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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
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
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
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
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
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
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
Predicting the human epigenome from DNA motifs. Whitaker JW, Chen Z, Wang W Nature methods 25240437 Nat Methods 2015 Mar
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
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
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
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
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
Genetics: Closing the distance on obesity culprits. Gorkin DU, Ren B Nature 24646989 Nature 2014 Mar 20
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
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
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
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
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
Next-generation genomics: an integrative approach. Hawkins RD, Hon GC, Ren B Nature reviews. Genetics 20531367 Nat Rev Genet 2010 Jul
'Leveling' the playing field for analyses of single-base resolution DNA methylomes. Schultz MD, Schmitz RJ, Ecker JR Trends in genetics : TIG 23131467 Trends Genet 2012 Dec
The DNA methylome. Pelizzola M, Ecker JR FEBS letters 21056564 FEBS Lett 2011 Jul 7
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
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
Genome organization and long-range regulation of gene expression by enhancers. Smallwood A, Ren B Current opinion in cell biology 23465541 Curr Opin Cell Biol 2013 Jun
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B Cell 23664764 Cell 2013 May 23
Mapping human epigenomes. Rivera CM, Ren B Cell 24074860 Cell 2013 Sep 26
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity. Wang SM, Zhang MQ Journal of cellular physiology 20143329 J Cell Physiol 2010 Jun
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
DNA methylation data analysis and its application to cancer research. Ma X, Wang YW, Zhang MQ, Gazdar AF Epigenomics 23750645 Epigenomics 2013 Jun
Developmental biology. Enhancing pluripotency and lineage specification. Xie W, Ren B Science (New York, N.Y.) 23869010 Science 2013 Jul 19
The 3D genome in transcriptional regulation and pluripotency. Gorkin DU, Leung D, Ren B Cell stem cell 24905166 Cell Stem Cell 2014 Jun 5
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
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
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
Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. Gu J, Xuan Z PloS one 24278370 PLoS One 2013
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
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
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
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
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
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
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
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
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
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
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
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
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
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA Cell 23953118 Cell 2013 Aug 15
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA Nature genetics 26502339 Nat Genet 2015 Dec
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
Taking Stock of Regulatory Variation. Maurano MT, Stamatoyannopoulos JA Cell systems 27135686 Cell Syst 2015 Jul 29
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
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
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A Cell 23664763 Cell 2013 May 23
High-throughput bisulfite sequencing in mammalian genomes. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A Methods (San Diego, Calif.) 19442738 Methods 2009 Jul
DNA methylation: roles in mammalian development. Smith ZD, Meissner A Nature reviews. Genetics 23400093 Nat Rev Genet 2013 Mar
Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC Proceedings of the National Academy of Sciences of the United States of America 21737748 Proc Natl Acad Sci U S A 2011 Sep 6
Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Adli M, Bernstein BE Nature protocols 21959244 Nat Protoc 2011 Sep 29
