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
      CytoSignal Detects Locations and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomic Data
      Liu J, Manabe H, Qian W, Wang Y, Gu Y, Chu AKY, Gadhvi G, Song Y, Ono N, Welch JD. bioRxiv, DOI:10.1101/2024.03.08.584153
    • Journal Article
      Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation: Bone marrow endosteal stem cells provide a robust source of bone-making osteoblasts both in normal and abnormal bone formation.
      Matsushita Y, Liu J, Chu AKY, Ono W, Welch JD, Ono N. Bioessays, 2024 Mar; 46 (3): e2300173 DOI:10.1002/bies.202300173
      PMID: 38161246
    • Presentation
      Single-cell multi-omic velocity reveals dynamic and decoupled gene regulation
      Welch J. 2024 Feb 28;
    • Preprint
      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. 2024 Feb 27; DOI:10.1101/2023.03.21.533528
      PMID: 36993393
    • Preprint
      Integrating single-cell multimodal epigenomic data using 1D-convolutional neural networks.
      Gao C, Welch JD. 2024 Feb 19; DOI:10.1101/2024.02.16.580655
      PMID: 38464242
    • Preprint
      Mapping Cell Fate Transition in Space and Time
      Gu Y, Liu J, Li C, Welch J. 2024 bioRxiv, DOI:10.1101/2024.02.12.579941
    • Preprint
      Predicting the Structural Impact of Human Alternative Splicing.
      Song Y, Zhang C, Omenn GS, O'Meara MJ, Welch JD. 2023 Dec 24; DOI:10.1101/2023.12.21.572928
      PMID: 38187531
    • Preprint
      Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.
      Varshney A, Manickam N, Orchard P, Tovar A, Zhang Z, Feng F, Erdos MR, Narisu N, Ventresca C, Nishino K, Rai V, Stringham HM, Jackson AU, Tamsen T, Gao C, Yang M, Koues OI, Welch JD, Burant CF, Williams LK, Jenkinson C, DeFronzo RA, Norton L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Mohlke KL, Kitzman JO, Koistinen HA, Liu J, Boehnke M, Collins FS, Scott LJ, Parker SCJ. 2023 Dec 15; DOI:10.1101/2023.12.15.571696
      PMID: 38168419
    Featured News & Stories
    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