Peter J Park

Peter J Park

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An enhanced genetic model of colorectal cancer progression history.

Genome Biol 2019 08 15;20(1):168. Epub 2019 Aug 15.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s13059-019-1782-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694562PMC
August 2019

Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance.

Nat Commun 2019 Aug 29;10(1):3908. Epub 2019 Aug 29.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41467-019-11857-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715686PMC
August 2019

Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma.

Cell 2019 Jun 30;177(7):1842-1857.e21. Epub 2019 May 30.

Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul 03080, Korea; Seoul National University Cancer Research Institute, Seoul 03080, Korea. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.013DOI Listing
June 2019

Detecting the mutational signature of homologous recombination deficiency in clinical samples.

Nat Genet 2019 05 15;51(5):912-919. Epub 2019 Apr 15.

Department of Biomedical Informatics and Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

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http://www.nature.com/articles/s41588-019-0390-2
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http://dx.doi.org/10.1038/s41588-019-0390-2DOI Listing
May 2019

Tibanna: software for scalable execution of portable pipelines on the cloud.

Bioinformatics 2019 May 11. Epub 2019 May 11.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz379DOI Listing
May 2019

Complete Genome Sequence of Rhodococcus erythropolis Phage Shuman.

Microbiol Resour Announc 2019 Mar 28;8(13). Epub 2019 Mar 28.

Department of Natural Sciences, Nyack College, Nyack, New York, USA

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http://dx.doi.org/10.1128/MRA.00113-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6439245PMC
March 2019

MicroRNA-29a activates a multi-component growth and invasion program in glioblastoma.

J Exp Clin Cancer Res 2019 Jan 25;38(1):36. Epub 2019 Jan 25.

Department of Neurological Surgery, University of Massachusetts Medical School, Albert Sherman Center AS6-1001, 368 Plantation Street, Worcester, MA, 01605, USA.

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https://jeccr.biomedcentral.com/articles/10.1186/s13046-019-
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http://dx.doi.org/10.1186/s13046-019-1026-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347789PMC
January 2019

Detecting Somatic Mutations in Normal Cells.

Trends Genet 2018 07 3;34(7):545-557. Epub 2018 May 3.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2018.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029698PMC
July 2018

A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases.

Cell Rep 2018 07;24(2):515-527

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.06.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092947PMC
July 2018

Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in .

Genes Dev 2017 10 25;31(19):1988-2002. Epub 2017 Oct 25.

Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gad.305987.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710143PMC
October 2017

Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas.

J Clin Oncol 2017 Sep 12;35(26):3065-3074. Epub 2017 May 12.

June-Koo Lee, Jeonghwan Youk, Seongyeol Park, Yohan An, Joon Kim, Young Seok Ju, Korea Advanced Institute of Science and Technology; Junehawk Lee, Korea Institute of Science and Technology Information, Daejeon; Sehui Kim, Bhumsuk Keam, Dong-Wan Kim, Dae Seog Heo, Young Tae Kim, Yoon Kyung Jeon, Doo Hyun Chung, Tae Min Kim, Seoul National University Hospital; Soyeon Kim, Bhumsuk Keam, Dong-Wan Kim, Dae Seog Heo, Young Tae Kim, Ja-Lok Ku, Yoon Kyung Jeon, Tae Min Kim, Seoul National University Cancer Research Institute; Jin-Soo Kim, Seoul Metropolitan Government-Seoul National University Boramae Medical Center; Se-Hoon Lee, Keunchil Park, Sungkyunkwan University School of Medicine; Doo Hyun Chung, Seoul National University College of Medicine, Seoul; Se Hyun Kim, Jong Seok Lee, Seoul National University Bundang Hospital, Seongnam, Republic of Korea; and Peter J. Park, Harvard Medical School, Boston, MA.

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http://dx.doi.org/10.1200/JCO.2016.71.9096DOI Listing
September 2017

The 4D nucleome project.

Nature 2017 09;549(7671):219-226

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature23884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617335PMC
September 2017

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.

Cancer Cell 2017 06 18;31(6):820-832.e3. Epub 2017 May 18.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502825PMC
June 2017

A molecular portrait of microsatellite instability across multiple cancers.

Nat Commun 2017 06 6;8:15180. Epub 2017 Jun 6.

Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms15180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467167PMC
June 2017

DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells.

Cell Stem Cell 2017 05 30;20(5):706-719.e7. Epub 2017 Mar 30.

Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524993PMC
May 2017

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation.

Mol Cell 2017 Apr 30;66(1):77-88.e5. Epub 2017 Mar 30.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.02.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394798PMC
April 2017

The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers.

