Xiuwei
Zhang

General Information

Email:
xiuwei.zhang@gatech.edu
Phone:
4048943885
Location - Building:
Coda
Location - Room:
S1241
Roles:
Professor (any rank)
Primary Unit:
School of Computational Science and Engineering
Website URL
https://xiuweizhang.wordpress.com/

Details

Degrees with subject and Postdoc Experience:
Degree Type
PhD
Subject
Studying evolution of gene regulation using machine learning
Year
2011
Institution
Ecole Polytechnique Federale de Lausanne (EPFL, aka Swiss Federal Institute of Technology in Lausanne)
Location
Lausanne, Switzerland
Degree Type
Postdoctoral scholar
Subject
Single cell genomics data analytics
Year
2012-2015
Institution
EMBL-European Bioinformatics Institute (EBI) & MRC LMB, University of Cambridge
Location
Cambridge, UK
Degree Type
Postdoctoral scholar
Subject
Developing computational methods for single cell genomics
Year
2016-2019
Institution
University of California, Berkeley
Location
California
Statement of Research Interests:

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)
– Temporal analysis of single cells: how cells change over pseudotime or real time through cell divisions. (Example projects: CellPath, LinRace)
– Spatial-omics and Spatial-temporal dynamics of cells (Example projects: scHybridNMF, CLARIFY, TemSOMap, SpaDecoder)
– Simulation of single cell omics (including temporal and spatial) data to evaluation computational methods. (Example projects: TedSim, scMultiSim)
– Inference of gene regulatory networks, cell-cell interactions, and cross-modality relationships in multi-omics data. (Example projects: CespGRN, CLARIFY)

Statement of Teaching Interests:

I teaching core computer science courses like Computational Science and Engineering Algorithms and domain related courses like Machine Learning in Computational Biology and Algorithms in Bioinformatics and Computational Biology.

Selection of recent research, scholarly, and creative activities:

H Li, Z Zhang, M Squires, X Chen, X Zhang. scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks. Nature Methods, 22: 982–993, 2025.

Z Zhang, X Zhao, M Bindra, P Qiu, and X Zhang. scDisInFact: Disentangled Learning for Integration and Prediction of Multi-Batch Multi-Condition Single-Cell RNA-Sequencing Data. Nature Communications, 15 (1): 912, 2024.

X Pan, H Li, P Putta, and X Zhang. LinRace: Cell Division History Reconstruction of Single Cells Using Paired Lineage Barcode and Gene Expression Data. Nature Communications 14 (1): 8388, 2023.

Z Zhang, H Sun, R Mariappan, X Chen, X Chen, M Jain, M Efremova, S Teichmann, V Rajan and X Zhang. scMoMaT jointly performs single cell mosaic integration and multi-modal bio- marker detection. Nature Communications, 14 (384), 2023

M Bafna, H Li, X Zhang. CLARIFY: Cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics. Bioinformatics, 39: i484–i493, 2023 (Proceeding of ISMB’23 )