Erosion of dosage compensation impacts human iPSC disease modeling. Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, Eggan K Cell stem cell 22560080 Cell Stem Cell 2012 May 4
Epigenetic obstacles encountered by transcription factors: reprogramming against all odds. Gifford CA, Meissner A Current opinion in genetics & development 22922161 Curr Opin Genet Dev 2012 Oct
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A Nature protocols 21412275 Nat Protoc 2011 Apr
Dissecting neural differentiation regulatory networks through epigenetic footprinting. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A Nature 25533951 Nature 2015 Feb 19
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A PLoS genetics 22174693 PLoS Genet 2011 Dec
Charting a dynamic DNA methylation landscape of the human genome. Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A Nature 23925113 Nature 2013 Aug 22
Locus-specific editing of histone modifications at endogenous enhancers. Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE Nature biotechnology 24013198 Nat Biotechnol 2013 Dec
Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N Stem cell reports 24052944 Stem Cell Reports 2013
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
Epigenetic modifications in pluripotent and differentiated cells. Meissner A Nature biotechnology 20944600 Nat Biotechnol 2010 Oct
Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. Zhan L, Li J, Jew B, Sul JH PLoS genetics 34516545 PLoS Genet 2021 Sep
Genetic and multi-omic risk assessment of Alzheimer's disease implicates core associated biological domains. Cary GA, Wiley JC, Gockley J, Keegan S, Amirtha Ganesh SS, Heath L, Butler RR 3rd, Mangravite LM, Logsdon BA, Longo FM, Levey A, Greenwood AK, Carter GW Alzheimer's & dementia (New York, N. Y.) 38650747 Alzheimers Dement (N Y) 2024 Apr-Jun
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
The Role of X Chromosome in Alzheimer's Disease Genetics. Belloy ME, Guen YL, Stewart I, Herz J, Sherva R, Zhang R, Merritt V, Panizzon MS, Hauger RL, VA Million Veteran Program, Gaziano JM, Logue M, Napolioni V, Greicius MD medRxiv : the preprint server for health sciences 38712163 medRxiv 2024 Apr 23
Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Adli M, Zhu J, Bernstein BE Nature methods 20622861 Nat Methods 2010 Aug
Mouse ooplasm confers context-specific reprogramming capacity. Chan MM, Smith ZD, Egli D, Regev A, Meissner A Nature genetics 22902786 Nat Genet 2012 Sep
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A Genome biology 23034176 Genome Biol 2012 Oct 3
Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. Hardison RC The Journal of biological chemistry 22952232 J Biol Chem 2012 Sep 7
An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE Cell reports 23707066 Cell Rep 2013 May 30
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Karnik R, Meissner A Cell stem cell 23827707 Cell Stem Cell 2013 Jul 3
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
Genome-wide chromatin state transitions associated with developmental and environmental cues. Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE Cell 23333102 Cell 2013 Jan 31
EPIGENOMIC FEATURES RELATED TO MICROGLIA ARE ASSOCIATED WITH ATTENUATED EFFECT OF APOE ε4 ON ALZHEIMER'S DISEASE RISK IN HUMANS. Ma Y, Yu L, Olah M, Smith R, Oatman SR, Allen M, Pishva E, Zhang B, Menon V, Ertekin-Taner N, Lunnon K, Bennett DA, Klein HU, De Jager PL Alzheimer's & dementia : the journal of the Alzheimer's Association 34393677 Alzheimers Dement 2020 Dec
Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. Ma Y, Dammer EB, Felsky D, Duong DM, Klein HU, White CC, Zhou M, Logsdon BA, McCabe C, Xu J, Wang M, Wingo TS, Lah JJ, Zhang B, Schneider J, Allen M, Wang X, Ertekin-Taner N, Seyfried NT, Levey AI, Bennett DA, De Jager PL Nature communications 34857756 Nat Commun 2021 Dec 2
Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer's disease. Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins JE Nature communications 39875385 Nat Commun 2025 Jan 28
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
Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells. Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE BMC genomics 23414147 BMC Genomics 2013 Feb 15
The simplest explanation: passive DNA demethylation in PGCs. Smith ZD, Meissner A The EMBO journal 23299938 EMBO J 2013 Feb 6
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG Genome research 22466170 Genome Res 2012 Jun
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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
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
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
