S. Cenk Sahinalp, Ph.D.

S. Cenk Sahinalp, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute
Cancer Data Science Laboratory


My research focuses on developing algorithmic methods for managing, storing, communicating and analyzing high-throughput cancer sequencing data.

Areas of Expertise

Algorithmic Methods
Tumor Heterogeneity and Progression
Single Cell Sequencing
Bimolecular Networks
Genotyping Repetitive Regions (e.g. genes involved in drug metabolism or coding immunoglobulins) of the Human Genome


Selected Publications

PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC
Genome Research. 29/11: 1860-1877, 2019. [ Journal Article ]

Sketching algorithms for genomic data analysis and querying in a secure enclave

Kockan, C., Zhu, K., Dokmai, K., Karpov, N., Kulekci, M.O., Woodruff. D.P.. & Sahinalp, S.C.
Nature Methods. 17(3): 295-301, 2020.
Full-Text Article
[ Journal Article ]

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC.
Genome Research. 27(9): 1573-88, 2017. [ Journal Article ]

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Numanagić I, Malikić S, Ford M, Qin X, Toji L, Radovich M, Skaar TC, Pratt VM, Berger B, Scherer S, Sahinalp SC..
Nature Communications. 9(1): 828, 2018. [ Journal Article ]

Comparison of high-throughput sequencing data compression tools

Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC.
Nature Methods. 13(12): 1005-8, 2016. [ Journal Article ]

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Special Volunteer
Kaiyuan Zhu
Computational Biologist (Contr.)
Mike Ford, M.S.
Predoctoral Visiting Fellow (Graduate Student)
Ananth Hari
Predoctoral Visiting Fellow (Graduate Student)
Chih Daniel Wu
Predoctoral Visiting Fellow (Graduate Student)
Cindy Li
Predoctoral Visiting Fellow (Graduate Student)
Yuelin Liu
Angela Cui, BS
Postdoctoral Fellow (Visiting)
Junyan Xu, Ph.D.
Postbaccalaureate Fellow (CRTA)
Suraj Joshi, BSc.
Jacob Gilbert
Jamin Day
Marina Knittel
Predoctoral Visiting Fellow (Graduate Student)
Zlatko-Salko Lagumdzja


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