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
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Postdoctoral ResearcherBroad Institute of Harvard and MIT, United States, 2018
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Center Membere-Health and Artificial Intelligence Initiative
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.
Welch Lab
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Zhang H, Patrick MT, Zhao J, Zhai X, Liu J, Li Z, Gu Y, Welch J, Zhou X, Modlin RL, Tsoi LC, Gudjonsson JE. J Allergy Clin Immunol, 2025 Mar; 155 (3): 678 - 687.Journal ArticleTechniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation.
DOI:10.1016/j.jaci.2025.01.009 PMID: 39837466 -
McLinden AP, Ibuki Y, Tadokoro K, Walker NM, Lu L, Ke F, Vittal R, Farver CF, Welch JD, Lama VN. bioRxiv,PreprintCharacterization of bronchovascular-bundle mesenchymal stromal cells regulating antibody-secreting cell niche in rejecting lung allografts
DOI:10.1101/2025.02.16.638532 -
Ravi VR, Korkmaz FT, De Ana CL, Lu L, Shao F-Z, 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 Rep, 2025 Feb 11; 115294Journal ArticleLung CD4+ resident memory T cells use airway secretory cells to stimulate and regulate onset of allergic airway neutrophilic disease.
DOI:10.1016/j.celrep.2025.115294 PMID: 39965565 -
Bonev B, Castelo-Branco G, 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, Ali Bayraktar O, Habib N, Nowakowski TJ. Nat Neurosci, 2025 Jan; 28 (1): 216Journal ArticleAuthor Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
DOI:10.1038/s41593-024-01858-2 PMID: 39681663 -
Gao C, Welch JD. Bioinformatics, 2024 Dec 26; 41 (1):Journal ArticleIntegrating single-cell multimodal epigenomic data using 1D convolutional neural networks.
DOI:10.1093/bioinformatics/btae705 PMID: 39820306 -
Lu L, Ono N, Welch JD. J Bone Miner Res, 2024 Dec 31; 40 (1): 20 - 26.Journal ArticleLinking transcriptome and morphology in bone cells at cellular resolution with generative AI.
DOI:10.1093/jbmr/zjae151 PMID: 39303095 -
Varshney A, Manickam N, Orchard P, Tovar A, Ventresca C, Zhang Z, Feng F, Mears J, Erdos MR, Narisu N, 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. 2024 Dec 17;PreprintPopulation-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.
DOI:10.1101/2023.12.15.571696 PMID: 38168419 -
Lu L, McLinden AP, Walker NM, Vittal R, Wang Y, Combs MP, Welch JD, Lama VN. bioRxiv,PreprintSingle-cell multi-omic analysis of post-transplant mesenchymal cells reveals molecular signatures and putative regulators of lung fibrosis
DOI:10.1101/2024.11.27.625698
Department News
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 2024 U-M Biosciences Faculty Achievement Recognition Award (MBioFAR).
Department News
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
Department News
J. Welch's "bold idea" is a "Research Scout" funded project
