David A Wheeler

David A Wheeler

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David A Wheeler

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An enhanced genetic model of colorectal cancer progression history.

Genome Biol 2019 Aug 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

Framework for microRNA variant annotation and prioritization using human population and disease datasets.

Hum Mutat 2019 Jan 8;40(1):73-89. Epub 2018 Nov 8.

Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030.

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http://doi.wiley.com/10.1002/humu.23668
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http://dx.doi.org/10.1002/humu.23668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400659PMC
January 2019

National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue.

Biopreserv Biobank 2018 Aug 19;16(4):247-250. Epub 2018 Jun 19.

4 Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute , Bethesda, Maryland.

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http://dx.doi.org/10.1089/bio.2018.0046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080192PMC
August 2018

Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma.

Eur Urol 2017 10 7;72(4):641-649. Epub 2017 Jun 7.

Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2017.05.048DOI Listing
October 2017

Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours.

Authors:
Aldo Scarpa David K Chang Katia Nones Vincenzo Corbo Ann-Marie Patch Peter Bailey Rita T Lawlor Amber L Johns David K Miller Andrea Mafficini Borislav Rusev Maria Scardoni Davide Antonello Stefano Barbi Katarzyna O Sikora Sara Cingarlini Caterina Vicentini Skye McKay Michael C J Quinn Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne McLean Craig Nourse Ehsan Nourbakhsh Peter J Wilson Matthew J Anderson J Lynn Fink Felicity Newell Nick Waddell Oliver Holmes Stephen H Kazakoff Conrad Leonard Scott Wood Qinying Xu Shivashankar Hiriyur Nagaraj Eliana Amato Irene Dalai Samantha Bersani Ivana Cataldo Angelo P Dei Tos Paola Capelli Maria Vittoria Davì Luca Landoni Anna Malpaga Marco Miotto Vicki L J Whitehall Barbara A Leggett Janelle L Harris Jonathan Harris Marc D Jones Jeremy Humphris Lorraine A Chantrill Venessa Chin Adnan M Nagrial Marina Pajic Christopher J Scarlett Andreia Pinho Ilse Rooman Christopher Toon Jianmin Wu Mark Pinese Mark Cowley Andrew Barbour Amanda Mawson Emily S Humphrey Emily K Colvin Angela Chou Jessica A Lovell Nigel B Jamieson Fraser Duthie Marie-Claude Gingras William E Fisher Rebecca A Dagg Loretta M S Lau Michael Lee Hilda A Pickett Roger R Reddel Jaswinder S Samra James G Kench Neil D Merrett Krishna Epari Nam Q Nguyen Nikolajs Zeps Massimo Falconi Michele Simbolo Giovanni Butturini George Van Buren Stefano Partelli Matteo Fassan Kum Kum Khanna Anthony J Gill David A Wheeler Richard A Gibbs Elizabeth A Musgrove Claudio Bassi Giampaolo Tortora Paolo Pederzoli John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2017 10 27;550(7677):548. Epub 2017 Sep 27.

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http://dx.doi.org/10.1038/nature24026DOI Listing
October 2017

Whole-genome landscape of pancreatic neuroendocrine tumours.

