Jason Ernst

Title(s)Professor, Biological Chemistry
SchoolMedicine
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    Title(s)Professor, Computational Medicine


    Collapse Biography 
    Collapse Education and Training
    University of Maryland, College Park, College Park, MDBS05/2002Computer Science and Mathematics
    Carnegie Mellon University, Pittsburgh, PAPhD08/2008Machine Learning
    Massachusetts Institute of Technology, Cambridge, MAPostdoc12/2011Computational Biology

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    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Whole genome sequence-based association analysis of African American individuals with bipolar disorder and schizophrenia. medRxiv. 2025 Feb 19. Li R, Taliun SAG, Liao K, Flickinger M, Sobell JL, Genovese G, Locke AE, Chiu RR, LeFaive J, Wang J, Martins T, Chapman S, Neumann A, Handsaker RE, Arnett DK, Barnes KC, Boerwinkle E, Braff D, Cade BE, Fornage M, Gibbs RA, Hoth KF, Hou L, Kooperberg C, Loos RJF, Metcalf GA, Montgomery CG, Morrison AC, Qin ZS, Redline S, Reiner AP, Rich SS, Rotter JI, Taylor KD, Viaud-Martinez KA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Genomic Psychiatry Cohort investigators, Bigdeli TB, Gabriel S, Zollner S, Smith AV, Abecasis G, McCarroll S, Pato MT, Pato CN, Boehnke M, Knowles J, Kang HM, Ophoff RA, Ernst J, Scott LJ. PMID: 39763555; PMCID: PMC11703280.
      View in: PubMed   Mentions:
    2. The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments. Res Sq. 2025 Feb 10. Li T, Alvarez M, Liu C, Abuhanna K, Sun Y, Ernst J, Plath K, Balliu B, Luo C, Zaitlen N. PMID: 39989953; PMCID: PMC11844637.
      View in: PubMed   Mentions:
    3. Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD mice. Cell. 2025 Feb 08. Wang N, Zhang S, Langfelder P, Ramanathan L, Gao F, Plascencia M, Vaca R, Gu X, Deng L, Dionisio LE, Vu H, Maciejewski E, Ernst J, Prasad BC, Vogt TF, Horvath S, Aaronson JS, Rosinski J, Yang XW. PMID: 39938516.
      View in: PubMed   Mentions:    Fields:    
    4. The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments. bioRxiv. 2025 Feb 08. Li T, Alvarez M, Liu C, Abuhanna K, Sun Y, Ernst J, Plath K, Balliu B, Luo C, Zaitlen N. PMID: 39975005; PMCID: PMC11839078.
      View in: PubMed   Mentions:
    5. Epigenetic predictors of species maximum life span and other life-history traits in mammals. Sci Adv. 2024 Jun 07; 10(23):eadm7273. 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. PMID: 38848365; PMCID: PMC11160467.
      View in: PubMed   Mentions: 6     Fields:    
    6. Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation. Cell Stem Cell. 2024 May 02; 31(5):754-771.e6. 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. PMID: 38701759; PMCID: PMC11126784.
      View in: PubMed   Mentions: 2     Fields:    
    7. Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior. Cell Genom. 2024 May 08; 4(5):100545. Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. PMID: 38697120; PMCID: PMC11099346.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    8. Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence and sex information. bioRxiv. 2024 Mar 21. Li R, Ernst J. PMID: 38562739; PMCID: PMC10983996.
      View in: PubMed   Mentions:
    9. Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior. bioRxiv. 2024 Jan 04. Chen PB, Chen R, LaPierre N, Chen Z, Mefford J, Marcus E, Heffel MG, Soto DC, Ernst J, Luo C, Flint J. PMID: 38260483; PMCID: PMC10802323.
      View in: PubMed   Mentions:
    10. Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription. Cell Genom. 2023 12 13; 3(12):100454. Flint J, Heffel MG, Chen Z, Mefford J, Marcus E, Chen PB, Ernst J, Luo C. PMID: 38116123; PMCID: PMC10726494.
      View in: PubMed   Mentions: 2     Fields:    
    11. Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species. bioRxiv. 2023 Nov 27. Maciejewski E, Horvath S, Ernst J. PMID: 38076978; PMCID: PMC10705269.
      View in: PubMed   Mentions:
    12. ChromGene: gene-based modeling of epigenomic data. Genome Biol. 2023 09 07; 24(1):203. Jaroszewicz A, Ernst J. PMID: 37679846; PMCID: PMC10486095.
