Publications

Peer-Reviewed Research Papers

2024 

• IGVF Consortium.  
  Deciphering the impact of genomic variation on function. 
  Nature, 633:47-57, 2024.
• Li CZ, Haghani A, Yan Q, Lu AT, Zhang J, Fei Z, Ernst J, Yang XW, Gladyshev VN, Robeck TR, Chavez AS, Cook JA, Dunnum JL, Raj K, Seluanov A, Gorbunova V, Horvath S.  
  Epigenetic predictors of species maximum life span and other life-history traits in mammals. 
  Science Advances, 10:eadm7273, 2024.
• Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. 
  Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior. 
  Cell Genomics, 4:100545, 2024.
• Nazim M, Lin CH, Feng AC, Xiao W, Yeom KH, Li M, Daly AE, Tan X, Vu H, Ernst J, Carey MF, Smale ST, Black DL.
  Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation.
  Cell Stem Cell, 31:754-771.e6, 2024.

2023

• Flint J, Heffel MG, Chen Z, Mefford J, Marcus E, Chen PB, Ernst J, Luo C. 
  Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription.
  Cell Genomics, 3:100454, 2023. 
• Jaroszewicz A, Ernst J.
  ChromGene: gene-based modeling of epigenomic data.
  Genome Biology, 24:203, 2023.
• Haghani A*#, Li CZ*, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O'Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S#.
  DNA methylation networks underlying mammalian traits.
  Science, 381:eabq5693, 2023.
• Lu AT*, Fei Z*, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S.
  Universal DNA methylation age across mammalian tissues.
  Nature Aging, 3:1144-1166, 2023.
• 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.
  Pan-primate studies of age and sex.
  Geroscience, 45:3187-3209, 2023.
• Vu H, Ernst J.
  Universal chromatin state annotation of the mouse genome.
  Genome Biology, 24:153, 2023.
• Vu H, Koch Z, Fiziev P, Ernst J.
  A framework for group-wise summarization and comparison of chromatin state annotations.
  Bioinformatics, 39:btac722, 2023.
• 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, 22:e13773, 2023.

2022

• 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, 13:783, 2022.
• Vu H, Ernst J.
  Universal annotation of the human genome through integration of over a thousand epigenomic datasets.
  Genome Biology, 23:9, 2022.
  Supporting Website
• 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, 44: 699-717, 2022.
• Lefaudeux D, Sen S, Jiang K, Hoffmann A, the UCLA Ribonomics Group.
  Kinetics of mRNA nuclear export regulate innate immune response gene expression.
  Nature Communications, 13, 7197, 2022.
  (Ernst J and Jaroszewicz A are part of the UCLA Ribonomics Group.)

2021

• 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.
  Front Cell Dev Biol, 9:787684, 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, 2441-2453, 2021.
• Catav A, Fu B, Zoabi Y, Weiss-Meilik A, Shomron N, Ernst J, Sankararaman S, Gilad-Bachrach R.
  Marginal Contribution Feature Importance - an Axiomatic Approach for Explaining Data.
  Proceedings of the 38th International Conference on Machine Learning, PMLR, 139:1324-1335, 2021.
• Kwon SB, Ernst J.
  Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.
  Communications Biology, 4:698, 2021.
• Kwon SB, Ernst J.
  Learning a genome-wide score of human-mouse conservation at the functional genomics level.
  Nature Communications, 12:2495, 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, 27:806-814, 2021.

2020

• Arneson A, Felsheim B, Chien J, Ernst J.
  ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation.
  NAR Genomics and Bioinformatics, 2:lqaa104, 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, 11:6168, 2020.
• Jaroszewicz A, Ernst J.
  An Integrative Approach for Fine-Mapping Chromatin Interactions.
  Bioinformatics, 36:1704-1711, 2020.

2019

• 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, 15:e1008481, 2019.
• Arneson A, Ernst J.
  Systematic discovery of conservation states for single-nucleotide annotation of the human genome.
  Communications Biology, 2:248, 2019.

2018

• 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, 9:3634, 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, 9:3391, 2018.
• Fiziev P, Ernst J.
  ChromTime: modeling spatio-temporal dynamics of chromatin marks.
  Genome Biology, 19:109, 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, 9:2606, 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, 9:754, 2018.

2017

• Ernst J#, Kellis M#.
  Chromatin-state discovery and genome annotation with ChromHMM.
  Nature Protocols, 12:2478-2492, 2017.
• Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M.
  Evidence of reduced recombination rate in human regulatory domains.
  Genome Biology, 18:193, 2017.
  (website with Enhancer-gene link predictions for Roadmap Epigenomics data)
• 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, 19:875-889, 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, 168:442-459, 2017.

2016

• Ernst J#, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M#.
  Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.
  Nature Biotechnology, 34:1180-1190, 2016.
• 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, 538:523-527, 2016.
• Rakshit K, Qian J, Ernst J, Matveyenko A.
  Circadian variation of the pancreatic islet transcriptome.
  Physiological Genomics, 48:677-687, 2016.
• Duong D, Zou J, Hormozdiari F, Sul JS, Ernst J, Han B, and Eskin E.
  Using genomic annotations increases statistical power to detect eGenes.
  Bioinformatics (Proceedings of ISMB 2016), 32: i156-i163, 2016.

