Jason Ernst

Jason Ernst

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Jason Ernst

Publications by authors named "Jason Ernst"

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

Authors:
Jennifer Zou Farhad Hormozdiari Brandon Jew Stephane E Castel Tuuli Lappalainen Jason Ernst Jae Hoon Sul Eleazar Eskin

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.

Authors:
Artur Jaroszewicz Jason Ernst

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.

Authors:
Adriana Arneson Jason Ernst

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.

Authors:
Adriana Arneson Jason Ernst

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

Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes.

Authors:
Gabriel B Ferguson Ben Van Handel Maxwell Bay Petko Fiziev Tonis Org Siyoung Lee Ruzanna Shkhyan Nicholas W Banks Mila Scheinberg Ling Wu Biagio Saitta Joseph Elphingstone A Noelle Larson Scott M Riester April D Pyle Nicholas M Bernthal Hanna Ka Mikkola Jason Ernst Andre J van Wijnen Michael Bonaguidi Denis Evseenko

Nat Commun 2018 09 7;9(1):3634. Epub 2018 Sep 7.

Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA, 90033, USA.

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http://dx.doi.org/10.1038/s41467-018-05573-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6128860PMC
September 2018

ChromTime: modeling spatio-temporal dynamics of chromatin marks.

Authors:
Petko Fiziev Jason Ernst

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.

Authors:
Soo Bin Kwon Jason Ernst

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

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Authors:
Pradeep Natarajan Gina M Peloso Seyedeh Maryam Zekavat May Montasser Andrea Ganna Mark Chaffin Amit V Khera Wei Zhou Jonathan M Bloom Jesse M Engreitz Jason Ernst Jeffrey R O'Connell Sanni E Ruotsalainen Maris Alver Ani Manichaikul W Craig Johnson James A Perry Timothy Poterba Cotton Seed Ida L Surakka Tonu Esko Samuli Ripatti Veikko Salomaa Adolfo Correa Ramachandran S Vasan Manolis Kellis Benjamin M Neale Eric S Lander Goncalo Abecasis Braxton Mitchell Stephen S Rich James G Wilson L Adrienne Cupples Jerome I Rotter Cristen J Willer Sekar Kathiresan

Nat Commun 2018 08 23;9(1):3391. Epub 2018 Aug 23.

Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA.

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http://dx.doi.org/10.1038/s41467-018-05747-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107638PMC
August 2018

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Authors:
Seyedeh M Zekavat Sanni Ruotsalainen Robert E Handsaker Maris Alver Jonathan Bloom Timothy Poterba Cotton Seed Jason Ernst Mark Chaffin Jesse Engreitz Gina M Peloso Ani Manichaikul Chaojie Yang Kathleen A Ryan Mao Fu W Craig Johnson Michael Tsai Matthew Budoff Ramachandran S Vasan L Adrienne Cupples Jerome I Rotter Stephen S Rich Wendy Post Braxton D Mitchell Adolfo Correa Andres Metspalu James G Wilson Veikko Salomaa Manolis Kellis Mark J Daly Benjamin M Neale Steven McCarroll Ida Surakka Tonu Esko Andrea Ganna Samuli Ripatti Sekar Kathiresan Pradeep Natarajan

Nat Commun 2018 08 23;9(1):3493. Epub 2018 Aug 23.

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1038/s41467-018-05975-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107495PMC
August 2018

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Authors:
Seyedeh M Zekavat Sanni Ruotsalainen Robert E Handsaker Maris Alver Jonathan Bloom Timothy Poterba Cotton Seed Jason Ernst Mark Chaffin Jesse Engreitz Gina M Peloso Ani Manichaikul Chaojie Yang Kathleen A Ryan Mao Fu W Craig Johnson Michael Tsai Matthew Budoff Ramachandran S Vasan L Adrienne Cupples Jerome I Rotter Stephen S Rich Wendy Post Braxton D Mitchell Adolfo Correa Andres Metspalu James G Wilson Veikko Salomaa Manolis Kellis Mark J Daly Benjamin M Neale Steven McCarroll Ida Surakka Tonu Esko Andrea Ganna Samuli Ripatti Sekar Kathiresan Pradeep Natarajan

Nat Commun 2018 07 4;9(1):2606. Epub 2018 Jul 4.

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1038/s41467-018-04668-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031652PMC
July 2018

Analysis of cardiomyocyte clonal expansion during mouse heart development and injury.

