Epigenomics
Epigenomics
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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 | PubMedLink |
|---|---|---|---|---|---|---|
| The DNA methylome. | Pelizzola M, Ecker JR | FEBS letters | 21056564 | FEBS Lett | 2011 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/21056564 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20852635 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21131980 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22341451 |
| DNA methylation data analysis and its application to cancer research. | Ma X, Wang YW, Zhang MQ, Gazdar AF | Epigenomics | 23750645 | Epigenomics | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23750645 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23443545 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23362228 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19736251 |
| Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity. | Wang SM, Zhang MQ | Journal of cellular physiology | 20143329 | J Cell Physiol | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20143329 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20452322 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28505334 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24757056 |
| Mapping human epigenomes. | Rivera CM, Ren B | Cell | 24074860 | Cell | 2013 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/24074860 |
| Genetics: Closing the distance on obesity culprits. | Gorkin DU, Ren B | Nature | 24646989 | Nature | 2014 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/24646989 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23075850 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22213113 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22730289 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23995138 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34663447 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20682449 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26960733 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23791644 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23482391 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23900278 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie W, Ren B | Science (New York, N.Y.) | 23869010 | Science | 2013 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/23869010 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23271069 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24141950 |
| Predicting the human epigenome from DNA motifs. | Whitaker JW, Chen Z, Wang W | Nature methods | 25240437 | Nat Methods | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25240437 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25461775 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24343027 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24752503 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25825433 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25842977 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25693563 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25693566 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25505163 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26268681 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26030523 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23099485 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23196972 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21289626 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22608086 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24078702 |
| Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. | Gu J, Xuan Z | PloS one | 24278370 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24278370 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23465541 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23664764 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23526891 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23293768 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19157957 |
| Next-generation genomics: an integrative approach. | Hawkins RD, Hon GC, Ren B | Nature reviews. Genetics | 20531367 | Nat Rev Genet | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20531367 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19829295 |
| '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 | https://www.ncbi.nlm.nih.gov/pubmed/23131467 |
| The 3D genome in transcriptional regulation and pluripotency. | Gorkin DU, Leung D, Ren B | Cell stem cell | 24905166 | Cell Stem Cell | 2014 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/24905166 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24077454 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24185094 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21478862 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25122670 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25591927 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21876557 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26085954 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25693564 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26415965 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21285249 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25580597 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26257180 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26282110 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25693567 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23953118 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26502339 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22576172 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22955828 |
| Taking Stock of Regulatory Variation. | Maurano MT, Stamatoyannopoulos JA | Cell systems | 27135686 | Cell Syst | 2015 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/27135686 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20852634 |
| The simplest explanation: passive DNA demethylation in PGCs. | Smith ZD, Meissner A | The EMBO journal | 23299938 | EMBO J | 2013 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/23299938 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20062050 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25490447 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30084846 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20978353 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23560082 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19781451 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24892707 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25419705 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25007794 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31877385 |
| Understanding the kidney one cell at a time. | Park J, Liu CL, Kim J, Susztak K | Kidney international | 31492507 | Kidney Int | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31492507 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31165727 |
| The interdependence of renal epithelial and endothelial metabolism and cell state. | Balzer MS, Susztak K | Science signaling | 32518144 | Sci Signal | 2020 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/32518144 |
| Repair problems in podocytes: Wnt, Notch, and glomerulosclerosis. | Kato H, Susztak K | Seminars in nephrology | 22958489 | Semin Nephrol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22958489 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26190114 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27188921 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26400545 |
| The transcriptomic signature of the aging podocyte. | Mukhi D, Susztak K | Kidney international | 33126968 | Kidney Int | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33126968 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29735694 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39137781 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36945458 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36732547 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28751525 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30237160 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29097680 |
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| Introduction: Systems Biology of Kidney Disease. | Sharma K, Susztak K, Pennathur S | Seminars in nephrology | 29602402 | Semin Nephrol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29602402 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29622724 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30596172 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34739325 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33859189 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35821371 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35450819 |
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| The next generation of therapeutics for chronic kidney disease. | Breyer MD, Susztak K | Nature reviews. Drug discovery | 27230798 | Nat Rev Drug Discov | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27230798 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29602395 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28970079 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28614350 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28404638 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28218918 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27760046 |
| Developing Treatments for Chronic Kidney Disease in the 21st Century. | Breyer MD, Susztak K | Seminars in nephrology | 27987541 | Semin Nephrol | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27987541 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28135296 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24876119 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25231882 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24011577 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30226866 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24916699 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26776520 |
| From mapping kidney function to mechanism and prediction. | Hirohama D, Susztak K | Nature reviews. Nephrology | 34819631 | Nat Rev Nephrol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34819631 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30844884 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34715018 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34608231 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34261756 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32541925 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32303282 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32392242 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32247630 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33301705 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33531352 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33465052 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34385711 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37022120 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37188670 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36522157 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38612525 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38614389 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38033715 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39048792 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39500311 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39511169 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/17065336 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/18443355 |
| Tracing the footsteps of glomerular insulin signaling in diabetic kidney disease. | Chang GY, Park AS, Susztak K | Kidney international | 21451535 | Kidney Int | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21451535 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26054542 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26293507 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26505625 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26198328 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26831199 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28575649 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28911167 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28835482 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23788618 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24480826 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24179169 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34177897 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35473814 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36914909 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27913625 |
