Searching journal content for Benjamin Raphael in author.

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  1. Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
    • Hongyu Zheng,
    • Hirak Sarkar,
    • and Benjamin J. Raphael
    Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
    OPEN ACCESS ARTICLE
  2. Method: Partial alignment of multislice spatially resolved transcriptomics data
    • Xinhao Liu,
    • Ron Zeira,
    • and Benjamin J. Raphael
    Genome Res. July 2023 33: 1124-1132; Published in Advance August 8, 2023, doi:10.1101/gr.277670.123
  3. Method: Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples
    • Sergey Aganezov and
    • Benjamin J. Raphael
    Genome Res. September 2020 30: 1274-1290; Published in Advance September 4, 2020, doi:10.1101/gr.256701.119
  4. Method: netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis
    • Rebecca Elyanow,
    • Bianca Dumitrascu,
    • Barbara E. Engelhardt,
    • and Benjamin J. Raphael
    Genome Res. February 2020 30: 195-204; Published in Advance January 28, 2020, doi:10.1101/gr.251603.119
  5. Method: Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors
    • Jack Kuipers,
    • Katharina Jahn,
    • Benjamin J. Raphael,
    • and Niko Beerenwinkel
    Genome Res. November 2017 27: 1885-1894; Published in Advance October 13, 2017, doi:10.1101/gr.220707.117
  6. Resource: GenomeVIP: a cloud platform for genomic variant discovery and interpretation
    • R. Jay Mashl,
    • Adam D. Scott,
    • Kuan-lin Huang,
    • Matthew A. Wyczalkowski,
    • Christopher J. Yoon,
    • Beifang Niu,
    • Erin DeNardo,
    • Venkata D. Yellapantula,
    • Robert E. Handsaker,
    • Ken Chen,
    • Daniel C. Koboldt,
    • Kai Ye,
    • David Fenyö,
    • Benjamin J. Raphael,
    • Michael C. Wendl,
    • and Li Ding
    Genome Res. August 2017 27: 1450-1459; Published in Advance May 18, 2017, doi:10.1101/gr.211656.116
  7. Method: De novo discovery of mutated driver pathways in cancer
    • Fabio Vandin,
    • Eli Upfal,
    • and Benjamin J. Raphael
    Genome Res. February 2012 22: 375-385; Published in Advance June 7, 2011, doi:10.1101/gr.120477.111
  8. Methods: Decoding the fine-scale structure of a breast cancer genome and transcriptome
    • Stanislav Volik,
    • Benjamin J. Raphael,
    • Guiqing Huang,
    • Michael R. Stratton,
    • Graham Bignel,
    • John Murnane,
    • John H. Brebner,
    • Krystyna Bajsarowicz,
    • Pamela L. Paris,
    • Quanzhou Tao,
    • David Kowbel,
    • Anna Lapuk,
    • Dmitri A. Shagin,
    • Irina A. Shagina,
    • Joe W. Gray,
    • Jan-Fang Cheng,
    • Pieter J. de Jong,
    • Pavel Pevzner,
    • and Colin Collins
    Genome Res. March 2006 16: 394-404; Published in Advance February 3, 2006, doi:10.1101/gr.4247306
  9. Methods: A novel method for multiple alignment of sequences with repeated and shuffled elements
    • Benjamin Raphael,
    • Degui Zhi,
    • Haixu Tang,
    • and Pavel Pevzner
    Genome Res. November 2004 14: 2336-2346; doi:10.1101/gr.2657504
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