Principal Investigator: Wesley Tansey

Machine Learning for Cancer

The Tansey lab focuses on solving frontier problems in cancer data science through the development of innovative statistical machine learning methods. Our work answers fundamental statistical and computing questions raised in both clinical and pre-clinical cancer research. The methods we develop are motivated by open problems in cancer research. How do we discover effective combination therapies when the search space of possible combinations is vast? Can we identify new biomarkers of therapeutic sensitivity or resistance from observational electronic health records? How do we build powerful-yet-interpretable multimodal models of medical images, laboratory tests, and clinical records that can inform and improve treatment decisions in the clinic? The goal of our lab is to distill these kinds of important scientific questions into precise mathematical statements, then derive answers in the form of computationally efficient and statistically principled methods. We are interested in a number of areas in statistics and computer science, including graphical models, Bayesian methods, deep learning, hypothesis testing, conditional density estimation, spatial smoothing, active learning, and causal inference. Ultimately, we seek to lay the statistical and computational foundations necessary to deliver on the promise of precision medicine: delivering the right treatment, for the right patient, at the right moment, and at the right dose.

View available career opportunities in the lab here.

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Recent Publications

Zhang H, Hunter MV, Chou J, Quinn JF, Zhou M, White RM, Tansey W. BayesTME: An end-to-end method for multiscale spatial transcriptional profiling of the tissue microenvironment. Cell Syst. 2023 Jul 19;14(7):605-619.e7. doi: 10.1016/j.cels.2023.06.003. PMID: 37473731; PMCID: PMC10368078.

Freeman BA, Jaro S, Park T, Keene S, Tansey W, Reznik E. MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization. Genome Biol. 2022 Sep 1;23(1):184. PMCID: PMC9438248

Tansey W, Tosh C, Blei DM. A Bayesian model of dose-response for cancer drug studies. aoas. Institute of Mathematical Statistics; 2022 Jun;16(2):680–705.

Tansey W, Li K, Zhang H, Linderman SW, Rabadan R, Blei DM, Wiggins CH. Dose-response modeling in high-throughput cancer drug screenings: an end-to-end approach. Biostatistics. 2022 Apr 13;23(2):643–665. PMCID: PMC9007438

Tansey W, Veitch V, Zhang H, Rabadan R, Blei DM. The Holdout Randomization Test for Feature Selection in Black Box Models. J Comput Graph Stat. Taylor & Francis; 2022 Jan 2;31(1):151–162.

Loper, J.H., Lei, L., Fithian, W., and Tansey, W. (2022). Smoothed nested testing on directed acyclic graphs. Biometrika 109, 457–471. https://doi.org/10.1093/biomet/asab041.

Selected Projects

MIRTH: Metabolite Imputation via Rank-Transformation and Harmonization B. A. Freeman*, S. Jaro*, T. Park, S. Keene, W. Tansey, E. Reznik Genome Biology, 2022.

BayesTME: A unified statistical framework for spatial transcriptomics H. Zhang, M. V. Hunter, J. Chou, J. F. Quinn, M. Zhou, R. White, and W. Tansey Biorxiv. doi: https://doi.org/10.1101/2022.07.08.499377

Dose-Response Modeling in High-Throughput Cancer Drug Screenings: An end-to-end approach W. Tansey, K. Li, H. Zhang, S. W. Linderman, D. M. Blei, R. Rabadan, and C. H. Wiggins Biostatistics, 2021.

 

Please visit Dr. Tansey’s faculty page and Google Scholar for more publications.

Lab Members

  • Karl Pichotta

    Senior Computational Biologist II
  • Tiffany Cordero

    Administrative Assistant
  • Amy Xie

    Graduate Student
  • Jacqueline Chou

    PhD Student
  • Jessica White

    PhD Student
  • Christopher Tosh

    Research Associate
  • Jeffery Quinn

    Bioinformatics Engineer IV
  • Haoran Zhang

    PhD student
  • Thomas Dougherty

    Graduate Student

Former Lab Members

  • Casey Bradshaw

    PhD Student
  • Brian Manzo

    PhD student
  • Mauricio Garcia Tec

    PhD student
  • Shounak Chattopadhyay

    PhD student