Joshua Welch, PhD
Associate Professor of Computational Medicine and Bioinformatics
Associate Professor of Electrical Engineering and Computer Science
[email protected]

Available to mentor
Joshua Welch, PhD
Associate Professor
  • Qualifications
  • Center Memberships
  • Research Overview
  • Links
  • Recent Publications
    • Qualifications
    • Postdoctoral Researcher
      Broad Institute of Harvard and MIT, United States, 2018
    Center Memberships
    • Center Member
      e-Health and Artificial Intelligence Initiative
    Research Overview

    I develop AI/ML approaches to decipher the link between molecular features and cellular phenotypes. By combining generative AI (autoencoders, diffusion models, and generative adversarial networks) with emerging single-cell experimental technologies, I aim to build predictive models of how cells will respond to genetic and chemical perturbations. Additionally, I perform experiments on iPS-derived neuron models to better model and treat neurodevelopment and neurological disease.

    Links
    • Welch Lab
    Recent Publications See All Publications
    • Preprint
      Single-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and putative regulators of lung fibrosis
      Lu L, McLinden AP, Walker NM, Vittal R, Wang Y, Combs MP, Welch JD, Lama VN. bioRxiv, DOI:10.1101/2024.11.27.625698
    • Journal Article
      HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages.
      Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. Nat Commun, 2024 Jun 29; 15 (1): 5514 DOI:10.1038/s41467-024-49635-w
      PMID: 38951492
    • Journal Article
      Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
      Bonev B, Gonçalo C-B, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Bayraktar O, Habib N, Nowakowski TJ. Nat Neurosci, 2024 Dec; 27 (12): 2292 - 2309. DOI:10.1038/s41593-024-01806-0
      PMID: 39627587
    • Journal Article
      TET2 promotes tumor antigen presentation and T cell IFN-γ, which is enhanced by vitamin C.
      Cheng M, Chu AKY, Li Z, Yang S, Smith MD, Zhang Q, Brown NG, Marzluff WF, Bardeesy N, Milner JJ, Welch JD, Xiong Y, Baldwin AS. JCI Insight, 2024 Nov 22; 9 (22): DOI:10.1172/jci.insight.175098
      PMID: 39388288
    • Preprint
      LUMIC: Latent diffUsion for Multiplexed Images of Cells.
      Hung A, Zhang CJ, Sexton JZ, O'Meara MJ, Welch JD. 2024 Nov 8; DOI:10.1101/2024.11.06.622339
      PMID: 39574699
    • Presentation
      Generative AI models for Predicting Cellular Dynamics, Gene Expression, and Morphology
      Welch J. 2024 Sep 20;
    • Journal Article
      Linking transcriptome and morphology in bone cells at cellular resolution with generative AI.
      Lu L, Ono N, Welch JD. J Bone Miner Res, 2024 Sep 20; DOI:10.1093/jbmr/zjae151
      PMID: 39303095
    • Journal Article
      Autophagy and machine learning: Unanswered questions.
      Yang Y, Pan Z, Sun J, Welch J, Klionsky DJ. Biochim Biophys Acta Mol Basis Dis, 2024 Aug; 1870 (6): 167263 DOI:10.1016/j.bbadis.2024.167263
      PMID: 38801963
    Featured News & Stories Portrait of Joshua Welch, PhD
    Department News
    Joshua Welch, PhD, is awarded a new Chan Zuckerberg Initiative grant
    Joshua Welch, Ph.D., an associate professor in the Department of Computational Medicine and Bioinformatics (DCMB) was awarded a Chan Zuckerberg Initiative (CZI) grant for his project titled: “Atlas-scale Hierarchical Identification of Cell Types and Functions.”
    Department News
    Joshua Welch receives U-M Biosciences Faculty Achievement Recognition Award
    Joshua Welch receives 2024 U-M Biosciences Faculty Achievement Recognition Award (MBioFAR).
    Department News
    2023 Faculty Promotions and Accolades
    2023 Faculty Promotions and Accolades at the U-M Department of Computational Medicine and Bioinformatics (DCMB).
    Department News
    J. Welch and J. Liu receive a Chan Zuckerberg Initiative grant
    J. Welch and J. Liu receive a Chan Zuckerberg Initiative grant
    Department News
    J. Welch's "bold idea" is a "Research Scout" funded project
    J. Welch's "bold idea" is a "Research Scout" funded project