Publications by authors named "Benjamin J Raphael"

104 Publications

NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks.

Authors:
Matthew A Reyna Uthsav Chitra Rebecca Elyanow Benjamin J Raphael

J Comput Biol 2021 Jan 5. Epub 2021 Jan 5.

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

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January 2021

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.

Authors:
Sergey Aganezov Benjamin J Raphael

Genome Res 2020 Sep 4;30(9):1274-1290. Epub 2020 Sep 4.

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

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September 2020

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.

Authors:
Simone Zaccaria Benjamin J Raphael

Nat Biotechnol 2021 Feb 2;39(2):207-214. Epub 2020 Sep 2.

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

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February 2021

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.

Authors:
Simone Zaccaria Benjamin J Raphael

Nat Commun 2020 09 2;11(1):4301. Epub 2020 Sep 2.

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

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September 2020

SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses.

Authors:
Gryte Satas Simone Zaccaria Geoffrey Mon Benjamin J Raphael

Cell Syst 2020 04;10(4):323-332.e8

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

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April 2020

Identifying tumor clones in sparse single-cell mutation data.

Authors:
Matthew A Myers Simone Zaccaria Benjamin J Raphael

Bioinformatics 2020 Jul;36(Supplement_1):i186-i193

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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July 2020

Copy number evolution with weighted aberrations in cancer.

Authors:
Ron Zeira Benjamin J Raphael

Bioinformatics 2020 Jul;36(Supplement_1):i344-i352

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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July 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 02 7;21(1):31. Epub 2020 Feb 7.

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

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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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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 02 5;11(1):729. Epub 2020 Feb 5.

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

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February 2020

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 02 28;30(2):195-204. Epub 2020 Jan 28.

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

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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 01;135(1):41-55

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

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January 2020

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Authors:
Matthew A Myers Gryte Satas Benjamin J Raphael

Cell Syst 2019 06 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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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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April 2019

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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September 2018

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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September 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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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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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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May 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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July 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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January 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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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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November 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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July 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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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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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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August 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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May 2017

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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September 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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August 2016