Nat Commun 2017 03 6;8:14648. Epub 2017 Mar 6.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/ncomms14648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343482PMC
March 2017

Validation of the Intensive Care Unit Early Warning Dashboard: Quality Improvement Utilizing a Retrospective Case-Control Evaluation.

Telemed J E Health 2017 02 8;23(2):88-95. Epub 2016 Jul 8.

4 Department of Pulmonary/Critical Care, Naval Medical Center San Diego , California.

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http://dx.doi.org/10.1089/tmj.2016.0073DOI Listing
February 2017

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice.

Nat Genet 2017 Feb 12;49(2):296-302. Epub 2016 Dec 12.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5285448PMC
February 2017

, the homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks.

G3 (Bethesda) 2017 02 9;7(2):625-635. Epub 2017 Feb 9.

Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115

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http://dx.doi.org/10.1534/g3.116.037788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295607PMC
February 2017

Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains.

Fly (Austin) 2015 ;9(4):178-82

b Division of Genetics; Brigham and Women's Hospital ; Boston , MA 02115.

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http://dx.doi.org/10.1080/19336934.2016.1151988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862425PMC
December 2016

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

PLoS Genet 2016 10 27;12(10):e1006385. Epub 2016 Oct 27.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America.

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http://dx.doi.org/10.1371/journal.pgen.1006385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082821PMC
October 2016

Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants.

Nucleic Acids Res 2016 07 3;44(13):6274-86. Epub 2016 Jun 3.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkw491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772337PMC
July 2016

Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.

Genome Biol 2016 06 3;17(1):120. Epub 2016 Jun 3.

Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s13059-016-0984-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893286PMC
June 2016

Mechanisms and Consequences of Cancer Genome Instability: Lessons from Genome Sequencing Studies.

Annu Rev Pathol 2016 05 22;11:283-312. Epub 2016 Feb 22.

Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115; email:

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http://dx.doi.org/10.1146/annurev-pathol-012615-044446DOI Listing
May 2016

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

Nat Commun 2016 05 6;7:11485. Epub 2016 May 6.

Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1038/ncomms11485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859066PMC
May 2016

Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing.

Am J Hum Genet 2016 05;98(5):843-856

Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Ludwig Center, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.03.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863662PMC
May 2016

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Cell Rep 2016 Mar 3;14(10):2476-89. Epub 2016 Mar 3.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794376PMC
March 2016

Resolving rates of mutation in the brain using single-neuron genomics.

Elife 2016 Feb 22;5. Epub 2016 Feb 22.

Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, United States.

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http://dx.doi.org/10.7554/eLife.12966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805530PMC
February 2016

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.

Proc Natl Acad Sci U S A 2015 Dec 2;112(49):15148-53. Epub 2015 Nov 2.

Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129; Howard Hughes Medical Institute, Chevy Chase, MD 20815; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114;

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http://dx.doi.org/10.1073/pnas.1518008112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679016PMC
December 2015

Intron retention is a widespread mechanism of tumor-suppressor inactivation.

Nat Genet 2015 Nov 5;47(11):1242-8. Epub 2015 Oct 5.

Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3414DOI Listing
November 2015

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.

Nat Biotechnol 2015 Nov 26;33(11):1173-81. Epub 2015 Oct 26.

Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847940PMC
November 2015

Somatic mutation in single human neurons tracks developmental and transcriptional history.

Science 2015 Oct;350(6256):94-98

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1126/science.aab1785DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664477PMC
October 2015

Genome-Wide Analysis of Wilms' Tumor 1-Controlled Gene Expression in Podocytes Reveals Key Regulatory Mechanisms.

J Am Soc Nephrol 2015 Sep 30;26(9):2097-104. Epub 2015 Jan 30.

Division of Nephrology, Department of Medicine and Harvard Stem Cell Institute, Cambridge, Massachusetts

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http://dx.doi.org/10.1681/ASN.2014090940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552122PMC
September 2015

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering.

BMC Bioinformatics 2015 Sep 3;16:278. Epub 2015 Sep 3.

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0704-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559005PMC
September 2015

Spatiotemporal Evolution of the Primary Glioblastoma Genome.

Cancer Cell 2015 Sep;28(3):318-28

Samsung Biomedical Research Institute, Samsung Medical Center, Seoul 06351, Korea; Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science and Technology (SAIHST), Sungkyunkwan University, Seoul 06351, Korea; Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2015.07.013DOI Listing
September 2015

Hallmarks of pluripotency.

Nature 2015 Sep;525(7570):469-78

Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature15515DOI Listing
September 2015

Failure to replicate the STAP cell phenomenon.

Nature 2015 Sep;525(7570):E6-9

Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature15513DOI Listing
September 2015

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.

