Matthew D Wilkerson

Matthew D Wilkerson

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Matthew D Wilkerson

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Neuroinflammatory astrocytes generated from cord blood-derived human induced pluripotent stem cells.

J Neuroinflammation 2019 Aug 9;16(1):164. Epub 2019 Aug 9.

Center for Neuroscience and Regenerative Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.

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http://dx.doi.org/10.1186/s12974-019-1553-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688278PMC
August 2019

Digitoxin Inhibits Epithelial-to-Mesenchymal-Transition in Hereditary Castration Resistant Prostate Cancer.

Front Oncol 2019 2;9:630. Epub 2019 Aug 2.

Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine-America's Medical School, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.

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http://dx.doi.org/10.3389/fonc.2019.00630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687970PMC
August 2019

Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis.

J Invest Dermatol 2019 Jun 6;139(6):1349-1361. Epub 2018 Dec 6.

Department of Dermatology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center (LCCC), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1016/j.jid.2018.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535139PMC
June 2019

A Computational Protocol for Detecting Somatic Mutations by Integrating DNA and RNA Sequencing.

Methods Mol Biol 2019 ;1878:109-124

Collaborative Health Initiative Research Program, The American Genome Center, Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA.

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http://link.springer.com/10.1007/978-1-4939-8868-6_6
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http://dx.doi.org/10.1007/978-1-4939-8868-6_6DOI Listing
May 2019

Chromaffin cell biology: inferences from The Cancer Genome Atlas.

Cell Tissue Res 2018 05 15;372(2):339-346. Epub 2018 Feb 15.

The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA.

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http://dx.doi.org/10.1007/s00441-018-2795-0DOI Listing
May 2018

Neonatal mouse cortical but not isogenic human astrocyte feeder layers enhance the functional maturation of induced pluripotent stem cell-derived neurons in culture.

Glia 2018 04 12;66(4):725-748. Epub 2017 Dec 12.

Center for Neuroscience and Regenerative Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland.

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http://dx.doi.org/10.1002/glia.23278DOI Listing
April 2018

"Soldier's Heart": A Genetic Basis for Elevated Cardiovascular Disease Risk Associated with Post-traumatic Stress Disorder.

Front Mol Neurosci 2016 23;9:87. Epub 2016 Sep 23.

Department of Psychiatry Uniformed Services University School of Medicine, Uniformed Services University of the Health SciencesBethesda, MD, USA; Center for the Study of Traumatic stress, Uniformed Services University of the Health SciencesBethesda, MD, USA.

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http://dx.doi.org/10.3389/fnmol.2016.00087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033971PMC
September 2016

MicroRNA Expression Profiling of the Armed Forces Health Surveillance Branch Cohort for Identification of "Enviro-miRs" Associated With Deployment-Based Environmental Exposure.

J Occup Environ Med 2016 08;58(8 Suppl 1):S97-S103

Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland (Dr Dalgard, Mr Polston, Mr Sukumar, Drs Wilkerson, Pollard); Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland (Drs Dalgard, Wilkerson, Pollard); The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland (Drs Dalgard, Wilkerson, Pollard); and Professor, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814 (Dr Mallon). The opinions expressed are those of the authors and do not necessarily reflect the official positions of the Uniformed Services University, the U.S. Departments of Defense, the Army and the Air Force, the 779th Aerospace Medical Squadron, the U.S. Army Public Health Center (Provisional), Emory University, Clarkson University, or the University of Rochester.

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http://dx.doi.org/10.1097/JOM.0000000000000764DOI Listing
August 2016

Validation of the Lung Subtyping Panel in Multiple Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Lung Tumor Gene Expression Data Sets.

Arch Pathol Lab Med 2016 Jun 2;140(6):536-42. Epub 2015 Oct 2.