Authors:
Konstantina-Ioanna Sereti Ngoc B Nguyen Paniz Kamran Peng Zhao Sara Ranjbarvaziri Shuin Park Shan Sabri James L Engel Kevin Sung Rajan P Kulkarni Yichen Ding Tzung K Hsiai Kathrin Plath Jason Ernst Debashis Sahoo Hanna K A Mikkola M Luisa Iruela-Arispe Reza Ardehali

Nat Commun 2018 02 21;9(1):754. Epub 2018 Feb 21.

Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.

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http://www.nature.com/articles/s41467-018-02891-z
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http://dx.doi.org/10.1038/s41467-018-02891-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821855PMC
February 2018

Chromatin-state discovery and genome annotation with ChromHMM.

Authors:
Jason Ernst Manolis Kellis

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.

Authors:
Yaping Liu Abhishek Sarkar Pouya Kheradpour Jason Ernst Manolis Kellis

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

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.

Authors:
Petko Fiziev Kadir C Akdemir John P Miller Emily Z Keung Neha S Samant Sneha Sharma Christopher A Natale Christopher J Terranova Mayinuer Maitituoheti Samirkumar B Amin Emmanuel Martinez-Ledesma Mayura Dhamdhere Jacob B Axelrad Amiksha Shah Christine S Cheng Harshad Mahadeshwar Sahil Seth Michelle C Barton Alexei Protopopov Kenneth Y Tsai Michael A Davies Benjamin A Garcia Ido Amit Lynda Chin Jason Ernst Kunal Rai

Cell Rep 2017 04;19(4):875-889

Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.03.078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473172PMC
April 2017

Cooperative Binding of Transcription Factors Orchestrates Reprogramming.

Authors:
Constantinos Chronis Petko Fiziev Bernadett Papp Stefan Butz Giancarlo Bonora Shan Sabri Jason Ernst Kathrin Plath

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.

Authors:
Jason Ernst Alexandre Melnikov Xiaolan Zhang Li Wang Peter Rogov Tarjei S Mikkelsen Manolis Kellis

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.

Authors:
Hyejung Won Luis de la Torre-Ubieta Jason L Stein Neelroop N Parikshak Jerry Huang Carli K Opland Michael J Gandal Gavin J Sutton Farhad Hormozdiari Daning Lu Changhoon Lee Eleazar Eskin Irina Voineagu Jason Ernst Daniel H Geschwind

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.

Authors:
Kuntol Rakshit Jingyi Qian Jason Ernst Aleksey V Matveyenko

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.

Authors:
Dat Duong Jennifer Zou Farhad Hormozdiari Jae Hoon Sul Jason Ernst Buhm Han Eleazar Eskin

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.

Authors:
Kunal Rai Kadir C Akdemir Lawrence N Kwong Petko Fiziev Chang-Jiun Wu Emily Z Keung Sneha Sharma Neha S Samant Maura Williams Jacob B Axelrad Amiksha Shah Dong Yang Elizabeth A Grimm Michelle C Barton Denai R Milton Timothy P Heffernan James W Horner Suhendan Ekmekcioglu Alexander J Lazar Jason Ernst Lynda Chin

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.

Authors:
Jason Ernst Manolis Kellis

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.

Authors:
Anshul Kundaje Wouter Meuleman Jason Ernst Misha Bilenky Angela Yen Alireza Heravi-Moussavi Pouya Kheradpour Zhizhuo Zhang Jianrong Wang Michael J Ziller Viren Amin John W Whitaker Matthew D Schultz Lucas D Ward Abhishek Sarkar Gerald Quon Richard S Sandstrom Matthew L Eaton Yi-Chieh Wu Andreas R Pfenning Xinchen Wang Melina Claussnitzer Yaping Liu Cristian Coarfa R Alan Harris Noam Shoresh Charles B Epstein Elizabeta Gjoneska Danny Leung Wei Xie R David Hawkins Ryan Lister Chibo Hong Philippe Gascard Andrew J Mungall Richard Moore Eric Chuah Angela Tam Theresa K Canfield R Scott Hansen Rajinder Kaul Peter J Sabo Mukul S Bansal Annaick Carles Jesse R Dixon Kai-How Farh Soheil Feizi Rosa Karlic Ah-Ram Kim Ashwinikumar Kulkarni Daofeng Li Rebecca Lowdon GiNell Elliott Tim R Mercer Shane J Neph Vitor Onuchic Paz Polak Nisha Rajagopal Pradipta Ray Richard C Sallari Kyle T Siebenthall Nicholas A Sinnott-Armstrong Michael Stevens Robert E Thurman Jie Wu Bo Zhang Xin Zhou Arthur E Beaudet Laurie A Boyer Philip L De Jager Peggy J Farnham Susan J Fisher David Haussler Steven J M Jones Wei Li Marco A Marra Michael T McManus Shamil Sunyaev James A Thomson Thea D Tlsty Li-Huei Tsai Wei Wang Robert A Waterland Michael Q Zhang Lisa H Chadwick Bradley E Bernstein Joseph F Costello Joseph R Ecker Martin Hirst Alexander Meissner Aleksandar Milosavljevic Bing Ren John A Stamatoyannopoulos Ting Wang Manolis Kellis

