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
Manage Your Profile
Qualifications
-
Postdoctoral ResearcherBroad Institute of Harvard and MIT, United States
2017 - 2018
Postdoctoral Research
Center Memberships
-
Center Membere-Health and Artificial Intelligence Initiative
-
Center MemberCenter for Cell Plasticity and Organ Design
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
-
McClellan BL, Peña Agudelo JA, Mujeeb AA, Dabaja AA, Zhu Z, Raghuram S, Varela ML, Tronrud C, Banerjee K, Wei A, Calatroni C, Zhang LH, Romero LC, Oh P, Alghamri MS, Robbins A, Perricone M, Wang Y, Shay B, Sajjakulnukit P, Lyssiotis CA, Welch JD, Schwendeman A, Lowenstein PR, Castro MG. Molecular Therapy Oncology, 2026 Jun 18; 34 (2):Journal ArticleReprogramming the immune suppressive tumor microenvironment in glioma enhances the efficacy of immune-mediated gene therapy
DOI:10.1016/j.omton.2026.201215 -
Liu J, Manabe H, Qian W, Orikasa S, Ghaemmaghami J, Wang Y, Gu Y, Chu AKY, Gadhvi G, Song Y, McClinden P, Lama VN, Ono N, Welch JD. Nat Genet, 2026 Jun 10;Journal ArticleCytoSignal detects locations and dynamics of ligand-receptor signaling at cellular resolution from spatial transcriptomic data.
DOI:10.1038/s41588-026-02624-9 PMID: 42271087 -
Welch J. 2026 Jun 11;PresentationInferring cell differentiation and migration from spatial transcriptomic data
-
Guzman SD, Duran P, Xiao Y, Song Y, Welch JD, He C, Aguilar CA. 2026 May 7;PreprintNuclear Speckles Regulate Splicing During Muscle Stem Cell Activation and Aging.
DOI:10.64898/2026.05.04.722644 PMID: 42146392 -
Lu L, McLinden AP, Walker NM, Vittal R, Wang Y, Fattahi F, Russell ST, Combs MP, Welch JD, Lama VN. JCI Insight, 2026 Apr 23;Journal ArticleSingle-cell multi-omic analysis of mesenchymal cells reveals molecular signatures and regulators of lung allograft fibrosis.
DOI:10.1172/jci.insight.196651 PMID: 42044158 -
Mehta MP, Vittal R, McLinden A, Lu L, Welch JD, Lama V. The Journal of Heart and Lung Transplantation, 2026 Apr 18; 45 (5): 54 - 55.Journal Article(116) Differential Midkine Expression in Mesenchymal Cells of Lung Transplant Chronic Lung Allograft Dysfunction (CLAD) Phenotypes
DOI:10.1016/j.healun.2026.02.122 -
Gu Y, Song Y, Blaauw D, Welch JD. PLoS Comput Biol, 2026 Mar 20; 22 (3): e1014060Journal ArticleBayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.
DOI:10.1371/journal.pcbi.1014060 PMID: 41860983 -
Onyango JA, Li C, Chen C, Disbennett WM, Virgilio MC, Painter MM, Terry VH, Ramnani B, Welch JD, Collins KL. 2026 Feb 23; bioRxiv,PreprintMechanisms of HIV Latency in Hematopoietic Progenitors: GFI1 as a Key Regulator
DOI:10.64898/2026.02.19.706859
Featured News & Stories
Health Lab
New algorithmic tool enables to scientists to see cells “talk” to one another
A new U-M study, featured in Nature Genetics, details a technique to infer cell-cell communication using spatial transcriptomics
Health Lab
An AI model accurately predicts how cells end up in position inside tissues
Understanding transitions from cell to tissue in space and over time: A new modeling tool from the Welch lab at Michigan Medicine.
Department News
A Welch lab publication is recognized in Molecular Systems Biology with a cover design
A Welch lab publication is recognized in Molecular Systems Biology with a cover design
The Welch lab developed PertubNet, a generative AI model that can predict shifts in cell state—changes in overall gene expression—in response to multiple types of unseen cellular perturbations, including responses to drugs.
This tool was published in Molecular Systems Biology (Volume 21, Issue 8, 4 August 2025.) and was recognized with the opportunity to design the cover of the journal.
Great Minds, Greater Discoveries Stories
Research Scout Scholar: Joshua Welch, PhD
Meet Dr. Joshua Welch, a Great Minds Research Scouts scholar at the U-M Medical School.
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.
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.
