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)
Crystal is awarded the Chia-Lun Lo International Student FellowshipDecember 1, 2023
Chen is awarded an NIH F31 fellowshipSeptember 20, 2023
R61DA059916 is awarded to Collins (PI) and Welch (PI)August 18, 2023
Crystal passes her PhD qualifying exam and achieves candidacyJuly 7, 2023
Yuxuan passes his PhD qualifying exam and achieves candidacyMay 18, 2023
Joshua Welch is promoted to Associate Professor with tenure (effective 9/1/23)May 11, 2023
Perspective piece about single-cell perturbation modeling published in Molecular Systems BiologyMay 4, 2023
Welch lab proposal advances to the top 16 of the ARPA-H DASH competitionApril 25, 2023
Collaborative paper with Noriaki Ono is published in Nature Communications