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

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.

Authors:
Philip L De Jager Gyan Srivastava Katie Lunnon Jeremy Burgess Leonard C Schalkwyk Lei Yu Matthew L Eaton Brendan T Keenan Jason Ernst Cristin McCabe Anna Tang Towfique Raj Joseph Replogle Wendy Brodeur Stacey Gabriel High S Chai Curtis Younkin Steven G Younkin Fanggeng Zou Moshe Szyf Charles B Epstein Julie A Schneider Bradley E Bernstein Alex Meissner Nilufer Ertekin-Taner Lori B Chibnik Manolis Kellis Jonathan Mill David A Bennett

Nat Neurosci 2014 Sep 17;17(9):1156-63. Epub 2014 Aug 17.

Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/nn.3786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292795PMC
September 2014

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

Authors:
Nisha Rajagopal Jason Ernst Pradipta Ray Jie Wu Michael Zhang Manolis Kellis Bing Ren

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.

Authors:
Ali Mortazavi Shirley Pepke Camden Jansen Georgi K Marinov Jason Ernst Manolis Kellis Ross C Hardison Richard M Myers Barbara J Wold

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.

Authors:
Nisha Rajagopal Wei Xie Yan Li Uli Wagner Wei Wang John Stamatoyannopoulos Jason Ernst Manolis Kellis Bing Ren

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

Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.

Authors:
Matthew Denholtz Giancarlo Bonora Constantinos Chronis Erik Splinter Wouter de Laat Jason Ernst Matteo Pellegrini Kathrin Plath

Cell Stem Cell 2013 Nov 12;13(5):602-16. Epub 2013 Sep 12.

Department of Biological Chemistry at the David Geffen School of Medicine, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1016/j.stem.2013.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825755PMC
November 2013

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

Authors:
Jason Ernst Manolis Kellis

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.

Authors:
Pouya Kheradpour Jason Ernst Alexandre Melnikov Peter Rogov Li Wang Xiaolan Zhang Jessica Alston Tarjei S Mikkelsen Manolis Kellis

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

Integrative annotation of chromatin elements from ENCODE data.

Authors:
Michael M Hoffman Jason Ernst Steven P Wilder Anshul Kundaje Robert S Harris Max Libbrecht Belinda Giardine Paul M Ellenbogen Jeffrey A Bilmes Ewan Birney Ross C Hardison Ian Dunham Manolis Kellis William Stafford Noble

Nucleic Acids Res 2013 Jan 5;41(2):827-41. Epub 2012 Dec 5.

Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195-5065, USA.

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http://compbio.mit.edu/publications/84_Hoffman_NAR_12.pdf
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http://nar.oxfordjournals.org/content/suppl/2012/11/27/gks12
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gks1284
Publisher Site
http://dx.doi.org/10.1093/nar/gks1284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553955PMC
January 2013

Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells.

Authors:
Bilian Jin Jason Ernst Rochelle L Tiedemann Hongyan Xu Suhas Sureshchandra Manolis Kellis Stephen Dalton Chen Liu Jeong-Hyeon Choi Keith D Robertson

Cell Rep 2012 Nov 21;2(5):1411-24. Epub 2012 Nov 21.

Cancer Research Center, Georgia Health Sciences University, Augusta, GA 30912, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S22111247120037
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http://dx.doi.org/10.1016/j.celrep.2012.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625945PMC
November 2012

Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma.