      View in: PubMed   Mentions: 2     Fields:    
    13. DNA methylation networks underlying mammalian traits. Science. 2023 08 11; 381(6658):eabq5693. 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. PMID: 37561875; PMCID: PMC11180965.
      View in: PubMed   Mentions: 35     Fields:    
    14. Pan-primate studies of age and sex. Geroscience. 2023 12; 45(6):3187-3209. 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. PMID: 37493860; PMCID: PMC10643767.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    15. Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types. bioRxiv. 2023 Jul 15. Dincer TU, Ernst J. PMID: 37503240; PMCID: PMC10369970.
      View in: PubMed   Mentions:
    16. Universal chromatin state annotation of the mouse genome. Genome Biol. 2023 06 27; 24(1):153. Vu H, Ernst J. PMID: 37370147; PMCID: PMC10294404.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    17. STAT3 promotes a youthful epigenetic state in articular chondrocytes. Aging Cell. 2023 02; 22(2):e13773. 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. PMID: 36638270; PMCID: PMC9924946.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    18. A framework for group-wise summarization and comparison of chromatin state annotations. Bioinformatics. 2023 01 01; 39(1). Vu H, Koch Z, Fiziev P, Ernst J. PMID: 36342196; PMCID: PMC9805555.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    19. A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun. 2022 02 10; 13(1):783. 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. PMID: 35145108; PMCID: PMC8831611.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansAnimalsCells
    20. Universal annotation of the human genome through integration of over a thousand epigenomic datasets. Genome Biol. 2022 01 06; 23(1):9. Vu H, Ernst J. PMID: 34991667; PMCID: PMC8734071.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    21. 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. 2021; 9:787684. 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. PMID: 34988079; PMCID: PMC8722677.
      View in: PubMed   Mentions: 3  
    22. Epigenetic clock and methylation studies in vervet monkeys. Geroscience. 2022 04; 44(2):699-717. 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. PMID: 34591235; PMCID: PMC9135907.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    23. Epigenetic clock and methylation studies in the rhesus macaque. Geroscience. 2021 10; 43(5):2441-2453. Horvath S, Zoller JA, Haghani A, Jasinska AJ, Raj K, Breeze CE, Ernst J, Vaughan KL, Mattison JA. PMID: 34487267; PMCID: PMC8599607.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    24. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome. Commun Biol. 2021 06 03; 4(1):698. Kwon SB, Ernst J. PMID: 34083758; PMCID: PMC8175581.
      View in: PubMed   Mentions: 2  Translation:HumansAnimalsCells
    25. Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition. Nat Med. 2021 05; 27(5):806-814. 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. PMID: 33958799; PMCID: PMC9009537.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    26. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nat Commun. 2021 05 03; 12(1):2495. Kwon SB, Ernst J. PMID: 33941776; PMCID: PMC8093196.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    27. Integration of evidence across human and model organism studies: A meeting report. Genes Brain Behav. 2021 Apr 23; e12738. 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. PMID: 33893716; PMCID: PMC8365690.
      View in: PubMed   Mentions: 8     Fields:    
    28. ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation. NAR Genom Bioinform. 2020 Dec; 2(4):lqaa104. Arneson A, Felsheim B, Chien J, Ernst J. PMID: 33543124; PMCID: PMC7745770.
      View in: PubMed   Mentions: 4  
    29. Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. Nat Commun. 2020 12 02; 11(1):6168. Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J. PMID: 33268804; PMCID: PMC7710766.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    30. Single-nucleotide conservation state annotation of the SARS-CoV-2 genome. bioRxiv. 2020 Nov 02. Kwon SB, Ernst J. PMID: 32699851; PMCID: PMC7373132.
      View in: PubMed   Mentions:
    31. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nat Commun. 2020 Apr 01; 11(1):1715. 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. PMID: 32238811; PMCID: PMC7113276.
      View in: PubMed   Mentions: 1     Fields:    
    32. An integrative approach for fine-mapping chromatin interactions. Bioinformatics. 2020 03 01; 36(6):1704-1711. Jaroszewicz A, Ernst J. PMID: 31742318; PMCID: PMC7425030.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    33. Leveraging allelic imbalance to refine fine-mapping for eQTL studies. PLoS Genet. 2019 12; 15(12):e1008481. Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. PMID: 31834882; PMCID: PMC6952111.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    34. Systematic discovery of conservation states for single-nucleotide annotation of the human genome. Commun Biol. 2019; 2:248. Arneson A, Ernst J. PMID: 31286065; PMCID: PMC6606595.
