Benjamin J Raphael

Benjamin J Raphael

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Benjamin J Raphael

Publications by authors named "Benjamin J Raphael"

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netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis.

Authors:
Rebecca Elyanow Bianca Dumitrascu Barbara E Engelhardt Benjamin J Raphael

Genome Res 2020 Feb 28;30(2):195-204. Epub 2020 Jan 28.

Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.

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http://dx.doi.org/10.1101/gr.251603.119DOI Listing
February 2020

Pathway and network analysis of more than 2500 whole cancer genomes.

Authors:
Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael

Nat Commun 2020 Feb 5;11(1):729. Epub 2020 Feb 5.

Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA.

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http://dx.doi.org/10.1038/s41467-020-14367-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002574PMC
February 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Authors:
Esther Rheinbay Morten Muhlig Nielsen Federico Abascal Jeremiah A Wala Ofer Shapira Grace Tiao Henrik Hornshøj Julian M Hess Randi Istrup Juul Ziao Lin Lars Feuerbach Radhakrishnan Sabarinathan Tobias Madsen Jaegil Kim Loris Mularoni Shimin Shuai Andrés Lanzós Carl Herrmann Yosef E Maruvka Ciyue Shen Samirkumar B Amin Pratiti Bandopadhayay Johanna Bertl Keith A Boroevich John Busanovich Joana Carlevaro-Fita Dimple Chakravarty Calvin Wing Yiu Chan David Craft Priyanka Dhingra Klev Diamanti Nuno A Fonseca Abel Gonzalez-Perez Qianyun Guo Mark P Hamilton Nicholas J Haradhvala Chen Hong Keren Isaev Todd A Johnson Malene Juul Andre Kahles Abdullah Kahraman Youngwook Kim Jan Komorowski Kiran Kumar Sushant Kumar Donghoon Lee Kjong-Van Lehmann Yilong Li Eric Minwei Liu Lucas Lochovsky Keunchil Park Oriol Pich Nicola D Roberts Gordon Saksena Steven E Schumacher Nikos Sidiropoulos Lina Sieverling Nasa Sinnott-Armstrong Chip Stewart David Tamborero Jose M C Tubio Husen M Umer Liis Uusküla-Reimand Claes Wadelius Lina Wadi Xiaotong Yao Cheng-Zhong Zhang Jing Zhang James E Haber Asger Hobolth Marcin Imielinski Manolis Kellis Michael S Lawrence Christian von Mering Hidewaki Nakagawa Benjamin J Raphael Mark A Rubin Chris Sander Lincoln D Stein Joshua M Stuart Tatsuhiko Tsunoda David A Wheeler Rory Johnson Jüri Reimand Mark Gerstein Ekta Khurana Peter J Campbell Núria López-Bigas Joachim Weischenfeldt Rameen Beroukhim Iñigo Martincorena Jakob Skou Pedersen Gad Getz

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
February 2020

Eleven grand challenges in single-cell data science.

Authors:
David Lähnemann Johannes Köster Ewa Szczurek Davis J McCarthy Stephanie C Hicks Mark D Robinson Catalina A Vallejos Kieran R Campbell Niko Beerenwinkel Ahmed Mahfouz Luca Pinello Pavel Skums Alexandros Stamatakis Camille Stephan-Otto Attolini Samuel Aparicio Jasmijn Baaijens Marleen Balvert Buys de Barbanson Antonio Cappuccio Giacomo Corleone Bas E Dutilh Maria Florescu Victor Guryev Rens Holmer Katharina Jahn Thamar Jessurun Lobo Emma M Keizer Indu Khatri Szymon M Kielbasa Jan O Korbel Alexey M Kozlov Tzu-Hao Kuo Boudewijn P F Lelieveldt Ion I Mandoiu John C Marioni Tobias Marschall Felix Mölder Amir Niknejad Lukasz Raczkowski Marcel Reinders Jeroen de Ridder Antoine-Emmanuel Saliba Antonios Somarakis Oliver Stegle Fabian J Theis Huan Yang Alex Zelikovsky Alice C McHardy Benjamin J Raphael Sohrab P Shah Alexander Schönhuth

Genome Biol 2020 Feb 7;21(1):31. Epub 2020 Feb 7.

Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s13059-020-1926-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007675PMC
February 2020

Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.

Authors:
Benshang Li Samuel W Brady Xiaotu Ma Shuhong Shen Yingchi Zhang Yongjin Li Karol Szlachta Li Dong Yu Liu Fan Yang Ningling Wang Diane A Flasch Matthew A Myers Heather L Mulder Lixia Ding Yanling Liu Liqing Tian Kohei Hagiwara Ke Xu Xin Zhou Edgar Sioson Tianyi Wang Liu Yang Jie Zhao Hui Zhang Ying Shao Hongye Sun Lele Sun Jiaoyang Cai Hui-Ying Sun Ting-Nien Lin Lijuan Du Hui Li Michael Rusch Michael N Edmonson John Easton Xiaofan Zhu Jingliao Zhang Cheng Cheng Benjamin J Raphael Jingyan Tang James R Downing Ludmil B Alexandrov Bin-Bing S Zhou Ching-Hon Pui Jun J Yang Jinghui Zhang

Blood 2020 Jan;135(1):41-55

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN.

