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Jason Ernst
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 2012
168172012
Integrative analysis of 111 reference human epigenomes
A Kundaje, W Meuleman, J Ernst, M Bilenky, A Yen, A Heravi-Moussavi, ...
Nature 518 (7539), 317-330, 2015
61242015
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
33042011
ChromHMM: automating chromatin-state discovery and characterization
J Ernst, M Kellis
Nature Methods 9 (3), 215-216, 2012
24752012
STEM: a tool for the analysis of short time series gene expression data
J Ernst, Z Bar-Joseph
BMC bioinformatics 7, 1-11, 2006
15072006
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS biology 9 (4), e1001046, 2011
14642011
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
12762011
Discovery and characterization of chromatin states for systematic annotation of the human genome
J Ernst, M Kellis
Nature Biotechnology 28, 817-825, 2010
12762010
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
10852010
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
9852011
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
9192014
Chromatin-state discovery and genome annotation with ChromHMM
J Ernst, M Kellis
Nature protocols 12 (12), 2478-2492, 2017
6952017
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
6062013
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
5762016
Clustering short time series gene expression data
J Ernst, GJ Nau, Z Bar-Joseph
Bioinformatics 21 (suppl_1), i159-i168, 2005
5722005
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
5132017
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
4202007
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
3942011
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
J Ernst, M Kellis
Nature biotechnology 33 (4), 364-376, 2015
3932015
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
3552013
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