About Me

I am Wei Zhang, a Research Associate at Computer Science and Engineering Department, University of Minnesota, Twin Cities. My advisors were Dr. Rui Kuang and Dr. Baolin Wu during my Ph.D. study.

I did my Bachelor thesis in Computer Science from Winona State University under Dr. Mingrui Zhang's supervision. From University of Minnesota, Twin Cities, I received my M.S. and Ph.D. in Computer Science from Computer Science and Engineering Department.

Research Interests

  • Computational Biology and Bioinformatics
  • Machine Learning
  • Biostatistics
  • Publications

    Peer-reviewed Publication Google Scholar

  • Lining Liang, Hao Sun, Wei Zhang, Mengdan Zhang, Xiao Yang, Rui Kuang, and Hui Zheng. Meta-Analysis of EMT Datasets Reveals Different Types of EMT. PLoS One, 2016. doi:10.1371/journal.pone.0156839

  • Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, and Rui Kuang. Network-based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PLoS Comput Biol, 2015. doi:10.1371/journal.pcbi.1004465 [Download]

  • Jae-Woong Chang*, Wei Zhang*, Hsin-Sung Yeh, Ebbing de Jong, Semo Jun, Kwan-Hyun Kim, Sun Sik Bae, Kenneth Beckman, TaeHyun Hwang, Kye-Seong Kim, Do-Hyung Kim, Rui Kuang, and Jeongsik Yong. mRNA 3'UTR Shortening is a Molecular Signature of mTORC1 Activation. Nature Communications, 2015. doi:10.1038/ncomms8218 (*Joint first authors)

  • Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy R Chien, Baolin Wu, and Rui Kuang. Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment. PLoS Comput Biol, 2013. doi:10.1371/journal.pcbi.1002975 [Download]

  • Jiaqi Yang, Wei Zhang, Baolin Wu. A note on statistical method for genotype calling of high-throughput SNP arrays. Journal of Applied Statistics, 2013. doi:10.1080/02664763.2013.785499

  • Wei Zhang, Nicholas Johnson, Baolin Wu, and Rui Kuang. Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations. Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Oct 2012. [Paper][Download]

  • TaeHyun Hwang, Wei Zhang, MaoQiang Xie, Jinfeng Liu, and Rui Kuang. Inferring Disease and Gene Set Associations with Rank Coherence in Networks. Bioinformatics, 27(19): 2692-2699, 2011. doi:10.1093/bioinformatics/btr463

  • Wei Zhang, Baryun Hwang, Baolin Wu, and Rui Kuang. Network propagation models for gene selection. Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Nov 2010. [Paper]

  • Mingrui Zhang, Wei Zhang, Hugues Sicotte, and Ping Yang. A New Validity Measure for a Correlation-Based Fuzzy C-means Clustering Algorithm. Conference Proc. The 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Sept 2009. [Paper]

  • Thesis

  • Wei Zhang. Computational Analysis of Transcript Interactions and Variants in Cancer. Ph.D Thesis (University of Minnesota, Twin Cities), 2015. [Paper]

  • Papers in Preparation

  • Wei Zhang, Jeremy Chien, Jeongsik Yong, and Rui Kuang. Network-based Machine Learning and Graph Algorithms for Precision Oncology. (Under review)

  • Jae-Woong Chang*, Wei Zhang*, Hsin-Sung Yeh, Ebbing de Jong, Chengguo Yao, Jung-Hee Lee, Hyun-Seo Lee, LeeAnn Higgins, Todd Markowski, Luke Erber, Yue Chen, TaeHyun Hwang, HoJin You, Yongsheng Shi, Timothy Griffin, Rui Kuang, and Jeongsik Yong. mTOR-coordinated Genome-wide Intronic Polyadenylation Reveals Multifaceted Gene Features. (*Joint first authors)

  • Raphael Petegrosso*, Wei Zhang*, Zhuliu Li, Yousef Saad, and Rui Kuang. Low-rank Label Propagation for Semi-supervised Learning with 100 Millions Samples. (*Joint first authors) [Paper]

  • Wei Zhang, Jae-Woong Chang, Hsin-Sung Yeh, Yue Chen, Rui Kuang, and Jeongsik Yong. Intronic Polyadenylation-mediated Reprogramming of Protein Interaction Networks in Cancers.

  • Jae-Woong Chang*, Wei Zhang*, Yongsheng Shi, Rui Kuang, and Jeongsik Yong. A New Integrative Model for Identifying Alternative Polyadenylation from PAS-Seq and RNA-Seq. (*Joint first authors)

  • Wei Zhang, Raphael Petegrosso, Jae-Woong Chang, Jeremy R Chien, Jeongsik Yong, and Rui Kuang. Comparative analysis of Isoform-level Gene Expression Estimated by NanoString, RNA-Seq, Exon-Array and qRT-PCR Platforms.

  • Wei Zhang, Rui Kuang, and Baolin Wu. Model Based Clustering Analysis of 16S rRNA Sequence.

  • Maoqiang Xie, Than Le, Xiang Yao, Hongyue Zhang, Wei Zhang, Taehyun Hwang and Rui Kuang. PheGenEx: a web explorer for prediction and analysis of phenome-genome association. [Webtool]
  • Internship

    me     Millennium: The Takeda Oncology Company

    Conference Posters and Presentations

  • Network-based Transcript Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC), Atlanta, GA, 2015. (Oral)

  • Network-based Transcript Quantification with RNA-Seq Data. International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA, 2014. (Poster)

  • Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Orlando, FL, 2012. (Oral)

  • Network-based Survival Analysis on Ovarian Cancer. International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA, 2012. (Oral)
  • Teaching Assistant

  • CSCI 8980 (Fall 2015): Next Generation Computing and Analytics for Cancer Genomics.
  • CSCI 5461 (Spring 2013 and Spring 2011): Functional Genomics, Systems Biology and Bioinformatics.
  • CSCI 8980 (Fall 2012): Emerging Bioinformatics Models for NGS and Biological Network Analysis.
  • CSCI 5481 (Fall 2011): Computational Techniques in Genomics.
  • Academic Awards

  • CNB-MAC Student Travel Grant, 2015
  • Best Poster Award, The 6th Annual Biomedical Informatics and Computational Biology Research Symposium, 2014
  • ACM-BCB Doctoral Student Travel Grant, 2012
  • 10th Place of NCS/MAA Mathematic Contest in Midwest of America, 2008
  • 4th Place of NCS/MAA Mathematic Contest in Midwest of America, 2007
  • 14th Place of NCS/MAA Mathematic Contest in Midwest of America, 2006
  • The views and opinions expressed in this page are strictly those of the page author.
    The contents of this page have not been reviewed or approved by the University of Minnesota.