Benjamin J. Raphael

112 papers A* 4B 26C 9Misc 5Journal 61Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Transport Clustering: Solving Low-Rank Optimal Transport via Clustering. CoRR Henri Schmidt, Peter Halmos, Benjamin J. Raphael
2025	J	`jnl`	Anomaly detection in spatial transcriptomics via spatially localized density comparison. Bioinform. Gary Hu, Julian Gold, Uthsav Chitra, Sunay Joshi, Benjamin J. Raphael
2025	J	`jnl`	Fast tumor phylogeny regression via tree-structured dual dynamic programming. Bioinform. Henri Schmidt, Yuanyuan Qi, Benjamin J. Raphael, Mohammed El-Kebir
2025	J	`jnl`	GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts. Bioinform. Uthsav Chitra, Shu Dan, Fenna M. Krienen, Benjamin J. Raphael
2025	A*	`conf`	Hierarchical Refinement: Optimal Transport to Infinity and Beyond. ICML Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael
2025	J	`jnl`	Hierarchical Refinement: Optimal Transport to Infinity and Beyond. CoRR Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael
2025	B	`conf`	Inferring Cell Differentiation Maps from Lineage Tracing Data. RECOMB Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael
2025	B	`conf`	Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. RECOMB Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael
2025	B	`conf`	Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. RECOMB Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael
2025	B	`conf`	The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. RECOMB Henri Schmidt, Benjamin J. Raphael
2024	J	`jnl`	A count-based model for delineating cell-cell interactions in spatial transcriptomics data. Bioinform. Hirak Sarkar, Uthsav Chitra, Julian Gold, Benjamin J. Raphael
2024	J	`jnl`	A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors. PLoS Comput. Biol. Henri Schmidt, Benjamin J. Raphael
2024	B	`conf`	DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. RECOMB Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael
2024	B	`conf`	Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. RECOMB Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael
2024	J	`jnl`	Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. Bioinform. Palash Sashittal, Viola Chen, Amey Pasarkar, Benjamin J. Raphael
2024	A*	`conf`	Low-Rank Optimal Transport through Factor Relaxation with Latent Coupling. NeurIPS Peter Halmos, Xinhao Liu, Julian Gold, Benjamin J. Raphael
2024	J	`jnl`	Low-Rank Optimal Transport through Factor Relaxation with Latent Coupling. CoRR Peter Halmos, Xinhao Liu, Julian Gold, Benjamin J. Raphael
2024	B	`conf`	Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. RECOMB Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael
2024	B	`conf`	Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. RECOMB Uyen Mai, Gillian Chu, Benjamin J. Raphael
2024	J	`jnl`	Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data. Bioinform. Uyen Mai, Gary Hu, Benjamin J. Raphael
2023	J	`jnl`	A zero-agnostic model for copy number evolution in cancer. PLoS Comput. Biol. Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
2022	C	`conf`	A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. WABI Pijus Simonaitis, Benjamin J. Raphael
2022	B	`conf`	Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. RECOMB Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael
2022	J	`jnl`	NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. J. Comput. Biol. Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
2022	B	`conf`	NetMix2: Unifying Network Propagation and Altered Subnetworks. RECOMB Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
2021	C	`conf`	Genome Halving and Aliquoting Under the Copy Number Distance. WABI Ron Zeira, Geoffrey Mon, Benjamin J. Raphael
2021	J	`jnl`	NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. J. Comput. Biol. Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael
2021	A*	`conf`	Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. ICML Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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 González-Pérez, 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
2020	J	`jnl`	Copy number evolution with weighted aberrations in cancer. Bioinform. Ron Zeira, Benjamin J. Raphael
2020	J	`jnl`	Identifying tumor clones in sparse single-cell mutation data. Bioinform. Matthew A. Myers, Simone Zaccaria, Benjamin J. Raphael
2020	B	`conf`	NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. RECOMB Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael
2020	J	`jnl`	Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. CoRR Uthsav Chitra, Kimberly Ding, Benjamin J. Raphael
2020	B	`conf`	Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. RECOMB Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael
2020	J	`jnl`	The evolutionary history of 2,658 cancers. Nat. 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
2019	J	`jnl`	12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 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
