Publications by authors named "Benjamin J Raphael"

104 Publications

NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks.

J Comput Biol 2021 Jan 5. Epub 2021 Jan 5.

Department of Computer Science, Princeton University, Princeton, New Jersey, USA.

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January 2021

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.

Genome Res 2020 Sep 4;30(9):1274-1290. Epub 2020 Sep 4.

Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.

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September 2020

Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.

Nat Biotechnol 2021 Feb 2;39(2):207-214. Epub 2020 Sep 2.

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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February 2021

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.

Nat Commun 2020 09 2;11(1):4301. Epub 2020 Sep 2.

Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA.

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September 2020

SCARLET: Single-cell tumor phylogeny inference with copy-number constrained mutation losses.

Cell Syst 2020 04;10(4):323-332.e8

Department of Computer Science, Princeton University, Princeton, NJ 08540.

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April 2020

Identifying tumor clones in sparse single-cell mutation data.

Bioinformatics 2020 Jul;36(Supplement_1):i186-i193

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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July 2020

Copy number evolution with weighted aberrations in cancer.

Bioinformatics 2020 Jul;36(Supplement_1):i344-i352

Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

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July 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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February 2020

netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis.

Genome Res 2020 02 28;30(2):195-204. Epub 2020 Jan 28.

Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.

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February 2020

CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Cell Syst 2019 06 19;8(6):514-522.e5. Epub 2019 Jun 19.

Department of Computer Science, Princeton University, Princeton, NJ 08540, USA. Electronic address:

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June 2019

Hierarchical HotNet: identifying hierarchies of altered subnetworks.

Bioinformatics 2018 09;34(17):i972-i980

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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September 2018

Using controls to limit false discovery in the era of big data.

BMC Bioinformatics 2018 Sep 14;19(1):323. Epub 2018 Sep 14.

Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI, 02912, USA.

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September 2018

Haplotype phasing in single-cell DNA-sequencing data.

Bioinformatics 2018 07;34(13):i211-i217

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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July 2018

Visible Machine Learning for Biomedicine.

Cell 2018 06;173(7):1562-1565

Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA; Cancer Cell Map Initiative, University of California San Diego, La Jolla, CA, USA; UCSD Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA. Electronic address:

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June 2018

Inferring parsimonious migration histories for metastatic cancers.

Nat Genet 2018 05 26;50(5):718-726. Epub 2018 Apr 26.

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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May 2018

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

J Comput Biol 2018 07 16;25(7):689-708. Epub 2018 Apr 16.

1 Department of Computer Science, Princeton University , Princeton, New Jersey.

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July 2018

Identifying simultaneous rearrangements in cancer genomes.

Bioinformatics 2018 Jan;34(2):346-352

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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January 2018

Identifying structural variants using linked-read sequencing data.

Bioinformatics 2018 Jan;34(2):353-360

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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January 2018

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors.

Genome Res 2017 11 13;27(11):1885-1894. Epub 2017 Oct 13.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland.

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November 2017

Tumor phylogeny inference using tree-constrained importance sampling.

Bioinformatics 2017 Jul;33(14):i152-i160

Department of Computer Science, Princeton University, Princeton, NJ, USA.

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July 2017

Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations.

Cancer Epidemiol Biomarkers Prev 2017 10 27;26(10):1531-1539. Epub 2017 Jul 27.

Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island.

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October 2017

Network propagation: a universal amplifier of genetic associations.

Nat Rev Genet 2017 09 12;18(9):551-562. Epub 2017 Jun 12.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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September 2017

Complexity and algorithms for copy-number evolution problems.

Algorithms Mol Biol 2017 16;12:13. Epub 2017 May 16.

School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

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May 2017

A weighted exact test for mutually exclusive mutations in cancer.

Bioinformatics 2016 09;32(17):i736-i745

Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.

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September 2016