I am an Assistant Professor and J. Z. Liang Early Career Chair Professor at the School of Computational Science and Engineering, College of Computing, Georgia Institute of Technology. My research group works on applying machine learning and optimization skills in method development and data analysis for single-cell RNA-Seq data and other types of data on single cell level. The goal is to study cellular mechanisms during differentiation, development of cells and disease progression.
Our research generally fall into the following four directions:
– Single cell multi-modal, multi-batch, multi-condition data integration and analysis. (Example projects: scDART, scMoMaT,scDisInFact)
– Inference of gene regulatory networks, cell-cell interactions, and cross-modality relationships in multi-omics data. (Example projects: CespGRN, CLARIFY)
– Temporal analysis of single cells: how cells change over pseudotime or real time through cell divisions. (Example projects: CellPath, LinRace)
– Spatial-omics (Example projects: scHybridNMF, CLARIFY)
– Simulation of single cell omics (including temporal and spatial) data to evaluation computational methods. (Example projects: TedSim, scMultiSim)
For some other projects see Publications.
Open Positions
I am looking for motivated PhD students to work on developing machine learning methods for single cell genomics data. Please email me your CV if you are interested.
Biography
I was a postdoc researcher in Prof. Nir Yosef‘s group at UC Berkeley. I obtained a PhD in computer science under the supervision of Prof. Bernard Moret, in the Laboratory for Computational Biology and Bioinformatics, EPFL (École Polytechnique Fédérale de Lausanne), Switzerland. Before moving to the United States, I was a postdoc researcher in Dr. Sarah Teichmann’s group, at the European Bioinformatics Institute (EBI) and Wellcome Trust Sanger Institute in Cambridge, UK. I was supported by a Fellowship for Prospective Researchers and an Advanced Postdoc.Mobility Fellowship from Swiss National Science Foundation (SNSF) from Aug. 2012 to Jul. 2015. I was a research fellow in the 2016 Simons Institute program on Algorithmic Challenges in Genomics. My Erdös number is 3.
Awards
NSF CAREER Award, 2022.
NIH Maximizing Investigators’ Research Award (MIRA) (R35 for ESI), 2021.
Academic Activities
Conference PC member:
RECOMB-CG (RECOMB comparative genomics) 2019, 2020, 2021, 2023; RECOMB 2022
WABI (Workshop on Algorithms in Bioinformatics) 2012, 2021
ECCB (European Conference on Computational Biology) 2012, 2014, 2016, 2019;
ISMB/ECCB2015, ISMB 2022, 2023.
Editorial Board:
Journal of Computational Biology
Journal Referee:
Nature Machine Intelligence, Nature Methods, Nature Communications, Nature Review Genetics, Genome Biology, Science Advances, Genome Research, Cell Reports, Cell Reports Methods, Cell Systems, Bioinformatics, Briefings in Bioinformatics, PLoS ONE, PLoS Computational Biology, BMC Bioinformatics, IEEE TCCB, BMC Molecular Biology, etc.
Conference organizer:
GSCS2022
Proposal Reviewer:
NSF BIO panel; Computing Innovation Fellows 2020, 2021; Research Grants Council (RGC) of Hong Kong.
Conference Referee:
RECOMB, ISMB, WABI, etc.
Links
Georgia Tech Machine Learning: ML@GT
The InQuBATE Training Program
Institute for Data Engineering and Science IDEaS
Xiuwei Zhang 