Publications

• Sarkar A, Liu NQ, Magallanes J, Tassey J, Lee S, Shkhyan R, Lee Y, Lu J, Ouyang Y, Tang H, Bian F, Tao L, Segil N, Ernst J, Lyons K, Horvath S, Evseenko D. STAT3 promotes a youthful epigenetic state in articular chondrocytes.. Aging cell, 2023.
• Vu H, Koch Z, Fiziev P, Ernst J. A framework for group-wise summarization and comparison of chromatin state annotations.. Bioinformatics (Oxford, England), 2023.
• Arneson A, Haghani A, Thompson MJ, Pellegrini M, Kwon SB, Vu H, Maciejewski E, Yao M, Li CZ, Lu AT, Morselli M, Rubbi L, Barnes B, Hansen KD, Zhou W, Breeze CE, Ernst J, Horvath S. A mammalian methylation array for profiling methylation levels at conserved sequences.. Nature communications, 2022.
• Vu H, Ernst J. Universal annotation of the human genome through integration of over a thousand epigenomic datasets.. Genome biology, 2022.
• Pezhouman A, Nguyen NB, Sercel AJ, Nguyen TL, Daraei A, Sabri S, Chapski DJ, Zheng M, Patananan AN, Ernst J, Plath K, Vondriska TM, Teitell MA, Ardehali R. Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation.. Frontiers in cell and developmental biology, 2021.
• Jasinska AJ, Haghani A, Zoller JA, Li CZ, Arneson A, Ernst J, Kavanagh K, Jorgensen MJ, Mattison JA, Wojta K, Choi OW, DeYoung J, Li X, Rao AW, Coppola G, Freimer NB, Woods RP, Horvath S. Epigenetic clock and methylation studies in vervet monkeys.. GeroScience, 2021.
• Horvath S, Zoller JA, Haghani A, Jasinska AJ, Raj K, Breeze CE, Ernst J, Vaughan KL, Mattison JA. Epigenetic clock and methylation studies in the rhesus macaque.. GeroScience, 2021.
• Kwon SB, Ernst J. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.. Communications biology, 2021.
• Carraro G, Langerman J, Sabri S, Lorenzana Z, Purkayastha A, Zhang G, Konda B, Aros CJ, Calvert BA, Szymaniak A, Wilson E, Mulligan M, Bhatt P, Lu J, Vijayaraj P, Yao C, Shia DW, Lund AJ, Israely E, Rickabaugh TM, Ernst J, Mense M, Randell SH, Vladar EK, Ryan AL, Plath K, Mahoney JE, Stripp BR, Gomperts BN. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition.. Nature medicine, 2021.
• Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level.. Nature communications, 2021.
• Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca-Bachman CE, Parker CC, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez-Roige S, Bandrowski A, Lu Q, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M, Williams RW. Integration of evidence across human and model organism studies: A meeting report.. Genes, brain, and behavior, 2021.
• Arneson A, Felsheim B, Chien J, Ernst J. ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation.. NAR genomics and bioinformatics, 2020.
• Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J. Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.. Nature communications, 2020.
• Kwon SB, Ernst J. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.. bioRxiv : the preprint server for biology, 2020.
• Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P, NHLBI TOPMed Lipids Working Group. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.. Nature communications, 2020.
• Jaroszewicz A, Ernst J. An integrative approach for fine-mapping chromatin interactions.. Bioinformatics (Oxford, England), 2020.
• Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. Leveraging allelic imbalance to refine fine-mapping for eQTL studies.. PLoS genetics, 2019.
• Arneson A, Ernst J. Systematic discovery of conservation states for single-nucleotide annotation of the human genome.. Communications biology, 2019.
• Ferguson GB, Van Handel B, Bay M, Fiziev P, Org T, Lee S, Shkhyan R, Banks NW, Scheinberg M, Wu L, Saitta B, Elphingstone J, Larson AN, Riester SM, Pyle AD, Bernthal NM, Mikkola HK, Ernst J, van Wijnen AJ, Bonaguidi M, Evseenko D. Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes.. Nature communications, 2018.
• Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S, NHLBI TOPMed Lipids Working Group. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.. Nature communications, 2018.
• Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P, NHLBI TOPMed Lipids Working Group. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.. Nature communications, 2018.
• Kwon SB, Ernst J. Investigating enhancer evolution with massively parallel reporter assays.. Genome biology, 2018.
• Fiziev P, Ernst J. ChromTime: modeling spatio-temporal dynamics of chromatin marks.. Genome biology, 2018.
• Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P, NHLBI TOPMed Lipids Working Group. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.. Nature communications, 2018.
• Sereti KI, Nguyen NB, Kamran P, Zhao P, Ranjbarvaziri S, Park S, Sabri S, Engel JL, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Plath K, Ernst J, Sahoo D, Mikkola HKA, Iruela-Arispe ML, Ardehali R. Analysis of cardiomyocyte clonal expansion during mouse heart development and injury.. Nature communications, 2018.
• Ernst J, Kellis M. Chromatin-state discovery and genome annotation with ChromHMM.. Nature protocols, 2017.
• Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M. Evidence of reduced recombination rate in human regulatory domains.. Genome biology, 2017.
• Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.. Cell reports, 2017.
• Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K. Cooperative Binding of Transcription Factors Orchestrates Reprogramming.. Cell, 2017.
• Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH. Chromosome conformation elucidates regulatory relationships in developing human brain.. Nature, 2016.
• Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.. Nature biotechnology, 2016.
• Rakshit K, Qian J, Ernst J, Matveyenko AV. Circadian variation of the pancreatic islet transcriptome.. Physiological genomics, 2016.
• Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. Using genomic annotations increases statistical power to detect eGenes.. Bioinformatics (Oxford, England), 2016.
• 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. Integrative analysis of 111 reference human epigenomes.. Nature, 2015.
• Ernst J, Kellis M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.. Nature biotechnology, 2015.
• De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.. Nature neuroscience, 2014.
• Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies.. G3 (Bethesda, Md.), 2014.
• Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.. Genome research, 2013.
• Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.. Cell stem cell, 2013.
• Ernst J, Kellis M. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types.. Genome research, 2013.
• Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.. Genome research, 2013.
• Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state.. PLoS computational biology, 2013.
• Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data.. Nucleic acids research, 2012.
• Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi JH, Robertson KD. Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells.. Cell reports, 2012.
• Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.. BMC systems biology, 2012.
• Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, Doheny KF, Friedman DS, Gaasterland D, Gaasterland T, Laurie C, Lee RK, Lichter PR, Loomis S, Liu Y, Medeiros FA, McCarty C, Mirel D, Moroi SE, Musch DC, Realini A, Rozsa FW, Schuman JS, Scott K, Singh K, Stein JD, Trager EH, Vanveldhuisen P, Vollrath D, Wollstein G, Yoneyama S, Zhang K, Weinreb RN, Ernst J, Kellis M, Masuda T, Zack D, Richards JE, Pericak-Vance M, Pasquale LR, Haines JL. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma.. PLoS genetics, 2012.
• Ernst J. Mapping enhancer and promoter interactions.. Cell research, 2012.
• Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization.. Nature methods, 2012.
• Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.. Cell, 2011.
• Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alf?ldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals.. Nature, 2011.
• Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.. Genome research, 2011.
• Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O'Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar Joseph Z, Morel PA. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque.. PloS one, 2011.
• Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types.. Nature, 2011.
• Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.. Nature, 2010.
• modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE.. Science (New York, N.Y.), 2010.
• Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome.. Nature biotechnology, 2010.
• Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome.. Genome research, 2010.
• Ernst J, Ghanem L, Bar-Joseph Z, McNamara M, Brown J, Steinman RA. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability.. PloS one, 2009.
• Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.. PLoS computational biology, 2008.
• Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN. Impact of the solvent capacity constraint on E. coli metabolism.. BMC systems biology, 2008.
• Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Reconstructing dynamic regulatory maps.. Molecular systems biology, 2007.
• Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data.. BMC bioinformatics, 2006.
• Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Combined static and dynamic analysis for determining the quality of time-series expression profiles.. Nature biotechnology, 2005.
• Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data.. Bioinformatics (Oxford, England), 2005.