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http://dx.doi.org/10.1182/blood.2019002220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940198PMC
January 2020

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Authors:
Matthew A Myers Gryte Satas Benjamin J Raphael

Cell Syst 2019 Jun 19;8(6):514-522.e5. Epub 2019 Jun 19.

Department of Computer Science, Princeton University, Princeton, NJ 08540, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.010DOI Listing
June 2019

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.

Authors:
Samuel W Brady Xiaotu Ma Armita Bahrami Gryte Satas Gang Wu Scott Newman Michael Rusch Daniel K Putnam Heather L Mulder Donald A Yergeau Michael N Edmonson John Easton Ludmil B Alexandrov Xiang Chen Elaine R Mardis Richard K Wilson James R Downing Alberto S Pappo Benjamin J Raphael Michael A Dyer Jinghui Zhang

Mol Cancer Res 2019 04 16;17(4):895-906. Epub 2019 Jan 16.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.

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http://mcr.aacrjournals.org/lookup/doi/10.1158/1541-7786.MCR
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http://dx.doi.org/10.1158/1541-7786.MCR-18-0620DOI Listing
April 2019

Using controls to limit false discovery in the era of big data.

Authors:
Matthew M Parks Benjamin J Raphael Charles E Lawrence

BMC Bioinformatics 2018 Sep 14;19(1):323. Epub 2018 Sep 14.

Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI, 02912, USA.

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http://dx.doi.org/10.1186/s12859-018-2356-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137876PMC
September 2018

Hierarchical HotNet: identifying hierarchies of altered subnetworks.

Authors:
Matthew A Reyna Mark D M Leiserson Benjamin J Raphael

Bioinformatics 2018 09;34(17):i972-i980

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129270PMC
September 2018

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Authors:
Simone Zaccaria Mohammed El-Kebir Gunnar W Klau Benjamin J Raphael

J Comput Biol 2018 07 16;25(7):689-708. Epub 2018 Apr 16.

1 Department of Computer Science, Princeton University , Princeton, New Jersey.

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http://www.liebertpub.com/doi/10.1089/cmb.2017.0253
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http://dx.doi.org/10.1089/cmb.2017.0253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067108PMC
July 2018

Haplotype phasing in single-cell DNA-sequencing data.

Authors:
Gryte Satas Benjamin J Raphael

Bioinformatics 2018 07;34(13):i211-i217

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022575PMC
July 2018

Visible Machine Learning for Biomedicine.

Authors:
Michael K Yu Jianzhu Ma Jasmin Fisher Jason F Kreisberg Benjamin J Raphael Trey Ideker

Cell 2018 06;173(7):1562-1565

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Cancer Cell Map Initiative, University of California San Diego, La Jolla, CA, USA; UCSD Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.05.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483071PMC
June 2018

Inferring parsimonious migration histories for metastatic cancers.

Authors:
Mohammed El-Kebir Gryte Satas Benjamin J Raphael

Nat Genet 2018 05 26;50(5):718-726. Epub 2018 Apr 26.

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1038/s41588-018-0106-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103651PMC
May 2018

Identifying structural variants using linked-read sequencing data.

Authors:
Rebecca Elyanow Hsin-Ta Wu Benjamin J Raphael

Bioinformatics 2018 Jan;34(2):353-360

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860216PMC
January 2018

Identifying simultaneous rearrangements in cancer genomes.

Authors:
Layla Oesper Simone Dantas Benjamin J Raphael

Bioinformatics 2018 Jan;34(2):346-352

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860217PMC
January 2018

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.

Authors:
Jack Kuipers Katharina Jahn Benjamin J Raphael Niko Beerenwinkel

Genome Res 2017 11 13;27(11):1885-1894. Epub 2017 Oct 13.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.

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http://dx.doi.org/10.1101/gr.220707.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668945PMC
November 2017

Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations.

Authors:
Priyanka Nakka Natalie P Archer Heng Xu Philip J Lupo Benjamin J Raphael Jun J Yang Sohini Ramachandran

Cancer Epidemiol Biomarkers Prev 2017 10 27;26(10):1531-1539. Epub 2017 Jul 27.

Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island.

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http://dx.doi.org/10.1158/1055-9965.EPI-17-0360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626662PMC
October 2017

Network propagation: a universal amplifier of genetic associations.

Authors:
Lenore Cowen Trey Ideker Benjamin J Raphael Roded Sharan

Nat Rev Genet 2017 09 12;18(9):551-562. Epub 2017 Jun 12.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://www.nature.com/doifinder/10.1038/nrg.2017.38
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http://dx.doi.org/10.1038/nrg.2017.38DOI Listing
September 2017

GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

Authors:
R Jay Mashl Adam D Scott Kuan-Lin Huang Matthew A Wyczalkowski Christopher J Yoon Beifang Niu Erin DeNardo Venkata D Yellapantula Robert E Handsaker Ken Chen Daniel C Koboldt Kai Ye David Fenyö Benjamin J Raphael Michael C Wendl Li Ding

Genome Res 2017 08 18;27(8):1450-1459. Epub 2017 May 18.

McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1101/gr.211656.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538560PMC
August 2017

Tumor phylogeny inference using tree-constrained importance sampling.

