Benjamin J. Raphael

Publication Activity (10 Years)

Years Active: 2003-2022
Publications (10 Years): 39

Top Topics

Maximum Likelihood

Von Mises Fisher

Top Venues

J. Comput. Biol.

Publications

Pijus Simonaitis, Benjamin J. Raphael
A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. WABI (2022)
Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
NetMix2: Unifying Network Propagation and Altered Subnetworks. RECOMB (2022)
Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael
Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. RECOMB (2022)
Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. J. Comput. Biol. 29 (12) (2022)
Ron Zeira, Geoffrey Mon, Benjamin J. Raphael
Genome Halving and Aliquoting Under the Copy Number Distance. WABI (2021)
Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. ICML (2021)
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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
Uthsav Chitra, Kimberly Ding, Benjamin J. Raphael
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. CoRR (2020)
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
The evolutionary history of 2,658 cancers. Nat. 578 (7793) (2020)
Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. RECOMB (2020)
Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael
Identifying tumor clones in sparse single-cell mutation data. Bioinform. 36 (Supplement-1) (2020)
Ron Zeira, Benjamin J. Raphael
Copy number evolution with weighted aberrations in cancer. Bioinform. 36 (Supplement-1) (2020)
Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael
Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. RECOMB (2020)
Uthsav Chitra, Benjamin J. Raphael
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. ICML (2019)
Matthew A. Myers, Gryte Satas, Benjamin J. Raphael
Inferring Tumor Evolution from Longitudinal Samples. RECOMB (2019)
Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael
netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data. RECOMB (2019)
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
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7 (2019)
Uthsav Chitra, Benjamin J. Raphael
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. CoRR (2019)
Matthew M. Parks, Benjamin J. Raphael, Charles E. Lawrence
Using controls to limit false discovery in the era of big data. BMC Bioinform. 19 (1) (2018)
Matthew A. Reyna, Mark D. M. Leiserson, Benjamin J. Raphael
Hierarchical HotNet: identifying hierarchies of altered subnetworks. Bioinform. 34 (17) (2018)
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. 25 (7) (2018)
Gryte Satas, Benjamin J. Raphael
Haplotype phasing in single-cell DNA-sequencing data. Bioinform. 34 (13) (2018)
Rebecca Elyanow, Hsin-Ta Wu, Benjamin J. Raphael
Identifying structural variants using linked-read sequencing data. Bioinform. 34 (2) (2018)
Layla Oesper, Simone Dantas, Benjamin J. Raphael
Identifying simultaneous rearrangements in cancer genomes. Bioinform. 34 (2) (2018)
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. RECOMB (2017)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12 (1) (2017)
Gryte Satas, Benjamin J. Raphael
Tumor phylogeny inference using tree-constrained importance sampling. Bioinform. 33 (14) (2017)
Caleb Weinreb, Benjamin J. Raphael
Identification of hierarchical chromatin domains. Bioinform. 32 (11) (2016)
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. CoRR (2016)
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB (2016)
Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael
A weighted exact test for mutually exclusive mutations in cancer. Bioinform. 32 (17) (2016)
Fabio Vandin, Benjamin J. Raphael, Eli Upfal
On the Sample Complexity of Cancer Pathways Identification. J. Comput. Biol. 23 (1) (2016)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Copy-Number Evolution Problems: Complexity and Algorithms. WABI (2016)
Fabio Vandin, Benjamin J. Raphael, Eli Upfal
On the Sample Complexity of Cancer Pathways Identification. RECOMB (2015)
Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal
Accurate Computation of Survival Statistics in Genome-Wide Studies. PLoS Comput. Biol. 11 (5) (2015)
Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael
CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. RECOMB (2015)
Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael
Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinform. 31 (12) (2015)
Benjamin J. Raphael, Fabio Vandin
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. J. Comput. Biol. 22 (6) (2015)
Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart
Session Introduction. Pacific Symposium on Biocomputing (2015)
Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael
Detecting independent and recurrent copy number aberrations using interval graphs. Bioinform. 30 (12) (2014)
Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael
A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types. ICCABS (2014)
Iman Hajirasouliha, Benjamin J. Raphael
Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures. WABI (2014)
Layla Oesper, Gryte Satas, Benjamin J. Raphael
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinform. 30 (24) (2014)
Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinform. 30 (12) (2014)
Benjamin J. Raphael, Fabio Vandin
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. RECOMB (2014)
Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael
Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinform. 30 (24) (2014)
Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal
Genome-Wide Survival Analysis of Somatic Mutations in Cancer. RECOMB (2013)
Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael
Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. RECOMB (2013)
Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance
Session introduction. Pacific Symposium on Biocomputing (2013)
Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz
Modeling cell heterogeneity: from single-cell variations to mixed cells populations. Pacific Symposium on Biocomputing (2013)
Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael
Simultaneous Identification of Multiple Driver Pathways in Cancer. PLoS Comput. Biol. 9 (5) (2013)
Layla Oesper, Benjamin J. Raphael
Workshop: Reconstructing the organization of cancer genomes. ICCABS (2013)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Identifying significant mutations in large cohorts of cancer genomes. ICCABS (2013)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Workshop: Algorithms for discovery of mutated pathways in cancer. ICCABS (2012)
Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael
Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. Pacific Symposium on Biocomputing (2012)
Benjamin J. Raphael
Chapter 6: Structural Variation and Medical Genomics. PLoS Comput. Biol. 8 (12) (2012)
Alejandro Cáceres, Suzanne S. Sindi, Benjamin J. Raphael, Mario Cáceres, Juan R. González
Identification of polymorphic inversions from genotypes. BMC Bioinform. 13 (2012)
Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael
Reconstructing cancer genomes from paired-end sequencing data. BMC Bioinform. 13 (S-6) (2012)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms Mol. Biol. 7 (2012)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. Computer 45 (3) (2012)
Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael
Reconstructing genome mixtures from partial adjacencies. BMC Bioinform. 13 (S-19) (2012)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Discovery of Mutated Driver Pathways in Cancer. RECOMB (2011)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Finding Driver Pathways in Cancer: Models and Algorithms. WABI (2011)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Algorithms for Detecting Significantly Mutated Pathways in Cancer. J. Comput. Biol. 18 (3) (2011)
Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir
Workshop: Characterization of structural variants with next generation DNA sequencing. ICCABS (2011)
Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael
Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinform. 12 (2011)
Crystal L. Kahn, Borislav H. Hristov, Benjamin J. Raphael
Parsimony and likelihood reconstruction of human segmental duplications. Bioinform. 26 (18) (2010)
Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol. Biol. 5 (2010)
Anna M. Ritz, Ali Bashir, Benjamin J. Raphael
Structural variation analysis with strobe reads. Bioinform. 26 (10) (2010)
Fabio Vandin, Eli Upfal, Benjamin J. Raphael
Algorithms for Detecting Significantly Mutated Pathways in Cancer. RECOMB (2010)
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
Optimizing PCR Assays for DNA-Based Cancer Diagnostics. J. Comput. Biol. 17 (3) (2010)
Suzanne S. Sindi, Benjamin J. Raphael
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. J. Comput. Biol. 17 (3) (2010)
Trevor M. O'Brien, Anna M. Ritz, Benjamin J. Raphael, David H. Laidlaw
Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements. IEEE Trans. Vis. Comput. Graph. 16 (6) (2010)
Crystal L. Kahn, Benjamin J. Raphael
A Parsimony Approach to Analysis of Human Segmental Duplications. Pacific Symposium on Biocomputing (2009)
Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael
Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. WABI (2009)
Suzanne S. Sindi, Benjamin J. Raphael
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. RECOMB (2009)
Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael
Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinform. 25 (1) (2009)
Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael
A geometric approach for classification and comparison of structural variants. Bioinform. 25 (12) (2009)
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
Optimizing PCR Assays for DNA Based Cancer Diagnostics. RECOMB (2009)
Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Comput. Biol. 4 (4) (2008)
Crystal L. Kahn, Benjamin J. Raphael
Analysis of segmental duplications via duplication distance. ECCB (2008)
Erik Corona, Benjamin J. Raphael, Eleazar Eskin
Identification of Deletion Polymorphisms from Haplotypes. RECOMB (2007)
Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna
Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinform. 23 (21) (2007)
Neil C. Jones, Degui Zhi, Benjamin J. Raphael
AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Mark Chaisson, Benjamin J. Raphael, Pavel A. Pevzner
Microinversions in mammalian evolution. Proc. Natl. Acad. Sci. USA 103 (52) (2006)
Benjamin J. Raphael, Lung-Tien Liu, George Varghese
A Uniform Projection Method for Motif Discovery in DNA Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (2) (2004)
Benjamin J. Raphael, Pavel A. Pevzner
Reconstructing tumor amplisomes. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner
Reconstructing tumor genome architectures. ECCB (2003)