Elisabeth Paymal

For 40 years, Brenda Franklin has been fiercely dedicated to supporting M&I scientists and the infrastructure they need to excel in their research.

Understanding transitions from cell to tissue in space and over time: A new modeling tool from the Welch lab at Michigan Medicine.

We are pleased to share with you the 2024–2025 Highlights from the University of Michigan Department of Microbiology and Immunology. This publication features the main achievements of M&I's community.

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. 

On June 13, 2025, he defended his thesis titled “Observability and higher-order methods for biomarker discovery,” and his mentor was professor Indika Rajapakse.

Eight faculty join the U-M Center for Computational Medicine and Bioinformatics Chad Brenner, PhD, Associate Professor of Otolaryngology-Head and Neck Surgery Associate Professor of Pharmacology, Cellular and Molecular Biology Academic Program Director, Medical School https://medschool.umich.edu/profile/3161/chad-brenner Irina Gaynanova, PhD, Associate Professor, Biostatistics, School of Public Health https://sph.umich.edu/faculty-profiles/gaynanova-irina.html Alex Gorodetsky, PhD, Associate Professor of Aerospace Engineering, College of Engineering https://aero.engin.umich.edu/people/gorodetsky-alex/ Vijayan (Vijay) Nair, PhD, Donald A. Darling Professor Emeritus of Statistics; Professor Emeritus of Industrial and Operations Engineering, College of Literature, Science and the Arts https://lsa.umich.edu/stats/people/faculty/vnn.html Xander Nuttle, PhD, Assistant Professor of Human Genetics, Medical School https://medschool.umich.edu/profile/13237/xander-nuttle Elliott SoRelle, PhD, Microbiology and Immunology, Medical School https://medschool.umich.edu/profile/13222/elliott-sorelle Yixin Wang, PhD, Assistant Professor of Statistics, College of Literature, Science and the Arts https://lsa.umich.edu/stats/people/faculty/yixinw.html Yang Xiao, PhD, Assistant Professor, Pathology, Medical School and Biomedical Engineering, College of Engineering https://bme.umich.edu/people/yang-xiao-ph-d/

The Gilbert S. Omenn Department of Computational Medicine and Bioinformatics is pleased to announce that Naoki Masuda, Ph.D., joined its faculty as Professor with Tenure, as of July 1, 2025. Professor Masuda is also joined by his lab team composed of two postdoctoral fellows and two graduate students. The Masuda lab is accepting new students and postdoctoral fellows. Masuda is an internationally recognized applied mathematician who develops theories, tools and computational methods to study networks. For the last 15 years, he has researched temporal networks –those that evolve over time– in a variety of contexts.

On June 9, 2025, Dr. Yang defended his dissertation titled: “Holistic Integration of Deep Learning Models for Mass Spectrometry-Based Peptide Identification.” His mentor was professor Alexey Nesvizhskii.

Joel Eliason, Ph.D., developed Bayesian statistical tools to analyze and interpret the spatial relationships between the different types of cells present in a tumorous environment. His results were presented in his Ph.D. dissertation, titled “Multiscale statistical models for understanding tumor microenvironment heterogeneity,” and defended on May 28, 2025. His mentor was Arvind Rao, Ph.D., DCMB, and he also worked closely in collaboration with Michele Peruzzi, Ph.D., a biostatistician in the School of Public Health and a CCMB member.

In M&I, we study adaptive immunology, also known as acquired immunology. The adaptive system is highly specific in that it distinguishes between different agents, recognizes a previously encountered agent, and adapts its response accordingly. When that agent is a pathogen, the adaptive response can help to clear that infection. A key feature of adaptive immunity is the development of immunological memory. This is the biology behind vaccines.

Every year, the Endowment for the Basic Sciences recognizes a faculty and a research staff with an award. This year, Adam Lauring, PhD, was recognized with an EBS Teaching Award, and Katie McBride with a Research Staff Award.

Every year, the Endowment for Basic Sciences (EBS) recognizes a faculty and a research staff with an award. This year, in DCMB, AJ Wing, PhD, was recognized with a Teaching Award, and Greg Farnum with a Research Staff Award.

Professor Kin Fai Au and his lab members Xiaoyu Cai, Qi Gao, Haoran Li, Puwen Tan, Dingjie Wang, and Yunhao Wang, with partners from Ohio State University, developed a new software that improves the accuracy of the quantification of gene isoforms for complex genes. Their software, called miniQuant, ranks genes with the uncertainty of isoform quantification. It integrates the complementary strengths of long reads and short reads of RNA sequencing data with optimal combinations in a gene- and data-specific manner to achieve more accurate isoform quantification. These findings are published in Nature Biotechnology.

On March 21, 2025, Faith Anderson Davis, Ph.D., defended her dissertation on Candida albicans, a fungus that naturally lives in small amounts on our mouth, skin and in our intestines. Her dissertation was titled “Adding complexity to models of Candida albicans human colonization: Natural isolates and polymicrobial interactions.” Her mentor was professor Teresa O’Meara.

Professors Yifan Wang, a parasitologist, and Christiane Wobus, a virologist, received the 2025 M&I Multiplier Award to pursue their collaborative investigation into how viral endosymbionts shape Toxoplasma virulence, immune evasion, and host interactions. Their project is titled: “Unmasking viral partners in parasites: dissecting the role of endogenous viruses in Toxoplasma gondii pathogenesis.”