Author

Timothy Pham

University of California San DiegoPrimary ORCID profile (0009-0000-4526-6353 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints

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Same name, identified by ORCID

Timothy PhamiD1 paper · Baylor College of Medicine

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:dimensionality reduction· 1 Research Focus:gene regulatory network inference· 1 Assay:GWAS summary statistics· 1

Frequent Co-Authors

Pablo TamayoiD· 2 shared William KimiD· 2 shared Alex Wenzel· 1 shared Amey Gupta· 1 shared Antony Castanza· 1 shared Bartholomew Tam· 1 shared David EbyiD· 1 shared Helga Thorvaldsdóttir· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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2 shared papersBioinformatics

Pablo TamayoORCID

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2 papers

Recent·Most cited

Variable sparsity non-negative matrix and tensor factorization algorithms and their applications in cancer genomics

Timothy Pham, Jiaqian Zhong, Joseph Hwang, Ronit Agarwala, Kun Zhang, Prashant Mali, William Kim, Pablo Tamayo

This paper introduces variable-sparsity matrix and tensor factorization algorithms for cancer genomics to improve biological interpretability and modeling of cancer subtypes and pathways.

bioRxiv · Oct 19, 2026 · PreprintBioinformatics

The Multi-scale Copula Index (MCI): a new information-theoretic measure of association and its applications in functional cancer genomics

Timothy Pham, Karina Meneses-Cime, Jiayan Ma, Bartholomew Tam, Amey Gupta, Michael R. Reich, Alex Wenzel, David Eby, Thorin T. Tabor, Helga Thorvaldsdóttir, Antony Castanza, Jill P. Mesirov, William Kim, Pablo Tamayo

The paper introduces the Multi-scale Copula Index (MCI), an information-theoretic measure of association, and demonstrates its utility in cancer genomics for capturing contextual associations in complex datasets.

bioRxiv · Oct 16, 2026 · PreprintBioinformatics