Authors:
Aldo Scarpa David K Chang Katia Nones Vincenzo Corbo Ann-Marie Patch Peter Bailey Rita T Lawlor Amber L Johns David K Miller Andrea Mafficini Borislav Rusev Maria Scardoni Davide Antonello Stefano Barbi Katarzyna O Sikora Sara Cingarlini Caterina Vicentini Skye McKay Michael C J Quinn Timothy J C Bruxner Angelika N Christ Ivon Harliwong Senel Idrisoglu Suzanne McLean Craig Nourse Ehsan Nourbakhsh Peter J Wilson Matthew J Anderson J Lynn Fink Felicity Newell Nick Waddell Oliver Holmes Stephen H Kazakoff Conrad Leonard Scott Wood Qinying Xu Shivashankar Hiriyur Nagaraj Eliana Amato Irene Dalai Samantha Bersani Ivana Cataldo Angelo P Dei Tos Paola Capelli Maria Vittoria Davì Luca Landoni Anna Malpaga Marco Miotto Vicki L J Whitehall Barbara A Leggett Janelle L Harris Jonathan Harris Marc D Jones Jeremy Humphris Lorraine A Chantrill Venessa Chin Adnan M Nagrial Marina Pajic Christopher J Scarlett Andreia Pinho Ilse Rooman Christopher Toon Jianmin Wu Mark Pinese Mark Cowley Andrew Barbour Amanda Mawson Emily S Humphrey Emily K Colvin Angela Chou Jessica A Lovell Nigel B Jamieson Fraser Duthie Marie-Claude Gingras William E Fisher Rebecca A Dagg Loretta M S Lau Michael Lee Hilda A Pickett Roger R Reddel Jaswinder S Samra James G Kench Neil D Merrett Krishna Epari Nam Q Nguyen Nikolajs Zeps Massimo Falconi Michele Simbolo Giovanni Butturini George Van Buren Stefano Partelli Matteo Fassan Kum Kum Khanna Anthony J Gill David A Wheeler Richard A Gibbs Elizabeth A Musgrove Claudio Bassi Giampaolo Tortora Paolo Pederzoli John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2017 03 15;543(7643):65-71. Epub 2017 Feb 15.

University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, 3010, Victoria, Australia.

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http://dx.doi.org/10.1038/nature21063DOI Listing
March 2017

Genomic Alterations of Adamantinomatous and Papillary Craniopharyngioma.

J Neuropathol Exp Neurol 2017 02;76(2):126-134

Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany.

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http://dx.doi.org/10.1093/jnen/nlw116DOI Listing
February 2017

Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera.

Blood 2016 11 19;128(18):2266-2270. Epub 2016 Sep 19.

Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT.

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http://dx.doi.org/10.1182/blood-2016-04-711283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5095759PMC
November 2016

Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle.

Cold Spring Harb Mol Case Stud 2016 Sep;2(5):a001057

Texas Children's Cancer Center and the Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA;; Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA;; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/mcs.a001057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5002928PMC
September 2016

Acquired uniparental disomy of chromosome 9p in hematologic malignancies.

Exp Hematol 2016 08 2;44(8):644-52. Epub 2015 Dec 2.

Division of Hematology, University of Utah School of Medicine and VAH, Salt Lake City, Utah. Electronic address:

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http://dx.doi.org/10.1016/j.exphem.2015.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5268131PMC
August 2016

Mixed-phenotype acute leukemia (MPAL) exhibits frequent mutations in DNMT3A and activated signaling genes.

Exp Hematol 2016 08 18;44(8):740-4. Epub 2016 May 18.

Cancer and Hematology Centers, Texas Children's Hospital/Baylor College of Medicine, Houston, TX. Electronic address:

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http://dx.doi.org/10.1016/j.exphem.2016.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956537PMC
August 2016

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.

Genome Biol 2016 08 24;17(1):178. Epub 2016 Aug 24.

Department of Bioinformatics and Computational Biology - Unit 1410, The University of Texas MD Anderson Cancer Center, P. O. Box 301402, Houston, 77230-1402, TX, USA.

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https://pdfs.semanticscholar.org/f720/841d49525c7f7167b41b51
Web Search
http://genomebiology.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13059-016-1029-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995747PMC
August 2016

Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs.

Pharmacogenet Genomics 2016 06;26(6):271-9

Departments of aMolecular and Human Genetics bBiochemistry and Molecular Biology cMolecular and Cellular Biology dHuman Genome Sequencing Center, Baylor College of Medicine eDepartment of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine fDepartment of Statistics, Rice University, Houston, Texas, USA.

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http://dx.doi.org/10.1097/FPC.0000000000000208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853247PMC
June 2016

SV-STAT accurately detects structural variation via alignment to reference-based assemblies.

Source Code Biol Med 2016 18;11. Epub 2016 Jun 18.

Structural and Computational Biology and Molecular Biophysics (SCBMB) Program, Baylor College of Medicine, Houston, TX 77030 USA ; Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030 USA ; W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX 77005 USA.

