Jason Ernst

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Manolis KellisProfessor of Computer Science, MIT and Broad InstituteVerified email at mit.edu
Ziv Bar-JosephProfessor of Computational Biology and Machine Learning, School of Computer Science, Carnegie Mellon UniversityVerified email at andrew.cmu.edu
Pouya KheradpourVerily Life SciencesVerified email at mit.edu
Anshul KundajeAssociate Professor, Dept. of Genetics, Dept. of Computer Science, Stanford UniversityVerified email at stanford.edu
Tarjei S. MikkelsenVerified email at alum.mit.edu
Petko (Pete) FizievIllumina Artificial Intelligence LabVerified email at illumina.com
Charles B. EpsteinThe Broad InstituteVerified email at broadinstitute.org
Bradley BernsteinProfessor of Pathology, Harvard UniversityVerified email at broadinstitute.org
matteo pellegriniuniversity of california Los AngelesVerified email at mcdb.ucla.edu
Eleazar EskinUniversity of California, Los AngelesVerified email at cs.ucla.edu
Lucas D. WardAlnylam PharmaceuticalsVerified email at alnylam.com
Manching KuGenentechVerified email at gene.com
Ross C. HardisonProfessor Emeritus of Biochemistry and Molecular Biology, The Pennsylvania State UniversityVerified email at psu.edu
Qasim BegMicrobiology Lecturer Boston UniversityVerified email at bu.edu
Zoltan N. OltvaiUniversity of RochesterVerified email at urmc.rochester.edu
constantinos chronisAssistant Professor at UICVerified email at uic.edu
Bing Ren, Ph.D.University of California, San DiegoVerified email at ucsd.edu
Ewan BirneyDirector, EMBL-EBIVerified email at ebi.ac.uk
Michael M. HoffmanChair and Senior Scientist, University Health Network/Associate Professor, University of TorontoVerified email at utoronto.ca
William Stafford NobleProfessor of Genome Sciences, University of WashingtonVerified email at uw.edu

Jason Ernst

Professor, University of California, Los Angeles

Verified email at ucla.edu - Homepage

Computational Biology Bioinformatics Genomics Epigenomics Machine Learning


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 2012	17661	2012
Integrative analysis of 111 reference human epigenomes Roadmap Epigenomics Consortium Integrative analysis coordination Kundaje ... Nature 518 (7539), 317-330, 2015	6526*	2015
Mapping and analysis of chromatin state dynamics in nine human cell types J Ernst, P Kheradpour, TS Mikkelsen, N Shoresh, LD Ward, CB Epstein, ... Nature 473 (7345), 43-49, 2011	3388	2011
ChromHMM: automating chromatin-state discovery and characterization J Ernst, M Kellis Nature Methods 9 (3), 215-216, 2012	2642	2012
STEM: a tool for the analysis of short time series gene expression data J Ernst, Z Bar-Joseph BMC bioinformatics 7, 1-11, 2006	1608	2006
A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011	1499	2011
Discovery and characterization of chromatin states for systematic annotation of the human genome J Ernst, M Kellis Nature Biotechnology 28, 817-825, 2010	1319	2010
A high-resolution map of human evolutionary constraint using 29 mammals K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ... Nature 478 (7370), 476-482, 2011	1304	2011
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE modENCODE Consortium, S Roy, J Ernst, PV Kharchenko, P Kheradpour, ... Science 330 (6012), 1787-1797, 2010	1113	2010
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci PL De Jager, G Srivastava, K Lunnon, J Burgess, LC Schalkwyk, L Yu, ... Nature neuroscience 17 (9), 1156-1163, 2014	1007	2014
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster PV Kharchenko, AA Alekseyenko, YB Schwartz, A Minoda, NC Riddle, ... Nature 471 (7339), 480-485, 2011	1007	2011
Chromatin-state discovery and genome annotation with ChromHMM J Ernst, M Kellis Nature protocols 12 (12), 2478-2492, 2017	810	2017
Integrative annotation of chromatin elements from ENCODE data MM Hoffman, J Ernst, SP Wilder, A Kundaje, RS Harris, M Libbrecht, ... Nucleic acids research, gks1284, 2013	636	2013
Chromosome conformation elucidates regulatory relationships in developing human brain H Won, L de La Torre-Ubieta, JL Stein, NN Parikshak, J Huang, ... Nature 538 (7626), 523-527, 2016	617	2016
Clustering short time series gene expression data J Ernst, GJ Nau, Z Bar-Joseph Bioinformatics 21 (suppl_1), i159-i168, 2005	586	2005
Cooperative binding of transcription factors orchestrates reprogramming C Chronis, P Fiziev, B Papp, S Butz, G Bonora, S Sabri, J Ernst, K Plath Cell 168 (3), 442-459. e20, 2017	553	2017
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity QK Beg, A Vazquez, J Ernst, MA de Menezes, Z Bar-Joseph, AL Barabási, ... Proceedings of the National Academy of Sciences 104 (31), 12663-12668, 2007	440	2007
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues J Ernst, M Kellis Nature biotechnology 33 (4), 364-376, 2015	422	2015
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells O Ram, A Goren, I Amit, N Shoresh, N Yosef, J Ernst, M Kellis, M Gymrek, ... Cell 147 (7), 1628-1639, 2011	403	2011
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay P Kheradpour, J Ernst, A Melnikov, P Rogov, L Wang, X Zhang, J Alston, ... Genome research 23 (5), 800-811, 2013	364	2013

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