Jason Ernst - Publications

Affiliations: 
Computer Science University of California, Los Angeles, Los Angeles, CA 
Area:
computational biology; bioinformatics; machine learning

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Vu H, Ernst J. Universal annotation of the human genome through integration of over a thousand epigenomic datasets. Genome Biology. 23: 9. PMID 34991667 DOI: 10.1186/s13059-021-02572-z  0.355
2021 Kwon SB, Ernst J. Learning a genome-wide score of human-mouse conservation at the functional genomics level. Nature Communications. 12: 2495. PMID 33941776 DOI: 10.1038/s41467-021-22653-8  0.391
2020 Arneson A, Felsheim B, Chien J, Ernst J. ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation. Nar Genomics and Bioinformatics. 2: lqaa104. PMID 33543124 DOI: 10.1093/nargab/lqaa104  0.351
2020 Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J. Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. Nature Communications. 11: 6168. PMID 33268804 DOI: 10.1038/s41467-020-19962-9  0.364
2020 Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, et al. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 11: 1715. PMID 32238811 DOI: 10.1038/S41467-020-15236-6  0.556
2019 Arneson A, Ernst J. Systematic discovery of conservation states for single-nucleotide annotation of the human genome. Communications Biology. 2: 248. PMID 31925086 DOI: 10.1038/s42003-019-0488-1  0.369
2019 Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E. Leveraging allelic imbalance to refine fine-mapping for eQTL studies. Plos Genetics. 15: e1008481. PMID 31834882 DOI: 10.1371/Journal.Pgen.1008481  0.47
2019 Jaroszewicz A, Ernst J. An Integrative Approach for Fine-Mapping Chromatin Interactions. Bioinformatics (Oxford, England). PMID 31742318 DOI: 10.1093/Bioinformatics/Btz843  0.403
2019 Arneson A, Ernst J. Systematic discovery of conservation states for single-nucleotide annotation of the human genome. Communications Biology. 2: 248. PMID 31286065 DOI: 10.1038/s42003-019-0488-1  0.369
2018 Ferguson GB, Van Handel B, Bay M, Fiziev P, Org T, Lee S, Shkhyan R, Banks NW, Scheinberg M, Wu L, Saitta B, Elphingstone J, Larson AN, Riester SM, Pyle AD, ... ... Ernst J, et al. Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes. Nature Communications. 9: 3634. PMID 30194383 DOI: 10.1038/S41467-018-05573-Y  0.43
2018 Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, et al. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 9: 3493. PMID 30140049 DOI: 10.1038/s41467-018-05975-y  0.473
2018 Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, et al. Deep-coverage whole genome sequences and blood lipids among 16,324 individuals. Nature Communications. 9: 3391. PMID 30140000 DOI: 10.1038/S41467-018-05747-8  0.631
2018 Kwon SB, Ernst J. Investigating enhancer evolution with massively parallel reporter assays. Genome Biology. 19: 114. PMID 30107810 DOI: 10.1186/S13059-018-1502-5  0.368
2018 Fiziev P, Ernst J. ChromTime: modeling spatio-temporal dynamics of chromatin marks. Genome Biology. 19: 109. PMID 30097049 DOI: 10.1186/S13059-018-1485-2  0.382
2018 Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, et al. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries. Nature Communications. 9: 2606. PMID 29973585 DOI: 10.1038/S41467-018-04668-W  0.554
2017 Ernst J, Kellis M. Chromatin-state discovery and genome annotation with ChromHMM. Nature Protocols. 12: 2478-2492. PMID 29120462 DOI: 10.1038/Nprot.2017.124  0.656
2017 Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M. Evidence of reduced recombination rate in human regulatory domains. Genome Biology. 18: 193. PMID 29058599 DOI: 10.1186/S13059-017-1308-X  0.777
2017 Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, ... ... Ernst J, et al. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Reports. 19: 875-889. PMID 28445736 DOI: 10.1016/J.Celrep.2017.03.078  0.419
2017 Chronis C, Fiziev P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K. Cooperative Binding of Transcription Factors Orchestrates Reprogramming. Cell. PMID 28111071 DOI: 10.1016/J.Cell.2016.12.016  0.372
2016 Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DH. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. PMID 27760116 DOI: 10.1038/Nature19847  0.466
2016 Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Nature Biotechnology. PMID 27701403 DOI: 10.1038/nbt.3678  0.607
2016 Rakshit K, Qian J, Ernst J, Matveyenko A. Circadian variation of the pancreatic islet transcriptome. Physiological Genomics. physiolgenomics.0001. PMID 27495157 DOI: 10.1152/Physiolgenomics.00019.2016  0.388
2016 Duong D, Zou J, Hormozdiari F, Sul JH, Ernst J, Han B, Eskin E. Using genomic annotations increases statistical power to detect eGenes. Bioinformatics (Oxford, England). 32: i156-i163. PMID 27307612 DOI: 10.1093/Bioinformatics/Btw272  0.427