2019	B	`conf`	Inferring Tumor Evolution from Longitudinal Samples. RECOMB Matthew A. Myers, Gryte Satas, Benjamin J. Raphael
2019	A*	`conf`	Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. ICML Uthsav Chitra, Benjamin J. Raphael
2019	J	`jnl`	Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. CoRR Uthsav Chitra, Benjamin J. Raphael
2019	B	`conf`	netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data. RECOMB Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael
2018	J	`jnl`	Haplotype phasing in single-cell DNA-sequencing data. Bioinform. Gryte Satas, Benjamin J. Raphael
2018	J	`jnl`	Hierarchical HotNet: identifying hierarchies of altered subnetworks. Bioinform. Matthew A. Reyna, Mark D. M. Leiserson, Benjamin J. Raphael
2018	J	`jnl`	Identifying simultaneous rearrangements in cancer genomes. Bioinform. Layla Oesper, Simone Dantas, Benjamin J. Raphael
2018	J	`jnl`	Identifying structural variants using linked-read sequencing data. Bioinform. Rebecca Elyanow, Hsin-Ta Wu, Benjamin J. Raphael
2018	J	`jnl`	Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2018	B	`ed.`	Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings RECOMB Benjamin J. Raphael
2018	J	`jnl`	Using controls to limit false discovery in the era of big data. BMC Bioinform. Matthew M. Parks, Benjamin J. Raphael, Charles E. Lawrence
2017	J	`jnl`	Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
2017	B	`conf`	The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. RECOMB Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2017	J	`jnl`	Tumor phylogeny inference using tree-constrained importance sampling. Bioinform. Gryte Satas, Benjamin J. Raphael
2016	J	`jnl`	A weighted exact test for mutually exclusive mutations in cancer. Bioinform. Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael
2016	C	`conf`	Copy-Number Evolution Problems: Complexity and Algorithms. WABI Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
2016	J	`jnl`	Identification of hierarchical chromatin domains. Bioinform. Caleb Weinreb, Benjamin J. Raphael
2016	J	`jnl`	Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. CoRR Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
2016	B	`conf`	Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
2016	J	`jnl`	On the Sample Complexity of Cancer Pathways Identification. J. Comput. Biol. Fabio Vandin, Benjamin J. Raphael, Eli Upfal
2015	J	`jnl`	Accurate Computation of Survival Statistics in Genome-Wide Studies. PLoS Comput. Biol. Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal
2015	B	`conf`	CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. RECOMB Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael
2015	B	`conf`	On the Sample Complexity of Cancer Pathways Identification. RECOMB Fabio Vandin, Benjamin J. Raphael, Eli Upfal
2015	J	`jnl`	Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinform. Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael
2015	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Søren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rätsch, Joshua M. Stuart
2015	J	`jnl`	Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. J. Comput. Biol. Benjamin J. Raphael, Fabio Vandin
2014	—	`conf`	A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types. ICCABS Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael
2014	J	`jnl`	A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinform. Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael
2014	J	`jnl`	Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinform. Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael
2014	J	`jnl`	Detecting independent and recurrent copy number aberrations using interval graphs. Bioinform. Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael
2014	J	`jnl`	Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinform. Layla Oesper, Gryte Satas, Benjamin J. Raphael
2014	C	`conf`	Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures. WABI Iman Hajirasouliha, Benjamin J. Raphael
2014	B	`conf`	Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. RECOMB Benjamin J. Raphael, Fabio Vandin
2013	B	`conf`	Genome-Wide Survival Analysis of Somatic Mutations in Cancer. RECOMB Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal
2013	—	`conf`	Identifying significant mutations in large cohorts of cancer genomes. ICCABS Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2013	B	`conf`	Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. RECOMB Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael
2013	Misc	`conf`	Modeling cell heterogeneity: from single-cell variations to mixed cells populations. Pacific Symposium on Biocomputing Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wójtowicz
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Gürkan Bebek, Mehmet Koyutürk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance
2013	J	`jnl`	Simultaneous Identification of Multiple Driver Pathways in Cancer. PLoS Comput. Biol. Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael
2013	—	`conf`	Workshop: Reconstructing the organization of cancer genomes. ICCABS Layla Oesper, Benjamin J. Raphael