A signature of circulating inflammatory proteins and development of end-stage renal disease in diabetes. Niewczas MA, Pavkov ME, Skupien J, Smiles A, Md Dom ZI, Wilson JM, Park J, Nair V, Schlafly A, Saulnier PJ, Satake E, Simeone CA, Shah H, Qiu C, Looker HC, Fiorina P, Ware CF, Sun JK, Doria A, Kretzler M, Susztak K, Duffin KL, Nelson RG, Krolewski AS Nature medicine 31011203 Nat Med 2019 May
Going from acute to chronic kidney injury with FoxO3. Gu X, Raman A, Susztak K The Journal of clinical investigation 31063992 J Clin Invest 2019 May 6
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
APOL1: The Balance Imposed by Infection, Selection, and Kidney Disease. Beckerman P, Susztak K Trends in molecular medicine 29886044 Trends Mol Med 2018 Aug
Katalin Susztak. Trends in molecular medicine 29980480 Trends Mol Med 2018 Aug
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
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
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
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
Epithelial Plasticity versus EMT in Kidney Fibrosis. Huang S, Susztak K Trends in molecular medicine 26700490 Trends Mol Med 2016 Jan
Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Doke T, Abedini A, Aldridge DL, Yang YW, Park J, Hernandez CM, Balzer MS, Shrestra R, Coppock G, Rico JMI, Han SY, Kim J, Xin S, Piliponsky AM, Angelozzi M, Lefebvre V, Siracusa MC, Hunter CA, Susztak K Nature immunology 35552540 Nat Immunol 2022 Jun
Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. Quinn GZ, Abedini A, Liu H, Ma Z, Cucchiara A, Havasi A, Hill J, Palmer MB, Susztak K Journal of the American Society of Nephrology : JASN 34348909 J Am Soc Nephrol 2021 Nov
Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease. Sheng X, Qiu C, Liu H, Gluck C, Hsu JY, He J, Hsu CY, Sha D, Weir MR, Isakova T, Raj D, Rincon-Choles H, Feldman HI, Townsend R, Li H, Susztak K Proceedings of the National Academy of Sciences of the United States of America 33144501 Proc Natl Acad Sci U S A 2020 Nov 17
Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. Guan Y, Liu H, Ma Z, Li SY, Park J, Sheng X, Susztak K Journal of the American Society of Nephrology : JASN 32127410 J Am Soc Nephrol 2020 Apr
A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. Guan Y, Liang X, Ma Z, Hu H, Liu H, Miao Z, Linkermann A, Hellwege JN, Voight BF, Susztak K Nature communications 34426578 Nat Commun 2021 Aug 23
APOL1 at 10 years: progress and next steps. Freedman BI, Kopp JB, Sampson MG, Susztak K Kidney international 33794228 Kidney Int 2021 Jun
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
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
The interdependence of renal epithelial and endothelial metabolism and cell state. Balzer MS, Susztak K Science signaling 32518144 Sci Signal 2020 Jun 9
Unmasking the elusive erythropoietin-producing 'Norn' cell. Abedini A, Klötzer KA, Susztak K Nature medicine 37130964 Nat Med 2023 May
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
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K Nature genetics 35710981 Nat Genet 2022 Jul
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
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
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
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
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
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
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
Fine tuning gene expression: the epigenome. Mohtat D, Susztak K Seminars in nephrology 21044758 Semin Nephrol 2010 Sep
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
APOL1 Variants: From Parasites to Kidney Function to Cardiovascular Disease. Reiner AP, Susztak K Arteriosclerosis, thrombosis, and vascular biology 26819463 Arterioscler Thromb Vasc Biol 2016 Feb
Podocytes: the Weakest Link in Diabetic Kidney Disease? Lin JS, Susztak K Current diabetes reports 27053072 Curr Diab Rep 2016 May
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
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
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
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
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
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
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
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
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
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
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
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
Unravelling the complex genetics of common kidney diseases: from variants to mechanisms. Sullivan KM, Susztak K Nature reviews. Nephrology 32514149 Nat Rev Nephrol 2020 Nov