2015 Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, ... ... Ernst J, et al. Dual Roles of RNF2 in Melanoma Progression. Cancer Discovery. PMID 26450788 DOI: 10.1158/2159-8290.Cd-15-0493  0.435
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.606
2015 Ernst J, Kellis M. Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nature Biotechnology. 33: 364-76. PMID 25690853 DOI: 10.1038/Nbt.3157  0.62
2014 De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nature Neuroscience. 17: 1156-63. PMID 25129075 DOI: 10.1038/Nn.3786  0.566
2014 Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda, Md.). 4: 2051-63. PMID 25122670 DOI: 10.1534/G3.114.013565  0.617
2013 Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Research. 23: 2136-48. PMID 24170599 DOI: 10.1101/Gr.158261.113  0.637
2013 Denholtz M, Bonora G, Chronis C, Splinter E, de Laat W, Ernst J, Pellegrini M, Plath K. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell. 13: 602-16. PMID 24035354 DOI: 10.1016/J.Stem.2013.08.013  0.459
2013 Ernst J, Kellis M. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Research. 23: 1142-54. PMID 23595227 DOI: 10.1101/Gr.144840.112  0.643
2013 Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B. RFECS: a random-forest based algorithm for enhancer identification from chromatin state. Plos Computational Biology. 9: e1002968. PMID 23526891 DOI: 10.1371/Journal.Pcbi.1002968  0.644
2013 Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Research. 23: 800-11. PMID 23512712 DOI: 10.1101/Gr.144899.112  0.813
2013 Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/Nar/Gks1284  0.708
2012 Jin B, Ernst J, Tiedemann RL, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi JH, Robertson KD. Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells. Cell Reports. 2: 1411-24. PMID 23177624 DOI: 10.1016/J.Celrep.2012.10.017  0.617
2012 Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. Bmc Systems Biology. 6: 104. PMID 22897824 DOI: 10.1186/1752-0509-6-104  0.723
2012 Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, ... ... Ernst J, et al. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. Plos Genetics. 8: e1002654. PMID 22570617 DOI: 10.1371/Journal.Pgen.1002654  0.61
2012 Ernst J. Mapping enhancer and promoter interactions. Cell Research. 22: 789-90. PMID 22453239 DOI: 10.1038/Cr.2012.49  0.379
2012 Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nature Methods. 9: 215-6. PMID 22373907 DOI: 10.1038/Nmeth.1906  0.616
2011 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, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 147: 1628-39. PMID 22196736 DOI: 10.1016/J.Cell.2011.09.057  0.623
2011 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, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  0.777
2011 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, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111  0.63
2011 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. 473: 43-9. PMID 21441907 DOI: 10.1038/Nature09906  0.823
2011 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, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725  0.685
2010 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, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.734
2010 Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology. 28: 817-25. PMID 20657582 DOI: 10.1038/Nbt.1662  0.704
2010 Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Research. 20: 526-36. PMID 20219943 DOI: 10.1101/Gr.096305.109  0.617
2009 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. 4: e7469. PMID 19829692 DOI: 10.1371/Journal.Pone.0007469  0.554
2008 Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. Plos Computational Biology. 4: e1000044. PMID 18369434 DOI: 10.1371/Journal.Pcbi.1000044  0.633
2008 Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN. Impact of the solvent capacity constraint on E. coli metabolism. Bmc Systems Biology. 2: 7. PMID 18215292 DOI: 10.1186/1752-0509-2-7  0.547
2008 Ernst J, Bar-Joseph Z, Ghanem L, Steinman RA. IL-3 Coordination of the Myeloblast Transcriptome by Modulating mRNA Stability Blood. 112: 3863-3863. DOI: 10.1182/Blood.V112.11.3863.3863  0.515
2007 Beg QK, Vazquez A, Ernst J, Menezes MAd, Bar-Joseph Z, Barabási A-, 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 of the United States of America. 104: 12663-12668. PMID 17652176 DOI: 10.1073/Pnas.0609845104  0.579
2007 Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Reconstructing dynamic regulatory maps. Molecular Systems Biology. 3: 74. PMID 17224918 DOI: 10.1038/Msb4100115  0.623
2006 Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. Bmc Bioinformatics. 7: 191. PMID 16597342 DOI: 10.1186/1471-2105-7-191  0.593
2005 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. 23: 1503-8. PMID 16333294 DOI: 10.1038/Nbt1164  0.615
2005 Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics (Oxford, England). 21: i159-68. PMID 15961453 DOI: 10.1093/Bioinformatics/Bti1022  0.577
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