Author

Mark Freeman

University Health Network

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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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 3 Research Focus:drug response / drug discovery· 3 Approach:statistical model· 3 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Petr SmirnoviD· 4 shared Benjamin Haibe‐KainsiD· 3 shared Zhaleh SafikhaniiD· 3 shared Nehmé El-HachemiD· 2 shared Venkata SK. ManemiD· 2 shared Victor KofiaiD· 2 shared Adrian She· 1 shared Alexander Maru· 1 shared

Activity by Year

2017-2019 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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4 shared papersBioinformatics

Petr SmirnovORCID

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4 papers

Recent·Most cited

Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy

Venkata SK. Manem, Meghan Lambie, Ian C. P. Smith, Petr Smirnov, Victor Kofia, Mark Freeman, Marianne Koritzinsky, Mohamed E. Abazeed, Benjamin Haibe‐Kains, Scott Victor Bratman

This study develops RadioGx, a computational platform to analyze radioresponse in radiogenomic databases, identifying molecular pathways and drug correlations with radiation response.

Cancer Research · Sep 26, 2019Peer-reviewedBioinformatics

PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies

Petr Smirnov, Victor Kofia, Alexander Maru, Mark Freeman, Chantal Ho, Nehmé El-Hachem, George-Alexandru Adam, Wail Ba-Alawi, Zhaleh Safikhani, Benjamin Haibe‐Kains

PharmacoDB integrates large pharmacogenomic studies to enable comparison and analysis of drug screening data by curating identifiers and standardizing drug response metrics.

Nucleic Acids Research · Sep 27, 2017Peer-reviewedBioinformatics

Revisiting inconsistency in large pharmacogenomic studies

Zhaleh Safikhani, Mark Freeman, Petr Smirnov, Nehme El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai Juul Birkbak, Christos Hatzis, Leming Shi, Andrew H Beck, Hugo JWL Aerts, John Quackenbush, Benjamin Haibe-Kains

This paper reanalyzes pharmacogenomic data from GDSC and CCLE, finding continued inconsistency in drug sensitivity measures despite improved statistical methods and expanded datasets.

F1000Research · Aug 11, 2017Peer-reviewedBioinformatics

Tissue specificity of in vitro drug sensitivity

Fupan Yao, Seyed Ali Madani Tonekaboni, Zhaleh Safikhani, Petr Smirnov, Nehmé El-Hachem, Mark Freeman, Venkata SK. Manem, Benjamin Haibe‐Kains

This study examines tissue-specific drug sensitivity in in vitro datasets and finds strong associations between tissue origin and drug response, but most preclinical findings do not align with clinical observations.

Journal of the American Medical Informatics Association · Jul 6, 2017Peer-reviewedBioinformatics