Jason Ernst

Title(s)Associate Professor, Biological Chemistry
SchoolMedicine
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    Other Positions
    Title(s)Associate Professor, Computational Medicine


    Collapse Research 
    Collapse Research Activities and Funding
    Deciphering the Relationship between Substance Use and Psychiatric Disorders from Whole Genome Sequencing Data
    NIH DP1DA044371Sep 1, 2017 - Jul 31, 2022
    Role: Principal Investigator

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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. 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:
    2. 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. Epigenetic clock and methylation studies in vervet monkeys. Geroscience. 2021 Sep 30. 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.
      View in: PubMed   Mentions:    Fields:    
    4. Correction to 'ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation'. NAR Genom Bioinform. 2021 Sep; 3(3):lqab084. Arneson A, Felsheim B, Chien J, Ernst J. PMID: 34532708; PMCID: PMC8439296.
      View in: PubMed   Mentions:
    5. 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:
    6. 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:
    7. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    8. 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:
    9. 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: 1     Fields:    
    10. 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:
    11. 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:
    12. 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:
    13. 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:
    14. 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:
    15. 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: 7     Fields:    Translation:HumansCells
    16. 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:
    17. 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: 9     Fields:    Translation:HumansAnimalsCells
    18. 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: 40     Fields:    Translation:HumansCells
    19. 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:    
    20. 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: 1     Fields:    Translation:HumansAnimalsCells
    21. 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: 1     Fields:    Translation:Cells
    22. 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: 24     Fields:    Translation:Humans
    23. 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: 34     Fields:    Translation:AnimalsCells
    24. 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: 125     Fields:    Translation:HumansAnimalsCells
    25. 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: 11     Fields:    Translation:HumansAnimalsCells
    26. 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: 26     Fields:    Translation:HumansCells
    27. 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: 143     Fields:    Translation:AnimalsCells
    28. 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: 177     Fields:    Translation:HumansCells
    29. 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: 43     Fields:    Translation:HumansCells
    30. 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: 17     Fields:    Translation:AnimalsCells
    31. 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: 6     Fields:    
    32. 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: 2079     Fields:    Translation:HumansCells
    33. 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: 140     Fields:    Translation:Humans
    34. 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: 294     Fields:    Translation:HumansCells
    35. 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: 13     Fields:    Translation:HumansAnimalsCells
    36. 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: 25     Fields:    Translation:HumansCells
    37. 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: 103     Fields:    Translation:AnimalsCells
    38. 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: 52     Fields:    Translation:HumansCells
    39. 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: 120     Fields:    Translation:HumansCells
    40. 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: 85     Fields:    Translation:HumansCells
    41. 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: 230     Fields:    Translation:HumansCells
    42. 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: 52     Fields:    Translation:HumansCells
    43. 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: 133     Fields:    Translation:HumansCells
    44. Mapping enhancer and promoter interactions. Cell Res. 2012 May; 22(5):789-90. Ernst J. PMID: 22453239; PMCID: PMC3343664.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    45. 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: 855     Fields:    Translation:HumansAnimalsCells
    46. 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: 180     Fields:    Translation:HumansCells
    47. 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: 479     Fields:    Translation:HumansAnimals
    48. 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: 85     Fields:    Translation:AnimalsCells
    49. 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: 1455     Fields:    Translation:HumansCells
    50. 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: 439     Fields:    Translation:AnimalsCells
    51. 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: 607     Fields:    Translation:AnimalsCells
    52. 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: 489     Fields:    Translation:HumansCells
    53. 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: 60     Fields:    Translation:HumansCells
    54. 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.
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    55. 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: 91     Fields:    Translation:Animals
    56. 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: 449     Fields:    Translation:Cells
    57. 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
    58. 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: 142     Fields:    Translation:HumansCells
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