Benjamin J. Raphael

According to our database, Benjamin J. Raphael authored at least 80 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

A zero-agnostic model for copy number evolution in cancer.

Henri Schmidt, Palash Sashittal, Benjamin J. Raphael

PLoS Comput. Biol., November, 2023

2022

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks.

Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael

J. Comput. Biol., 2022

A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements.

Pijus Simonaitis, Benjamin J. Raphael

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics.

Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2022

NetMix2: Unifying Network Propagation and Altered Subnetworks.

Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2022

2021

Genome Halving and Aliquoting Under the Copy Number Distance.

Ron Zeira, Geoffrey Mon, Benjamin J. Raphael

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies.

Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael

Proceedings of the 38th International Conference on Machine Learning, 2021

2020

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

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah 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, André 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, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora

Nat., 2020

The evolutionary history of 2,658 cancers.

Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit G. Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven E. Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, David J. Adams, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils, Matthew Fittall, Dale W. Garsed, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge, Peter Van Loo

Nat., 2020

Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies.

Uthsav Chitra, Kimberly Ding, Benjamin J. Raphael

CoRR, 2020

Copy number evolution with weighted aberrations in cancer.

Ron Zeira, Benjamin J. Raphael

Bioinform., 2020

Identifying tumor clones in sparse single-cell mutation data.

Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael

Bioinform., 2020

Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses.

Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2020

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

Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2020

2019

12 Grand Challenges in Single-Cell Data Science.

David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. 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 J. T. 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

PeerJ Prepr., 2019

Inferring Tumor Evolution from Longitudinal Samples.

Matthew A. Myers, Gryte Satas, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2019

netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data.

Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2019

Random Walks on Hypergraphs with Edge-Dependent Vertex Weights.

Uthsav Chitra, Benjamin J. Raphael

Proceedings of the 36th International Conference on Machine Learning, 2019

2018

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael

J. Comput. Biol., 2018

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

Matthew M. Parks, Benjamin J. Raphael, Charles E. Lawrence

BMC Bioinform., 2018

Haplotype phasing in single-cell DNA-sequencing data.

Gryte Satas, Benjamin J. Raphael

Bioinform., 2018

Hierarchical HotNet: identifying hierarchies of altered subnetworks.

Matthew A. Reyna, Mark D. M. Leiserson, Benjamin J. Raphael

Bioinform., 2018

Identifying simultaneous rearrangements in cancer genomes.

Layla Oesper, Simone Dantas, Benjamin J. Raphael

Bioinform., 2018

Identifying structural variants using linked-read sequencing data.

Rebecca Elyanow, Hsin-Ta Wu, Benjamin J. Raphael

Bioinform., 2018

2017

Tumor phylogeny inference using tree-constrained importance sampling.

Gryte Satas, Benjamin J. Raphael

Bioinform., 2017

Complexity and algorithms for copy-number evolution problems.

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

Algorithms Mol. Biol., 2017

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.

Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2017

2016

On the Sample Complexity of Cancer Pathways Identification.

Fabio Vandin, Benjamin J. Raphael, Eli Upfal

J. Comput. Biol., 2016

Identification of hierarchical chromatin domains.

Caleb Weinreb, Benjamin J. Raphael

Bioinform., 2016

A weighted exact test for mutually exclusive mutations in cancer.

Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael

Bioinform., 2016

Copy-Number Evolution Problems: Complexity and Algorithms.

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

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing.

Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

Accurate Computation of Survival Statistics in Genome-Wide Studies.

Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal

PLoS Comput. Biol., 2015

Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data.

Benjamin J. Raphael, Fabio Vandin

J. Comput. Biol., 2015

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

Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael

Bioinform., 2015

CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer.

Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2015

Session Introduction.

Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

Detecting independent and recurrent copy number aberrations using interval graphs.

Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael

Bioinform., 2014

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

Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael

Bioinform., 2014

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

Layla Oesper, Gryte Satas, Benjamin J. Raphael

Bioinform., 2014

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

Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael

Bioinform., 2014

Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures.