Authors:
Gryte Satas Benjamin J Raphael

Bioinformatics 2017 Jul;33(14):i152-i160

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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https://academic.oup.com/bioinformatics/article/33/14/i152/3
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http://dx.doi.org/10.1093/bioinformatics/btx270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870673PMC
July 2017

Complexity and algorithms for copy-number evolution problems.

Authors:
Mohammed El-Kebir Benjamin J Raphael Ron Shamir Roded Sharan Simone Zaccaria Meirav Zehavi Ron Zeira

Algorithms Mol Biol 2017 16;12:13. Epub 2017 May 16.

School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1186/s13015-017-0103-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433102PMC
May 2017

Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases.

Authors:
Priyanka Nakka Benjamin J Raphael Sohini Ramachandran

Genetics 2016 Oct 3;204(2):783-798. Epub 2016 Aug 3.

Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912

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http://dx.doi.org/10.1534/genetics.116.188391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068862PMC
October 2016

A weighted exact test for mutually exclusive mutations in cancer.

Authors:
Mark D M Leiserson Matthew A Reyna Benjamin J Raphael

Bioinformatics 2016 09;32(17):i736-i745

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013919PMC
September 2016

Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Authors:
Mark D M Leiserson Hsin-Ta Wu Fabio Vandin Benjamin J Raphael

Genome Biol 2016 Aug 2;17(1):168. Epub 2016 Aug 2.

Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI, 02912, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13059-016-1034-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970302PMC
August 2016

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Authors:
Siyuan Zheng Andrew D Cherniack Ninad Dewal Richard A Moffitt Ludmila Danilova Bradley A Murray Antonio M Lerario Tobias Else Theo A Knijnenburg Giovanni Ciriello Seungchan Kim Guillaume Assie Olena Morozova Rehan Akbani Juliann Shih Katherine A Hoadley Toni K Choueiri Jens Waldmann Ozgur Mete A Gordon Robertson Hsin-Ta Wu Benjamin J Raphael Lina Shao Matthew Meyerson Michael J Demeure Felix Beuschlein Anthony J Gill Stan B Sidhu Madson Q Almeida Maria C B V Fragoso Leslie M Cope Electron Kebebew Mouhammed A Habra Timothy G Whitsett Kimberly J Bussey William E Rainey Sylvia L Asa Jérôme Bertherat Martin Fassnacht David A Wheeler Gary D Hammer Thomas J Giordano Roel G W Verhaak

Cancer Cell 2016 08 8;30(2):363. Epub 2016 Aug 8.

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http://dx.doi.org/10.1016/j.ccell.2016.07.013DOI Listing
August 2016

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures.

Authors:
Mohammed El-Kebir Gryte Satas Layla Oesper Benjamin J Raphael

Cell Syst 2016 07;3(1):43-53

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.07.004DOI Listing
July 2016

Identification of hierarchical chromatin domains.

Authors:
Caleb Weinreb Benjamin J Raphael

Bioinformatics 2016 06 26;32(11):1601-9. Epub 2015 Aug 26.

Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4892410PMC
June 2016

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Authors:
Siyuan Zheng Andrew D Cherniack Ninad Dewal Richard A Moffitt Ludmila Danilova Bradley A Murray Antonio M Lerario Tobias Else Theo A Knijnenburg Giovanni Ciriello Seungchan Kim Guillaume Assie Olena Morozova Rehan Akbani Juliann Shih Katherine A Hoadley Toni K Choueiri Jens Waldmann Ozgur Mete A Gordon Robertson Hsin-Ta Wu Benjamin J Raphael Lina Shao Matthew Meyerson Michael J Demeure Felix Beuschlein Anthony J Gill Stan B Sidhu Madson Q Almeida Maria C B V Fragoso Leslie M Cope Electron Kebebew Mouhammed A Habra Timothy G Whitsett Kimberly J Bussey William E Rainey Sylvia L Asa Jérôme Bertherat Martin Fassnacht David A Wheeler Gary D Hammer Thomas J Giordano Roel G W Verhaak

Cancer Cell 2016 05;29(5):723-736

Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864952PMC
May 2016

Integrated analysis of germline and somatic variants in ovarian cancer.

Authors:
Krishna L Kanchi Kimberly J Johnson Charles Lu Michael D McLellan Mark D M Leiserson Michael C Wendl Qunyuan Zhang Daniel C Koboldt Mingchao Xie Cyriac Kandoth Joshua F McMichael Matthew A Wyczalkowski David E Larson Heather K Schmidt Christopher A Miller Robert S Fulton Paul T Spellman Elaine R Mardis Todd E Druley Timothy A Graubert Paul J Goodfellow Benjamin J Raphael Richard K Wilson Li Ding

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

Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.

Authors:
Mark D M Leiserson Fabio Vandin Hsin-Ta Wu Benjamin J Raphael

Nat Genet 2016 Feb;48(2):106-8

Department of Computer Science, Brown University, Providence, Rhode Island, USA.

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http://dx.doi.org/10.1038/ng.3491DOI Listing
February 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

N Engl J Med 2016 Jan 4;374(2):135-45. Epub 2015 Nov 4.

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https://www.genome.gov/Multimedia/Slides/TCGA4/06_Linehan.pd
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http://www.nejm.org/doi/abs/10.1056/NEJMoa1505917
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http://dx.doi.org/10.1056/NEJMoa1505917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775252PMC
January 2016

On the Sample Complexity of Cancer Pathways Identification.