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http://dx.doi.org/10.1186/s13029-016-0051-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4913042PMC
June 2016

Clonal Dynamics In Vivo of Virus Integration Sites of T Cells Expressing a Safety Switch.

Mol Ther 2016 04 7;24(4):736-45. Epub 2015 Dec 7.

Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/mt.2015.217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886929PMC
April 2016

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.

BMC Bioinformatics 2016 Apr 27;17:188. Epub 2016 Apr 27.

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12859-016-1031-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847212PMC
April 2016

Genomic analyses identify molecular subtypes of pancreatic cancer.

Authors:
Peter Bailey David K Chang Katia Nones Amber L Johns Ann-Marie Patch Marie-Claude Gingras David K Miller Angelika N Christ Tim J C Bruxner Michael C Quinn Craig Nourse L Charles Murtaugh Ivon Harliwong Senel Idrisoglu Suzanne Manning Ehsan Nourbakhsh Shivangi Wani Lynn Fink Oliver Holmes Venessa Chin Matthew J Anderson Stephen Kazakoff Conrad Leonard Felicity Newell Nick Waddell Scott Wood Qinying Xu Peter J Wilson Nicole Cloonan Karin S Kassahn Darrin Taylor Kelly Quek Alan Robertson Lorena Pantano Laura Mincarelli Luis N Sanchez Lisa Evers Jianmin Wu Mark Pinese Mark J Cowley Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Lorraine A Chantrill Amanda Mawson Jeremy Humphris Angela Chou Marina Pajic Christopher J Scarlett Andreia V Pinho Marc Giry-Laterriere Ilse Rooman Jaswinder S Samra James G Kench Jessica A Lovell Neil D Merrett Christopher W Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Kim Moran-Jones Nigel B Jamieson Janet S Graham Fraser Duthie Karin Oien Jane Hair Robert Grützmann Anirban Maitra Christine A Iacobuzio-Donahue Christopher L Wolfgang Richard A Morgan Rita T Lawlor Vincenzo Corbo Claudio Bassi Borislav Rusev Paola Capelli Roberto Salvia Giampaolo Tortora Debabrata Mukhopadhyay Gloria M Petersen Donna M Munzy William E Fisher Saadia A Karim James R Eshleman Ralph H Hruban Christian Pilarsky Jennifer P Morton Owen J Sansom Aldo Scarpa Elizabeth A Musgrove Ulla-Maja Hagbo Bailey Oliver Hofmann Robert L Sutherland David A Wheeler Anthony J Gill Richard A Gibbs John V Pearson Nicola Waddell Andrew V Biankin Sean M Grimmond

Nature 2016 Mar 24;531(7592):47-52. Epub 2016 Feb 24.

Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1038/nature16965DOI Listing
March 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

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

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair.

Cell 2016 Jan 21;164(3):538-49. Epub 2016 Jan 21.

Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.12.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753048PMC
January 2016

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Nat Commun 2015 Dec 9;6:10001. Epub 2015 Dec 9.

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms10001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682041PMC
December 2015

BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.

Mod Pathol 2015 Apr 31;28(4):575-86. Epub 2014 Oct 31.

1] Department of Pathology, Texas Children's Hospital, Houston, TX, USA [2] Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA [3] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA [4] Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1038/modpathol.2014.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385430PMC
April 2015

Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis.

Blood 2014 Nov 8;124(19):3007-15. Epub 2014 Sep 8.

Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Human Genome Sequencing Center, Division of Pediatric Hematology-Oncology, Department of Pediatrics, Program in Translational Biology and Molecular Medicine, and.

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http://dx.doi.org/10.1182/blood-2014-05-577825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224195PMC
November 2014

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types.

Nat Commun 2014 Nov 20;5:5274. Epub 2014 Nov 20.

1] Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms6274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467577PMC
November 2014

Genomic sequencing for cancer diagnosis and therapy.

Annu Rev Med 2014 21;65:33-48. Epub 2013 Nov 21.

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030; email:

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http://dx.doi.org/10.1146/annurev-med-120811-171056DOI Listing
September 2014

Novel somatic and germline mutations in intracranial germ cell tumours.