Bioinformatics 2015 Jul 27;31(13):2066-74. Epub 2015 Feb 27.

Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Information and Computer Engineering, Ajou University, Suwon 443-749, South Korea, Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110799, Korea, Systems Biomedical Informatics Research Center, Seoul National University, Seoul 110799, Korea, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia, The University of New South Wales, Sydney, NSW 2052, Australia, Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481846PMC
July 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila.

Genes Dev 2015 Jun;29(11):1136-50

Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;

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http://dx.doi.org/10.1101/gad.260562.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470282PMC
June 2015

Standard for improving emergency information interoperability: the HL7 data elements for emergency department systems.

J Am Med Inform Assoc 2015 May 13;22(3):529-35. Epub 2015 Mar 13.

Homer Warner Center for Informatics Research, Intermountain Healthcare, South Office Building, 2nd Floor, 5171 South Cottonwood Street, Salt Lake City, UT 84107, USA.

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http://dx.doi.org/10.1093/jamia/ocu040DOI Listing
May 2015

Identification of rare germline copy number variations over-represented in five human cancer types.

Mol Cancer 2015 Feb 3;14:25. Epub 2015 Feb 3.

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s12943-015-0292-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381456PMC
February 2015

Cell lineage analysis in human brain using endogenous retroelements.

Neuron 2015 Jan;85(1):49-59

Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2014.12.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299461PMC
January 2015

Rearranging the chromatin for pluripotency.

Cell Cycle 2014 15;13(2):167-8. Epub 2013 Nov 15.

Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine; Harvard Stem Cell Institute; Boston, MA USA; Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology; Harvard University and Harvard Medical School; Cambridge, MA USA.

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http://dx.doi.org/10.4161/cc.27028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906226PMC
December 2014

p53 prevents neurodegeneration by regulating synaptic genes.

Proc Natl Acad Sci U S A 2014 Dec 1;111(50):18055-60. Epub 2014 Dec 1.

Departments of Pathology and

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http://dx.doi.org/10.1073/pnas.1419083111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273405PMC
December 2014

A genome-wide view of microsatellite instability: old stories of cancer mutations revisited with new sequencing technologies.

Cancer Res 2014 Nov 4;74(22):6377-82. Epub 2014 Nov 4.

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

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http://dx.doi.org/10.1158/0008-5472.CAN-14-1225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233171PMC
November 2014

Guided visual exploration of genomic stratifications in cancer.

Nat Methods 2014 Sep;11(9):884-885

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

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http://dx.doi.org/10.1038/nmeth.3088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196637PMC
September 2014

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming.

Nat Commun 2014 Aug 27;5:4719. Epub 2014 Aug 27.

1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms5719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217530PMC
August 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Impact of sequencing depth in ChIP-seq experiments.

Nucleic Acids Res 2014 May 5;42(9):e74. Epub 2014 Mar 5.

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA Division of Genetics, Brigham and Women's Hospital & Harvard Medical School, Boston, MA 02115, USA Informatics Program, Children's Hospital, Boston, MA 02115, USA

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http://nar.oxfordjournals.org/content/42/9/e74.full.pdf
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http://dx.doi.org/10.1093/nar/gku178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027199PMC
May 2014

Large-scale quality analysis of published ChIP-seq data.

G3 (Bethesda) 2014 Feb 19;4(2):209-23. Epub 2014 Feb 19.

Division of Biology, California Institute of Technology, Pasadena, California 91125.

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http://dx.doi.org/10.1534/g3.113.008680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931556PMC
February 2014

Transcriptional control of a whole chromosome: emerging models for dosage compensation.

Nat Struct Mol Biol 2014 Feb 5;21(2):118-25. Epub 2014 Feb 5.

1] Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342042PMC
February 2014

Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome.

Cell 2013 Nov 31;155(4):948-62. Epub 2013 Oct 31.

Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00928674130128
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http://dx.doi.org/10.1016/j.cell.2013.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891052PMC
November 2013

The landscape of microsatellite instability in colorectal and endometrial cancer genomes.

Cell 2013 Nov;155(4):858-68

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea.

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http://dx.doi.org/10.1016/j.cell.2013.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871995PMC
November 2013

Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.

Mol Cell Biol 2013 Aug 17;33(16):3274-85. Epub 2013 Jun 17.

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1128/MCB.00275-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753906PMC
August 2013

Nozzle: a report generation toolkit for data analysis pipelines.

Bioinformatics 2013 Apr 17;29(8):1089-91. Epub 2013 Feb 17.

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

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http://dx.doi.org/10.1093/bioinformatics/btt085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624805PMC
April 2013