Author

S. Malikic

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 5

Signature Assays, Organisms & Methods

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Research Focus:clustering· 3 Research Focus:differential expression· 3 Organism:human· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Approach:experimental assay· 2 Organism:mouse· 2 Assay:scRNA-seq· 2

Frequent Co-Authors

C. Sahinalp· 3 shared A. Sassano· 2 shared C. Gruen· 2 shared C. H. Wu· 2 shared C. Jolly· 2 shared C.-P. Day· 2 shared D. G. Livitz· 2 shared D. Rosebrock· 2 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersCancer Biology

C. Sahinalp

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5 papers

Recent·Most cited

Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

M. G. Hirsch, S. Pal, F. R. Mehrabadi, S. Malikic, C. Gruen, A. Sassano, E. Perez-Guijarro, G. Merlino, C. Sahinalp, E. Molloy, C.-P. Day, T. M. Przytycka

The paper models gene expression adaptation in tumor subclones using stochastic processes and finds non-genetic mechanisms drive subclonal evolution and treatment response.

bioRxiv · Apr 17, 2024 · PreprintCancer Biology

Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History

C. H. Wu, S. Joshi, W. Robinson, P. F. Robbins, R. Schwartz, C. Sahinalp, S. Malikic

This paper introduces DETOPT, a method for accurately placing SNVs affected by CNAs in tumor progression trees, showing improved accuracy on simulated data and biologically plausible results on breast cancer metastases.

bioRxiv · Mar 10, 2024 · PreprintCancer Biology

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

C. Gruen, H. H. Yang, A. Sassano, E. Wu, V. Gopalan, K. L. Marie, A. Castro, F. R. Mehrabadi, C. H. Wu, I. Church, G. A. Needle, C. Smith, S. Chin, J. Ebersole, C. Marcelus, , E. Perez-Guijarro

The paper analyzes melanoma clonal sublines to uncover how intratumoral heterogeneity drives resistance to immunotherapy.

bioRxiv · Apr 3, 2023 · PreprintCancer Biology

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

S. C. Dentro, I. Leshchiner, K. Haase, M. Tarabichi, J. Wintersinger, A. G. Deshwar, K. Yu, Y. Rubanova, G. Macintyre, J. Demeulemeester, I. Vazquez-Garcia, K. Kleinheinz, D. G. Livitz, S. Malikic, N. Donmez, , Q. D. Morris

This study characterizes intra-tumor heterogeneity across 2,658 human cancer genomes, identifying subclonal mutations and evolutionary patterns across 38 cancer types.

Cell · Apr 1, 2021Peer-reviewedCancer Biology

The evolutionary history of 2,658 cancers

M. Gerstung, C. Jolly, I. Leshchiner, S. C. Dentro, S. Gonzalez Rosado, D. Rosebrock, T. J. Mitchell, Y. Rubanova, P. Anur, K. Yu, M. Tarabichi, A. Deshwar, J. Wintersinger, K. Kleinheinz, I. Vazquez-Garcia, , Spellman

This study uses whole-genome sequencing of cancer samples to reconstruct the evolutionary history of 39 cancer types, identifying early and late-stage mutational patterns and driver genes.

bioRxiv · Sep 12, 2018Cancer Biology