Authors:
Fabio Vandin Benjamin J Raphael Eli Upfal

J Comput Biol 2016 Jan 8;23(1):30-41. Epub 2015 Dec 8.

2 Department of Computer Science, Brown University , Providence, Rhode Island.

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http://dx.doi.org/10.1089/cmb.2015.0100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700400PMC
January 2016

Open adjacencies and k-breaks: detecting simultaneous rearrangements in cancer genomes.

Authors:
Caleb Weinreb Layla Oesper Benjamin J Raphael

BMC Genomics 2014 17;15 Suppl 6:S4. Epub 2014 Oct 17.

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http://dx.doi.org/10.1186/1471-2164-15-S6-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239675PMC
December 2015

Patterns and functional implications of rare germline variants across 12 cancer types.

Authors:
Charles Lu Mingchao Xie Michael C Wendl Jiayin Wang Michael D McLellan Mark D M Leiserson Kuan-Lin Huang Matthew A Wyczalkowski Reyka Jayasinghe Tapahsama Banerjee Jie Ning Piyush Tripathi Qunyuan Zhang Beifang Niu Kai Ye Heather K Schmidt Robert S Fulton Joshua F McMichael Prag Batra Cyriac Kandoth Maheetha Bharadwaj Daniel C Koboldt Christopher A Miller Krishna L Kanchi James M Eldred David E Larson John S Welch Ming You Bradley A Ozenberger Ramaswamy Govindan Matthew J Walter Matthew J Ellis Elaine R Mardis Timothy A Graubert John F Dipersio Timothy J Ley Richard K Wilson Paul J Goodfellow Benjamin J Raphael Feng Chen Kimberly J Johnson Jeffrey D Parvin Li Ding

Nat Commun 2015 Dec 22;6:10086. Epub 2015 Dec 22.

The McDonnell Genome Institute, Washington University in St. Louis, Forest Park Avenue, Campus Box 8501, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/ncomms10086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703835PMC
December 2015

Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.

Authors:
Stephen M Doris Deborah R Smith Julia N Beamesderfer Benjamin J Raphael Judith A Nathanson Susan A Gerbi

RNA 2015 Oct 17;21(10):1719-30. Epub 2015 Aug 17.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1261/rna.051144.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574749PMC
October 2015

CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Authors:
Mark D M Leiserson Hsin-Ta Wu Fabio Vandin Benjamin J Raphael

Genome Biol 2015 Aug 8;16:160. Epub 2015 Aug 8.

Department of Computer Science, Brown University, 115 Waterman Street, Providence, 02912, RI, USA.

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August 2015

Pathway and network analysis of cancer genomes.

Authors:
Pau Creixell Jüri Reimand Syed Haider Guanming Wu Tatsuhiro Shibata Miguel Vazquez Ville Mustonen Abel Gonzalez-Perez John Pearson Chris Sander Benjamin J Raphael Debora S Marks B F Francis Ouellette Alfonso Valencia Gary D Bader Paul C Boutros Joshua M Stuart Rune Linding Nuria Lopez-Bigas Lincoln D Stein

Nat Methods 2015 Jul;12(7):615-621

Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717906PMC
July 2015

Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data.

Authors:
Benjamin J Raphael Fabio Vandin

J Comput Biol 2015 Jun 18;22(6):510-27. Epub 2015 Mar 18.

1Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island.

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http://dx.doi.org/10.1089/cmb.2014.0161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449706PMC
June 2015

MAGI: visualization and collaborative annotation of genomic aberrations.

Authors:
Mark D M Leiserson Connor C Gramazio Jason Hu Hsin-Ta Wu David H Laidlaw Benjamin J Raphael

Nat Methods 2015 Jun;12(6):483-4

1] Department of Computer Science, Brown University, Providence, Rhode Island, USA. [2] Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA.

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June 2015

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.

Authors:
Mohammed El-Kebir Layla Oesper Hannah Acheson-Field Benjamin J Raphael

Bioinformatics 2015 Jun;31(12):i62-70

Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542783PMC
June 2015

Accurate computation of survival statistics in genome-wide studies.

Authors:
Fabio Vandin Alexandra Papoutsaki Benjamin J Raphael Eli Upfal

PLoS Comput Biol 2015 May 7;11(5):e1004071. Epub 2015 May 7.

Department of Computer Science, Brown University, Providence, Rhode Island, United States of America.

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May 2015

Detecting non-allelic homologous recombination from high-throughput sequencing data.

Authors:
Matthew M Parks Charles E Lawrence Benjamin J Raphael

Genome Biol 2015 Apr 8;16:72. Epub 2015 Apr 8.

Center for Computational Molecular Biology, Brown University, Providence, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425883PMC
April 2015

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.

Authors:
Mark D M Leiserson Fabio Vandin Hsin-Ta Wu Jason R Dobson Jonathan V Eldridge Jacob L Thomas Alexandra Papoutsaki Younhun Kim Beifang Niu Michael McLellan Michael S Lawrence Abel Gonzalez-Perez David Tamborero Yuwei Cheng Gregory A Ryslik Nuria Lopez-Bigas Gad Getz Li Ding Benjamin J Raphael

Nat Genet 2015 Feb 15;47(2):106-14. Epub 2014 Dec 15.

