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

Available to mentor
Joshua Welch, PhD
Associate Professor
  • Qualifications
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  • Research Overview
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    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
    • Journal Article
      Epithelial - CD4 + Tissue Resident Memory Crosstalk Dictates Allergic Airway Neutrophilic Disease
      Ravi VR, Korkmaz FT, Lyon De Ana C, Lu L, Shao F-Z, Odom C, Barker K, Ramanujan AR, Niszczak E, Goltry W, Martin I, Ha C, Quinton LJ, Jones MR, Fine A, Welch J, Chen F, Belkina A, Mizgerd JP, Shenoy AT. American Journal of Respiratory and Critical Care Medicine, 2025 May 15; 211 (Abstracts): a1083 - a1083. DOI:10.1164/ajrccm.2025.211.abstracts.a1083
    • Journal Article
      Single-cell, Multi-omics on Lung Transplant-Derived Mesenchymal Cells Identifies the Transcription Factor C/EBPD as a Key Pro-fibrotic Regulator
      Mclinden AP, Lu L, Walker NM, Vittal R, Welch J, Lama VN. American Journal of Respiratory and Critical Care Medicine, 2025 May 15; 211 (Abstracts): a3356 - a3356. DOI:10.1164/ajrccm.2025.211.abstracts.a3356
    • Journal Article
      (1662) Single-Cell Multi-Omic Analysis of Post-Transplant Mesenchymal Cells Reveals Key Molecular Signatures Regulating Aspects of Allograft Dysfunction
      McLinden AP, Lu L, Walker N, Vittal R, Welch JD, Lama VN. The Journal of Heart and Lung Transplantation, 2025 Apr 27; 44 (4): s778 DOI:10.1016/j.healun.2025.02.1677
    • Journal Article
      CytoSimplex: visualizing single-cell fates and transitions on a simplex
      Liu J, Wang Y, Li C, Gu Y, Ono N, Welch J. Bioinformatics, 2025 Apr 1; 41 (4): DOI:10.1093/bioinformatics/btaf119
      PMID: 40119904
    • Journal Article
      Lung CD4<sup>+</sup> resident memory T cells use airway secretory cells to stimulate and regulate onset of allergic airway neutrophilic disease
      Ravi VR, Korkmaz FT, De Ana CL, Lu L, Shao FZ, Odom CV, Barker KA, Ramanujan A, Niszczak EN, Goltry WN, Martin IMC, Ha CT, Quinton LJ, Jones MR, Fine A, Welch JD, Chen F, Belkina AC, Mizgerd JP, Shenoy AT. Cell Reports, 2025 Mar 25; 44 (3): DOI:10.1016/j.celrep.2025.115294
      PMID: 39965565
    • Journal Article
      Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation
      Zhang H, Patrick MT, Zhao J, Zhai X, Liu J, Li Z, Gu Y, Welch J, Zhou X, Modlin RL, Tsoi LC, Gudjonsson JE. Journal of Allergy and Clinical Immunology, 2025 Mar 1; 155 (3): 678 - 687. DOI:10.1016/j.jaci.2025.01.009
      PMID: 39837466
    • Preprint
      Characterization of bronchovascular-bundle mesenchymal stromal cells regulating antibody-secreting cell niche in rejecting lung allografts
      McLinden AP, Ibuki Y, Tadokoro K, Walker NM, Lu L, Ke F, Vittal R, Farver CF, Welch JD, Lama VN. 2025 Feb 23; bioRxiv, DOI:10.1101/2025.02.16.638532
    • Preprint
      HPV integration in head and neck cancer: downstream splicing events and expression ratios linked with poor outcomes.
      Li S, Xia S, Lawas M, Kulshreshtha A, Garb BF, Perera AC, Li C, Qin T, Welch JD, D'Silva NJ, Rozek LS, Sartor MA. 2025 Jan 20; DOI:10.1101/2025.01.17.633627
      PMID: 39896613
    Featured News & Stories Thomas Chen, MS
    Department News
    Thomas Chen, M.S.: From U-M to Harvard/MIT
    Thomas Chen, M.S., graduated in Spring 2025 from the Gilbert S. Omenn Department of Computational Medicine and Bioinformatics (DCMB) with a Master's in Science degree. He started his bioinformatics studies at U-M as a senior student majoring in Microbiology, and attended DCMB’s Accelerated MS program. In June 2025, he will pursue his training to become a scientist-physician at the Harvard/MIT MD-PhD Program.
         Jialin Liu, Ph.D., visits Zion National Park
    Department News
    Jialin Liu defended his Ph.D. dissertation on spatial transcriptomic
    On March 21, 2025, Jialin Liu, Ph.D., defended his doctoral dissertation titled “Mapping Cell Fate Transitions from Single-Cell Multi-Omic and Spatial Transcriptomic Data.” His mentor was professor Joshua Welch, Associate Professor in the Gilbert S. Omenn Department of Computational Medicine and Bioinformatics (DCMB) and the Department of Computer Science and Engineering at the University of Michigan.
         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