Yu Zhang

Dr Yu Zhang is an associate professor in the Machine Learning Lab at the College of Computer Science and Technology of Jilin University. He is the director of the Mathematical Modeling course. He also teaches courses such as C#, .NET, Machine Learning, and Computing Methods.

He is an International Affiliate in Medical & Molecular Genetics, Department of Medical & Molecular Genetics, Indiana University School of Medicine. He was a visiting scholar at Indiana University School of Medicine from July 2018 to Auguest 2019 and a visiting scholar at University of Georgia from July 2011 to July 2012. He received his bachelor’s, master’s and doctoral degree in Mathematics from Jilin University.

In addition to algorithms, he also specializes in a variety of computer languages and software engineering techniques. As a bioinformatics researcher, he is accumulating reputation for developing computer programs.

He is now responsible for the research on Biclustering-based study of alternative drug resistance mechanisms on cancer drug screening and clinical transcriptomics data. [Supported by National Natural Science Foundation of China (NSFC) under Grant No. 61972175, 2020.01 - 2023.12, Funding: 590,000 CNY]

Recent Publications

M3S: A comprehensive model selection for multi-modal single-cell RNA sequencing data Y Zhang, C Wan, P Wang, W Chang, Y Huo, J Chen, Q Ma, S Cao, … BMC Bioinformatics 20 (Suppl 24), 672 1 2019

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data J Xie, A Ma, Y Zhang, B Liu, S Cao, C Wang, J Xu, C Zhang, Q Ma Bioinformatics 36 (4), 1143–1149 5* 2019

LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data C Wan, W Chang, Y Zhang, F Shah, X Lu, Y Zang, A Zhang, S Cao, … Nucleic acids research 47 (18), e111-e111 3 2019

A new deconvolution algorithm for accurate assessing immune and stromal cell populations in mouse transcriptomic data X Lu, S Tu, W Chang, Y Huo, P Wang, Y Zhang, C Zhang, S Cao Cancer Research 79 (13 Supplement), 2453-2453 2019

A semi-supervised approach for cell phenotypic and functional estimation in tissue microenvironment W Chang, C Wan, Y Zhang, K So, B Richardson, Y Sun, X Zhang, … bioRxiv, 426593 1 2019

Multi-label deep learning for gene function annotation in cancer pathways R Guan, X Wang, MQ Yang, Y Zhang, F Zhou, C Yang, Y Liang Scientific reports 8 (1), 267 10 2018

ICTD: Inference of cell types and deconvolution–a next-generation deconvolution method for accurate assess cell population and activities in tumor microenvironment. W Chang, C Wan, Y Zhang, K So, B Richardson, Y Sun, X Zhang, … bioRxiv, 426593 1 2018

MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network Y Zhang, S Cao, J Zhao, B Alsaihati, Q Ma, C Zhang Quantitative Biology 6 (1), 40-55 2 2018

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data Y Zhang, J Xie, J Yang, A Fennell, C Zhang, Q Ma Bioinformatics 33 (3), 450-452 42 2017

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation Y Li, X Shi, Y Liang, J Xie, Y Zhang, Q Ma BMC bioinformatics 18 (1), 51 6 2017

Analyzing gene expression time-courses based on multi-resolution shape mixture model Y Li, Y He, Y Zhang Mathematical Biosciences 281, 74-81 2016

Comprehensive characterization of the genomic alterations in human gastric cancer J Cui, Y Yin, Q Ma, G Wang, V Olman, Y Zhang, WC Chou, CS Hong, … International Journal of Cancer 137 (1), 86-95 47 2015

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data Z Chang, G Li, J Liu, Y Zhang, C Ashby, D Liu, CL Cramer, X Huang Genome biology 16 (1), 30 172 2015

CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes X Mao, X Chen, Y Zhang, S Pangle, Y Xu PloS one 7 (12), e51252 6 2012

SEAS: A system for SEED-based pathway enrichment analysis X Mao, Y Zhang, Y Xu PloS one 6 (7), e22556 5 2011

Analysis of gene expression data based on density and biological knowledge X Zhou, H Sun, DP Wang, Y Zhang, Y Zhou Frontier of Computer Science and Technology (FCST), 2010 Fifth International … 1 2010

Gender Classification with Support Vector Machines Based on Non-tensor Pre-wavelets L Ying, Z Yu, Z Shishun Computer Research and Development, 2010 Second International Conference on … 3 2010