Welcome to the Welch Lab

Our research aims to address fundamental problems in both biomedical research and computer science by developing new tools tailored to rapidly emerging high-throughput sequencing technologies. Broadly, we seek to understand what genes define the complement of cell types and cell states within healthy tissue, how cells differentiate to their final fates, and how dysregulation of genes within specific cell types contributes to human disease. As computational method developers, we seek to both employ and advance the methods of machine learning, particularly for unsupervised analysis of high-dimensional data.

Most recently, I have focused on developing open-source software for the processing, analysis, and modeling of single-cell sequencing data. Key contributions in this area include LIGER, a general approach for integrating single-cell transcriptomic, epigenomic and spatial transcriptomic data; online iNMF, a scalable and iterative algorithm for single-cell data integration; and MultiVelo, a tool for modeling cell fate transitions from single-cell multi-omic data. I have applied these methods in collaboration with biological scientists to study stem cell differentiation, somatic cell reprogramming, and the mammalian brain.

The Welch Lab has openings for multiple positions, including Postdoctoral Fellow, PhD Student, Bioinformatician, and Software Engineer! (more info)

News

July 1, 2024

Collaborative paper with Collins lab published in Nature Communications

June 19, 2024

Perspective on AI for algorithmic biology is published in Cell Systems

May 14, 2024

Weizhou passes his PhD qualifying exam and achieves candidacy

March 11, 2024

April successfully defends her dissertation and earns her PhD in Bioinformatics

January 23, 2024

Joshua Welch wins the University of Michigan mBioFAR award

January 18, 2024

Chao successfully defends his dissertation and earns his PhD in Bioinformatics

January 1, 2024

Jialin and Angel's collaborative paper with Noriaki Ono is published in Bioessays

December 4, 2023

Crystal is awarded the Chia-Lun Lo International Student Fellowship

December 1, 2023

Chen is awarded an NIH F31 fellowship

... see all News