| APOL1 at 10 years: progress and next steps. | Freedman BI, Kopp JB, Sampson MG, Susztak K | Kidney international | 33794228 | Kidney Int | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33794228 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30702441 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30275566 |
| APOL1: The Balance Imposed by Infection, Selection, and Kidney Disease. | Beckerman P, Susztak K | Trends in molecular medicine | 29886044 | Trends Mol Med | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29886044 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31011203 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31063992 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31167971 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39059357 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29709239 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37023747 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38051585 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36764286 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36787250 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38287030 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39286974 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39566842 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19277126 |
| Fine tuning gene expression: the epigenome. | Mohtat D, Susztak K | Seminars in nephrology | 21044758 | Semin Nephrol | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21044758 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24675284 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24098934 |
| ADCK4 "reenergizes" nephrotic syndrome. | Malaga-Dieguez L, Susztak K | The Journal of clinical investigation | 24270414 | J Clin Invest | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24270414 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24516231 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30850438 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28724797 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28727768 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31474566 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30578418 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30625149 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30076412 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34456921 |
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| Analyzing the cancer methylome through targeted bisulfite sequencing. | Lee EJ, Luo J, Wilson JM, Shi H | Cancer letters | 23200671 | Cancer Lett | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/23200671 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21346760 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21596650 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22306810 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27461342 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21706001 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23175612 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22725639 |
| Proteomics and melanoma: a current perspective. | Shields BD, Tackett AJ, Shalin SC | Global dermatology | 30214824 | Glob Dermatol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30214824 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21884633 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22433969 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21709819 |
| Microscopes and Mass Spectrometers. | Shields B, Shalin SC, Tackett AJ | Journal of proteomics & bioinformatics | 29910559 | J Proteomics Bioinform | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/29910559 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23364797 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19581291 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21883366 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23408432 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23075270 |
| Drug discovery: Reader's block. | Taverna SD, Cole PA | Nature | 21179160 | Nature | 2010 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/21179160 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21273814 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22840409 |
| Proteomic technologies for the study of osteosarcoma. | Byrum SD, Washam CL, Montgomery CO, Tackett AJ, Suva LJ | Sarcoma | 22550414 | Sarcoma | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22550414 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23976835 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23381856 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19621382 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22982377 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25104842 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24470334 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22183593 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25106422 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25419056 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21325313 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/19494183 |
| Sensitive single-molecule protein quantification and protein complex detection in a microarray format. | Tessler LA, Mitra RD | Proteomics | 22038904 | Proteomics | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22038904 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22287102 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20147217 |
| Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. | Varley KE, Mitra RD | Genome research | 20627893 | Genome Res | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20627893 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26027919 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23248290 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25498963 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25289806 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25009286 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22703188 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25062021 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23589626 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21041413 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22760212 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21471402 |
| "Calling cards" for DNA-binding proteins in mammalian cells. | Wang H, Mayhew D, Chen X, Johnston M, Mitra RD | Genetics | 22214611 | Genetics | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22214611 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32941613 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23610441 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23018789 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20088589 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21981444 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21919532 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20421412 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22816516 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22586076 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27694895 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/20434984 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23246990 |
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| Transcriptional regulation and its misregulation in disease. | Lee TI, Young RA | Cell | 23498934 | Cell | 2013 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/23498934 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37085492 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28786976 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28742274 |
| Deconstructing and targeting the genomic architecture of human neurodegeneration. | De Jager PL, Yang HS, Bennett DA | Nature neuroscience | 30258235 | Nat Neurosci | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30258235 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30140277 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37493860 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36424430 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32733030 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34680427 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34040149 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36199750 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32839459 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32877673 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33837133 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35896049 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39231932 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25375876 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27399073 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29317593 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27681803 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23571780 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23708142 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23482655 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25230996 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25653292 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24598707 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26469902 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29078839 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34153464 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35951002 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35974141 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33120085 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33571421 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33716367 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34020725 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35907208 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33838873 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33846280 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35770850 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36709307 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37239387 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35105862 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28322283 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31144443 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26786711 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22395465 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27522519 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26457534 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26479702 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25347937 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26876477 |
| The mitochondrial epigenome: a role in Alzheimer's disease? | Devall M, Mill J, Lunnon K | Epigenomics | 25531259 | Epigenomics | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25531259 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26619357 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30691483 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32007278 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32745807 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33815817 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25585531 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/23631413 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31847916 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26883014 |
| From promises to practical strategies in epigenetic epidemiology. | Mill J, Heijmans BT | Nature reviews. Genetics | 23817309 | Nat Rev Genet | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23817309 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24038819 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/22714879 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/24679604 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/25129077 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28011714 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/21908516 |