Nature 2014 Jul 4;511(7508):241-5. Epub 2014 Jun 4.

1] Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas 77030, USA [2] Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA [3] Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532372PMC
July 2014

Effects of TP53 mutational status on gene expression patterns across 10 human cancer types.

J Pathol 2014 Apr 29;232(5):522-33. Epub 2014 Jan 29.

Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.

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http://dx.doi.org/10.1002/path.4321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362779PMC
April 2014

From human genome to cancer genome: the first decade.

Genome Res 2013 Jul;23(7):1054-62

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.157602.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698498PMC
July 2013

Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing.

Pediatr Blood Cancer 2013 Jun 19;60(6):E1-3. Epub 2012 Dec 19.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1002/pbc.24417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926299PMC
June 2013

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Authors:
Andrew V Biankin Nicola Waddell Karin S Kassahn Marie-Claude Gingras Lakshmi B Muthuswamy Amber L Johns David K Miller Peter J Wilson Ann-Marie Patch Jianmin Wu David K Chang Mark J Cowley Brooke B Gardiner Sarah Song Ivon Harliwong Senel Idrisoglu Craig Nourse Ehsan Nourbakhsh Suzanne Manning Shivangi Wani Milena Gongora Marina Pajic Christopher J Scarlett Anthony J Gill Andreia V Pinho Ilse Rooman Matthew Anderson Oliver Holmes Conrad Leonard Darrin Taylor Scott Wood Qinying Xu Katia Nones J Lynn Fink Angelika Christ Tim Bruxner Nicole Cloonan Gabriel Kolle Felicity Newell Mark Pinese R Scott Mead Jeremy L Humphris Warren Kaplan Marc D Jones Emily K Colvin Adnan M Nagrial Emily S Humphrey Angela Chou Venessa T Chin Lorraine A Chantrill Amanda Mawson Jaswinder S Samra James G Kench Jessica A Lovell Roger J Daly Neil D Merrett Christopher Toon Krishna Epari Nam Q Nguyen Andrew Barbour Nikolajs Zeps Nipun Kakkar Fengmei Zhao Yuan Qing Wu Min Wang Donna M Muzny William E Fisher F Charles Brunicardi Sally E Hodges Jeffrey G Reid Jennifer Drummond Kyle Chang Yi Han Lora R Lewis Huyen Dinh Christian J Buhay Timothy Beck Lee Timms Michelle Sam Kimberly Begley Andrew Brown Deepa Pai Ami Panchal Nicholas Buchner Richard De Borja Robert E Denroche Christina K Yung Stefano Serra Nicole Onetto Debabrata Mukhopadhyay Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Steven Gallinger Ralph H Hruban Anirban Maitra Christine A Iacobuzio-Donahue Richard D Schulick Christopher L Wolfgang Richard A Morgan Rita T Lawlor Paola Capelli Vincenzo Corbo Maria Scardoni Giampaolo Tortora Margaret A Tempero Karen M Mann Nancy A Jenkins Pedro A Perez-Mancera David J Adams David A Largaespada Lodewyk F A Wessels Alistair G Rust Lincoln D Stein David A Tuveson Neal G Copeland Elizabeth A Musgrove Aldo Scarpa James R Eshleman Thomas J Hudson Robert L Sutherland David A Wheeler John V Pearson John D McPherson Richard A Gibbs Sean M Grimmond

Nature 2012 Nov 24;491(7424):399-405. Epub 2012 Oct 24.

The Kinghorn Cancer Centre, 370 Victoria Street, Darlinghurst, Sydney, New South Wales 2010, Australia.

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http://dx.doi.org/10.1038/nature11547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530898PMC
November 2012

Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children.

Physiol Genomics 2011 Sep 19;43(18):1029-37. Epub 2011 Jul 19.

Department of Pediatrics, Baylor College of Medicine, US Department of Agriculture/Agricultural Research Service Children's Nutrition Research Center, Houston, TX, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00019.2011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180738PMC
September 2011

Building a comprehensive genomic program for hepatocellular carcinoma.

