Mark D Leiserson

Mark D M Leiserson

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Mark D Leiserson

Mark D M Leiserson

Publications by authors named "Mark D M Leiserson"

24Publications

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1PubMed Central Citations

Modeling clinical and molecular covariates of mutational process activity in cancer.

Bioinformatics 2019 Jul;35(14):i492-i500

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612886PMC
July 2019

Functional protein representations from biological networks enable diverse cross-species inference.

Nucleic Acids Res 2019 May;47(9):e51

Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA.

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http://dx.doi.org/10.1093/nar/gkz132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511848PMC
May 2019

Criticality in tumor evolution and clinical outcome.

Proc Natl Acad Sci U S A 2018 11 7;115(47):E11101-E11110. Epub 2018 Nov 7.

Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742;

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http://dx.doi.org/10.1073/pnas.1807256115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255199PMC
November 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

Precision Oncology: The Road Ahead.

Trends Mol Med 2017 10 5;23(10):874-898. Epub 2017 Sep 5.

Tumor Initiation and Maintenance Program, NCI designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Technion Integrated Cancer Center, Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, 31096, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.molmed.2017.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718207PMC
October 2017

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

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

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

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

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

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

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

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.

BMC Bioinformatics 2013 Jan 18;14:23. Epub 2013 Jan 18.

Department of Computer Science, Tufts University, Medford, MA 02155, USA.

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http://dx.doi.org/10.1186/1471-2105-14-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614884PMC
January 2013

Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut.

J Comput Biol 2011 Nov 1;18(11):1399-409. Epub 2011 Sep 1.

Department of Computer Science, Tufts University, Medford, Massachusetts 02155, USA.

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http://dx.doi.org/10.1089/cmb.2011.0191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216108PMC
November 2011