Salem Malikic, Ph.D.

Salem Malikic, Ph.D.

  • Center for Cancer Research
  • National Cancer Institute


Salem Malikic is a computational biologist working on biological sequence data analysis and design and development of computational methods for studying intra-tumor heterogeneity and history of tumor evolution. Dr. Malikic joined the Cancer Data Science Laboratory in September 2020.

Areas of Expertise

Combinatorial Optimization
Probabilistic Modelling
Cancer Genetics And Evolution
High-throughput Sequencing Data


Selected Key Publications

Clonality inference in multiple tumor samples using phylogeny

Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 31(9): 1349-56, 2015. [ Journal Article ]

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 Res. 29(11): 1860-1877, 2019. [ Journal Article ]

Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data

Malikic S, Jahn K, Kuipers J, Sahinalp SC, Beerenwinkel N.
Nat Commun. 10(1): 2750, 2019. [ 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.
Nat Commun. 9(1): 9(1), 2018. [ Journal Article ]

A multi-labeled tree dissimilarity measure for comparing "clonal trees" of tumor progression

Karpov N, Malikic S, Rahman MK, Sahinalp SC.
Algorithms Mol Biol. 14: 17, 2019. [ Journal Article ]