Salem Malikić

National Institutes of Health — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

37h-index18.1kcitations117works3.52yr avg
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Research Topics

Cancer Genomics and Diagnostics(77), Single-cell and spatial transcriptomics(23), Genetic factors in colorectal cancer(20), Genomics and Phylogenetic Studies(12), Genomics and Rare Diseases(12)

Publications66 total

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing
2025Open Access
LCPan: efficient variation graph construction using Locally Consistent Parsing
arXiv (Cornell University)·2025Open Access
Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories
2025Open Access
Abstract 7497: Nanopore sequencing of single-cell derived sublines provides insights into melanoma heterogeneity and evolution
Cancer Research·2025
Abstract 2848: Severus: A tool for detecting and characterizing complex structural variants in cancer using long-read sequencing
Cancer Research·2025
Abstract 3898: Integrating structural variants and single nucleotide variants to uncover evolutionary trajectories in melanoma
Cancer Research·2025
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing
Nature Biotechnology·2025· 17 citedOpen Access
A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data
Lecture notes in computer science·2025· 1 cited
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones
Cell Systems·2024· 10 citedOpen Access
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Nature Biotechnology·2024· 5 citedOpen Access
Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones
2024· 3 citedOpen Access
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
2024· 19 citedOpen Access
Abstract 6924: Structural variant dynamics in melanoma: Unraveling tumor heterogeneity and evolution
Cancer Research·2024
Abstract 7407: Melanoma clonal subline analysis reveals genetic factors driving intra-tumor heterogeneity
Cancer Research·2024
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
2024Open Access
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
Lecture notes in computer science·2024
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Genome Research·2023· 10 citedOpen Access
Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms
2023· 5 citedOpen Access
Abstract 127: Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models
Cancer Research·2023
Author Correction: The evolutionary history of 2,658 cancers
Nature·2023· 4 citedOpen Access
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Frequent Co-authors

S. Cenk Şahinalp(31), Nilgun Donmez(21), Ignaty Leshchiner(19), Yulia Rubanova(19), Jeff Wintersinger(19), Martin Peifer(19), Clemency Jolly(18), Stefan C. Dentro(18), Daniel Rosebrock(18), Pavana Anur(18), Amit G. Deshwar(18), Kortine Kleinheinz(18), Kerstin Haase(18), Geoff Macintyre(18), Dimitri Livitz(18), Jonas Demeulemeester(18), Gad Getz(18), Marcin Imieliński(18), Florian Markowetz(18), Moritz Gerstung(17)