From the Clinical Development Department, GeneCentric Diagnostics, Durham, North Carolina (Drs Faruki, Mayhew, and Lai-Goldman); the Lineberger Comprehensive Cancer Center (Mr Fan and Drs Hayes and Perou) and the Department of Genetics (Drs Wilkerson and Perou), University of North Carolina, Chapel Hill; and the Center for Molecular Biology and Pathology, Laboratory Corporation of America Holdings, Research Triangle Park, North Carolina (Mr Parker and Drs Kam-Morgan, Eisenberg, and Horten).

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http://dx.doi.org/10.5858/arpa.2015-0113-OADOI Listing
June 2016

Cafeteria diet-induced obesity causes oxidative damage in white adipose.

Biochem Biophys Res Commun 2016 Apr 28;473(2):545-50. Epub 2016 Mar 28.

Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2016.03.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862365PMC
April 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

Oncometabolite D-2-Hydroxyglutarate Inhibits ALKBH DNA Repair Enzymes and Sensitizes IDH Mutant Cells to Alkylating Agents.

Cell Rep 2015 Dec 10;13(11):2353-2361. Epub 2015 Dec 10.

Molecular and Cell Biology Lab of Key Laboratory of Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, College of Life Science, Fudan University, Shanghai 200032, China; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://www.cell.com/cell-reports/pdf/S2211-1247(15)01329-7.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471501329
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http://dx.doi.org/10.1016/j.celrep.2015.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694633PMC
December 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

Coexistent ARID1A-PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling.

Nat Commun 2015 Jan 27;6:6118. Epub 2015 Jan 27.

1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1038/ncomms7118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308813PMC
January 2015

Alterations of LKB1 and KRAS and risk of brain metastasis: comprehensive characterization by mutation analysis, copy number, and gene expression in non-small-cell lung carcinoma.

Lung Cancer 2014 Nov 30;86(2):255-61. Epub 2014 Aug 30.

The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, United States; Department of Internal Medicine, Division of Hematology/Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, United States. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2014.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362696PMC
November 2014

ABRA: improved coding indel detection via assembly-based realignment.

Bioinformatics 2014 Oct 6;30(19):2813-5. Epub 2014 Jun 6.

Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4173014PMC
October 2014

SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples.

Nucleic Acids Res 2014 Aug 16;42(14):e113. Epub 2014 Jul 16.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Multidisciplinary Thoracic Oncology Program, Division of Medical Oncology, Department of Internal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

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http://dx.doi.org/10.1093/nar/gku521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132703PMC
August 2014

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors.

Nucleic Acids Res 2014 Jul 26;42(13):e107. Epub 2014 Jun 26.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

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http://dx.doi.org/10.1093/nar/gku489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117748PMC
July 2014

An educational intervention to improve internal medicine interns' awareness of hazards of hospitalization in acutely ill older adults.

J Am Geriatr Soc 2014 Apr 11;62(4):727-33. Epub 2014 Mar 11.

Geriatrics Division, Department of Medicine, Duke University, Durham, North Carolina.

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http://dx.doi.org/10.1111/jgs.12733DOI Listing
April 2014

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients.

J Clin Oncol 2014 Jan 9;32(2):121-8. Epub 2013 Dec 9.

Youngwook Kim, Ji-ae Yoon, Yoomi Lee, Yeong Kyung Yoo, and Keunchil Park, Samsung Medical Center, Samsung Biomedical Research Institute; Jong-Mu Sun, Hong Kwan Kim, Yong Soo Choi, Kwhanmien Kim, Young Mog Shim, Yoon-La Choi, Jhingook Kim, Jin Seok Ahn, Myung-Ju Ahn, and Keunchil Park, Samsung Medical Center, Sungkyunkwan University School of Medicine; Sukki Cho, Seoul National University Bundang Hospital, College of Medicine, Seoul National University, Seoul; In-Jae Oh, Kyu-Sik Kim, Sang-Yun Song, Kook-Ju Na, and Young-Chul Kim, Chonnam National University Hwasun Hospital, Jeonnam, Republic of Korea; Peter S. Hammerman, Jaegil Kim, Chandra Sekhar Pedamallu, Kristian Cibulskis, Michael S. Lawrence, Petar Stojanov, Scott L. Carter, Aaron McKenna, Chip Stewart, Andrey Y. Sivachenko, Gad Getz, and Matthew Meyerson, Broad Institute of Harvard and MIT, Cambridge; Matthew Meyerson, Harvard Medical School; Peter S. Hammerman and Chandra Sekhar Pedamallu, Dana-Farber Cancer Institute; Gad Getz, Massachusetts General Hospital Cancer Center, Boston, MA; and Matthew D. Wilkerson and D. Neil Hayes, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.