1] Department of Computer Science, Brown University, Providence, Rhode Island, USA. [2] Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444046PMC
February 2015

Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease.

Authors:
Alexander S Brodsky Andrew Fischer Daniel H Miller Souriya Vang Shannon MacLaughlan Hsin-Ta Wu Jovian Yu Margaret Steinhoff Colin Collins Peter J S Smith Benjamin J Raphael Laurent Brard

PLoS One 2014 14;9(4):e94476. Epub 2014 Apr 14.

Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Southern Illinois University School of Medicine, Springfield, Illinois, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986100PMC
January 2015

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data.

Authors:
Layla Oesper Gryte Satas Benjamin J Raphael

Bioinformatics 2014 Dec 8;30(24):3532-40. Epub 2014 Oct 8.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253833PMC
December 2014

Characterization of structural variants with single molecule and hybrid sequencing approaches.

Authors:
Anna Ritz Ali Bashir Suzanne Sindi David Hsu Iman Hajirasouliha Benjamin J Raphael

Bioinformatics 2014 Dec 28;30(24):3458-66. Epub 2014 Oct 28.

Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI.

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December 2014

Expanding the computational toolbox for mining cancer genomes.

Authors:
Li Ding Michael C Wendl Joshua F McMichael Benjamin J Raphael

Nat Rev Genet 2014 Aug 8;15(8):556-70. Epub 2014 Jul 8.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, Rhode Island 02912, USA.

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August 2014

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Authors:
Katherine A Hoadley Christina Yau Denise M Wolf Andrew D Cherniack David Tamborero Sam Ng Max D M Leiserson Beifang Niu Michael D McLellan Vladislav Uzunangelov Jiashan Zhang Cyriac Kandoth Rehan Akbani Hui Shen Larsson Omberg Andy Chu Adam A Margolin Laura J Van't Veer Nuria Lopez-Bigas Peter W Laird Benjamin J Raphael Li Ding A Gordon Robertson Lauren A Byers Gordon B Mills John N Weinstein Carter Van Waes Zhong Chen Eric A Collisson Christopher C Benz Charles M Perou Joshua M Stuart

Cell 2014 Aug 7;158(4):929-944. Epub 2014 Aug 7.

Department of Biomolecular Engineering, Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.06.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152462PMC
August 2014

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.

Authors:
Benjamin J Raphael Jason R Dobson Layla Oesper Fabio Vandin

Genome Med 2014 30;6(1). Epub 2014 Jan 30.

Department of Computer Science, Brown University, 115 Waterman Street, Providence, RI 02912, USA ; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.

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June 2014

Detecting independent and recurrent copy number aberrations using interval graphs.

Authors:
Hsin-Ta Wu Iman Hajirasouliha Benjamin J Raphael

Bioinformatics 2014 Jun;30(12):i195-203

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu276DOI Listing
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June 2014

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.

Authors:
Iman Hajirasouliha Ahmad Mahmoody Benjamin J Raphael

Bioinformatics 2014 Jun;30(12):i78-86

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, 02906, USADepartment of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, 02906, USA.

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June 2014

Simultaneous identification of multiple driver pathways in cancer.

Authors:
Mark D M Leiserson Dima Blokh Roded Sharan Benjamin J Raphael

PLoS Comput Biol 2013 23;9(5):e1003054. Epub 2013 May 23.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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March 2014

Discovery of mutated subnetworks associated with clinical data in cancer.

Authors:
Fabio Vandin Patrick Clay Eli Upfal Benjamin J Raphael

Pac Symp Biocomput 2012 :55-66

Department of Computer Science, and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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December 2013

Modeling cell heterogeneity: from single-cell variations to mixed cells.

Authors:
Eric Batchelor Maricel G Kann Teresa M Przytycka Benjamin J Raphael Damian Wojtowicz

Pac Symp Biocomput 2013 :445-50

Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA.

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December 2013

Network analysis of GWAS data.

Authors:
Mark D M Leiserson Jonathan V Eldridge Sohini Ramachandran Benjamin J Raphael

Curr Opin Genet Dev 2013 Dec 26;23(6):602-10. Epub 2013 Nov 26.

Department of Computer Science, Brown University, Providence, RI 02912, United States; Center for Computational Molecular Biology, Brown University, Providence, RI 02912, United States.

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http://dx.doi.org/10.1016/j.gde.2013.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867794PMC
December 2013

Advances for studying clonal evolution in cancer.

Authors:
Li Ding Benjamin J Raphael Feng Chen Michael C Wendl

Cancer Lett 2013 Nov 23;340(2):212-9. Epub 2013 Jan 23.

Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address:

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November 2013

Making connections: using networks to stratify human tumors.

Authors:
Benjamin J Raphael

Nat Methods 2013 Nov;10(11):1077-8

Department of Computer Science and Center for Computational Molecular Biology Brown University, Providence, Rhode Island, USA.

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November 2013

Mutational landscape and significance across 12 major cancer types.

Authors:
Cyriac Kandoth Michael D McLellan Fabio Vandin Kai Ye Beifang Niu Charles Lu Mingchao Xie Qunyuan Zhang Joshua F McMichael Matthew A Wyczalkowski Mark D M Leiserson Christopher A Miller John S Welch Matthew J Walter Michael C Wendl Timothy J Ley Richard K Wilson Benjamin J Raphael Li Ding

Nature 2013 Oct;502(7471):333-339

The Genome Institute, Washington University in St Louis, Missouri 63108, USA.

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October 2013

The mutational landscape of adenoid cystic carcinoma.

Authors:
Allen S Ho Kasthuri Kannan David M Roy Luc G T Morris Ian Ganly Nora Katabi Deepa Ramaswami Logan A Walsh Stephanie Eng Jason T Huse Jianan Zhang Igor Dolgalev Kety Huberman Adriana Heguy Agnes Viale Marija Drobnjak Margaret A Leversha Christine E Rice Bhuvanesh Singh N Gopalakrishna Iyer C Rene Leemans Elisabeth Bloemena Robert L Ferris Raja R Seethala Benjamin E Gross Yupu Liang Rileen Sinha Luke Peng Benjamin J Raphael Sevin Turcan Yongxing Gong Nikolaus Schultz Seungwon Kim Simion Chiosea Jatin P Shah Chris Sander William Lee Timothy A Chan

Nat Genet 2013 Jul 19;45(7):791-8. Epub 2013 May 19.

Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1038/ng.2643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708595PMC
July 2013

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.

Authors:
Layla Oesper Ahmad Mahmoody Benjamin J Raphael

Genome Biol 2013 Jul 29;14(7):R80. Epub 2013 Jul 29.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054893PMC
July 2013

Chapter 6: Structural variation and medical genomics.

Authors:
Benjamin J Raphael

PLoS Comput Biol 2012 27;8(12):e1002821. Epub 2012 Dec 27.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531322PMC
May 2013

Reconstructing genome mixtures from partial adjacencies.

Authors:
Ahmad Mahmoody Crystal L Kahn Benjamin J Raphael

BMC Bioinformatics 2012 19;13 Suppl 19:S9. Epub 2012 Dec 19.

Department of Computer Science, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S19-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526445PMC
May 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Authors:
Timothy J Ley Christopher Miller Li Ding Benjamin J Raphael Andrew J Mungall A Gordon Robertson Katherine Hoadley Timothy J Triche Peter W Laird Jack D Baty Lucinda L Fulton Robert Fulton Sharon E Heath Joelle Kalicki-Veizer Cyriac Kandoth Jeffery M Klco Daniel C Koboldt Krishna-Latha Kanchi Shashikant Kulkarni Tamara L Lamprecht David E Larson Ling Lin Charles Lu Michael D McLellan Joshua F McMichael Jacqueline Payton Heather Schmidt David H Spencer Michael H Tomasson John W Wallis Lukas D Wartman Mark A Watson John Welch Michael C Wendl Adrian Ally Miruna Balasundaram Inanc Birol Yaron Butterfield Readman Chiu Andy Chu Eric Chuah Hye-Jung Chun Richard Corbett Noreen Dhalla Ranabir Guin An He Carrie Hirst Martin Hirst Robert A Holt Steven Jones Aly Karsan Darlene Lee Haiyan I Li Marco A Marra Michael Mayo Richard A Moore Karen Mungall Jeremy Parker Erin Pleasance Patrick Plettner Jacquie Schein Dominik Stoll Lucas Swanson Angela Tam Nina Thiessen Richard Varhol Natasja Wye Yongjun Zhao Stacey Gabriel Gad Getz Carrie Sougnez Lihua Zou Mark D M Leiserson Fabio Vandin Hsin-Ta Wu Frederick Applebaum Stephen B Baylin Rehan Akbani Bradley M Broom Ken Chen Thomas C Motter Khanh Nguyen John N Weinstein Nianziang Zhang Martin L Ferguson Christopher Adams Aaron Black Jay Bowen Julie Gastier-Foster Thomas Grossman Tara Lichtenberg Lisa Wise Tanja Davidsen John A Demchok Kenna R Mills Shaw Margi Sheth Heidi J Sofia Liming Yang James R Downing Greg Eley

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells.

Authors:
Lulu Cao Yiyuan Ding Norris Hung Kebing Yu Anna Ritz Benjamin J Raphael Arthur R Salomon

PLoS One 2012 11;7(10):e46725. Epub 2012 Oct 11.

Department of Chemistry, Brown University, Providence, Rhode Island, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3469622PMC
April 2013

An integrative probabilistic model for identification of structural variation in sequencing data.

Authors:
Suzanne S Sindi Selim Onal Luke C Peng Hsin-Ta Wu Benjamin J Raphael

Genome Biol 2012 ;13(3):R22

Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439973PMC
September 2012

Finding driver pathways in cancer: models and algorithms.

Authors:
Fabio Vandin Eli Upfal Benjamin J Raphael

Algorithms Mol Biol 2012 Sep 6;7(1):23. Epub 2012 Sep 6.

Department of Computer Science, and Center for Computational Molecular Biology Brown University, 115 Waterman St,, 4th Flr, Providence, RI 02912, USA.

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http://dx.doi.org/10.1186/1748-7188-7-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544164PMC
September 2012

The mutational landscape of lethal castration-resistant prostate cancer.

Authors:
Catherine S Grasso Yi-Mi Wu Dan R Robinson Xuhong Cao Saravana M Dhanasekaran Amjad P Khan Michael J Quist Xiaojun Jing Robert J Lonigro J Chad Brenner Irfan A Asangani Bushra Ateeq Sang Y Chun Javed Siddiqui Lee Sam Matt Anstett Rohit Mehra John R Prensner Nallasivam Palanisamy Gregory A Ryslik Fabio Vandin Benjamin J Raphael Lakshmi P Kunju Daniel R Rhodes Kenneth J Pienta Arul M Chinnaiyan Scott A Tomlins

Nature 2012 Jul;487(7406):239-43

Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1038/nature11125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396711PMC
July 2012

Reconstructing cancer genomes from paired-end sequencing data.

Authors:
Layla Oesper Anna Ritz Sarah J Aerni Ryan Drebin Benjamin J Raphael

BMC Bioinformatics 2012 Apr 19;13 Suppl 6:S10. Epub 2012 Apr 19.

Department of Computer Science, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S6-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358655PMC
April 2012

De novo discovery of mutated driver pathways in cancer.

Authors:
Fabio Vandin Eli Upfal Benjamin J Raphael

Genome Res 2012 Feb 7;22(2):375-85. Epub 2011 Jun 7.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1101/gr.120477.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266044PMC
February 2012

Identification of polymorphic inversions from genotypes.

Authors:
Alejandro Cáceres Suzanne S Sindi Benjamin J Raphael Mario Cáceres Juan R González

BMC Bioinformatics 2012 Feb 9;13:28. Epub 2012 Feb 9.

Center for Research in Environmental Epidemiology, and Institut Municipal d'Investigació Mèdica, Barcelona 08003, Spain.

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http://dx.doi.org/10.1186/1471-2105-13-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296650PMC
February 2012

Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes.

Authors:
Kian Huat Lim Luciana Ferraris Madeleine E Filloux Benjamin J Raphael William G Fairbrother

Proc Natl Acad Sci U S A 2011 Jul 17;108(27):11093-8. Epub 2011 Jun 17.

Department of Molecular and Cellular Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.

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http://dx.doi.org/10.1073/pnas.1101135108DOI Listing
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July 2011

Integrated genomics of ovarian xenograft tumor progression and chemotherapy response.

Authors:
Ashley Stuckey Andrew Fischer Daniel H Miller Sara Hillenmeyer Kyu K Kim Anna Ritz Rakesh K Singh Benjamin J Raphael Laurent Brard Alexander S Brodsky

BMC Cancer 2011 Jul 22;11:308. Epub 2011 Jul 22.

Molecular Therapeutics Laboratory, Program in Women’s Oncology, Department of Obstetrics and Gynecology, Women and Infants7 Hospital, Alpert Medical School of Brown University, Providence, RI 02905, USA.

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http://dx.doi.org/10.1186/1471-2407-11-308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155912PMC
July 2011

Detection of recurrent rearrangement breakpoints from copy number data.

Authors:
Anna Ritz Pamela L Paris Michael M Ittmann Colin Collins Benjamin J Raphael

BMC Bioinformatics 2011 Apr 21;12:114. Epub 2011 Apr 21.

Department of Computer Science, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1186/1471-2105-12-114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112242PMC
April 2011

Algorithms for detecting significantly mutated pathways in cancer.

Authors:
Fabio Vandin Eli Upfal Benjamin J Raphael

J Comput Biol 2011 Mar;18(3):507-22

Department of Computer Science, Brown University, Providence, Rhode Island, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2010.0265
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March 2011

Gremlin: an interactive visualization model for analyzing genomic rearrangements.

Authors:
Trevor M O'Brien Anna M Ritz Benjamin J Raphael David H Laidlaw

IEEE Trans Vis Comput Graph 2010 Nov-Dec;16(6):918-26

Computer Science Department, Brown University, Providence, RI 02912, USA.

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December 2010

Parsimony and likelihood reconstruction of human segmental duplications.

Authors:
Crystal L Kahn Borislav H Hristov Benjamin J Raphael

Bioinformatics 2010 Sep;26(18):i446-52

Department of Computer Science, Brown University, Providence, RI 02912, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935423PMC
September 2010

Structural variation analysis with strobe reads.

Authors:
Anna Ritz Ali Bashir Benjamin J Raphael

Bioinformatics 2010 May 8;26(10):1291-8. Epub 2010 Apr 8.

Department of Computer Science, Brown University, Providence, RI 02912, USA.

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May 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Optimizing PCR assays for DNA-based cancer diagnostics.

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J Comput Biol 2010 Mar;17(3):369-81

Department of Computer Science, University of California, San Diego, La Jolla, California 92129, USA.

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March 2010

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Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.

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March 2010

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes.

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January 2010

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Mol Cell Proteomics 2009 Nov 14;8(11):2418-31. Epub 2009 Jul 14.

Department of Molecular Biology, Brown University, Providence, Rhode Island 02912, USA.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M800307-MCP2
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November 2009

A geometric approach for classification and comparison of structural variants.

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Bioinformatics 2009 Jun;25(12):i222-30

Division of Applied Mathematics, Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp208DOI Listing
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June 2009

Computational identification of CDR3 sequence archetypes among immunoglobulin sequences in chronic lymphocytic leukemia.

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Leuk Res 2009 Mar 21;33(3):368-76. Epub 2008 Jul 21.

The Rebecca and John Moores Cancer Center, University of California, San Diego, CA, USA.

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March 2009

A parsimony approach to analysis of human segmental duplications.

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Crystal L Kahn Benjamin J Raphael

Pac Symp Biocomput 2009 :126-37

Box 1910, Brown University, Department of Computer Science & Center for Computational Molecular Biology, Providence, RI 02912, USA.

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March 2009

Discovery of phosphorylation motif mixtures in phosphoproteomics data.

Authors:
Anna Ritz Gregory Shakhnarovich Arthur R Salomon Benjamin J Raphael

Bioinformatics 2009 Jan 7;25(1):14-21. Epub 2008 Nov 7.

Department of Computer Science, Brown University, Toyota Technological Institute at Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638929PMC
January 2009

Analysis of segmental duplications via duplication distance.

Authors:
Crystal L Kahn Benjamin J Raphael

Bioinformatics 2008 Aug;24(16):i133-8

Department of Computer Science, Brown University, Providence, RI, USA.

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August 2008

A sequence-based survey of the complex structural organization of tumor genomes.

Authors:
Benjamin J Raphael Stanislav Volik Peng Yu Chunxiao Wu Guiqing Huang Elena V Linardopoulou Barbara J Trask Frederic Waldman Joseph Costello Kenneth J Pienta Gordon B Mills Krystyna Bajsarowicz Yasuko Kobayashi Shivaranjani Sridharan Pamela L Paris Quanzhou Tao Sarah J Aerni Raymond P Brown Ali Bashir Joe W Gray Jan-Fang Cheng Pieter de Jong Mikhail Nefedov Thomas Ried Hesed M Padilla-Nash Colin C Collins

Genome Biol 2008 25;9(3):R59. Epub 2008 Mar 25.

Department of Computer Science & Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912-1910, USA.

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http://dx.doi.org/10.1186/gb-2008-9-3-r59DOI Listing
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June 2008

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.

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PLoS Comput Biol 2008 Apr 25;4(4):e1000051. Epub 2008 Apr 25.

Bioinformatics Graduate Program, University of California San Diego, San Diego, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278375PMC
April 2008

Optimization of primer design for the detection of variable genomic lesions in cancer.

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Ali Bashir Yu-Tsueng Liu Benjamin J Raphael Dennis Carson Vineet Bafna

Bioinformatics 2007 Nov 30;23(21):2807-15. Epub 2007 Aug 30.

Bioinformatics Program, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm390DOI Listing
November 2007

Quantitative time-resolved phosphoproteomic analysis of mast cell signaling.

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Lulu Cao Kebing Yu Cindy Banh Vinh Nguyen Anna Ritz Benjamin J Raphael Yuko Kawakami Toshiaki Kawakami Arthur R Salomon

J Immunol 2007 Nov;179(9):5864-76

Department of Chemistry, Brown University, Providence, RI 02912, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727709PMC
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November 2007

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

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Shibu Yooseph Granger Sutton Douglas B Rusch Aaron L Halpern Shannon J Williamson Karin Remington Jonathan A Eisen Karla B Heidelberg Gerard Manning Weizhong Li Lukasz Jaroszewski Piotr Cieplak Christopher S Miller Huiying Li Susan T Mashiyama Marcin P Joachimiak Christopher van Belle John-Marc Chandonia David A Soergel Yufeng Zhai Kannan Natarajan Shaun Lee Benjamin J Raphael Vineet Bafna Robert Friedman Steven E Brenner Adam Godzik David Eisenberg Jack E Dixon Susan S Taylor Robert L Strausberg Marvin Frazier J Craig Venter

PLoS Biol 2007 Mar;5(3):e16

J. Craig Venter Institute, Rockville, Maryland, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821046PMC
March 2007

Identifying repeat domains in large genomes.

Authors:
Degui Zhi Benjamin J Raphael Alkes L Price Haixu Tang Pavel A Pevzner

Genome Biol 2006 31;7(1):R7. Epub 2006 Jan 31.

Bioinformatics Program, University of California, San Diego, CA 92093-0419, USA.

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August 2006

AliWABA: alignment on the web through an A-Bruijn approach.

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Neil C Jones Degui Zhi Benjamin J Raphael

Nucleic Acids Res 2006 Jul;34(Web Server issue):W613-6

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

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July 2006

Decoding the fine-scale structure of a breast cancer genome and transcriptome.

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Stanislav Volik Benjamin J Raphael Guiqing Huang Michael R Stratton Graham Bignel John Murnane John H Brebner Krystyna Bajsarowicz Pamela L Paris Quanzhou Tao David Kowbel Anna Lapuk Dmitri A Shagin Irina A Shagina Joe W Gray Jan-Fang Cheng Pieter J de Jong Pavel Pevzner Colin Collins

Genome Res 2006 Mar 3;16(3):394-404. Epub 2006 Feb 3.

Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA.

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http://dx.doi.org/10.1101/gr.4247306DOI Listing
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March 2006

Reconstructing tumor amplisomes.

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Benjamin J Raphael Pavel A Pevzner

Bioinformatics 2004 Aug;20 Suppl 1:i265-73

Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0114, USA.

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August 2004

Reconstructing tumor genome architectures.

Authors:
Benjamin J Raphael Stanislav Volik Colin Collins Pavel A Pevzner

Bioinformatics 2003 Oct;19 Suppl 2:ii162-71

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093-0114, USA.

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October 2003