Author

Thomas O. McDonald

Harvard UniversityORCID 0000-0002-5272-0187Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Bioinformatics· 1 Cancer Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:cell type annotation· 2 Research Focus:drug response / drug discovery· 2 Assay:scRNA-seq· 2 Research Focus:trajectory inference· 2 Approach:Bayesian inference· 1 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

Franziska Michor AiD· 4 shared Herbert LevineiD· 2 shared Shubham TripathiiD· 2 shared Yu-Chen ChengiD· 2 shared Yun ZhangiD· 2 shared Arantxa Romero-Toledo· 1 shared Benjamin OakesiD· 1 shared BV Harshavardhan· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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4 shared papersSystems Biology

Franziska Michor AORCID

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4 papers

Recent·Most cited

PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses

Yu-Chen Cheng, Hyemin Gu, Thomas O. McDonald, Wenbo Wu, Shubham Tripathi, Cristina Guarducci, Douglas Russo, Daniel L. Abravanel, Madeline Bailey, Yue Wang, Yun Zhang, Yannis Pantazis, Herbert Levine, Rinath M. Jeselsohn, Markos A. Katsoulakis, Franziska Michor A

Cell Systems · Aug 1, 2026Peer-reviewedBioinformatics

Multi-region biopsies and patient-derived neurosphere cultures reveal spatial divergence in glioblastoma.

Roberto Salatino, Jacob Geisberg, Arantxa Romero-Toledo, Benjamin Oakes, Jerome C. Nwachukwu, Dobeen Hwang, Cristina Vincentelli, Oszkar Szentirmai, Thomas O. McDonald, K.W. Nettles, Franziska Michor A, Michalina Janiszewska

This study shows that multi-region neurospheres from glioblastoma tumors retain spatial diversity and drug response patterns linked to their original biopsies, highlighting their importance for modeling intratumor heterogeneity.

bioRxiv · Apr 10, 2026 · PreprintCancer Biology

BESTDR: Bayesian quantification of mechanism-specific drug response in cell culture

Thomas O. McDonald, Simone Bruno, James P. Roney, Ioannis K. Zervantonakis, Franziska Michor A

BESTDR quantifies drug response mechanisms using Bayesian modeling of cell state transitions, improving accuracy in dose-response analysis across cell lines.

bioRxiv · Feb 5, 2025 · PreprintSystems Biology

Reconstruction of single cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition

Yu-Chen Cheng, Yun Zhang, Shubham Tripathi, BV Harshavardhan, Mohit Kumar Jolly, Geoffrey R. Schiebinger, Herbert Levine, Thomas O. McDonald, Franziska Michor A

This study uses optimal transport analysis on scRNA-seq data to reconstruct EMT trajectories in MCF10A cells, identifying three distinct fates and novel genes associated with different EMT states.

bioRxiv · Sep 19, 2023 · PreprintSystems Biology