Authors:
Janey L Wiggs Brian L Yaspan Michael A Hauser Jae H Kang R Rand Allingham Lana M Olson Wael Abdrabou Bao J Fan Dan Y Wang Wendy Brodeur Donald L Budenz Joseph Caprioli Andrew Crenshaw Kristy Crooks Elizabeth Delbono Kimberly F Doheny David S Friedman Douglas Gaasterland Terry Gaasterland Cathy Laurie Richard K Lee Paul R Lichter Stephanie Loomis Yutao Liu Felipe A Medeiros Cathy McCarty Daniel Mirel Sayoko E Moroi David C Musch Anthony Realini Frank W Rozsa Joel S Schuman Kathleen Scott Kuldev Singh Joshua D Stein Edward H Trager Paul Vanveldhuisen Douglas Vollrath Gadi Wollstein Sachiko Yoneyama Kang Zhang Robert N Weinreb Jason Ernst Manolis Kellis Tomohiro Masuda Don Zack Julia E Richards Margaret Pericak-Vance Louis R Pasquale Jonathan L Haines

PLoS Genet 2012 26;8(4):e1002654. Epub 2012 Apr 26.

Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343074PMC
September 2012

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

Authors:
Marcel H Schulz William E Devanny Anthony Gitter Shan Zhong Jason Ernst Ziv Bar-Joseph

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

ChromHMM: automating chromatin-state discovery and characterization.

Authors:
Jason Ernst Manolis Kellis

Nat Methods 2012 Feb 28;9(3):215-6. Epub 2012 Feb 28.

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http://dx.doi.org/10.1038/nmeth.1906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577932PMC
February 2012

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.

Authors:
Oren Ram Alon Goren Ido Amit Noam Shoresh Nir Yosef Jason Ernst Manolis Kellis Melissa Gymrek Robbyn Issner Michael Coyne Timothy Durham Xiaolan Zhang Julie Donaghey Charles B Epstein Aviv Regev Bradley E Bernstein

Cell 2011 Dec;147(7):1628-39

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cell.2011.09.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312319PMC
December 2011

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque.

Authors:
Guy Zinman Rachel Brower-Sinning Chineye H Emeche Jason Ernst Grace Tzu-Wei Huang Shaun Mahony Amy J Myers Dawn M O'Dee JoAnne L Flynn Gerard J Nau Ted M Ross Russell D Salter Panayiotis V Benos Ziv Bar Joseph Penelope A Morel

PLoS One 2011 18;6(7):e22401. Epub 2011 Jul 18.

Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022401PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138787PMC
November 2011

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Authors:
Weisheng Wu Yong Cheng Cheryl A Keller Jason Ernst Swathi Ashok Kumar Tejaswini Mishra Christapher Morrissey Christine M Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E Crawford Terrence S Furey Manolis Kellis Webb Miller James Taylor Stephan C Schuster Yu Zhang Francesca Chiaromonte Gerd A Blobel Mitchell J Weiss Ross C Hardison

Genome Res 2011 Oct 27;21(10):1659-71. Epub 2011 Jul 27.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.125088.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202283PMC
October 2011

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

Authors:
Kerstin Lindblad-Toh Manuel Garber Or Zuk Michael F Lin Brian J Parker Stefan Washietl Pouya Kheradpour Jason Ernst Gregory Jordan Evan Mauceli Lucas D Ward Craig B Lowe Alisha K Holloway Michele Clamp Sante Gnerre Jessica Alföldi Kathryn Beal Jean Chang Hiram Clawson James Cuff Federica Di Palma Stephen Fitzgerald Paul Flicek Mitchell Guttman Melissa J Hubisz David B Jaffe Irwin Jungreis W James Kent Dennis Kostka Marcia Lara Andre L Martins Tim Massingham Ida Moltke Brian J Raney Matthew D Rasmussen Jim Robinson Alexander Stark Albert J Vilella Jiayu Wen Xiaohui Xie Michael C Zody Jen Baldwin Toby Bloom Chee Whye Chin Dave Heiman Robert Nicol Chad Nusbaum Sarah Young Jane Wilkinson Kim C Worley Christie L Kovar Donna M Muzny Richard A Gibbs Andrew Cree Huyen H Dihn Gerald Fowler Shalili Jhangiani Vandita Joshi Sandra Lee Lora R Lewis Lynne V Nazareth Geoffrey Okwuonu Jireh Santibanez Wesley C Warren Elaine R Mardis George M Weinstock Richard K Wilson Kim Delehaunty David Dooling Catrina Fronik Lucinda Fulton Bob Fulton Tina Graves Patrick Minx Erica Sodergren Ewan Birney Elliott H Margulies Javier Herrero Eric D Green David Haussler Adam Siepel Nick Goldman Katherine S Pollard Jakob S Pedersen Eric S Lander Manolis Kellis

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

Mapping and analysis of chromatin state dynamics in nine human cell types.

