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 | 3248 | 2011 |
ChromHMM: automating chromatin-state discovery and characterization J Ernst, M Kellis Nature Methods 9 (3), 215-216, 2012 | 2422 | 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 | 1444 | 2006 |
A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011 | 1440 | 2011 |
Discovery and characterization of chromatin states for systematic annotation of the human genome J Ernst, M Kellis Nature Biotechnology 28, 817-825, 2010 | 1265 | 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 | 1252 | 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 | 1070 | 2010 |
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 | 973 | 2011 |
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 | 897 | 2014 |
Chromatin-state discovery and genome annotation with ChromHMM J Ernst, M Kellis Nature protocols 12 (12), 2478-2492, 2017 | 652 | 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 | 598 | 2013 |
Clustering short time series gene expression data J Ernst, GJ Nau, Z Bar-Joseph Bioinformatics 21 (suppl_1), i159-i168, 2005 | 569 | 2005 |
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 | 562 | 2016 |
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 | 486 | 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 | 415 | 2007 |
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 | 391 | 2011 |
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues J Ernst, M Kellis Nature biotechnology 33 (4), 364-376, 2015 | 385 | 2015 |
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 | 341 | 2013 |
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 | 336 | 2012 |
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 | 287 | 2013 |
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 | 244 | 2013 |
Reconstructing dynamic regulatory maps J Ernst, O Vainas, CT Harbison, I Simon, Z Bar‐Joseph Molecular systems biology 3 (1), 74, 2007 | 240 | 2007 |
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 | 163 | 2018 |
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 | 160 | 2023 |
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 | 159 | 2016 |
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 | 147 | 2011 |
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 | 141 | 2012 |
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 | 138 | 2008 |
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 | 133 | 2010 |
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 | 128 | 2008 |
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 | 124 | 2022 |
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 | 123 | 2012 |
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 | 116 | 2013 |
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 | 110 | 2021 |
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 | 100 | 2018 |
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 | 93 | 2018 |
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 | 88 | 2017 |
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 | 50 | 2013 |
Universal annotation of the human genome through integration of over a thousand epigenomic datasets H Vu, J Ernst Genome biology 23, 1-37, 2022 | 47 | 2022 |
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 | 47 | 2018 |
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 | 45 | 2014 |
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 | 40 | 2017 |
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 | 38 | 2021 |
Circadian variation of the pancreatic islet transcriptome K Rakshit, J Qian, J Ernst, AV Matveyenko Physiological Genomics 48 (9), 677-687, 2016 | 38 | 2016 |
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 | 36 | 2005 |
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 | 35 | 2011 |
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 | 21 | 2022 |
Systematic discovery of conservation states for single-nucleotide annotation of the human genome A Arneson, J Ernst Communications biology 2 (1), 248, 2019 | 20 | 2019 |
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 | 20 | 2016 |
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 | 16 | 2021 |
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 | 16 | 2009 |
Learning a genome-wide score of human-mouse conservation at the functional genomics level SB Kwon, J Ernst Nature Communications 12 (1), 2495, 2021 | 14 | 2021 |
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 | 11 | 2018 |
Mapping enhancer and promoter interactions J Ernst Cell Research 22 (5), 789-790, 2012 | 11 | 2012 |
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 | 10 | 2021 |
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 | 9 | 2023 |
An integrative approach for fine-mapping chromatin interactions A Jaroszewicz, J Ernst Bioinformatics 36 (6), 1704-1711, 2020 | 8 | 2020 |
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 | 6 | 2022 |
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 | 5 | 2021 |
Computational methods for analyzing and modeling gene regulation dynamics J Ernst Carnegie Mellon University, 2008 | 5 | 2008 |
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 | 4 | 2017 |
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 | 3 | 2020 |
Universal chromatin state annotation of the mouse genome H Vu, J Ernst Genome biology 24 (1), 153, 2023 | 2 | 2023 |
Single-nucleotide conservation state annotation of the SARS-CoV-2 genome SB Kwon, J Ernst Communications Biology 4 (1), 698, 2021 | 2 | 2021 |
Investigating enhancer evolution with massively parallel reporter assays SB Kwon, J Ernst Genome biology 19, 1-3, 2018 | 2 | 2018 |
ChromGene: gene-based modeling of epigenomic data A Jaroszewicz, J Ernst Genome Biology 24 (1), 203, 2023 | 1 | 2023 |
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 | 1 | 2023 |
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 | 1 | 2023 |
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 | 1 | 2023 |
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 | 1 | 2020 |
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 |