Loss of IL-27Rα Results in Enhanced Tubulointerstitial Fibrosis Associated with Elevated Th17 Responses. Coppock GM, Aronson LR, Park J, Qiu C, Park J, DeLong JH, Radaelli E, Suszták K, Hunter CA Journal of immunology (Baltimore, Md. : 1950) 32522836 J Immunol 2020 Jul 15
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
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
Introduction: Systems Biology of Kidney Disease. Sharma K, Susztak K, Pennathur S Seminars in nephrology 29602402 Semin Nephrol 2018 Mar
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
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
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
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
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
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
Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue. Gluck C, Ko YA, Susztak K Current diabetes reports 28364354 Curr Diab Rep 2017 May
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
Podocytopathies. Kopp JB, Anders HJ, Susztak K, Podestà MA, Remuzzi G, Hildebrandt F, Romagnani P Nature reviews. Disease primers 32792490 Nat Rev Dis Primers 2020 Aug 13
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
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
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
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists. Abedini A, Sánchez-Navaro A, Wu J, Klötzer KA, Ma Z, Poudel B, Doke T, Balzer MS, Frederick J, Cernecka H, Liu H, Liang X, Vitale S, Kolkhof P, Susztak K The Journal of clinical investigation 37906287 J Clin Invest 2024 Jan 2
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
The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L, Koesterer R, Gilbert C, Welch RP, Kudtarkar P, Hoang Q, Boughton AP, Singh P, Sun Y, Duby M, Moriondo A, Nguyen T, Smadbeck P, Alexander BR, Brandes M, Carmichael M, Dornbos P, Green T, Huellas-Bruskiewicz KC, Ji Y, Kluge A, McMahon AC, Mercader JM, Ruebenacker O, Sengupta S, Spalding D, Taliun D, AMP-T2D Consortium, Smith P, Thomas MK, Akolkar B, Brosnan MJ, Cherkas A, Chu AY, Fauman EB, Fox CS, Kamphaus TN, Miller MR, Nguyen L, Parsa A, Reilly DF, Ruetten H, Wholley D, Zaghloul NA, Abecasis GR, Altshuler D, Keane TM, McCarthy MI, Gaulton KJ, Florez JC, Boehnke M, Burtt NP, Flannick J Cell metabolism 36963395 Cell Metab 2023 Apr 4
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
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
Emerging role of autophagy in kidney function, diseases and aging. Huber TB, Edelstein CL, Hartleben B, Inoki K, Jiang M, Koya D, Kume S, Lieberthal W, Pallet N, Quiroga A, Ravichandran K, Susztak K, Yoshida S, Dong Z Autophagy 22692002 Autophagy 2012 Jul 1
Smad1 as a biomarker for diabetic nephropathy. Kato H, Si H, Hostetter T, Susztak K Diabetes 18511448 Diabetes 2008 Jun
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
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
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
Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. Gu X, Yang H, Sheng X, Ko YA, Qiu C, Park J, Huang S, Kember R, Judy RL, Park J, Damrauer SM, Nadkarni G, Loos RJF, My VTH, Chaudhary K, Bottinger EP, Paranjpe I, Saha A, Brown C, Akilesh S, Hung AM, Palmer M, Baras A, Overton JD, Reid J, Ritchie M, Rader DJ, Susztak K Science translational medicine 33441424 Sci Transl Med 2021 Jan 13
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
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
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
The evolving understanding of the contribution of lipid metabolism to diabetic kidney disease. Stadler K, Goldberg IJ, Susztak K Current diabetes reports 25957525 Curr Diab Rep 2015 Jul
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
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Total daily activity declines more rapidly with increasing age in older adults. Buchman AS, Wilson RS, Yu L, James BD, Boyle PA, Bennett DA Archives of gerontology and geriatrics 24007938 Arch Gerontol Geriatr 2014 Jan-Feb
Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies. Yang J, Yu L, Gaiteri C, Srivastava GP, Chibnik LB, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA The international journal of biochemistry & cell biology 26003740 Int J Biochem Cell Biol 2015 Oct
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Change in risk of Alzheimer disease over time. Hebert LE, Bienias JL, Aggarwal NT, Wilson RS, Bennett DA, Shah RC, Evans DA Neurology 20805524 Neurology 2010 Aug 31
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Association of genetic variants in and promoter hypermethylation of CDH1 with gastric cancer: a meta-analysis. Jing H, Dai F, Zhao C, Yang J, Li L, Kota P, Mao L, Xiang K, Zheng C, Yang J Medicine 25340495 Medicine (Baltimore) 2014 Oct
