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ORCIDBenjamin J. Raphael
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- affiliation: Princeton University, Princeton, NJ, USA
- affiliation (former): Brown University, Providence, RI, USA
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Journal Articles
- 2024
[j51]Palash Sashittal, Viola Chen, Amey Pasarkar, Benjamin J. Raphael:
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. Bioinform. 40(Supplement_1): i218-i227 (2024)- [j50]Uyen Mai, Gary Hu, Benjamin J. Raphael:
Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data. Bioinform. 40(Supplement_1): i228-i236 (2024) - [j49]Hirak Sarkar, Uthsav Chitra
, Julian Gold, Benjamin J. Raphael:
A count-based model for delineating cell-cell interactions in spatial transcriptomics data. Bioinform. 40(Supplement_1): i481-i489 (2024) - [j48]Henri Schmidt, Benjamin J. Raphael:
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors. PLoS Comput. Biol. 20(12): 1012631 (2024) - 2023
- [j47]Henri Schmidt, Palash Sashittal, Benjamin J. Raphael:
A zero-agnostic model for copy number evolution in cancer. PLoS Comput. Biol. 19(11) (2023) - 2022
- [j46]Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael:
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. J. Comput. Biol. 29(12): 1305-1323 (2022) - 2021
- [j45]Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael:
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. J. Comput. Biol. 28(5): 469-484 (2021) - 2020
- [j44]Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael:
Identifying tumor clones in sparse single-cell mutation data. Bioinform. 36(Supplement-1): i186-i193 (2020) - [j43]Ron Zeira, Benjamin J. Raphael:
Copy number evolution with weighted aberrations in cancer. Bioinform. 36(Supplement-1): i344-i352 (2020) - [j42]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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j41]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): 122-128 (2020) - 2018
- [j40]Layla Oesper, Simone Dantas, Benjamin J. Raphael:
Identifying simultaneous rearrangements in cancer genomes. Bioinform. 34(2): 346-352 (2018) - [j39]Rebecca Elyanow, Hsin-Ta Wu, Benjamin J. Raphael:
Identifying structural variants using linked-read sequencing data. Bioinform. 34(2): 353-360 (2018) - [j38]Gryte Satas, Benjamin J. Raphael:
Haplotype phasing in single-cell DNA-sequencing data. Bioinform. 34(13): i211-i217 (2018) - [j37]Matthew A. Reyna, Mark D. M. Leiserson, Benjamin J. Raphael:
Hierarchical HotNet: identifying hierarchies of altered subnetworks. Bioinform. 34(17): i972-i980 (2018) - [j36]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): 323:1-323:8 (2018) - [j35]Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael:
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. 25(7): 689-708 (2018) - 2017
- [j34]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): 13:1-13:11 (2017) - [j33]Gryte Satas, Benjamin J. Raphael:
Tumor phylogeny inference using tree-constrained importance sampling. Bioinform. 33(14): i152-i160 (2017) - 2016
- [j32]Caleb Weinreb, Benjamin J. Raphael:
Identification of hierarchical chromatin domains. Bioinform. 32(11): 1601-1609 (2016) - [j31]Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael:
A weighted exact test for mutually exclusive mutations in cancer. Bioinform. 32(17): 736-745 (2016) - [j30]Fabio Vandin, Benjamin J. Raphael, Eli Upfal:
On the Sample Complexity of Cancer Pathways Identification. J. Comput. Biol. 23(1): 30-41 (2016) - 2015
- [j29]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): 62-70 (2015) - [j28]Benjamin J. Raphael, Fabio Vandin:
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. J. Comput. Biol. 22(6): 510-527 (2015) - [j27]Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal:
Accurate Computation of Survival Statistics in Genome-Wide Studies. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j26]Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael:
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinform. 30(12): 78-86 (2014) - [j25]Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael:
Detecting independent and recurrent copy number aberrations using interval graphs. Bioinform. 30(12): 195-203 (2014) - [j24]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): 3458-3466 (2014) - [j23]Layla Oesper, Gryte Satas, Benjamin J. Raphael:
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinform. 30(24): 3532-3540 (2014) - 2013
- [j22]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) - 2012
- [j21]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms Mol. Biol. 7: 23 (2012) - [j20]Alejandro Cáceres, Suzanne S. Sindi, Benjamin J. Raphael, Mario Cáceres, Juan R. González:
Identification of polymorphic inversions from genotypes. BMC Bioinform. 13: 28 (2012) - [j19]Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael:
Reconstructing genome mixtures from partial adjacencies. BMC Bioinform. 13(S-19): S9 (2012) - [j18]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): S10 (2012) - [j17]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. Computer 45(3): 39-46 (2012) - [j16]Benjamin J. Raphael:
