Publications by authors named "Paul Spellman"

100Publications

Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.

Cancer Cell 2020 Oct 26. Epub 2020 Oct 26.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2020.10.008DOI Listing
October 2020

Diurnal stability of cell-free DNA and cell-free RNA in human plasma samples.

Sci Rep 2020 10 5;10(1):16456. Epub 2020 Oct 5.

Knight Cancer Institute, Cancer Early Detection Advanced Research Center (CEDAR), Oregon Health & Science University, Portland, OR, 97201, USA.

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http://dx.doi.org/10.1038/s41598-020-73350-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7536441PMC
October 2020

Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6.

RNA 2020 06 6;26(6):724-738. Epub 2020 Mar 6.

Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1261/rna.073114.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7266157PMC
June 2020

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets.

Cancer Cell 2019 04 28;35(4):588-602.e10. Epub 2019 Mar 28.

MRC Centre for Reproductive Health, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh EH16 4TJ, UK; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York 10461, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2019.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472943PMC
April 2019

Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity.

PLoS One 2019 25;14(3):e0205623. Epub 2019 Mar 25.

Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205623PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433232PMC
November 2019

Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer.

Cold Spring Harb Mol Case Stud 2019 04 1;5(2). Epub 2019 Apr 1.

Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU) Portland, Oregon 97201, USA.

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http://dx.doi.org/10.1101/mcs.a003772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549569PMC
April 2019

Alternative Splicing in Tumors - A Path to Immunogenicity?

N Engl J Med 2019 02;380(9):877-880

From the Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora (J.E.S.); and the Department of Molecular and Medical Genetics, Oregon Health and Science University, and the Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Portland (P.T.S.).

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http://dx.doi.org/10.1056/NEJMcibr1814237DOI Listing
February 2019

Long-Term Correction of Diabetes in Mice by In Vivo Reprogramming of Pancreatic Ducts.

Mol Ther 2018 05 21;26(5):1327-1342. Epub 2018 Feb 21.

Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymthe.2018.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993989PMC
May 2018

Physiologically activated mammary fibroblasts promote postpartum mammary cancer.

JCI Insight 2017 03 23;2(6):e89206. Epub 2017 Mar 23.

Department of Cell, Developmental and Cancer Biology.

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http://dx.doi.org/10.1172/jci.insight.89206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358521PMC
March 2017

Circulating-tumor DNA as an early detection and diagnostic tool.

Curr Opin Genet Dev 2017 Feb 23;42:14-21. Epub 2017 Jan 23.

Oregon Health and Science University Department of Biomedical Engineering, Mail Code CL3G, 2730 SW Moody Ave., Portland, OR 97201-5042, United States; Oregon Health and Science University Knight Cancer Institute, Mail Code CR145, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, United States; Oregon Health and Science University Center for Spatial System Biomedicine, Collaborative Life Sciences Building, 2730 SW Moody Ave, Mail Code CL3G, Portland, OR 97201-5042, United States. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.12.003DOI Listing
February 2017

ΔN-ASPP2, a novel isoform of the ASPP2 tumor suppressor, promotes cellular survival.

Biochem Biophys Res Commun 2017 Jan 8;482(4):1271-1277. Epub 2016 Dec 8.

Department of Medicine, Division of Hematology and Medical Oncology and the Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2016.12.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237613PMC
January 2017

FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer.

Proc Natl Acad Sci U S A 2016 10 6;113(43):E6600-E6609. Epub 2016 Oct 6.

Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Department of Medicine, Baylor College of Medicine, Houston, TX 77030;

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http://dx.doi.org/10.1073/pnas.1612835113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087040PMC
October 2016

Patient-specific factors influence somatic variation patterns in von Hippel-Lindau disease renal tumours.

Nat Commun 2016 05 13;7:11588. Epub 2016 May 13.

Department of Molecular &Medical Genetics, Oregon Health &Science University, Mail Code: CL6S, 2730 SW Moody St, Portland, Oregon 97201, USA.

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http://dx.doi.org/10.1038/ncomms11588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869254PMC
May 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

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

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma.

JAMA Oncol 2015 Jul;1(4):486-94

Department of Pathology, University of Texas MD Anderson Cancer Center, Houston2Institute for Systems Biology/MD Anderson Cancer Center Genome Data Analysis Center, The Cancer Genome Atlas, Bethesda, Maryland.

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http://oncology.jamanetwork.com/article.aspx?doi=10.1001/jam
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http://dx.doi.org/10.1001/jamaoncol.2015.1432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608536PMC
July 2015

Stacked Predictive Sparse Decomposition for Classification of Histology Sections.

Int J Comput Vis 2015 May 23;113(1):3-18. Epub 2014 Dec 23.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051579PMC
http://dx.doi.org/10.1007/s11263-014-0790-9DOI Listing
May 2015

A humanized leucine zipper-TRAIL hybrid induces apoptosis of tumors both in vitro and in vivo.