The association between apolipoprotein E and gallstone disease: an updated meta-analysis. Li L, Qiao X, Wang X, Liu D, Xue Q, Han L, Dai F, Ma G, Yang Z, Zhang T, Yang S, Cai S, Gao M, Yang J BMC medical genetics 31200656 BMC Med Genet 2019 Jun 14
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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
Prioritizing Parkinson's disease genes using population-scale transcriptomic data. Li YI, Wong G, Humphrey J, Raj T Nature communications 30824768 Nat Commun 2019 Mar 1
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
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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
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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
Novel methods for integration and visualization of genomics and genetics data in Alzheimer's disease. Bihlmeyer NA, Merrill E, Lambert Y, Srivastava GP, Clark TW, Hyman BT, Das S Alzheimer's & dementia : the journal of the Alzheimer's Association 30935898 Alzheimers Dement 2019 Jun
Seasonal plasticity of cognition and related biological measures in adults with and without Alzheimer disease: Analysis of multiple cohorts. Lim ASP, Gaiteri C, Yu L, Sohail S, Swardfager W, Tasaki S, Schneider JA, Paquet C, Stuss DT, Masellis M, Black SE, Hugon J, Buchman AS, Barnes LL, Bennett DA, De Jager PL PLoS medicine 30180184 PLoS Med 2018 Sep
Age and the association of dementia-related pathology with trajectories of cognitive decline. Jansen WJ, Wilson RS, Visser PJ, Nag S, Schneider JA, James BD, Leurgans SE, Capuano AW, Bennett DA, Boyle PA Neurobiology of aging 29078129 Neurobiol Aging 2018 Jan
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
Cognitive decline following incident and preexisting diabetes mellitus in a population sample. Rajan KB, Arvanitakis Z, Lynch EB, McAninch EA, Wilson RS, Weuve J, Barnes LL, Bianco AC, Evans DA Neurology 27655734 Neurology 2016 Oct 18
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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
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
Shared Causal Paths underlying Alzheimer's dementia and Type 2 Diabetes. Hu Z, Jiao R, Wang P, Zhu Y, Zhao J, De Jager P, Bennett DA, Jin L, Xiong M Scientific reports 32139775 Sci Rep 2020 Mar 5
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification. Moon S, Lee H Bioinformatics (Oxford, England) 35157023 Bioinformatics 2022 Apr 12
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
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
Mendelian randomization analysis identified genes pleiotropically associated with the risk and prognosis of COVID-19. Liu D, Yang J, Feng B, Lu W, Zhao C, Li L The Journal of infection 33259846 J Infect 2021 Jan
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
The association between genetic variants in lactotransferrin and dental caries: a meta- and gene-based analysis. Li X, Su Y, Liu D, Yang J BMC medical genetics 32460726 BMC Med Genet 2020 May 27
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
Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men. Grodstein F, Lemos B, Yu L, Iatrou A, De Jager PL, Bennett DA Frontiers in neuroscience 33488342 Front Neurosci 2020
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
MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state. You SF, Brase L, Filipello F, Iyer AK, Del-Aguila J, He J, D'Oliveira Albanus R, Budde J, Norton J, Gentsch J, Dräger NM, Sattler SM, Kampmann M, Piccio L, Morris JC, Perrin RJ, McDade E, Dominantly Inherited Alzheimer Network, Paul SM, Cashikar AG, Benitez BA, Harari O, Karch CM medRxiv : the preprint server for health sciences 36798226 medRxiv 2023 Feb 8
Metabolomic and lipidomic signatures in autosomal dominant and late-onset Alzheimer's disease brains. Novotny BC, Fernandez MV, Wang C, Budde JP, Bergmann K, Eteleeb AM, Bradley J, Webster C, Ebl C, Norton J, Gentsch J, Dube U, Wang F, Morris JC, Bateman RJ, Perrin RJ, McDade E, Xiong C, Chhatwal J, Dominantly Inherited Alzheimer Network (DIAN) Study Group, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's Disease Metabolomics Consortium (ADMC), Goate A, Farlow M, Schofield P, Chui H, Karch CM, Cruchaga C, Benitez BA, Harari O Alzheimer's & dementia : the journal of the Alzheimer's Association 36251323 Alzheimers Dement 2023 May
Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G. Smullen M, Olson MN, Murray LF, Suresh M, Yan G, Dawes P, Barton NJ, Mason JN, Zhang Y, Fernandez-Fontaine AA, Church GM, Mastroeni D, Wang Q, Lim ET, Chan Y, Readhead B Scientific reports 37369829 Sci Rep 2023 Jun 27
