Chip Stewart

Chip Stewart

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Chip Stewart

Chip Stewart

Publications by authors named "Chip Stewart"

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A (fire)cloud-based DNA methylation data preprocessing and quality control platform.

BMC Bioinformatics 2019 Mar 29;20(1):160. Epub 2019 Mar 29.

Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-019-2750-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440105PMC
March 2019

Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma.

Cancer Cell 2018 08;34(2):242-255.e5

Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Thyroid Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Internal Medicine, Division of Endocrinology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121811PMC
August 2018

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.

Cell Rep 2016 Apr 14;15(4):857-865. Epub 2016 Apr 14.

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, 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.celrep.2016.03.075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850357PMC
April 2016

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

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PLoS One 2014 5;9(3):e90581. Epub 2014 Mar 5.

Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944147PMC
January 2015

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.

Genome Res 2014 Jul 13;24(7):1053-63. Epub 2014 May 13.

Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA; Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.163659.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079962PMC
July 2014

Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing.

Cell 2014 Mar;156(6):1298-1311

Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.02.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040459PMC
March 2014

Landscape of genomic alterations in cervical carcinomas.

Nature 2014 Feb 25;506(7488):371-5. Epub 2013 Dec 25.

1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [4].

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http://dx.doi.org/10.1038/nature12881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161954PMC
February 2014

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas.

Nat Genet 2014 Feb 12;46(2):161-5. Epub 2014 Jan 12.

1] Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA. [4] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [5].

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http://dx.doi.org/10.1038/ng.2868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982316PMC
February 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

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.

