Searching journal content for S. Cenk Sahinalp in author.

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  1. Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
    • Natnatee Dokmai,
    • Kaiyuan Zhu,
    • S. Cenk Sahinalp,
    • and Hyunghoon Cho
    Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
    OPEN ACCESS ARTICLE
  2. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    OPEN ACCESS ARTICLE
  3. Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
    • Yuelin Liu,
    • Xuan Cindy Li,
    • Farid Rashidi Mehrabadi,
    • Alejandro A. Schäffer,
    • Drew Pratt,
    • David R. Crawford,
    • Salem Malikić,
    • Erin K. Molloy,
    • Vishaka Gopalan,
    • Stephen M. Mount,
    • Eytan Ruppin,
    • Kenneth D. Aldape,
    • and S. Cenk Sahinalp
    Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
  4. Method: An efficient genotyper and star-allele caller for pharmacogenomics
    • Ananth Hari,
    • Qinghui Zhou,
    • Nina Gonzaludo,
    • John Harting,
    • Stuart A. Scott,
    • Xiang Qin,
    • Steve Scherer,
    • S. Cenk Sahinalp,
    • and Ibrahim Numanagić
    Genome Res. January 2023 33: 61-70; Published in Advance January 19, 2023, doi:10.1101/gr.277075.122
  5. Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
    • Salem Malikic,
    • Farid Rashidi Mehrabadi,
    • Simone Ciccolella,
    • Md. Khaledur Rahman,
    • Camir Ricketts,
    • Ehsan Haghshenas,
    • Daniel Seidman,
    • Faraz Hach,
    • Iman Hajirasouliha,
    • and S. Cenk Sahinalp
    Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
    OPEN ACCESS ARTICLE
  6. Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
    • Raunak Shrestha,
    • Ermin Hodzic,
    • Thomas Sauerwald,
    • Phuong Dao,
    • Kendric Wang,
    • Jake Yeung,
    • Shawn Anderson,
    • Fabio Vandin,
    • Gholamreza Haffari,
    • Colin C. Collins,
    • and S. Cenk Sahinalp
    Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
  7. Method: nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    • Andrew McPherson,
    • Chunxiao Wu,
    • Alexander W. Wyatt,
    • Sohrab Shah,
    • Colin Collins,
    • and S. Cenk Sahinalp
    Genome Res. November 2012 22: 2250-2261; Published in Advance June 28, 2012, doi:10.1101/gr.136572.111
  8. Resource: Simultaneous structural variation discovery among multiple paired-end sequenced genomes
    • Fereydoun Hormozdiari,
    • Iman Hajirasouliha,
    • Andrew McPherson,
    • Evan E. Eichler,
    • and S. Cenk Sahinalp
    Genome Res. December 2011 21: 2203-2212; Published in Advance November 2, 2011, doi:10.1101/gr.120501.111
  9. Research: Alu repeat discovery and characterization within human genomes
    • Fereydoun Hormozdiari,
    • Can Alkan,
    • Mario Ventura,
    • Iman Hajirasouliha,
    • Maika Malig,
    • Faraz Hach,
    • Deniz Yorukoglu,
    • Phuong Dao,
    • Marzieh Bakhshi,
    • S. Cenk Sahinalp,
    • and Evan E. Eichler
    Genome Res. June 2011 21: 840-849; Published in Advance December 3, 2010, doi:10.1101/gr.115956.110
  10. Methods: Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Fereydoun Hormozdiari,
    • Can Alkan,
    • Evan E. Eichler,
    • and S. Cenk Sahinalp
    Genome Res. July 2009 19: 1270-1278; Published in Advance May 15, 2009, doi:10.1101/gr.088633.108
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