2015

• Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar A, Ernst J, Chin L.
  Dual Roles of RNF2 in Melanoma Progression.
  Cancer Discovery, 5:1314-1327, 2015.
• Ernst J#, Kellis M#.
  Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.
  Nature Biotechnology, 33:364-376, 2015. (see News and Views by Ebert and Bock and Cover)
• 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, 518:317-330, 2015.
  Supporting Website

2014

• Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, and Ren B.
  Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies.
  G3, 4:2051-2063, 2014.
• 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, 17:1156-63, 2014.
  (News and Views)

2013

• Mortazavi A*, Pepke S*, Jansen CS, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers R, Wold B.
  Integrating and mining the chromatin landscape of cell type specificity using Self-Organizing Maps.
  Genome Research, 23: 2136-2148, 2013.
• Denholtz M*, Bonora G*, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, and 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, 13:602-616, 2013.
• Ernst J, Kellis M.
  Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types.
  Genome Research, 23:1142-1154, 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, 23:800-811, 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, 9:e1002968, 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, 41:827-841, 2013.

2012

• Ernst J, Kellis M.
  ChromHMM: automating chromatin-state discovery and characterization.
  Nature Methods, 9:215-216, 2012.
  Supporting Website
• ENCODE Project Consortium.
  An integrated encyclopedia of DNA elements in the human genome.
  Nature 489:57-74, 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 2:1411-1424, 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 6:104, 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, Kuldev 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 8: e1002654, 2012.

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 473: 43-49, 2011.
  Supporting Website
• 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*, Alfoldi 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, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, 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 478: 476-482, 2011.https://2010
  Supporting Website
• 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 R, Bishop EP, Canfield TP, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH, Park PJ.
  Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
  Nature 471: 480-485, 2011.
• 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 147: 1628-1639, 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 21: 1659-1671, 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 6:e22401, 2011.
• ENCODE Project Consortium.
  A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
  PLoS Biology 9: e1001046, 2011.

2010

• Ernst J, Kellis M.
  Discovery and characterization of chromatin states for systematic annotation of the human genome.
  Nature Biotechnology 28: 817-825, 2010.
  Supporting Website
• Ernst J, Plasterer HL, Simon I, Bar-Joseph Z.
  Integrating multiple evidence sources to predict transcription factor binding in the human genome.
  Genome Research 20: 526-536, 2010.
  Supporting Website
• 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 330: 1787-1797, 2010.
  Supporting Website

2009

• 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 4: e7469, 2009.

2008

• Ernst J, Beg QK, Kay KA, Balazsi G, Oltvai ZN, Bar-Joseph Z.
  A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli.
  PLoS Computational Biology 4: e1000044, 2008.
  Supporting Website
• Vazquez A*, Beg QK*, de Menezes MA, Ernst J, Bar-Joseph Z, Barabasi A-L, Boros LG, Oltvai ZN.
  Impact of the solvent capacity constraint on E. coli metabolism.
  BMC Systems Biology, 2:7, 2008.

2007

• Ernst J, Vainas O, Harbison CT, Simon I, and Bar-Joseph Z.
  Reconstructing dynamic regulatory maps.
  Nature-EMBO Molecular Systems Biology, 3:74, 2007.
  Supporting website
• Beg QK*, Vazquez A*, Ernst J, de Menezes MA, Bar-Joseph Z, Barabasi A-L, Oltvai ZN.
  Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.
  Proceedings of the National Academy of Sciences, 104: 12663-12668, 2007.

2006 

• Ernst J, Bar-Joseph Z.
  STEM: a tool for the analysis of short time series gene expression data.
  BMC Bioinformatics, 7:191, 2006.
  Supporting website

2005

• Ernst J, Nau GJ, Bar-Joseph Z.
  Clustering Short Time Series Gene Expression Data.
  Bioinformatics (Proceedings of ISMB 2005), 21 Suppl. 1, i159-i168, 2005.
  Supporting website
• 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, 23: 1503-1508, 2005.
  Supporting website

Commentaries

• Implications of the first complete human genome assembly.
  Genome Research, 32:595-598, 2022.
  (Ernst J contributed one of 12-short commentaries)
• Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca-Bachman CE, Parker CC, Ursu O, 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, Qing L, 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 Behavior, e12738, 2021.
• Kwon SB, Ernst J.
  Investigating enhancer evolution with massively parallel reporter assays.
  Genome Biology, 19:114, 2018.
• Ernst J.
  Mapping enhancer and promoter interactions.
  Cell Research, 22:789-790, 2012.

Thesis

• Ernst J.
  Computational Methods for Modeling and Analyzing Gene Regulation Dynamics (PDF).
  PhD thesis, Carnegie Mellon University, CMU-ML-08-110, 2008.