Authors:
Jason Ernst Pouya Kheradpour Tarjei S Mikkelsen Noam Shoresh Lucas D Ward Charles B Epstein Xiaolan Zhang Li Wang Robbyn Issner Michael Coyne Manching Ku Timothy Durham Manolis Kellis Bradley E Bernstein

Nature 2011 May 23;473(7345):43-9. Epub 2011 Mar 23.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature09906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773PMC
May 2011

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Authors:
Peter V Kharchenko Artyom A Alekseyenko Yuri B Schwartz Aki Minoda Nicole C Riddle Jason Ernst Peter J Sabo Erica Larschan Andrey A Gorchakov Tingting Gu Daniela Linder-Basso Annette Plachetka Gregory Shanower Michael Y Tolstorukov Lovelace J Luquette Ruibin Xi Youngsook L Jung Richard W Park Eric P Bishop Theresa K Canfield Richard Sandstrom Robert E Thurman David M MacAlpine John A Stamatoyannopoulos Manolis Kellis Sarah C R Elgin Mitzi I Kuroda Vincenzo Pirrotta Gary H Karpen Peter J Park

Nature 2011 Mar 22;471(7339):480-5. Epub 2010 Dec 22.

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature09725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109908PMC
March 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Authors:
Sushmita Roy Jason Ernst Peter V Kharchenko Pouya Kheradpour Nicolas Negre Matthew L Eaton Jane M Landolin Christopher A Bristow Lijia Ma Michael F Lin Stefan Washietl Bradley I Arshinoff Ferhat Ay Patrick E Meyer Nicolas Robine Nicole L Washington Luisa Di Stefano Eugene Berezikov Christopher D Brown Rogerio Candeias Joseph W Carlson Adrian Carr Irwin Jungreis Daniel Marbach Rachel Sealfon Michael Y Tolstorukov Sebastian Will Artyom A Alekseyenko Carlo Artieri Benjamin W Booth Angela N Brooks Qi Dai Carrie A Davis Michael O Duff Xin Feng Andrey A Gorchakov Tingting Gu Jorja G Henikoff Philipp Kapranov Renhua Li Heather K MacAlpine John Malone Aki Minoda Jared Nordman Katsutomo Okamura Marc Perry Sara K Powell Nicole C Riddle Akiko Sakai Anastasia Samsonova Jeremy E Sandler Yuri B Schwartz Noa Sher Rebecca Spokony David Sturgill Marijke van Baren Kenneth H Wan Li Yang Charles Yu Elise Feingold Peter Good Mark Guyer Rebecca Lowdon Kami Ahmad Justen Andrews Bonnie Berger Steven E Brenner Michael R Brent Lucy Cherbas Sarah C R Elgin Thomas R Gingeras Robert Grossman Roger A Hoskins Thomas C Kaufman William Kent Mitzi I Kuroda Terry Orr-Weaver Norbert Perrimon Vincenzo Pirrotta James W Posakony Bing Ren Steven Russell Peter Cherbas Brenton R Graveley Suzanna Lewis Gos Micklem Brian Oliver Peter J Park Susan E Celniker Steven Henikoff Gary H Karpen Eric C Lai David M MacAlpine Lincoln D Stein Kevin P White Manolis Kellis

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
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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.

Authors:
Jason Ernst Manolis Kellis

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.

Authors:
Jason Ernst Heather L Plasterer Itamar Simon Ziv Bar-Joseph

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.

Authors:
Jason Ernst Louis Ghanem Ziv Bar-Joseph Michael McNamara Jason Brown Richard A Steinman

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.

Authors:
Jason Ernst Qasim K Beg Krin A Kay Gábor Balázsi Zoltán N Oltvai Ziv Bar-Joseph

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.

Authors:
Alexei Vazquez Qasim K Beg Marcio A Demenezes Jason Ernst Ziv Bar-Joseph Albert-László Barabási László G Boros Zoltán N Oltvai

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.

Authors:
Jason Ernst Oded Vainas Christopher T Harbison Itamar Simon Ziv Bar-Joseph

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.

Authors:
Jason Ernst Ziv Bar-Joseph

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.

Authors:
Itamar Simon Zahava Siegfried Jason Ernst Ziv Bar-Joseph

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.

Authors:
Jason Ernst Gerard J Nau Ziv Bar-Joseph

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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http://dx.doi.org/10.1093/bioinformatics/bti1022DOI Listing
June 2005