AutoFocus: a hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction. Schweickart A, Chetnik K, Batra R, Kaddurah-Daouk R, Suhre K, Halama A, Krumsiek J Communications biology 39237774 Commun Biol 2024 Sep 6
Targeted co-expression networks for the study of traits. Gómez-Pascual A, Rocamora-Pérez G, Ibanez L, Botía JA Scientific reports 39030261 Sci Rep 2024 Jul 19
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
Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics. Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ Science advances 38781333 Sci Adv 2024 May 24
APOE genotype-specific methylation patterns are linked to Alzheimer disease pathology and estrogen response. Panitch R, Sahelijo N, Hu J, Nho K, Bennett DA, Lunetta KL, Au R, Stein TD, Farrer LA, Jun GR Translational psychiatry 38424036 Transl Psychiatry 2024 Feb 29
Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci. Grodstein F, Lemos B, Yang J, de Paiva Lopes K, Vialle RA, Seyfried N, Wang Y, Shireby G, Hannon E, Thomas A, Brookes K, Mill J, De Jager PL, Bennett DA Epigenetics 39169872 Epigenetics 2024 Dec
Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Alzheimer's Disease Genetics Consortium, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C Alzheimer's & dementia : the journal of the Alzheimer's Association 38958117 Alzheimers Dement 2024 Aug
Sex-specific Associations of Gene Expression with Alzheimer's Disease Neuropathology and Ante-mortem Cognitive Performance. Seto M, Clifton M, Gomez ML, Coughlan G, Gifford KA, Jefferson AL, De Jager PL, Bennett DA, Wang Y, Barnes LL, Schneider JA, Hohman TJ, Buckley RF, Dumitrescu L bioRxiv : the preprint server for biology 39803447 bioRxiv 2025 Jan 2
Exploring the role of the epigenome in multiple sclerosis: a window onto cell-specific transcriptional potential. Kaliszewska A, De Jager PL Journal of neuroimmunology 22297167 J Neuroimmunol 2012 Jul 15
Occupational cognitive requirements and late-life cognitive aging. Pool LR, Weuve J, Wilson RS, Bültmann U, Evans DA, Mendes de Leon CF Neurology 26984944 Neurology 2016 Apr 12
Genetic variants in Alzheimer disease - molecular and brain network approaches. Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA Nature reviews. Neurology 27282653 Nat Rev Neurol 2016 Jul
Incident parkinsonism in older adults without Parkinson disease. Buchman AS, Leurgans SE, Yu L, Wilson RS, Lim AS, James BD, Shulman JM, Bennett DA Neurology 27488597 Neurology 2016 Sep 6
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
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
Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19. Piras IS, Huentelman MJ, Walker JE, Arce R, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Suszczewicz KE, Borja CL, Desforges M, Deture M, Dickson DW, Beach TG, Serrano GE medRxiv : the preprint server for health sciences 34545375 medRxiv 2021 Sep 15
Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease. Bennett DA, Yu L, De Jager PL Biochemical pharmacology 24508835 Biochem Pharmacol 2014 Apr 15
Effect of breastfeeding on childhood BMI and obesity: the China Family Panel Studies. Jing H, Xu H, Wan J, Yang Y, Ding H, Chen M, Li L, Lv P, Hu J, Yang J Medicine 25170931 Medicine (Baltimore) 2014 Aug
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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
Toward an integrated genetic and epigenetic approach to Alzheimer's disease. Mill J Neurobiology of aging 21497948 Neurobiol Aging 2011 Jul
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
Commentary: The seven plagues of epigenetic epidemiology. Heijmans BT, Mill J International journal of epidemiology 22269254 Int J Epidemiol 2012 Feb
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
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
Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains. Hannon E, Marzi SJ, Schalkwyk LS, Mill J Molecular brain 30691483 Mol Brain 2019 Jan 28
Psychosis-associated DNA methylomic variation in Alzheimer's disease cortex. Pishva E, Creese B, Smith AR, Viechtbauer W, Proitsi P, van den Hove DLA, Ballard C, Mill J, Lunnon K Neurobiology of aging 32007278 Neurobiol Aging 2020 May
The mitochondrial epigenome: a role in Alzheimer's disease? Devall M, Mill J, Lunnon K Epigenomics 25531259 Epigenomics 2014
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
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Hannon E, Dempster E, Viana J, Burrage J, Smith AR, Macdonald R, St Clair D, Mustard C, Breen G, Therman S, Kaprio J, Toulopoulou T, Hulshoff Pol HE, Bohlken MM, Kahn RS, Nenadic I, Hultman CM, Murray RM, Collier DA, Bass N, Gurling H, McQuillin A, Schalkwyk L, Mill J Genome biology 27572077 Genome Biol 2016 Aug 30
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

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