I am an Assistant 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 current projects include:
– CellPath: Inference of multiple trajectories in single cell RNA-seq data from RNA velocity; | preprint | Python package |
– DeepTI: a single cell trajectory inference method using graph convolutional neural networks
– SpatialClustering (now named scHybridNMF): cell type identification integrating both gene-expression and cell location data, | preprint |
– VeloSim: an in silico simulator which generates single cell gene-expression data including spliced counts, unspliced counts, true RNA velocity, given any structure of cell development including trees and cycles. | preprint | R package |
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.
Conference PC member:
RECOMB-CG (RECOMB comparative genomics) 2019, 2020, 2021
WABI (Workshop on Algorithms in Bioinformatics) 2012, 2021
ECCB (European Conference on Computational Biology) 2012, 2014, 2016, 2019
NSF BIO, Computing Innovation Fellows 2020, Research Grants Council (RGC) of Hong Kong.
Cell Reports, Cell Reports Methods, Bioinformatics, PLoS ONE, PLoS Computational Biology, BMC Bioinformatics, IEEE TCCB, BMC Molecular Biology, etc.
RECOMB, ISMB, WABI, etc.
To be added.