Authors:
Marcel den Hoed Mark Eijgelsheim Tõnu Esko Bianca J J M Brundel David S Peal David M Evans Ilja M Nolte Ayellet V Segrè Hilma Holm Robert E Handsaker Harm-Jan Westra Toby Johnson Aaron Isaacs Jian Yang Alicia Lundby Jing Hua Zhao Young Jin Kim Min Jin Go Peter Almgren Murielle Bochud Gabrielle Boucher Marilyn C Cornelis Daniel Gudbjartsson David Hadley Pim van der Harst Caroline Hayward Martin den Heijer Wilmar Igl Anne U Jackson Zoltán Kutalik Jian'an Luan John P Kemp Kati Kristiansson Claes Ladenvall Mattias Lorentzon May E Montasser Omer T Njajou Paul F O'Reilly Sandosh Padmanabhan Beate St Pourcain Tuomo Rankinen Perttu Salo Toshiko Tanaka Nicholas J Timpson Veronique Vitart Lindsay Waite William Wheeler Weihua Zhang Harmen H M Draisma Mary F Feitosa Kathleen F Kerr Penelope A Lind Evelin Mihailov N Charlotte Onland-Moret Ci Song Michael N Weedon Weijia Xie Loic Yengo Devin Absher Christine M Albert Alvaro Alonso Dan E Arking Paul I W de Bakker Beverley Balkau Cristina Barlassina Paola Benaglio Joshua C Bis Nabila Bouatia-Naji Søren Brage Stephen J Chanock Peter S Chines Mina Chung Dawood Darbar Christian Dina Marcus Dörr Paul Elliott Stephan B Felix Krista Fischer Christian Fuchsberger Eco J C de Geus Philippe Goyette Vilmundur Gudnason Tamara B Harris Anna-Liisa Hartikainen Aki S Havulinna Susan R Heckbert Andrew A Hicks Albert Hofman Suzanne Holewijn Femke Hoogstra-Berends Jouke-Jan Hottenga Majken K Jensen Asa Johansson Juhani Junttila Stefan Kääb Bart Kanon Shamika Ketkar Kay-Tee Khaw Joshua W Knowles Angrad S Kooner Jan A Kors Meena Kumari Lili Milani Päivi Laiho Edward G Lakatta Claudia Langenberg Maarten Leusink Yongmei Liu Robert N Luben Kathryn L Lunetta Stacey N Lynch Marcello R P Markus Pedro Marques-Vidal Irene Mateo Leach Wendy L McArdle Steven A McCarroll Sarah E Medland Kathryn A Miller Grant W Montgomery Alanna C Morrison Martina Müller-Nurasyid Pau Navarro Mari Nelis Jeffrey R O'Connell Christopher J O'Donnell Ken K Ong Anne B Newman Annette Peters Ozren Polasek Anneli Pouta Peter P Pramstaller Bruce M Psaty Dabeeru C Rao Susan M Ring Elizabeth J Rossin Diana Rudan Serena Sanna Robert A Scott Jaban S Sehmi Stephen Sharp Jordan T Shin Andrew B Singleton Albert V Smith Nicole Soranzo Tim D Spector Chip Stewart Heather M Stringham Kirill V Tarasov André G Uitterlinden Liesbeth Vandenput Shih-Jen Hwang John B Whitfield Cisca Wijmenga Sarah H Wild Gonneke Willemsen James F Wilson Jacqueline C M Witteman Andrew Wong Quenna Wong Yalda Jamshidi Paavo Zitting Jolanda M A Boer Dorret I Boomsma Ingrid B Borecki Cornelia M van Duijn Ulf Ekelund Nita G Forouhi Philippe Froguel Aroon Hingorani Erik Ingelsson Mika Kivimaki Richard A Kronmal Diana Kuh Lars Lind Nicholas G Martin Ben A Oostra Nancy L Pedersen Thomas Quertermous Jerome I Rotter Yvonne T van der Schouw W M Monique Verschuren Mark Walker Demetrius Albanes David O Arnar Themistocles L Assimes Stefania Bandinelli Michael Boehnke Rudolf A de Boer Claude Bouchard W L Mark Caulfield John C Chambers Gary Curhan Daniele Cusi Johan Eriksson Luigi Ferrucci Wiek H van Gilst Nicola Glorioso Jacqueline de Graaf Leif Groop Ulf Gyllensten Wen-Chi Hsueh Frank B Hu Heikki V Huikuri David J Hunter Carlos Iribarren Bo Isomaa Marjo-Riitta Jarvelin Antti Jula Mika Kähönen Lambertus A Kiemeney Melanie M van der Klauw Jaspal S Kooner Peter Kraft Licia Iacoviello Terho Lehtimäki Marja-Liisa L Lokki Braxton D Mitchell Gerjan Navis Markku S Nieminen Claes Ohlsson Neil R Poulter Lu Qi Olli T Raitakari Eric B Rimm John D Rioux Federica Rizzi Igor Rudan Veikko Salomaa Peter S Sever Denis C Shields Alan R Shuldiner Juha Sinisalo Alice V Stanton Ronald P Stolk David P Strachan Jean-Claude Tardif Unnur Thorsteinsdottir Jaako Tuomilehto Dirk J van Veldhuisen Jarmo Virtamo Jorma Viikari Peter Vollenweider Gérard Waeber Elisabeth Widen Yoon Shin Cho Jesper V Olsen Peter M Visscher Cristen Willer Lude Franke Jeanette Erdmann John R Thompson Arne Pfeufer Nona Sotoodehnia Christopher Newton-Cheh Patrick T Ellinor Bruno H Ch Stricker Andres Metspalu Markus Perola Jacques S Beckmann George Davey Smith Kari Stefansson Nicholas J Wareham Patricia B Munroe Ody C M Sibon David J Milan Harold Snieder Nilesh J Samani Ruth J F Loos

Nat Genet 2013 Jun 14;45(6):621-31. Epub 2013 Apr 14.

Medical Research Council MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.

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http://www.nature.com/protocolexchange/system/uploads/2514/o
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http://www.nature.com/doifinder/10.1038/ng.2610
Publisher Site
http://dx.doi.org/10.1038/ng.2610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696959PMC
June 2013

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Bioinformatics 2013 Mar 12;29(5):656-7. Epub 2013 Jan 12.

Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582267PMC
March 2013

Expression divergence measured by transcriptome sequencing of four yeast species.

BMC Genomics 2011 Dec 29;12:635. Epub 2011 Dec 29.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-3961, USA.

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http://dx.doi.org/10.1186/1471-2164-12-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296765PMC
December 2011

Electroporation of a multicellular system: asymptotic model analysis.

Conf Proc IEEE Eng Med Biol Soc 2004 ;7:5444-6

Harvard-MIT Division of Health Sciences & Technology, MIT, Cambridge, MA, USA.

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http://ieeexplore.ieee.org/document/1404521/
Publisher Site
http://dx.doi.org/10.1109/IEMBS.2004.1404521DOI Listing
June 2007