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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
16483*2012
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium Integrative analysis coordination Kundaje ...
Nature 518 (7539), 317-330, 2015
5927*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
32482011
ChromHMM: automating chromatin-state discovery and characterization
J Ernst, M Kellis
Nature Methods 9 (3), 215-216, 2012
24222012
STEM: a tool for the analysis of short time series gene expression data
J Ernst, Z Bar-Joseph
BMC bioinformatics 7, 1-11, 2006
14442006
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS biology 9 (4), e1001046, 2011
14402011
Discovery and characterization of chromatin states for systematic annotation of the human genome
J Ernst, M Kellis
Nature Biotechnology 28, 817-825, 2010
12652010
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
12522011
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
10702010
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
9732011
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
8972014
Chromatin-state discovery and genome annotation with ChromHMM
J Ernst, M Kellis
Nature protocols 12 (12), 2478-2492, 2017
6522017
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
5982013
Clustering short time series gene expression data
J Ernst, GJ Nau, Z Bar-Joseph
Bioinformatics 21 (suppl_1), i159-i168, 2005
5692005
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
5622016
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
4862017
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
4152007
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
3912011
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
J Ernst, M Kellis
Nature biotechnology 33 (4), 364-376, 2015
3852015
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
3412013
Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma
JL Wiggs, BL Yaspan, MA Hauser, JH Kang, RR Allingham, LM Olson, ...
PLoS Genetics 8 (4), e1002654, 2012
3362012
Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization
M Denholtz, G Bonora, C Chronis, E Splinter, W De Laat, J Ernst, ...
Cell stem cell 13 (5), 602-616, 2013
2872013
RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
N Rajagopal, W Xie, Y Li, U Wagner, W Wang, J Stamatoyannopoulos, ...
PLOS Computational Biology 9 (3), e1002968, 2013
2442013
Reconstructing dynamic regulatory maps
J Ernst, O Vainas, CT Harbison, I Simon, Z Bar‐Joseph
Molecular systems biology 3 (1), 74, 2007
2402007
Deep-coverage whole genome sequences and blood lipids among 16,324 individuals
P Natarajan, GM Peloso, SM Zekavat, M Montasser, A Ganna, M Chaffin, ...
Nature communications 9 (1), 3391, 2018
1632018
Universal DNA methylation age across mammalian tissues
AT Lu, Z Fei, A Haghani, TR Robeck, JA Zoller, CZ Li, R Lowe, Q Yan, ...
Nature aging, 1-23, 2023
1602023
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions
J Ernst, A Melnikov, X Zhang, L Wang, P Rogov, TS Mikkelsen, M Kellis
Nature biotechnology 34 (11), 1180-1190, 2016
1592016
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
W Wu, Y Cheng, CA Keller, J Ernst, SA Kumar, T Mishra, C Morrissey, ...
Genome research 21 (10), 1659-1671, 2011
1472011
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data
MH Schulz, WE Devanny, A Gitter, S Zhong, J Ernst, Z Bar-Joseph
BMC Systems Biology 6 (1), 104, 2012
1412012
A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli
J Ernst, QK Beg, KA Kay, G Balázsi, ZN Oltvai, Z Bar-Joseph
PLoS computational biology 4 (3), e1000044, 2008
1382008
Integrating multiple evidence sources to predict transcription factor binding in the human genome
J Ernst, HL Plasterer, I Simon, Z Bar-Joseph
Genome research 20 (4), 526-536, 2010
1332010
Impact of the solvent capacity constraint on E. coli metabolism
A Vazquez, QK Beg, MA de Menezes, J Ernst, Z Bar-Joseph, AL Barabasi, ...
BMC systems biology 2 (1), 7, 2008
1282008
A mammalian methylation array for profiling methylation levels at conserved sequences
A Arneson, A Haghani, MJ Thompson, M Pellegrini, SB Kwon, H Vu, ...
Nature communications 13 (1), 783, 2022
1242022
Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells
B Jin, J Ernst, RL Tiedemann, H Xu, S Sureshchandra, M Kellis, S Dalton, ...
Cell reports 2 (5), 1411-1424, 2012
1232012
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
J Ernst, M Kellis
Genome research 23 (7), 1142-1154, 2013
1162013
Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition
G Carraro, J Langerman, S Sabri, Z Lorenzana, A Purkayastha, G Zhang, ...
Nature medicine 27 (5), 806-814, 2021
1102021
Analysis of cardiomyocyte clonal expansion during mouse heart development and injury
KI Sereti, NB Nguyen, P Kamran, P Zhao, S Ranjbarvaziri, S Park, S Sabri, ...