PLoS One 2015 7;10(4):e0122980. Epub 2015 Apr 7.

Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122980PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388654PMC
March 2016

Classification of Histology Sections via Multispectral Convolutional Sparse Coding.

Conf Comput Vis Pattern Recognit Workshops 2014 Jun;2014:3081-3088

University of California, Riverside, U.S.A.

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http://dx.doi.org/10.1109/CVPR.2014.394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279924PMC
June 2014

Detecting cancer by monitoring circulating tumor DNA.

Nat Med 2014 May;20(5):474-5

Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1038/nm.3564DOI Listing
May 2014

Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching.

Med Image Comput Comput Assist Interv 2013 ;16(Pt 2):91-8

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998828PMC
http://dx.doi.org/10.1007/978-3-642-40763-5_12DOI Listing
April 2014

Integrated analysis of germline and somatic variants in ovarian cancer.

Nat Commun 2014 ;5:3156

1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA [4] Department of Medicine, Washington University, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/ncomms4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025965PMC
March 2016

CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING.

Proc IEEE Int Symp Biomed Imaging 2013 Apr;2013

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.

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http://dx.doi.org/10.1109/ISBI.2013.6556499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850768PMC
April 2013

Classification of Tumor Histology via Morphometric Context.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit 2013 Jun;2013

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.

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http://dx.doi.org/10.1109/CVPR.2013.286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3850786PMC
June 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
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http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
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http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

A robust prognostic signature for hormone-positive node-negative breast cancer.

Genome Med 2013 11;5(10):92. Epub 2013 Oct 11.

Department of Cancer and DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley 94720, CA, USA ; Department of Biomedical Engineering, Center for Spatial Systems Biomedicine, Knight Cancer Institute, Oregon Health and Science University, 3303 SW Bond Ave, Portland, 97239, OR, USA.

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http://dx.doi.org/10.1186/gm496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961800PMC
May 2014

HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression.

Springerplus 2013 15;2:386. Epub 2013 Aug 15.

Division of Hematology and Medical Oncology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, MC L586, Portland, OR 97239 USA ; Portland VA Medical Center, 3710 SW US Veterans Hospital Road, Portland, OR 97239 USA ; Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239 USA.

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http://dx.doi.org/10.1186/2193-1801-2-386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791222PMC
October 2013

Methods and challenges in timing chromosomal abnormalities within cancer samples.

Bioinformatics 2013 Dec 23;29(24):3113-20. Epub 2013 Sep 23.

Department of Statistics, University of California, Berkeley, 367 Evans Hall Berkeley, CA 94720-3860, USA, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA and Department of Dermatology, University of California, San Francisco, CA 94115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842754PMC
December 2013

Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer.

Nucleic Acids Res 2013 Oct 24;41(18):8464-74. Epub 2013 Jul 24.

Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea, Bioinformatics Institute, Seoul National University, Seoul 151-744, Korea, School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA, The Ohio State University Comprehensive Cancer Center Nucleic Acid Shared Resource-Illumina Core, Columbus, OH 43210, USA, School of Computer Science and Engineering, Seoul National University, Seoul 151-742, Korea, OHSU Knight Cancer Institute, Portland, OR 97239, USA, Department of Molecular Medicine/Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA, Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.1093/nar/gkt643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794600PMC
October 2013

Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells.

Mol Cancer 2013 Apr 26;12:32. Epub 2013 Apr 26.

Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA2015, Tampa, FL 33620, USA.

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http://molecular-cancer.biomedcentral.com/articles/10.1186/1
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http://dx.doi.org/10.1186/1476-4598-12-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644492PMC
April 2013

GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.