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http://dx.doi.org/10.1200/JCO.2013.50.8556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062710PMC
January 2014

Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors.

Cancer Discov 2013 Dec 27;3(12):1355-63. Epub 2013 Sep 27.

Departments of 1Medicine and 2Medical Oncology and Cancer Vaccine Center, Dana-Farber Cancer Institute; 3Harvard Medical School; 4Ludwig Institute for Cancer Research; 5Department of Neurosurgery, Massachusetts General Hospital; 6Belfer Institute for Applied Cancer Science; 7Department of Pathology, Brigham and Women's Hospital, Boston; 8Broad Institute, Cambridge, Massachusetts; 9UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and 10Department of Molecular Pharmacology and Therapeutics, Oncology Institute, Loyola University, Chicago, Illinois; 11Department of Physiology, University of Valencia, Valencia, Spain.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864135PMC
December 2013

BlackOPs: increasing confidence in variant detection through mappability filtering.

Nucleic Acids Res 2013 Oct 8;41(19):e178. Epub 2013 Aug 8.

Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC 27599, USA, The Genome Institute at Washington University, St. Louis, MO 63108, USA, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA and Division of Medical Oncology, Department of Internal Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/nar/gkt692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799449PMC
October 2013

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.

Bioinformatics 2010 Jun 28;26(12):1572-3. Epub 2010 Apr 28.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881355PMC
June 2010

SWISS MADE: Standardized WithIn Class Sum of Squares to evaluate methodologies and dataset elements.

PLoS One 2010 Mar 26;5(3):e9905. Epub 2010 Mar 26.

Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009905PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845619PMC
March 2010

Common introns within orthologous genes: software and application to plants.

Brief Bioinform 2009 Nov;10(6):631-44

University of North Carolina, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1093/bib/bbp051DOI Listing
November 2009

PlantGDB: a resource for comparative plant genomics.

Nucleic Acids Res 2008 Jan 6;36(Database issue):D959-65. Epub 2007 Dec 6.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/nar/gkm1041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238959PMC
January 2008

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.

Genome Biol 2006 ;7(7):R58

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA.

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http://dx.doi.org/10.1186/gb-2006-7-7-r58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779557PMC
May 2007

Tracembler--software for in-silico chromosome walking in unassembled genomes.

BMC Bioinformatics 2007 May 9;8:151. Epub 2007 May 9.

Department of Genetics, Development & Cell Biology, Iowa State University, Ames, Iowa 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-8-151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876249PMC
May 2007

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

Genome Biol 2006 ;7(11):R111

Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011-3260, USA.

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http://dx.doi.org/10.1186/gb-2006-7-11-r111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794590PMC
March 2007

Comparative plant genomics resources at PlantGDB.

Plant Physiol 2005 Oct;139(2):610-8

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, 50011-3260, USA.

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http://www.plantphysiol.org/lookup/doi/10.1104/pp.104.059212
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http://dx.doi.org/10.1104/pp.104.059212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1255980PMC
October 2005

Community-based gene structure annotation.

Trends Plant Sci 2005 Jan;10(1):9-14

Department of Genetics, Development and Cell Biology, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011, USA.

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http://dx.doi.org/10.1016/j.tplants.2004.11.002DOI Listing
January 2005