January 23, 2024

Joshua Welch receives a 2024 U-M Mid-career Biosciences Faculty Achievement Recognition Award (MBioFAR)

This very competitive award supports highly innovative bioscience research and emphasizes the scientific value and importance of this work. 

Dr. Joshua Welch outstanding research is recognized by a prestigious U-M MBioFAR award. This very competitive award supports highly innovative bioscience research and emphasizes the scientific value and importance of this work. Dr. Welch is Associate Professor in the Department of Computational Medicine and Bioinformatics (DCMB), Medical School, and in the Department of Electrical Engineering and Computer Science (EECS), division of Computer Science and Engineering (CSE), College of Engineering. 

“We are proud of Josh Welch’s recognition with the U-M MBioFAR Award. He is a brilliant scientist bridging computational medicine & bioinformatics, computer sciences, and brain biology. And he is a magnet and an inspiration for students.”
—Gil Omenn, MD, PhD, Harold T. Shapiro Distinguished University Professor, Director, Center for Computational Medicine and Bioinformatics

Joshua Welch’s research focuses on developing machine learning and artificial intelligence approaches for analyzing single-cell and spatial transcriptomic data. For more than a decade, he has been fascinated by the question of how a single genome encodes the blueprint for so many distinct cellular phenotypes. He is particularly interested in how gene regulatory mechanisms create thousands of distinct types of neurons, and how these regulatory mechanisms break down in disease. 

His group has developed a number of computational approaches that use machine learning and AI to find new answers to these questions using new experimental technologies, such as single-cell genomics and spatial transcriptomics. These new experimental data types provide exciting new windows into the gene regulatory control system, but require sophisticated computational approaches to understand the data.

“This is a very well-deserved honor for Josh Welch who is a pathbreaker in applying single cell spatial transcriptomics and biomedical data science methods to neuro- and developmental biology. His deep scientific impacts, enabling new science and exciting new collaborations, are just beginning to reverberate internationally.”
—Brian Athey, PhD, Michael Savageau Collegiate Professor & Chair Department of Computational Medicine & Bioinformatics

More recently, Welch and his team have used emerging generative AI approaches to build predictive models that link genotype to phenotype at cellular resolution. For example, they developed an AI approach similar to DALLE-2 that can draw a picture of a neuron’s morphology based on the genes that it expresses. They also developed a model that predicts how individual cells will respond to new drug treatment or a new genetic perturbation induced by CRISPR.

With this award, Dr. Welch will support his new wet lab where he will perform experiments on cellular perturbations, in particular in neurons, collecting new data to develop computational models. This leading-edge research might bring new insights into neurodegenerative diseases such as ALS and Alzheimer’s.

“Even though I’m a computer scientist by training, I’ve taken the step of opening a molecular biology lab because I’m so excited about the possibilities of co-developing experimental and computational approaches that inform each other. I think combining perturbation assays with generative AI in this way is really promising.”
—Joshua Welch, PhD, Associate Professor in the Department of Computational Medicine and Bioinformatics (DCMB), Medical School, and in the Department of Computer Science and Engineering (CSE), College of Engineering. 

In this work, Dr. Welch collaborates with several U-M scientists, including Dr. Sami Barmada, Angela Dobson Welch and Lyndon Welch Research Professor, Associate Professor, Department of Neurology, himself a recipient of the 2022 MBioFAR award.

At the award ceremony, January 16, 2024, Dr. Welch expressed his gratitude for U-M Scientific leadership recognition as well as for Drs. Brian Athey, Michael Savageau Collegiate Professor and DCMB Chair, Jun Li, Professor of Computational Medicine and Bioinformatics, Associate Chair for Research, DCMB, and Professor of Human Genetics, and Gil Omenn, Harold T. Shapiro Distinguished University Professor, Director of the Center for Computational Medicine and Bioinformatics, for their support and mentoring. 

About MBioFAR
The MBioFAR award recognizes and provides the most meritorious mid-career faculty with additional discretionary resources to facilitate innovative and higher-risk research that might not otherwise be supported by conventional granting agencies. MBioFAR was created to help ensure continued extraordinary productivity, impact, and a high-level of job satisfaction for our most outstanding faculty at the most productive phase of their career. This award emphasizes their value and their work’s importance. Faculty are confidentially nominated, and only one to five awards are made per year. Each MBioFAR awardee receives $250,000 per year for two years of discretionary research funds that can be spent at the discretion of the investigator on their research or academic activities. 

MBioFAR is managed by the Biosciences Initiative (BSI) whose mission is to strengthen research and education in the biosciences across the University through strategic leadership and coordination. 

In The Record

 

Josh Welch, PhD

Joshua Welch, Ph.D.

Associate Professor of Computational Medicine and Bioinformatics
Associate Professor of Electrical Engineering and Computer Science