World J Surg 2011 Aug;35(8):1746-50

Michael E. DeBakey Department of Surgery, Baylor College of Medicine, One Baylor Plaza, Jewish Bldg #404D, Houston, TX 77030, USA.

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http://dx.doi.org/10.1007/s00268-010-0954-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137964PMC
August 2011

Overview of the development of personalized genomic medicine and surgery.

World J Surg 2011 Aug;35(8):1693-9

Michael E. DeBakey Department of Surgery, Baylor College of Medicine, 1709 Dryden Street, Suite 1500, Houston, TX 77030, USA.

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http://dx.doi.org/10.1007/s00268-011-1056-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281749PMC
August 2011

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation.

Authors:
Florencia Pereyra Xiaoming Jia Paul J McLaren Amalio Telenti Paul I W de Bakker Bruce D Walker Stephan Ripke Chanson J Brumme Sara L Pulit Mary Carrington Carl M Kadie Jonathan M Carlson David Heckerman Robert R Graham Robert M Plenge Steven G Deeks Lauren Gianniny Gabriel Crawford Jordan Sullivan Elena Gonzalez Leela Davies Amy Camargo Jamie M Moore Nicole Beattie Supriya Gupta Andrew Crenshaw Noël P Burtt Candace Guiducci Namrata Gupta Xiaojiang Gao Ying Qi Yuko Yuki Alicja Piechocka-Trocha Emily Cutrell Rachel Rosenberg Kristin L Moss Paul Lemay Jessica O'Leary Todd Schaefer Pranshu Verma Ildiko Toth Brian Block Brett Baker Alissa Rothchild Jeffrey Lian Jacqueline Proudfoot Donna Marie L Alvino Seanna Vine Marylyn M Addo Todd M Allen Marcus Altfeld Matthew R Henn Sylvie Le Gall Hendrik Streeck David W Haas Daniel R Kuritzkes Gregory K Robbins Robert W Shafer Roy M Gulick Cecilia M Shikuma Richard Haubrich Sharon Riddler Paul E Sax Eric S Daar Heather J Ribaudo Brian Agan Shanu Agarwal Richard L Ahern Brady L Allen Sherly Altidor Eric L Altschuler Sujata Ambardar Kathryn Anastos Ben Anderson Val Anderson Ushan Andrady Diana Antoniskis David Bangsberg Daniel Barbaro William Barrie J Bartczak Simon Barton Patricia Basden Nesli Basgoz Suzane Bazner Nicholaos C Bellos Anne M Benson Judith Berger Nicole F Bernard Annette M Bernard Christopher Birch Stanley J Bodner Robert K Bolan Emilie T Boudreaux Meg Bradley James F Braun Jon E Brndjar Stephen J Brown Katherine Brown Sheldon T Brown Jedidiah Burack Larry M Bush Virginia Cafaro Omobolaji Campbell John Campbell Robert H Carlson J Kevin Carmichael Kathleen K Casey Chris Cavacuiti Gregory Celestin Steven T Chambers Nancy Chez Lisa M Chirch Paul J Cimoch Daniel Cohen Lillian E Cohn Brian Conway David A Cooper Brian Cornelson David T Cox Michael V Cristofano George Cuchural Julie L Czartoski Joseph M Dahman Jennifer S Daly Benjamin T Davis Kristine Davis Sheila M Davod Edwin DeJesus Craig A Dietz Eleanor Dunham Michael E Dunn Todd B Ellerin Joseph J Eron John J W Fangman Claire E Farel Helen Ferlazzo Sarah Fidler Anita Fleenor-Ford Renee Frankel Kenneth A Freedberg Neel K French Jonathan D Fuchs Jon D Fuller Jonna Gaberman Joel E Gallant Rajesh T Gandhi Efrain Garcia Donald Garmon Joseph C Gathe Cyril R Gaultier Wondwoosen Gebre Frank D Gilman Ian Gilson Paul A Goepfert Michael S Gottlieb Claudia Goulston Richard K Groger T Douglas Gurley Stuart Haber Robin Hardwicke W David Hardy P Richard Harrigan Trevor N Hawkins Sonya Heath Frederick M Hecht W Keith Henry Melissa Hladek Robert P Hoffman James M Horton Ricky K Hsu Gregory D Huhn Peter Hunt Mark J Hupert Mark L Illeman Hans Jaeger Robert M Jellinger Mina John Jennifer A Johnson Kristin L Johnson Heather Johnson Kay Johnson Jennifer Joly Wilbert C Jordan Carol A Kauffman Homayoon Khanlou Robert K Killian Arthur Y Kim David D Kim Clifford A Kinder Jeffrey T Kirchner Laura Kogelman Erna Milunka Kojic P Todd Korthuis Wayne Kurisu Douglas S Kwon Melissa LaMar Harry Lampiris Massimiliano Lanzafame Michael M Lederman David M Lee Jean M L Lee Marah J Lee Edward T Y Lee Janice Lemoine Jay A Levy Josep M Llibre Michael A Liguori Susan J Little Anne Y Liu Alvaro J Lopez Mono R Loutfy Dawn Loy Debbie Y Mohammed Alan Man Michael K Mansour Vincent C Marconi Martin Markowitz Rui Marques Jeffrey N Martin Harold L Martin Kenneth Hugh Mayer M Juliana McElrath Theresa A McGhee Barbara H McGovern Katherine McGowan Dawn McIntyre Gavin X Mcleod Prema Menezes Greg Mesa Craig E Metroka Dirk Meyer-Olson Andy O Miller Kate Montgomery Karam C Mounzer Ellen H Nagami Iris Nagin Ronald G Nahass Margret O Nelson Craig Nielsen David L Norene David H O'Connor Bisola O Ojikutu Jason Okulicz Olakunle O Oladehin Edward C Oldfield Susan A Olender Mario Ostrowski William F Owen Eunice Pae Jeffrey Parsonnet Andrew M Pavlatos Aaron M Perlmutter Michael N Pierce Jonathan M Pincus Leandro Pisani Lawrence Jay Price Laurie Proia Richard C Prokesch Heather Calderon Pujet Moti Ramgopal Almas Rathod Michael Rausch J Ravishankar Frank S Rhame Constance Shamuyarira Richards Douglas D Richman Berta Rodes Milagros Rodriguez Richard C Rose Eric S Rosenberg Daniel Rosenthal Polly E Ross David S Rubin Elease Rumbaugh Luis Saenz Michelle R Salvaggio William C Sanchez Veeraf M Sanjana Steven Santiago Wolfgang Schmidt Hanneke Schuitemaker Philip M Sestak Peter Shalit William Shay Vivian N Shirvani Vanessa I Silebi James M Sizemore Paul R Skolnik Marcia Sokol-Anderson James M Sosman Paul Stabile Jack T Stapleton Sheree Starrett Francine Stein Hans-Jurgen Stellbrink F Lisa Sterman Valerie E Stone David R Stone Giuseppe Tambussi Randy A Taplitz Ellen M Tedaldi Amalio Telenti William Theisen Richard Torres Lorraine Tosiello Cecile Tremblay Marc A Tribble Phuong D Trinh Alice Tsao Peggy Ueda Anthony Vaccaro Emilia Valadas Thanes J Vanig Isabel Vecino Vilma M Vega Wenoah Veikley Barbara H Wade Charles Walworth Chingchai Wanidworanun Douglas J Ward Daniel A Warner Robert D Weber Duncan Webster Steve Weis David A Wheeler David J White Ed Wilkins Alan Winston Clifford G Wlodaver Angelique van't Wout David P Wright Otto O Yang David L Yurdin Brandon W Zabukovic Kimon C Zachary Beth Zeeman Meng Zhao

Science 2010 Dec 4;330(6010):1551-7. Epub 2010 Nov 4.

Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA.

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http://dx.doi.org/10.1126/science.1195271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235490PMC
December 2010

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.

PLoS One 2010 Jan 27;5(1):e8910. Epub 2010 Jan 27.

Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008910PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811727PMC
January 2010