      View in: PubMed   Mentions: 12  Translation:HumansCells
    35. Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes. Nat Commun. 2018 09 07; 9(1):3634. 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. PMID: 30194383; PMCID: PMC6128860.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    36. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. Nat Commun. 2018 08 23; 9(1):3391. 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. PMID: 30140000; PMCID: PMC6107638.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansCells
    37. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nat Commun. 2018 08 23; 9(1):3493. 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. PMID: 30140049; PMCID: PMC6107495.
      View in: PubMed   Mentions: 1     Fields:    
    38. Investigating enhancer evolution with massively parallel reporter assays. Genome Biol. 2018 08 14; 19(1):114. Kwon SB, Ernst J. PMID: 30107810; PMCID: PMC6090676.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    39. ChromTime: modeling spatio-temporal dynamics of chromatin marks. Genome Biol. 2018 08 10; 19(1):109. Fiziev P, Ernst J. PMID: 30097049; PMCID: PMC6085762.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    40. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nat Commun. 2018 07 04; 9(1):2606. 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. PMID: 29973585; PMCID: PMC6031652.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    41. Analysis of cardiomyocyte clonal expansion during mouse heart development and injury. Nat Commun. 2018 02 21; 9(1):754. 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. PMID: 29467410; PMCID: PMC5821855.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    42. Chromatin-state discovery and genome annotation with ChromHMM. Nat Protoc. 2017 Dec; 12(12):2478-2492. Ernst J, Kellis M. PMID: 29120462; PMCID: PMC5945550.
      View in: PubMed   Mentions: 365     Fields:    Translation:HumansAnimalsCells
    43. Evidence of reduced recombination rate in human regulatory domains. Genome Biol. 2017 10 20; 18(1):193. Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M. PMID: 29058599; PMCID: PMC5651596.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    44. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep. 2017 04 25; 19(4):875-889. 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. PMID: 28445736; PMCID: PMC5473172.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    45. Cooperative Binding of Transcription Factors Orchestrates Reprogramming. Cell. 2017 01 26; 168(3):442-459.e20. Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K. PMID: 28111071; PMCID: PMC5302508.
      View in: PubMed   Mentions: 272     Fields:    Translation:AnimalsCells
    46. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. 2016 10 27; 538(7626):523-527. 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. PMID: 27760116; PMCID: PMC5358922.
      View in: PubMed   Mentions: 290     Fields:    Translation:HumansCells
    47. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Nat Biotechnol. 2016 Nov; 34(11):1180-1190. Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M. PMID: 27701403; PMCID: PMC5125825.
      View in: PubMed   Mentions: 82     Fields:    Translation:HumansCells
    48. Circadian variation of the pancreatic islet transcriptome. Physiol Genomics. 2016 09 01; 48(9):677-87. Rakshit K, Qian J, Ernst J, Matveyenko AV. PMID: 27495157; PMCID: PMC5111880.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    49. Using genomic annotations increases statistical power to detect eGenes. Bioinformatics. 2016 06 15; 32(12):i156-i163. Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. PMID: 27307612; PMCID: PMC4908356.
      View in: PubMed   Mentions: 8     Fields:    
    50. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. 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. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed   Mentions: 3195     Fields:    Translation:HumansCells
    51. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat Biotechnol. 2015 Apr; 33(4):364-76. Ernst J, Kellis M. PMID: 25690853; PMCID: PMC4512306.
      View in: PubMed   Mentions: 195     Fields:    Translation:Humans
    52. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014 Sep; 17(9):1156-63. 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. PMID: 25129075; PMCID: PMC4292795.
      View in: PubMed   Mentions: 457     Fields:    Translation:HumansCells
    53. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda). 2014 Aug 12; 4(11):2051-63. Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. PMID: 25122670; PMCID: PMC4232531.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    54. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Res. 2013 Dec; 23(12):2136-48. Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. PMID: 24170599; PMCID: PMC3847782.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    55. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell. 2013 Nov 07; 13(5):602-16. Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. PMID: 24035354; PMCID: PMC3825755.