Nature communications 9 (1), 754, 2018
1002018
Deep coverage whole genome sequences and plasma lipoprotein (a) in individuals of European and African ancestries
SM Zekavat, S Ruotsalainen, RE Handsaker, M Alver, J Bloom, T Poterba, ...
Nature communications 9 (1), 2606, 2018
932018
Systematic epigenomic analysis reveals chromatin states associated with melanoma progression
P Fiziev, KC Akdemir, JP Miller, EZ Keung, NS Samant, S Sharma, ...
Cell reports 19 (4), 875-889, 2017
882017
Dual Roles of RNF2 in Melanoma Progression
K Rai, KC Akdemir, LN Kwong, P Fiziev, CJ Wu, EZ Keung, S Sharma, ...
Cancer discovery, CD-15-0493, 2015
64*2015
Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
A Mortazavi, S Pepke, C Jansen, GK Marinov, J Ernst, M Kellis, ...
Genome research 23 (12), 2136-2148, 2013
502013
Universal annotation of the human genome through integration of over a thousand epigenomic datasets
H Vu, J Ernst
Genome biology 23, 1-37, 2022
472022
Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes
GB Ferguson, B Van Handel, M Bay, P Fiziev, T Org, S Lee, R Shkhyan, ...
Nature communications 9 (1), 3634, 2018
472018
Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies
N Rajagopal, J Ernst, P Ray, J Wu, M Zhang, M Kellis, B Ren
G3: Genes, Genomes, Genetics 4 (11), 2051-2063, 2014
452014
DNA methylation networks underlying mammalian traits
A Haghani, CZ Li, TR Robeck, J Zhang, AT Lu, J Ablaeva, ...
Science 381 (6658), eabq5693, 2023
41*2023
Evidence of reduced recombination rate in human regulatory domains
Y Liu, A Sarkar, P Kheradpour, J Ernst, M Kellis
Genome biology 18, 1-11, 2017
402017
Epigenetic clock and methylation studies in the rhesus macaque
S Horvath, JA Zoller, A Haghani, AJ Jasinska, K Raj, CE Breeze, J Ernst, ...
GeroScience 43, 2441-2453, 2021
382021
Circadian variation of the pancreatic islet transcriptome
K Rakshit, J Qian, J Ernst, AV Matveyenko
Physiological Genomics 48 (9), 677-687, 2016
382016
Combined static and dynamic analysis for determining the quality of time-series expression profiles
I Simon, Z Siegfried, J Ernst, Z Bar-Joseph
Nature biotechnology 23 (12), 1503-1508, 2005
362005
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque
G Zinman, R Brower-Sinning, CH Emeche, J Ernst, GTW Huang, ...
PloS one 6 (7), e22401, 2011
352011
Leveraging allelic imbalance to refine fine-mapping for eQTL studies
J Zou, F Hormozdiari, B Jew, SE Castel, T Lappalainen, J Ernst, JH Sul, ...
PLoS genetics 15 (12), e1008481, 2019
27*2019
Marginal contribution feature importance-an axiomatic approach for explaining data
A Catav, B Fu, Y Zoabi, ALW Meilik, N Shomron, J Ernst, S Sankararaman, ...
International Conference on Machine Learning, 1324-1335, 2021
24*2021
Epigenetic clock and methylation studies in vervet monkeys
AJ Jasinska, A Haghani, JA Zoller, CZ Li, A Arneson, J Ernst, K Kavanagh, ...
GeroScience, 1-19, 2022
212022
Systematic discovery of conservation states for single-nucleotide annotation of the human genome
A Arneson, J Ernst
Communications biology 2 (1), 248, 2019
202019
Using genomic annotations increases statistical power to detect eGenes
D Duong, J Zou, F Hormozdiari, JH Sul, J Ernst, B Han, E Eskin
Bioinformatics 32 (12), i156-i163, 2016
202016
Epigenetic predictors of maximum lifespan and other life history traits in mammals
CZ Li, A Haghani, TR Robeck, D Villar, AT Lu, J Zhang, CG Faulkes, H Vu, ...
BioRxiv, 2021.05. 16.444078, 2021
162021
IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability
J Ernst, L Ghanem, Z Bar-Joseph, M McNamara, J Brown, RA Steinman
PLoS One 4 (10), e7469, 2009
162009
Learning a genome-wide score of human-mouse conservation at the functional genomics level
SB Kwon, J Ernst
Nature Communications 12 (1), 2495, 2021
142021
Pan-primate studies of age and sex
S Horvath, A Haghani, JA Zoller, AT Lu, J Ernst, M Pellegrini, AJ Jasinska, ...
