Jason Ernst, Ph.D.

Work Email Address:
jason.ernst@ucla.edu Mailing Address:
UCLA Biological Chemistry
615 Charles E Young Dr South
314 BSRB
Los Angeles, CA 90095

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Jason Ernst, Ph.D.

Department / Division Affiliations
Assistant Professor, Biological Chemistry
Member, ACCESS Program: Dept. of Biological Chemistry, ACCESS Program, Access Bioinformatics Home Area, Access Cell and Developmental Biology Home Area, Access Gene Regulation Home Area, Access Genetics and Genomics Home Area

Research Interest:

My research interests are in computational biology and bioinformatics. I develop and applying machine learning methods for the analysis of high-throughput experimental data to address problems in epigenomics and gene regulation


Jason joined the faculty at UCLA in the Department of Biological Chemistry in 2012. Prior to that, he was a postdoc in the Computational Biology Group led by Manolis Kellis in the Computer Science and Artificial Intelligence Laboratory at MIT and affiliated with the Broad Institute. In 2008, Jason completed a PhD advised by Ziv Bar-Joseph where he was part of the Systems Biology Group, Machine Learning Deparment, and School of Computer Science at Carnegie Mellon University. Jason also earned BS degrees in Computer Science and Mathematics from the University of Maryland College Park. He is a receipient of a NSF Postdoctoral Fellowship, a Siebel Scholarship, and a Goldwater scholarship.


Ernst J, Kellis M ChromHMM: automating chromatin-state discovery and characterization. Nature methods. 2012; 9(3): 215-6.
Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE. Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells. Cell. 2011; 147(7): 1628-39.
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. 2011; 478(7370): 476-82.
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 2011; 21(10): 1659-71.
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473(7345): 43-9.
The ENCODE Project Consortium. A User's Guide to the Encyclopedia of DNA Elements (ENCODE) . PLoS Biology. 2011; 9: e1001046.
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. 2011; 471(7339): 480-5.
Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O'Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar-Joseph Z, Morel PA. Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PloS One. 2011; 6(7): e22401.
The 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. 2010; 330(6012): 1787-97.
Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology. 2010; 28(8): 817-25.
Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Research. 2010; 20(4): 526-36.
Ernst J, Ghanem L, Bar-Joseph Z, McNamara M, Brown J, Steinman RA. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PloS One. 2009; 4(10): e7469.
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. 2008; 4(3): e1000044.
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. 2008; 2(3): 7.
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. 2007; 104: 12663-12668.
Ernst J, Vainas O, Harbison CT, Simon I, and Bar-Joseph Z. Reconstructing dynamic regulatory maps. Molecular Systems Biology. 2007; 3(3): 74.
Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006; 7(3): 191.
Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nature Biotechnology. 2005; 23(12): 1503-8.
Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics (Proceedings of ISMB 2005). 2005; 21 Suppl 1(12): i159-68.

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