Ben Raphael
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Ben Raphael

Princeton University

20032025

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  • 2024

    DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

    Halmos, P., Liu, X., Gold, J., Chen, F., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 434-437 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics

    Ma, C., Balaban, M., Liu, J., Chen, S., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 466-469 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning

    Chitra, U., Arnold, B. J., Sarkar, H., Ma, C., Lopez-Darwin, S., Sanno, K. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 368-371 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data

    Mai, U., Chu, G. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 360-363 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2022

    A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements

    Simonaitis, P. & Raphael, B. J., Sep 1 2022, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022. Boucher, C. & Rahmann, S. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 21. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 242).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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

    Ma, C., Chitra, U., Zhang, S. & Raphael, B. J., 2022, Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings. Pe’er, I. (ed.). Springer Science and Business Media Deutschland GmbH, p. 372-373 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13278 LNBI).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • NetMix2: Unifying Network Propagation and Altered Subnetworks

    Chitra, U., Park, T. Y. & Raphael, B. J., 2022, Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings. Pe’er, I. (ed.). Springer Science and Business Media Deutschland GmbH, p. 193-208 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13278 LNBI).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2021

    Genome halving and aliquoting under the copy number distance

    Zeira, R., Mon, G. & Raphael, B. J., Jul 1 2021, 21st International Workshop on Algorithms in Bioinformatics, WABI 2021. Carbone, A. & El-Kebir, M. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 18. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 201).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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

    Chitra, U., Ding, K., Lee, J. C. H. & Raphael, B. J., 2021, Proceedings of the 38th International Conference on Machine Learning, ICML 2021. ML Research Press, p. 1908-1919 12 p. (Proceedings of Machine Learning Research; vol. 139).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2020

    Netmix: a network-structured mixture model for reduced-bias estimation of altered subnetworks

    Reyna, M. A., Chitra, U., Elyanow, R. & Raphael, B. J., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 169-185 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access

  • Single-cell tumor phylogeny inference with copy-number constrained mutation losses

    Satas, G., Zaccaria, S., Mon, G. & Raphael, B. J., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 273 1 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
  • 2019

    Random walks on hypergraphs with edge-dependent vertex weights

    Chitra, U. & Raphael, B. J., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 2002-2011 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Scopus citations
  • 2017

    The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

    Zaccaria, S., El-Kebir, M., Klau, G. W. & Raphael, B. J., 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer Verlag, p. 318-335 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

    Princeton University

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    9 Scopus citations
  • 2016

    Copy-number evolution problems: Complexity and algorithms

    El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M. & Zeira, R., 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Frith, M. & Pedersen, C. N. S. (eds.). Springer Verlag, p. 137-149 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9838 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    12 Scopus citations
  • 2015

    CoMET: A statistical approach to identify combinations of mutually exclusive alterations in cancer

    Leiserson, M. D. M., Wu, H. T., Vandin, F. & Raphael, B. J., 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer Verlag, p. 202-204 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations

  • On the sample complexity of cancer pathways identification

    Vandin, F., Raphael, B. J. & Upfal, E., 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer Verlag, p. 326-337 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    1 Scopus citations
  • 2014

    Reconstructing mutational history in multiply sampled tumors using perfect phylogeny mixtures

    Hajirasouliha, I. & Raphael, B. J., 2014, Algorithms in Bioinformatics - 14th International Workshop, WABI 2014, Proceedings. Springer Verlag, p. 354-367 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8701 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    11 Scopus citations

  • Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data

    Raphael, B. J. & Vandin, F., 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, p. 250-264 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations
  • 2013

    Genome-wide survival analysis of somatic mutations in cancer

    Vandin, F., Papoutsaki, A., Raphael, B. J. & Upfal, E., 2013, Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. p. 285-286 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7821 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

    Oesper, L., Mahmoody, A. & Raphael, B. J., 2013, Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. p. 171-172 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7821 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations
  • 2012

    Workshop: Algorithms for discovery of mutated pathways in cancer

    Vandin, F., Upfal, E. & Raphael, B. J., 2012, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 6182678. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2011

    De Novo Discovery of Mutated Driver Pathways in Cancer

    Vandin, F., Upfal, E. & Raphael, B. J., 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. Bafna, V. & Sahinalp, S. C. (eds.). Springer Verlag, p. 499-500 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6577 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
    3 Scopus citations

  • Finding driver pathways in cancer: Models and algorithms

    Vandin, F., Upfal, E. & Raphael, B. J., 2011, Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Proceedings. p. 314-325 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6833 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
  • 2010

    Algorithms for detecting significantly mutated pathways in cancer

    Vandin, F., Upfal, E. & Raphael, B. J., 2010, Research in Computational Molecular Biology - 14th Annual International Conference, RECOMB 2010, Proceedings. p. 506-521 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6044 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    16 Scopus citations
  • 2009

    A parsimony approach to analysis of human segmental duplications

    Kahn, C. L. & Raphael, B. J., 2009, Pacific Symposium on Biocomputing 2009, PSB 2009. p. 126-137 12 p. (Pacific Symposium on Biocomputing 2009, PSB 2009).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Scopus citations

  • Efficient algorithms for analyzing segmental duplications, deletions, and inversions in genomes

    Kahn, C. L., Mozes, S. & Raphael, B. J., 2009, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 169-180 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Identification and frequency estimation of inversion polymorphisms from haplotype data

    Sindi, S. S. & Raphael, B. J., 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 418-433 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    3 Scopus citations

  • Optimizing PCR assays for DNA based cancer diagnostics

    Bashir, A., Lu, Q., Carson, D., Raphael, B., Liu, Y. T. & Bafna, V., 2009, Research in Computational Molecular Biology - 13th Annual International Conference, RECOMB 2009, Proceedings. p. 220-235 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5541 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2007

    Identification of deletion polymorphisms from haplotypes

    Corona, E., Raphael, B. & Eskin, E., 2007, Research in Computational Molecular Biology - 11th Annual International Conference, RECOMB 2007, Proceedings. Springer Verlag, p. 354-365 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4453 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    6 Scopus citations