Authors:
Paul D P Pharoah Ya-Yu Tsai Susan J Ramus Catherine M Phelan Ellen L Goode Kate Lawrenson Melissa Buckley Brooke L Fridley Jonathan P Tyrer Howard Shen Rachel Weber Rod Karevan Melissa C Larson Honglin Song Daniel C Tessier François Bacot Daniel Vincent Julie M Cunningham Joe Dennis Ed Dicks Katja K Aben Hoda Anton-Culver Natalia Antonenkova Sebastian M Armasu Laura Baglietto Elisa V Bandera Matthias W Beckmann Michael J Birrer Greg Bloom Natalia Bogdanova James D Brenton Louise A Brinton Angela Brooks-Wilson Robert Brown Ralf Butzow Ian Campbell Michael E Carney Renato S Carvalho Jenny Chang-Claude Y Anne Chen Zhihua Chen Wong-Ho Chow Mine S Cicek Gerhard Coetzee Linda S Cook Daniel W Cramer Cezary Cybulski Agnieszka Dansonka-Mieszkowska Evelyn Despierre Jennifer A Doherty Thilo Dörk Andreas du Bois Matthias Dürst Diana Eccles Robert Edwards Arif B Ekici Peter A Fasching David Fenstermacher James Flanagan Yu-Tang Gao Montserrat Garcia-Closas Aleksandra Gentry-Maharaj Graham Giles Anxhela Gjyshi Martin Gore Jacek Gronwald Qi Guo Mari K Halle Philipp Harter Alexander Hein Florian Heitz Peter Hillemanns Maureen Hoatlin Estrid Høgdall Claus K Høgdall Satoyo Hosono Anna Jakubowska Allan Jensen Kimberly R Kalli Beth Y Karlan Linda E Kelemen Lambertus A Kiemeney Susanne Krüger Kjaer Gottfried E Konecny Camilla Krakstad Jolanta Kupryjanczyk Diether Lambrechts Sandrina Lambrechts Nhu D Le Nathan Lee Janet Lee Arto Leminen Boon Kiong Lim Jolanta Lissowska Jan Lubiński Lene Lundvall Galina Lurie Leon F A G Massuger Keitaro Matsuo Valerie McGuire John R McLaughlin Usha Menon Francesmary Modugno Kirsten B Moysich Toru Nakanishi Steven A Narod Roberta B Ness Heli Nevanlinna Stefan Nickels Houtan Noushmehr Kunle Odunsi Sara Olson Irene Orlow James Paul Tanja Pejovic Liisa M Pelttari Jenny Permuth-Wey Malcolm C Pike Elizabeth M Poole Xiaotao Qu Harvey A Risch Lorna Rodriguez-Rodriguez Mary Anne Rossing Anja Rudolph Ingo Runnebaum Iwona K Rzepecka Helga B Salvesen Ira Schwaab Gianluca Severi Hui Shen Vijayalakshmi Shridhar Xiao-Ou Shu Weiva Sieh Melissa C Southey Paul Spellman Kazuo Tajima Soo-Hwang Teo Kathryn L Terry Pamela J Thompson Agnieszka Timorek Shelley S Tworoger Anne M van Altena David van den Berg Ignace Vergote Robert A Vierkant Allison F Vitonis Shan Wang-Gohrke Nicolas Wentzensen Alice S Whittemore Elisabeth Wik Boris Winterhoff Yin Ling Woo Anna H Wu Hannah P Yang Wei Zheng Argyrios Ziogas Famida Zulkifli Marc T Goodman Per Hall Douglas F Easton Celeste L Pearce Andrew Berchuck Georgia Chenevix-Trench Edwin Iversen Alvaro N A Monteiro Simon A Gayther Joellen M Schildkraut Thomas A Sellers

Nat Genet 2013 Apr;45(4):362-70, 370e1-2

The Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.2564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693183PMC
April 2013

Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology.

Proc IEEE Int Conf Comput Vis 2013 :169-176

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A.

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http://dx.doi.org/10.1109/ICCV.2013.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998824PMC
January 2013

Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.

IEEE Trans Med Imaging 2013 Apr 4;32(4):670-82. Epub 2012 Dec 4.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1109/TMI.2012.2231420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728287PMC
April 2013

Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.

IEEE Trans Biomed Eng 2012 Dec 10;59(12):3460-7. Epub 2012 Sep 10.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1109/TBME.2012.2218107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728286PMC
December 2012

Bayesian inference of signaling network topology in a cancer cell line.

Bioinformatics 2012 Nov 24;28(21):2804-10. Epub 2012 Aug 24.

Department of Biochemistry, The Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bts514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476330PMC
November 2012

Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing.

Cancer Discov 2012 Jan;2(1):23-4

Department of Pathology, and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA.

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http://dx.doi.org/10.1158/2159-8290.CD-11-0319DOI Listing
January 2012

Morphometic analysis of TCGA glioblastoma multiforme.

BMC Bioinformatics 2011 Dec 20;12:484. Epub 2011 Dec 20.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1186/1471-2105-12-484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271112PMC
December 2011

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

Bioinformatics 2011 Aug 11;27(15):2038-46. Epub 2011 Jun 11.

Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137217PMC
August 2011

A new treasure in the breast cancer gene hunt.

Nat Med 2011 Apr;17(4):422-3

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http://dx.doi.org/10.1038/nm0411-422DOI Listing
April 2011

Unifying gene expression measures from multiple platforms using factor analysis.

PLoS One 2011 Mar 11;6(3):e17691. Epub 2011 Mar 11.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059153PMC
March 2011

Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI.

Integr Biol (Camb) 2011 Apr 18;3(4):490-6. Epub 2011 Mar 18.

Department of Radiation Oncology, University of California, San Francisco Comprehensive Cancer Center, 1600 Divisadero Street H1031, San Francisco, CA 94143-1708, USA.

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http://xlink.rsc.org/?DOI=c0ib00089b
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http://dx.doi.org/10.1039/c0ib00089bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698966PMC
April 2011

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
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