Jason Ernst

Jason Ernst

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Jason Ernst

Jason Ernst

Publications by authors named "Jason Ernst"

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51Publications

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Leveraging allelic imbalance to refine fine-mapping for eQTL studies.

PLoS Genet 2019 Dec 13;15(12):e1008481. Epub 2019 Dec 13.

Computer Science Department, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952111PMC
December 2019

An Integrative Approach for Fine-Mapping Chromatin Interactions.

Bioinformatics 2019 Nov 19. Epub 2019 Nov 19.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz843DOI Listing
November 2019

Systematic discovery of conservation states for single-nucleotide annotation of the human genome.

Commun Biol 2019 2;2:248. Epub 2019 Jul 2.

1Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095 USA.

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http://dx.doi.org/10.1038/s42003-019-0488-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606595PMC
July 2019

Systematic discovery of conservation states for single-nucleotide annotation of the human genome.

Commun Biol 2019 Jul 2;2(1):248. Epub 2019 Jul 2.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1038/s42003-019-0488-1DOI Listing
July 2019

ChromTime: modeling spatio-temporal dynamics of chromatin marks.

Genome Biol 2018 08 10;19(1):109. Epub 2018 Aug 10.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1485-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085762PMC
August 2018

Investigating enhancer evolution with massively parallel reporter assays.

Genome Biol 2018 08 14;19(1):114. Epub 2018 Aug 14.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1186/s13059-018-1502-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090676PMC
August 2018

Chromatin-state discovery and genome annotation with ChromHMM.

Nat Protoc 2017 Dec 9;12(12):2478-2492. Epub 2017 Nov 9.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nprot.2017.124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945550PMC
December 2017

Evidence of reduced recombination rate in human regulatory domains.

Genome Biol 2017 10 20;18(1):193. Epub 2017 Oct 20.

Computer Science and Artificial Intelligence Lab (CSAIL), Massachusetts Institute of Technology, Massachusetts, USA.

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http://dx.doi.org/10.1186/s13059-017-1308-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651596PMC
October 2017

Cooperative Binding of Transcription Factors Orchestrates Reprogramming.

Cell 2017 01 19;168(3):442-459.e20. Epub 2017 Jan 19.

David Geffen School of Medicine, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Bioinformatics Program, Los Angeles, CA 90095, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674163173
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http://dx.doi.org/10.1016/j.cell.2016.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302508PMC
January 2017

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Nat Biotechnol 2016 Nov 3;34(11):1180-1190. Epub 2016 Oct 3.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125825PMC
November 2016

Chromosome conformation elucidates regulatory relationships in developing human brain.

Nature 2016 10 19;538(7626):523-527. Epub 2016 Oct 19.

Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/nature19847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358922PMC
October 2016

Circadian variation of the pancreatic islet transcriptome.

Physiol Genomics 2016 09 5;48(9):677-87. Epub 2016 Aug 5.

Department of Physiology and Biomedical Engineering, Mayo Clinic School of Medicine, Mayo Clinic Rochester, Rochester, Minnesota; Department of Medicine, Division of Endocrinology, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, California; and

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http://dx.doi.org/10.1152/physiolgenomics.00019.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111880PMC
September 2016

Using genomic annotations increases statistical power to detect eGenes.

Bioinformatics 2016 06;32(12):i156-i163

Department of Computer Science Department of Human Genetics, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908356PMC
June 2016

Dual Roles of RNF2 in Melanoma Progression.

Cancer Discov 2015 Dec 8;5(12):1314-27. Epub 2015 Oct 8.

Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas. Institute for Health Transformation, The University of Texas System, Houston, Texas.

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http://dx.doi.org/10.1158/2159-8290.CD-15-0493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670809PMC
December 2015

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.

Nat Biotechnol 2015 Apr 18;33(4):364-76. Epub 2015 Feb 18.

1] MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512306PMC
April 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies.

G3 (Bethesda) 2014 Aug 12;4(11):2051-63. Epub 2014 Aug 12.

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653 Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, California 92093

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http://dx.doi.org/10.1534/g3.114.013565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232531PMC
August 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Genome Res 2013 Dec 29;23(12):2136-48. Epub 2013 Oct 29.

Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA;

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http://dx.doi.org/10.1101/gr.158261.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847782PMC
December 2013

RFECS: a random-forest based algorithm for enhancer identification from chromatin state.

PLoS Comput Biol 2013 14;9(3):e1002968. Epub 2013 Mar 14.

Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597546PMC
November 2013

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types.

Genome Res 2013 Jul 17;23(7):1142-54. Epub 2013 Apr 17.

Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, USA.

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http://dx.doi.org/10.1101/gr.144840.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698507PMC
July 2013

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay.

Genome Res 2013 May 19;23(5):800-11. Epub 2013 Mar 19.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.144899.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638136PMC
May 2013

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.

BMC Syst Biol 2012 Aug 16;6:104. Epub 2012 Aug 16.

Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1752-0509-6-104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464930PMC
August 2012

Mapping enhancer and promoter interactions.

Authors:
Jason Ernst

Cell Res 2012 May 27;22(5):789-90. Epub 2012 Mar 27.

Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.

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http://www.nature.com/articles/cr201249
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http://dx.doi.org/10.1038/cr.2012.49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343664PMC
May 2012

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
Publisher Site
http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Discovery and characterization of chromatin states for systematic annotation of the human genome.

Nat Biotechnol 2010 Aug 25;28(8):817-25. Epub 2010 Jul 25.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.1662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919626PMC
August 2010

Integrating multiple evidence sources to predict transcription factor binding in the human genome.

Genome Res 2010 Apr 10;20(4):526-36. Epub 2010 Mar 10.

Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1101/gr.096305.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847756PMC
April 2010

IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability.

PLoS One 2009 Oct 15;4(10):e7469. Epub 2009 Oct 15.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, Massachusetts, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007469PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758590PMC
October 2009

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.

PLoS Comput Biol 2008 Mar 28;4(3):e1000044. Epub 2008 Mar 28.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266799PMC
March 2008

Impact of the solvent capacity constraint on E. coli metabolism.

BMC Syst Biol 2008 Jan 23;2. Epub 2008 Jan 23.

The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1186/1752-0509-2-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270259PMC
January 2008

Reconstructing dynamic regulatory maps.

Mol Syst Biol 2007 16;3:74. Epub 2007 Jan 16.

Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1038/msb4100115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800355PMC
February 2007

STEM: a tool for the analysis of short time series gene expression data.

BMC Bioinformatics 2006 Apr 5;7:191. Epub 2006 Apr 5.

Center for Automated and Learning and Discovery, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

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http://dx.doi.org/10.1186/1471-2105-7-191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456994PMC
April 2006

Combined static and dynamic analysis for determining the quality of time-series expression profiles.

Nat Biotechnol 2005 Dec;23(12):1503-8

Dept. Molecular Biology, Hebrew University Medical School, Jerusalem, Israel 91120.

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http://dx.doi.org/10.1038/nbt1164DOI Listing
December 2005

Clustering short time series gene expression data.

Bioinformatics 2005 Jun;21 Suppl 1:i159-68

Center for Automated Learning and Discovery, School of Computer Science, Carnegie Mellon University 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti1022DOI Listing
June 2005