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)


December 4, 2023

Crystal is awarded the Chia-Lun Lo International Student Fellowship

December 1, 2023

Chen is awarded an NIH F31 fellowship

September 20, 2023

R61DA059916 is awarded to Collins (PI) and Welch (PI)

August 18, 2023

Crystal passes her PhD qualifying exam and achieves candidacy

July 7, 2023

Yuxuan passes his PhD qualifying exam and achieves candidacy

May 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 Biology

May 4, 2023

Welch lab proposal advances to the top 16 of the ARPA-H DASH competition

April 25, 2023

Collaborative paper with Noriaki Ono is published in Nature Communications

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