Jason Ernst, Ph.D.

Jaroszewicz Artur, Ernst Jason   An integrative approach for fine-mapping chromatin interactions Bioinformatics (Oxford, England), 2020; 36(6): 1704-1711.

Zou Jennifer, Hormozdiari Farhad, Jew Brandon, Castel Stephane E, Lappalainen Tuuli, Ernst Jason, Sul Jae Hoon, Eskin Eleazar   Leveraging allelic imbalance to refine fine-mapping for eQTL studies PLoS genetics, 2019; 15(12): e1008481.

Arneson Adriana, Ernst Jason   Systematic discovery of conservation states for single-nucleotide annotation of the human genome Communications biology, 2019; 2(12): 248.

Ferguson Gabriel B, Van Handel Ben, Bay Maxwell, Fiziev Petko, Org Tonis, Lee Siyoung, Shkhyan Ruzanna, Banks Nicholas W, Scheinberg Mila, Wu Ling, Saitta Biagio, Elphingstone Joseph, Larson A Noelle, Riester Scott M, Pyle April D, Bernthal Nicholas M, Mikkola Hanna Ka, Ernst Jason, van Wijnen Andre J, Bonaguidi Michael, Evseenko Denis   Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes Nature communications, 2018; 9(1): 3634.

Fiziev Petko, Ernst Jason   ChromTime: modeling spatio-temporal dynamics of chromatin marks Genome biology, 2018; 19(1): 109.

Natarajan Pradeep, Peloso Gina M, Zekavat Seyedeh Maryam, Montasser May, Ganna Andrea, Chaffin Mark, Khera Amit V, Zhou Wei, Bloom Jonathan M, Engreitz Jesse M, Ernst Jason, O’Connell Jeffrey R, Ruotsalainen Sanni E, Alver Maris, Manichaikul Ani, Johnson W Craig, Perry James A, Poterba Timothy, Seed Cotton, Surakka Ida L, Esko Tonu, Ripatti Samuli, Salomaa Veikko, Correa Adolfo, Vasan Ramachandran S, Kellis Manolis, Neale Benjamin M, Lander Eric S, Abecasis Goncalo, Mitchell Braxton, Rich Stephen S, Wilson James G, Cupples L Adrienne, Rotter Jerome I, Willer Cristen J, Kathiresan Sekar, Kathiresan Sekar   Deep-coverage whole genome sequences and blood lipids among 16,324 individuals Nature communications, 2018; 9(1): 3391.

Ernst Jason, Kellis Manolis   Chromatin-state discovery and genome annotation with ChromHMM Nature protocols, 2017; 12(12): 2478-2492.

Fiziev Petko, Akdemir Kadir C, Miller John P, Keung Emily Z, Samant Neha S, Sharma Sneha, Natale Christopher A, Terranova Christopher J, Maitituoheti Mayinuer, Amin Samirkumar B, Martinez-Ledesma Emmanuel, Dhamdhere Mayura, Axelrad Jacob B, Shah Amiksha, Cheng Christine S, Mahadeshwar Harshad, Seth Sahil, Barton Michelle C, Protopopov Alexei, Tsai Kenneth Y, Davies Michael A, Garcia Benjamin A, Amit Ido, Chin Lynda, Ernst Jason, Rai Kunal   Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression Cell reports, 2017; 19(4): 875-889.

Chronis Constantinos, Fiziev Petko, Papp Bernadett, Butz Stefan, Bonora Giancarlo, Sabri Shan, Ernst Jason, Plath Kathrin   Cooperative Binding of Transcription Factors Orchestrates Reprogramming Cell, 2017; 168(3): 442-459.e20.

Ernst Jason, Melnikov Alexandre, Zhang Xiaolan, Wang Li, Rogov Peter, Mikkelsen Tarjei S, Kellis Manolis   Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions Nature biotechnology, 2016; 34(11): 1180-1190.

Won Hyejung, de la Torre-Ubieta Luis, Stein Jason L, Parikshak Neelroop N, Huang Jerry, Opland Carli K, Gandal Michael J, Sutton Gavin J, Hormozdiari Farhad, Lu Daning, Lee Changhoon, Eskin Eleazar, Voineagu Irina, Ernst Jason, Geschwind Daniel H   Chromosome conformation elucidates regulatory relationships in developing human brain Nature, 2016; 538(7626): 523-527.

Ernst Jason, Kellis Manolis   Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues Nature biotechnology, 2015; 33(4): 364-76.

Ernst Jason, Kellis Manolis   Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types Genome research, 2013; 23(7): 1142-54.

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.