Peer Reviewed Publications

(see also Google Scholar and PubMed)

Jump to year:[2014|2013|2012|2011|2010|2009|2008|2007|2006|2005]

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.

  • 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.
    Nat Neurosci, 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 2,000 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.
    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 and Reviews

  • 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.
    PhD thesis, Carnegie Mellon University, CMU-ML-08-110, 2008.