GeroScience 45 (6), 3187-3209, 2023
11*2023
ChromTime: modeling spatio-temporal dynamics of chromatin marks
P Fiziev, J Ernst
Genome biology 19, 1-18, 2018
112018
Mapping enhancer and promoter interactions
J Ernst
Cell Research 22 (5), 789-790, 2012
112012
Integration of evidence across human and model organism studies: A meeting report
RHC Palmer, EC Johnson, H Won, R Polimanti, M Kapoor, A Chitre, ...
Genes, Brain and Behavior 20 (6), e12738, 2021
102021
STAT3 promotes a youthful epigenetic state in articular chondrocytes
A Sarkar, NQ Liu, J Magallanes, J Tassey, S Lee, R Shkhyan, Y Lee, J Lu, ...
Aging Cell 22 (2), e13773, 2023
92023
An integrative approach for fine-mapping chromatin interactions
A Jaroszewicz, J Ernst
Bioinformatics 36 (6), 1704-1711, 2020
82020
Implications of the first complete human genome assembly
C Alkan, L Carbone, M Dennis, J Ernst, G Evrony, S Girirajan, DCY Leung, ...
Genome Research, 2022
62022
Transcriptional, electrophysiological, and metabolic characterizations of hESC-derived first and second heart fields demonstrate a potential role of TBX5 in cardiomyocyte …
A Pezhouman, NB Nguyen, AJ Sercel, TL Nguyen, A Daraei, S Sabri, ...
Frontiers in Cell and Developmental Biology 9, 787684, 2021
52021
Computational methods for analyzing and modeling gene regulation dynamics
J Ernst
Carnegie Mellon University, 2008
52008
Genome-wide regulatory model from MPRA data predicts functional regions, eQTLs, and GWAS hits
Y Li, AH Shi, R Tewhey, PC Sabeti, J Ernst, M Kellis
Biorxiv, 110171, 2017
42017
ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation
A Arneson, B Felsheim, J Chien, J Ernst
NAR Genomics and Bioinformatics 2 (4), lqaa104, 2020
32020
Universal chromatin state annotation of the mouse genome
H Vu, J Ernst
Genome biology 24 (1), 153, 2023
22023
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome
SB Kwon, J Ernst
Communications Biology 4 (1), 698, 2021
22021
Investigating enhancer evolution with massively parallel reporter assays
SB Kwon, J Ernst
Genome biology 19, 1-3, 2018
22018
ChromGene: gene-based modeling of epigenomic data
A Jaroszewicz, J Ernst
Genome Biology 24 (1), 203, 2023
12023
Epigenetic predictors of species maximum lifespan and other life history traits in mammals
CZ Li, A Haghani, Q Yan, AT Lu, J Zhang, Z Fei, J Ernst, X Yang, ...
bioRxiv, 2023.11. 02.565286, 2023
12023
Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation
M Nazim, CH Lin, AC Feng, KH Yeom, M Li, AE Daly, X Tan, H Vu, J Ernst, ...
bioRxiv, 2023.09. 10.556946, 2023
12023
A framework for group-wise summarization and comparison of chromatin state annotations
H Vu, Z Koch, P Fiziev, J Ernst
Bioinformatics 39 (1), btac722, 2023
12023
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations
O Grujic, TN Phung, SB Kwon, A Arneson, Y Lee, KE Lohmueller, J Ernst
Nature communications 11 (1), 6168, 2020
12020
Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence and sex information
R Li, J Ernst
bioRxiv, 2024.03. 20.585624, 2024
2024
Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior
PB Chen, R Chen, NRS LaPierre, Z Chen, J Mefford, E Marcus, M Heffel, ...
bioRxiv, 2024.01. 03.574060, 2024
2024
Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription
J Flint, MG Heffel, Z Chen, J Mefford, E Marcus, PB Chen, J Ernst, C Luo
Cell Genomics 3 (12), 2023
2023
The Impact of Genomic Variation on Function (IGVF) Consortium
I Consortium
arXiv preprint arXiv:2307.13708, 2023
2023
Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types
TU Dincer, J Ernst
bioRxiv, 2023
2023
Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.
E Maciejewski, S Horvath, J Ernst
bioRxiv, 2023.11. 26.568769, 2023
2023
Chromatin state modeling across individuals reveals global patterns of histone modifications
J Zou, J Ernst
bioRxiv, 2022.08. 02.502571, 2022
2022
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