Iman Hajirasouliha, Benjamin J. Raphael

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types.

Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013

Simultaneous Identification of Multiple Driver Pathways in Cancer.

Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael

PLoS Comput. Biol., 2013

Genome-Wide Survival Analysis of Somatic Mutations in Cancer.

Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal

Proceedings of the Research in Computational Molecular Biology, 2013

Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data.

Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2013

Session introduction.

Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

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

Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Identifying significant mutations in large cohorts of cancer genomes.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

Workshop: Reconstructing the organization of cancer genomes.

Layla Oesper, Benjamin J. Raphael

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

2012

Chapter 6: Structural Variation and Medical Genomics.

Benjamin J. Raphael

PLoS Comput. Biol., 2012

Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

Computer, 2012

Reconstructing cancer genomes from paired-end sequencing data.

Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael

BMC Bioinform., 2012

Reconstructing genome mixtures from partial adjacencies.

Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael

BMC Bioinform., 2012

Identification of polymorphic inversions from genotypes.

Alejandro Cáceres, Suzanne S. Sindi, Benjamin J. Raphael, Mario Cáceres, Juan R. González

BMC Bioinform., 2012

Finding Driver Pathways in Cancer: Models and Algorithms.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

Algorithms Mol. Biol., 2012

Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer.

Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

Workshop: Algorithms for discovery of mutated pathways in cancer.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011

Algorithms for Detecting Significantly Mutated Pathways in Cancer.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

J. Comput. Biol., 2011

Detection of recurrent rearrangement breakpoints from copy number data.

Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael

BMC Bioinform., 2011

<i>De Novo</i> Discovery of Mutated Driver Pathways in Cancer.

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2011

Workshop: Characterization of structural variants with next generation DNA sequencing.

Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements.

Trevor M. O'Brien, Anna M. Ritz, Benjamin J. Raphael, David H. Laidlaw

IEEE Trans. Vis. Comput. Graph., 2010

Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data.

Suzanne S. Sindi, Benjamin J. Raphael

J. Comput. Biol., 2010

Optimizing PCR Assays for DNA-Based Cancer Diagnostics.

Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna

J. Comput. Biol., 2010

Structural variation analysis with strobe reads.

Anna M. Ritz, Ali Bashir, Benjamin J. Raphael

Bioinform., 2010

Parsimony and likelihood reconstruction of human segmental duplications.

Crystal L. Kahn, Borislav H. Hristov, Benjamin J. Raphael

Bioinform., 2010

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

Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael

Algorithms Mol. Biol., 2010

2009

A geometric approach for classification and comparison of structural variants.

Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael

Bioinform., 2009

Discovery of phosphorylation motif mixtures in phosphoproteomics data.

Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael

Bioinform., 2009

A Parsimony Approach to Analysis of Human Segmental Duplications.

Crystal L. Kahn, Benjamin J. Raphael

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.

Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael

PLoS Comput. Biol., 2008

Analysis of segmental duplications via duplication distance.

Crystal L. Kahn, Benjamin J. Raphael

Proceedings of the ECCB'08 Proceedings, 2008

2007

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

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

Bioinform., 2007

Identification of Deletion Polymorphisms from Haplotypes.

Erik Corona, Benjamin J. Raphael, Eleazar Eskin

Proceedings of the Research in Computational Molecular Biology, 2007

2006

Microinversions in mammalian evolution.

Mark Chaisson, Benjamin J. Raphael, Pavel A. Pevzner

Proc. Natl. Acad. Sci. USA, 2006

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

Neil C. Jones, Degui Zhi, Benjamin J. Raphael

Nucleic Acids Res., 2006

2004

A Uniform Projection Method for Motif Discovery in DNA Sequences.

Benjamin J. Raphael, Lung-Tien Liu, George Varghese

IEEE ACM Trans. Comput. Biol. Bioinform., 2004

Reconstructing tumor amplisomes.

Benjamin J. Raphael, Pavel A. Pevzner

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

Reconstructing tumor genome architectures.

Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003