Chapter 6: Structural Variation and Medical Genomics. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j15]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: 114 (2011) - [j14]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Algorithms for Detecting Significantly Mutated Pathways in Cancer. J. Comput. Biol. 18(3): 507-522 (2011) - 2010
- [j13]Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael:
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol. Biol. 5: 11 (2010) - [j12]Anna M. Ritz, Ali Bashir, Benjamin J. Raphael:
Structural variation analysis with strobe reads. Bioinform. 26(10): 1291-1298 (2010) - [j11]Crystal L. Kahn, Borislav H. Hristov, Benjamin J. Raphael:
Parsimony and likelihood reconstruction of human segmental duplications. Bioinform. 26(18) (2010) - [j10]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): 369-381 (2010) - [j9]Suzanne S. Sindi, Benjamin J. Raphael:
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. J. Comput. Biol. 17(3): 517-531 (2010) - [j8]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): 918-926 (2010) - 2009
- [j7]Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael:
Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinform. 25(1): 14-21 (2009) - [j6]Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael:
A geometric approach for classification and comparison of structural variants. Bioinform. 25(12) (2009) - 2008
- [j5]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) - 2007
- [j4]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): 2807-2815 (2007) - 2006
- [j3]Neil Christopher Jones, Degui Zhi, Benjamin J. Raphael:
AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res. 34(Web-Server-Issue): 613-616 (2006) - [j2]Mark Chaisson, Benjamin J. Raphael, Pavel A. Pevzner:
Microinversions in mammalian evolution. Proc. Natl. Acad. Sci. USA 103(52): 19824-19829 (2006) - 2004
- [j1]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): 91-94 (2004)
Conference and Workshop Papers
- 2025
- [c48]Henri Schmidt, Benjamin J. Raphael:
The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. RECOMB 2025: 273-276 - [c47]Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael:
Inferring Cell Differentiation Maps from Lineage Tracing Data. RECOMB 2025: 312-315 - [c46]Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael:
Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. RECOMB 2025: 358-361 - [c45]Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael:
Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. RECOMB 2025: 367-370 - 2024
- [c44]Peter Halmos, Xinhao Liu, Julian Gold, Benjamin J. Raphael:
Low-Rank Optimal Transport through Factor Relaxation with Latent Coupling. NeurIPS 2024 - [c43]Uyen Mai, Gillian Chu, Benjamin J. Raphael:
Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. RECOMB 2024: 360-363 - [c42]Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael:
Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. RECOMB 2024: 368-371 - [c41]Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael:
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. RECOMB 2024: 434-437 - [c40]Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael:
Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. RECOMB 2024: 466-469 - 2022
- [c39]Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael:
NetMix2: Unifying Network Propagation and Altered Subnetworks. RECOMB 2022: 193-208 - [c38]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: 372-373 - [c37]Pijus Simonaitis, Benjamin J. Raphael:
A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. WABI 2022: 21:1-21:22 - 2021
- [c36]Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael:
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. ICML 2021: 1908-1919 - [c35]Ron Zeira, Geoffrey Mon, Benjamin J. Raphael:
Genome Halving and Aliquoting Under the Copy Number Distance. WABI 2021: 18:1-18:25 - 2020
- [c34]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: 169-185 - [c33]Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael:
Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. RECOMB 2020: 273 - 2019
- [c32]Uthsav Chitra, Benjamin J. Raphael:
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. ICML 2019: 1172-1181 - [c31]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: 297-298 - [c30]Matthew A. Myers, Gryte Satas, Benjamin J. Raphael:
Inferring Tumor Evolution from Longitudinal Samples. RECOMB 2019: 311 - 2017
- [c29]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: 318-335 - 2016
- [c28]Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael:
Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB 2016: 251 - [c27]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: 137-149 - 2015
- [c26]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: 8-9 - [c25]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: 202-204 - [c24]Fabio Vandin, Benjamin J. Raphael, Eli Upfal:
On the Sample Complexity of Cancer Pathways Identification. RECOMB 2015: 326-337 - 2014
- [c23]Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael:
A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types. ICCABS 2014: 1 - [c22]Benjamin J. Raphael, Fabio Vandin:
Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. RECOMB 2014: 250-264 - [c21]Iman Hajirasouliha, Benjamin J. Raphael:
Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures. WABI 2014: 354-367 - 2013
- [c20]Layla Oesper, Benjamin J. Raphael:
Workshop: Reconstructing the organization of cancer genomes. ICCABS 2013: 1 - [c19]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Identifying significant mutations in large cohorts of cancer genomes. ICCABS 2013: 1 - [c18]Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance:
Session introduction. Pacific Symposium on Biocomputing 2013: 307-309 - [c17]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: 445-450 - [c16]Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael:
Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. RECOMB 2013: 171-172 - [c15]Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal:
Genome-Wide Survival Analysis of Somatic Mutations in Cancer. RECOMB 2013: 285-286 - 2012
- [c14]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Workshop: Algorithms for discovery of mutated pathways in cancer. ICCABS 2012: 1 - [c13]Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael:
Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. Pacific Symposium on Biocomputing 2012: 55-66 - 2011
- [c12]Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir:
Workshop: Characterization of structural variants with next generation DNA sequencing. ICCABS 2011: 275 - [c11]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
De Novo Discovery of Mutated Driver Pathways in Cancer. RECOMB 2011: 499-500 - [c10]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Finding Driver Pathways in Cancer: Models and Algorithms. WABI 2011: 314-325 - 2010
- [c9]Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
Algorithms for Detecting Significantly Mutated Pathways in Cancer. RECOMB 2010: 506-521 - 2009
- [c8]Crystal L. Kahn, Benjamin J. Raphael:
A Parsimony Approach to Analysis of Human Segmental Duplications. Pacific Symposium on Biocomputing 2009: 126-137 - [c7]Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna:
Optimizing PCR Assays for DNA Based Cancer Diagnostics. RECOMB 2009: 220-235 - [c6]Suzanne S. Sindi, Benjamin J. Raphael:
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. RECOMB 2009: 418-433 - [c5]Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael:
Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. WABI 2009: 169-180 - 2008
- [c4]Crystal L. Kahn, Benjamin J. Raphael:
Analysis of segmental duplications via duplication distance. ECCB 2008: 133-138 - 2007
- [c3]Erik Corona, Benjamin J. Raphael, Eleazar Eskin:
Identification of Deletion Polymorphisms from Haplotypes. RECOMB 2007: 354-365 - 2004
- [c2]Benjamin J. Raphael, Pavel A. Pevzner:
Reconstructing tumor amplisomes. ISMB/ECCB (Supplement of Bioinformatics) 2004: 265-273 - 2003
- [c1]Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner:
Reconstructing tumor genome architectures. ECCB 2003: 162-171
Editorship
- 2018
- [e3]Benjamin J. Raphael:
Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings. Lecture Notes in Computer Science 10812, Springer 2018, ISBN 978-3-319-89928-2 [contents] - 2012
- [e2]Benjamin J. Raphael, Jijun Tang:
Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings. Lecture Notes in Computer Science 7534, Springer 2012, ISBN 978-3-642-33121-3 [contents] - 2006
- [e1]Eleazar Eskin, Trey Ideker, Benjamin J. Raphael, Christopher T. Workman:
Systems Biology and Regulatory Genomics, Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers. Lecture Notes in Computer Science 4023, Springer 2006, ISBN 978-3-540-48293-2 [contents]
Informal and Other Publications
- 2025
- [i6]Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael:
Hierarchical Refinement: Optimal Transport to Infinity and Beyond. CoRR abs/2503.03025 (2025) - 2024
- [i5]Peter Halmos, Xinhao Liu, Julian Gold, Benjamin J. Raphael:
Low-Rank Optimal Transport through Factor Relaxation with Latent Coupling. CoRR abs/2411.10555 (2024) - 2020
- [i4]Uthsav Chitra, Kimberly Ding, Benjamin J. Raphael:
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. CoRR abs/2007.07878 (2020) - 2019
- [i3]Uthsav Chitra, Benjamin J. Raphael:
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. CoRR abs/1905.08287 (2019) - [i2]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: e27885 (2019) - 2016
- [i1]Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael:
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. CoRR abs/1604.02605 (2016)
Coauthor Index
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Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
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Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
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Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
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OpenAlex data
Load additional information about publications from 
.
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last updated on 2025-10-30 00:58 CET by the dblp team
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