Publications

2021
Ziqi Zhang, Xiuwei Zhang. VeloSim: Simulating single cell gene-expression and RNA velocity. bioRxiv.

2020
Vaibhav Rajan, Ziqi Zhang, Carl Kingsford, Xiuwei Zhang. Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming, Bioinformatics, accepted.
• Harsh Shrivastava, Xiuwei Zhang, Le Song, Srinivas Aluru. An Unrolled Deep Learning Framework for Single Cell Gene Regulatory Networks. RECOMB 2021, accepted.
• Ziqi Zhang, Xiuwei Zhang. Inference of multiple trajectories in single cell RNA-seq data from RNA velocity BioRxiv.
• Sooyoun Oh, Haesun Park, Xiuwei Zhang, Hybrid Clustering of single-cell gene-expression and cell spatial information via integrated NMF and k-means. BioRxiv.

For a full list of publications please see Google Scholar Profile.

Software

1. R package for SymSim : a simulator for single cell RNA-Seq data with the following applications
• Benchmark a wide range of computational methods for single cell RNA-Seq data analysis, including clustering, trajectory inference, differentially expressed gene detection.
• Analyze the effects of various confouding factors in the data on the performance of downstream analysis.
• Estimate how many cells we need to sequence to detect a rare population under various realistic scenarios.

2. Matlab code for ProPhyC : a framework of phylogenetic transfer of knowledge to improve accuracy of biological networks for a family of species.