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)
April successfully defends her dissertation and earns her PhD in Bioinformatics
January 23, 2024Joshua Welch wins the University of Michigan mBioFAR award
January 18, 2024Chao successfully defends his dissertation and earns his PhD in Bioinformatics
January 1, 2024Jialin and Angel's collaborative paper with Noriaki Ono is published in Bioessays
December 4, 2023Crystal is awarded the Chia-Lun Lo International Student Fellowship
December 1, 2023Chen is awarded an NIH F31 fellowship
September 20, 2023R61DA059916 is awarded to Collins (PI) and Welch (PI)
August 18, 2023Crystal passes her PhD qualifying exam and achieves candidacy
July 7, 2023Yuxuan passes his PhD qualifying exam and achieves candidacy