      View in: PubMed   Mentions: 151     Fields:    Translation:AnimalsCells
    56. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Res. 2013 Jul; 23(7):1142-54. Ernst J, Kellis M. PMID: 23595227; PMCID: PMC3698507.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    57. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 2013 May; 23(5):800-11. Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. PMID: 23512712; PMCID: PMC3638136.
      View in: PubMed   Mentions: 183     Fields:    Translation:HumansCells
    58. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput Biol. 2013; 9(3):e1002968. Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. PMID: 23526891; PMCID: PMC3597546.
      View in: PubMed   Mentions: 117     Fields:    Translation:HumansCells
    59. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013 Jan; 41(2):827-41. 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. PMID: 23221638; PMCID: PMC3553955.
      View in: PubMed   Mentions: 305     Fields:    Translation:HumansCells
    60. Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells. Cell Rep. 2012 Nov 29; 2(5):1411-24. Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi JH, Robertson KD. PMID: 23177624; PMCID: PMC3625945.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    61. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. BMC Syst Biol. 2012 Aug 16; 6:104. Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. PMID: 22897824; PMCID: PMC3464930.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    62. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. PLoS Genet. 2012; 8(4):e1002654. 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. PMID: 22570617; PMCID: PMC3343074.
      View in: PubMed   Mentions: 155     Fields:    Translation:HumansCells
    63. Mapping enhancer and promoter interactions. Cell Res. 2012 May; 22(5):789-90. Ernst J. PMID: 22453239; PMCID: PMC3343664.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    64. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012 Feb 28; 9(3):215-6. Ernst J, Kellis M. PMID: 22373907; PMCID: PMC3577932.
      View in: PubMed   Mentions: 1273     Fields:    Translation:HumansAnimalsCells
    65. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. 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. PMID: 22196736; PMCID: PMC3312319.
      View in: PubMed   Mentions: 203     Fields:    Translation:HumansCells
    66. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82. 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, Alföldi 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. PMID: 21993624; PMCID: PMC3207357.
      View in: PubMed   Mentions: 605     Fields:    Translation:HumansAnimals
    67. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct; 21(10):1659-71. 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. PMID: 21795386; PMCID: PMC3202283.
      View in: PubMed   Mentions: 94     Fields:    Translation:AnimalsCells
    68. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One. 2011; 6(7):e22401. 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. PMID: 21789257; PMCID: PMC3138787.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    69. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 05; 473(7345):43-9. 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. PMID: 21441907; PMCID: PMC3088773.
      View in: PubMed   Mentions: 1719     Fields:    Translation:HumansCells
    70. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5. 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. PMID: 21179089; PMCID: PMC3109908.
      View in: PubMed   Mentions: 532     Fields:    Translation:AnimalsCells
    71. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. 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. PMID: 21177974; PMCID: PMC3192495.
      View in: PubMed   Mentions: 723     Fields:    Translation:AnimalsCells
    72. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug; 28(8):817-25. Ernst J, Kellis M. PMID: 20657582; PMCID: PMC2919626.
      View in: PubMed   Mentions: 580     Fields:    Translation:HumansCells
    73. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res. 2010 Apr; 20(4):526-36. Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. PMID: 20219943; PMCID: PMC2847756.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    74. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PLoS One. 2009 Oct 15; 4(10):e7469. Ernst J, Ghanem L, Bar-Joseph Z, McNamara M, Brown J, Steinman RA. PMID: 19829692; PMCID: PMC2758590.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    75. A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol. 2008 Mar 28; 4(3):e1000044. Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. PMID: 18369434; PMCID: PMC2266799.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    76. Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol. 2008 Jan 23; 2:7. Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN. PMID: 18215292; PMCID: PMC2270259.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    77. Reconstructing dynamic regulatory maps. Mol Syst Biol. 2007; 3:74. Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. PMID: 17224918; PMCID: PMC1800355.
      View in: PubMed   Mentions: 97     Fields:    Translation:Animals
    78. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006 Apr 05; 7:191. Ernst J, Bar-Joseph Z. PMID: 16597342; PMCID: PMC1456994.
      View in: PubMed   Mentions: 781     Fields:    Translation:Cells
    79. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol. 2005 Dec; 23(12):1503-8. Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. PMID: 16333294.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    80. Clustering short time series gene expression data. Bioinformatics. 2005 Jun; 21 Suppl 1:i159-68. Ernst J, Nau GJ, Bar-Joseph Z. PMID: 15961453.
      View in: PubMed   Mentions: 173     Fields:    Translation:HumansCells
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