Turecki G, O'Donovan MC, Schalkwyk LC, Bray NJ, Mill J | Nature neuroscience | 26619357 | Nat Neurosci | 2016 Jan |
| Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains. | Hannon E, Marzi SJ, Schalkwyk LS, Mill J | Molecular brain | 30691483 | Mol Brain | 2019 Jan 28 |
| Psychosis-associated DNA methylomic variation in Alzheimer's disease cortex. | Pishva E, Creese B, Smith AR, Viechtbauer W, Proitsi P, van den Hove DLA, Ballard C, Mill J, Lunnon K | Neurobiology of aging | 32007278 | Neurobiol Aging | 2020 May |
| An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene. | Roubroeks JAY, Smith AR, Smith RG, Pishva E, Ibrahim Z, Sattlecker M, Hannon EJ, Kłoszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Wahlund LO, Aarsland D, Proitsi P, Hodges A, Lovestone S, Newhouse SJ, Dobson RJB, Mill J, van den Hove DLA, Lunnon K | Neurobiology of aging | 32745807 | Neurobiol Aging | 2020 Nov |
| The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain. | Smith AR, Smith RG, Macdonald R, Marzi SJ, Burrage J, Troakes C, Al-Sarraj S, Mill J, Lunnon K | Future science OA | 33815817 | Future Sci OA | 2021 Feb 9 |
| Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus. | Lunnon K, Smith RG, Cooper I, Greenbaum L, Mill J, Beeri MS | Neurobiology of aging | 25585531 | Neurobiol Aging | 2015 Mar |
| A data-driven approach to preprocessing Illumina 450K methylation array data. | Pidsley R, Y Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC | BMC genomics | 23631413 | BMC Genomics | 2013 May 1 |
| Systematic underestimation of the epigenetic clock and age acceleration in older subjects. | El Khoury LY, Gorrie-Stone T, Smart M, Hughes A, Bao Y, Andrayas A, Burrage J, Hannon E, Kumari M, Mill J, Schalkwyk LC | Genome biology | 31847916 | Genome Biol | 2019 Dec 17 |
| Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. | Lunnon K, Hannon E, Smith RG, Dempster E, Wong C, Burrage J, Troakes C, Al-Sarraj S, Kepa A, Schalkwyk L, Mill J | Genome biology | 26883014 | Genome Biol | 2016 Feb 16 |
| From promises to practical strategies in epigenetic epidemiology. | Mill J, Heijmans BT | Nature reviews. Genetics | 23817309 | Nat Rev Genet | 2013 Aug |
| Epigenetic studies in Alzheimer's disease: current findings, caveats, and considerations for future studies. | Lunnon K, Mill J | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 24038819 | Am J Med Genet B Neuropsychiatr Genet | 2013 Dec |
| Stochastic choice of allelic expression in human neural stem cells. | Jeffries AR, Perfect LW, Ledderose J, Schalkwyk LC, Bray NJ, Mill J, Price J | Stem cells (Dayton, Ohio) | 22714879 | Stem Cells | 2012 Sep |
| Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. | Condliffe D, Wong A, Troakes C, Proitsi P, Patel Y, Chouliaras L, Fernandes C, Cooper J, Lovestone S, Schalkwyk L, Mill J, Lunnon K | Neurobiology of aging | 24679604 | Neurobiol Aging | 2014 Aug |
| Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. | Lunnon K, Smith R, Hannon E, De Jager PL, Srivastava G, Volta M, Troakes C, Al-Sarraj S, Burrage J, Macdonald R, Condliffe D, Harries LW, Katsel P, Haroutunian V, Kaminsky Z, Joachim C, Powell J, Lovestone S, Bennett DA, Schalkwyk LC, Mill J | Nature neuroscience | 25129077 | Nat Neurosci | 2014 Sep |
| Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions. | Viana J, Hannon E, Dempster E, Pidsley R, Macdonald R, Knox O, Spiers H, Troakes C, Al-Saraj S, Turecki G, Schalkwyk LC, Mill J | Human molecular genetics | 28011714 | Hum Mol Genet | 2017 Jan 1 |
| Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. | Dempster EL, Pidsley R, Schalkwyk LC, Owens S, Georgiades A, Kane F, Kalidindi S, Picchioni M, Kravariti E, Toulopoulou T, Murray RM, Mill J | Human molecular genetics | 21908516 | Hum Mol Genet | 2011 Dec 15 |