2012	J	`jnl`	Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. Computer Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2012	C	`ed.`	Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings WABI Benjamin J. Raphael, Jijun Tang
2012	J	`jnl`	Chapter 6: Structural Variation and Medical Genomics. PLoS Comput. Biol. Benjamin J. Raphael
2012	Misc	`conf`	Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. Pacific Symposium on Biocomputing Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael
2012	J	`jnl`	Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms Mol. Biol. Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2012	J	`jnl`	Identification of polymorphic inversions from genotypes. BMC Bioinform. Alejandro Cáceres, Suzanne S. Sindi, Benjamin J. Raphael, Mario Cáceres, Juan R. González
2012	J	`jnl`	Reconstructing cancer genomes from paired-end sequencing data. BMC Bioinform. Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael
2012	J	`jnl`	Reconstructing genome mixtures from partial adjacencies. BMC Bioinform. Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael
2012	—	`conf`	Workshop: Algorithms for discovery of mutated pathways in cancer. ICCABS Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2011	J	`jnl`	Algorithms for Detecting Significantly Mutated Pathways in Cancer. J. Comput. Biol. Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2011	J	`jnl`	Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinform. Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael
2011	C	`conf`	Finding Driver Pathways in Cancer: Models and Algorithms. WABI Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2011	—	`conf`	Workshop: Characterization of structural variants with next generation DNA sequencing. ICCABS Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir
2010	B	`conf`	Algorithms for Detecting Significantly Mutated Pathways in Cancer. RECOMB Fabio Vandin, Eli Upfal, Benjamin J. Raphael
2010	J	`jnl`	Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol. Biol. Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael
2010	J	`jnl`	Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements. IEEE Trans. Vis. Comput. Graph. Trevor M. O'Brien, Anna M. Ritz, Benjamin J. Raphael, David H. Laidlaw
2010	J	`jnl`	Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. J. Comput. Biol. Suzanne S. Sindi, Benjamin J. Raphael
2010	J	`jnl`	Optimizing PCR Assays for DNA-Based Cancer Diagnostics. J. Comput. Biol. Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2010	J	`jnl`	Parsimony and likelihood reconstruction of human segmental duplications. Bioinform. Crystal L. Kahn, Borislav H. Hristov, Benjamin J. Raphael
2010	J	`jnl`	Structural variation analysis with strobe reads. Bioinform. Anna M. Ritz, Ali Bashir, Benjamin J. Raphael
2009	Misc	`conf`	A Parsimony Approach to Analysis of Human Segmental Duplications. Pacific Symposium on Biocomputing Crystal L. Kahn, Benjamin J. Raphael
2009	J	`jnl`	A geometric approach for classification and comparison of structural variants. Bioinform. Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael
2009	J	`jnl`	Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinform. Anna M. Ritz, Gregory Shakhnarovich, Arthur R. Salomon, Benjamin J. Raphael
2009	C	`conf`	Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. WABI Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael
2009	B	`conf`	Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. RECOMB Suzanne S. Sindi, Benjamin J. Raphael
2009	B	`conf`	Optimizing PCR Assays for DNA Based Cancer Diagnostics. RECOMB Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2008	C	`conf`	Analysis of segmental duplications via duplication distance. ECCB Crystal L. Kahn, Benjamin J. Raphael
2008	J	`jnl`	Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Comput. Biol. Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
2007	B	`conf`	Identification of Deletion Polymorphisms from Haplotypes. RECOMB Erik Corona, Benjamin J. Raphael, Eleazar Eskin
2007	J	`jnl`	Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinform. Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna
2006	J	`jnl`	AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res. Neil Christopher Jones, Degui Zhi, Benjamin J. Raphael
2006	J	`jnl`	Microinversions in mammalian evolution. Proc. Natl. Acad. Sci. USA Mark Chaisson, Benjamin J. Raphael, Pavel A. Pevzner
2006	—	`ed.`	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 Systems Biology and Regulatory Genomics Eleazar Eskin, Trey Ideker, Benjamin J. Raphael, Christopher T. Workman
2004	J	`jnl`	A Uniform Projection Method for Motif Discovery in DNA Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. Benjamin J. Raphael, Lung-Tien Liu, George Varghese
2004	—	`conf`	Reconstructing tumor amplisomes. ISMB/ECCB (Supplement of Bioinformatics) Benjamin J. Raphael, Pavel A. Pevzner
2003	C	`conf`	Reconstructing tumor genome architectures. ECCB Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner