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Benjamin J. Raphael
Person information
- affiliation: Princeton University, Princeton, NJ, USA
- affiliation (former): Brown University, Providence, RI, USA
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2020 – today
- 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 - 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
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. J. Comput. Biol. 29(12): 1305-1323 (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
Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. RECOMB 2022: 372-373 - [c37]Pijus Simonaitis
A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. WABI 2022: 21:1-21:22 - 2021
- [j45]Matthew A. Reyna, Uthsav Chitra
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. J. Comput. Biol. 28(5): 469-484 (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
Genome Halving and Aliquoting Under the Copy Number Distance. WABI 2021: 18:1-18:25 - 2020
- [j44]Matthew A. Myers
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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j41]Moritz Gerstung
The evolutionary history of 2,658 cancers. Nat. 578(7793): 122-128 (2020) - [c34]Matthew A. Reyna, Uthsav Chitra
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. RECOMB 2020: 169-185 - [c33]Gryte Satas, Simone Zaccaria
Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. RECOMB 2020: 273 - [i4]Uthsav Chitra, Kimberly Ding, Benjamin J. Raphael:
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. CoRR abs/2007.07878 (2020)
2010 – 2019
- 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 - [i3]Uthsav Chitra, Benjamin J. Raphael:
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. CoRR abs/1905.08287 (2019) - [i2]David Laehnemann
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [j40]Layla Oesper, Simone Dantas, Benjamin J. Raphael
Identifying simultaneous rearrangements in cancer genomes. Bioinform. 34(2): 346-352 (2018) - [j39]Rebecca Elyanow
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
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. 25(7): 689-708 (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] - 2017
- [j34]Mohammed El-Kebir
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) - [c29]Simone Zaccaria
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. RECOMB 2017: 318-335 - 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) - [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
Copy-Number Evolution Problems: Complexity and Algorithms. WABI 2016: 137-149 - [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) - 2015
- [j29]Mohammed El-Kebir
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) - [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
- [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
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) - [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
- [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) - [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
- [j21]Fabio Vandin, Eli Upfal
Finding Driver Pathways in Cancer: Models and Algorithms. Algorithms Mol. Biol. 7: 23 (2012) - [j20]Alejandro Cáceres
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
Reconstructing cancer genomes from paired-end sequencing data. BMC Bioinform. 13(S-6): S10 (2012) - [j17]Fabio Vandin, Eli Upfal
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) - [c14]Fabio Vandin, Eli Upfal
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 - [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] - 2011
- [j15]Anna M. Ritz
Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinform. 12: 114 (2011) - [j14]Fabio Vandin, Eli Upfal
Algorithms for Detecting Significantly Mutated Pathways in Cancer. J. Comput. Biol. 18(3): 507-522 (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
De Novo Discovery of Mutated Driver Pathways in Cancer. RECOMB 2011: 499-500 - [c10]Fabio Vandin, Eli Upfal
Finding Driver Pathways in Cancer: Models and Algorithms. WABI 2011: 314-325 - 2010
- [j13]Crystal L. Kahn, Shay Mozes
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. Algorithms Mol. Biol. 5: 11 (2010) - [j12]Anna M. Ritz
Structural variation analysis with strobe reads. Bioinform. 26(10): 1291-1298 (2010) - [j11]Crystal L. Kahn, Borislav H. Hristov
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
Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements. IEEE Trans. Vis. Comput. Graph. 16(6): 918-926 (2010) - [c9]Fabio Vandin, Eli Upfal
Algorithms for Detecting Significantly Mutated Pathways in Cancer. RECOMB 2010: 506-521
2000 – 2009
- 2009
- [j7]Anna M. Ritz
Discovery of phosphorylation motif mixtures in phosphoproteomics data. Bioinform. 25(1): 14-21 (2009) - [j6]Suzanne S. Sindi, Elena Helman, Ali Bashir
A geometric approach for classification and comparison of structural variants. Bioinform. 25(12) (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
Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. WABI 2009: 169-180 - 2008
- [j5]Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Comput. Biol. 4(4) (2008) - [c4]Crystal L. Kahn, Benjamin J. Raphael:
Analysis of segmental duplications via duplication distance. ECCB 2008: 133-138 - 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) - [c3]Erik Corona, Benjamin J. Raphael, Eleazar Eskin:
Identification of Deletion Polymorphisms from Haplotypes. RECOMB 2007: 354-365 - 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) - [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] - 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) - [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
Coauthor Index
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