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.

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

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

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

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Tumor phylogeny inference using tree-constrained importance sampling.

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.

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.

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.

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.

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

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

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.

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

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

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

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

On the Sample Complexity of Cancer Pathways Identification.

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

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

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.

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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http://genomebiology.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13059-015-0700-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531541PMC
August 2015

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

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.

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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http://dx.doi.org/10.1038/nmeth.3412DOI Listing
June 2015

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

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.

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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http://dx.doi.org/10.1371/journal.pcbi.1004071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423942PMC
May 2015

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

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://dx.doi.org/10.1186/s13059-015-0633-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425883PMC
April 2015

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

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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094476PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986100PMC
January 2015

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

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://dx.doi.org/10.1093/bioinformatics/btu651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253833PMC
December 2014

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

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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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253835PMC
December 2014

Expanding the computational toolbox for mining cancer genomes.

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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http://www.nature.com/articles/nrg3767
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http://dx.doi.org/10.1038/nrg3767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168012PMC
August 2014

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

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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http://dx.doi.org/10.1186/gm524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978567PMC
June 2014

Detecting independent and recurrent copy number aberrations using interval graphs.

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058951PMC
June 2014

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

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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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058927PMC
June 2014

Simultaneous identification of multiple driver pathways in cancer.

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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http://dx.plos.org/10.1371/journal.pcbi.1003054
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http://dx.doi.org/10.1371/journal.pcbi.1003054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662702PMC
March 2014

Discovery of mutated subnetworks associated with clinical data in cancer.

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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http://psb.stanford.edu/psb-online/proceedings/psb12/vandin.
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December 2013

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

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.

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.

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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https://linkinghub.elsevier.com/retrieve/pii/S03043835130003
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http://dx.doi.org/10.1016/j.canlet.2012.12.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783624PMC
November 2013

Making connections: using networks to stratify human tumors.

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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http://dx.doi.org/10.1038/nmeth.2704DOI Listing
November 2013

Chapter 6: Structural variation and medical genomics.

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.

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.

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

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http://dx.doi.org/10.1056/NEJMoa1301689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

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

Genome Biol 2012 ;13(3):R22

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

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http://dx.doi.org/10.1186/gb-2012-13-3-r22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439973PMC
September 2012

Finding driver pathways in cancer: models and algorithms.

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

Reconstructing cancer genomes from paired-end sequencing data.

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.

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.

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.

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131313PMC
July 2011

Integrated genomics of ovarian xenograft tumor progression and chemotherapy response.

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.

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.

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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http://dx.doi.org/10.1089/cmb.2010.0265DOI Listing
March 2011

Gremlin: an interactive visualization model for analyzing genomic rearrangements.

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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http://dx.doi.org/10.1109/TVCG.2010.163DOI Listing
December 2010

Parsimony and likelihood reconstruction of human segmental duplications.

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.

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

Optimizing PCR assays for DNA-based cancer diagnostics.

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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http://dx.doi.org/10.1089/cmb.2009.0203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213025PMC
March 2010

Identification and frequency estimation of inversion polymorphisms from haplotype data.

J Comput Biol 2010 Mar;17(3):517-31

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

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http://dx.doi.org/10.1089/cmb.2009.0185DOI Listing
March 2010

A geometric approach for classification and comparison of structural variants.

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687962PMC
June 2009

A parsimony approach to analysis of human segmental duplications.

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.

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.

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

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

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http://dx.doi.org/10.1093/bioinformatics/btn292DOI Listing
August 2008

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

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.

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

Identifying repeat domains in large genomes.

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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http://dx.doi.org/10.1186/gb-2006-7-1-r7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431705PMC
August 2006

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

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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http://dx.doi.org/10.1093/nar/gkl288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538870PMC
July 2006

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

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1415204PMC
March 2006

Reconstructing tumor amplisomes.

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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http://dx.doi.org/10.1093/bioinformatics/bth931DOI Listing
August 2004

Reconstructing tumor genome architectures.

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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http://dx.doi.org/10.1093/bioinformatics/btg1074DOI Listing
October 2003