About Me

I am Wei Zhang, an assistant professor at the Department of Computer Science and a core member for the Genomics and Bioinformatics Cluster at University of Central Florida. My primary research interest is computational biology, an interdisciplinary research area where computational, mathematical and statistical methods are applied to solve biology problems. My research covers several important topics in cancer transcriptome, spanning from technique-driven research that aims at developing graph-based learning algorithms for cancer transcriptome analysis with prior knowledge, to hypothesis-driven investigation of specific biological problems.

I received my Ph.D and M.S. from the Computer Science and Engineering Department at University of Minnesota-Twin Cities. My advisor are Dr. Rui Kuang and Dr. Baolin Wu. I did my Bachelor thesis in Computer Science from Winona State University under Dr. Mingrui Zhang's supervision. Before joining UCF in 2017, I was a research associate at University of Minnesota for two years.

Research Interests

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

  • Spring 2019: COT3100H Introduction to Discrete Structure
  • Fall 2018: COP5537 Network Optimization
  • Spring 2018: COT3100H Introduction to Discrete Structure
  • Fall 2017: COP5537 Network Optimization
  • Publications

    Peer-reviewed Publication Google Scholar ORCID

  • Raphael Petegrosso, Zhuliu Li, Molly Srour, Yousef Saad, Wei Zhang, and Rui Kuang. Scalable Remote Homology Detection and Fold Recognition in Massive Protein Networks. PROTEINS: Structure, Function, and Bioinformatics, 2019. (Accepted)

  • Shaahin Angizi, Jiao Sun, Wei Zhang, and Deliang Fan. AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM. Design Automation Conference (DAC), June 2019. (Accepted)

  • Shaahin Angizi, Jiao Sun, Wei Zhang, and Deliang Fan. GraphS: A Graph Processing Accelerator Leveraging SOT-MRAM. Design, Automation and Test in Europe (DATE), Mar 2019. (Accepted)

  • Jae-Woong Chang*, Wei Zhang*, Hsin-Sung Yeh, Meeyeon Park, Chengguo Yao, Yongsheng Shi, Rui Kuang#, and Jeongsik Yong#. An Integrative Model for Alternative Polyadenylation, IntMAP, Delineates mTOR-modulated Endoplasmic Reticulum Stress Response. Nucleic Acids Research, 2018. (*Joint first authors) doi:10.1093/nar/gky340 [Download]

  • Sk. Kayum Alam, Matteo Astone, Ping Liu, Stephanie Hall, Abbygail Coyle, Erin Dankert, Dane Hoffman, Wei Zhang, Rui Kuang, Anja Roden, Aaron Mansfield, and Luke Hoeppner. DARPP-32 and t-DARPP Promote Non-small Cell Lung Cancer Growth Through Regulation of IKKα-dependent Cell Migration. Communication Biology, 2018. doi:10.1038/s42003-018-0050-6

  • Xiaoyu Xiang, Yuanguo Wang, Hongbin Zhang, Jinhua Piao, Selvaraj Muthusamy, Lei Wang, Yibin Deng, Wei Zhang, Rui Kuang, Daniel D. Billadeau, Shengbing Huang, Jinping Lai, Raul Urrutia, and Ningling Kang. Vasodilator-stimulated phosphoprotein promotes liver metastasis of gastrointestinal cancer by activating a β1-integrin-FAK-YAP1/TAZ signaling pathway. npj Precision Oncology, 2018. doi:10.1038/s41698-017-0045-7

  • Wei Zhang, Jeremy Chien, Jeongsik Yong, and Rui Kuang. Network-based Machine Learning and Graph Theory Algorithms for Precision Oncology. npj Precision Oncology, 2017. doi:10.1038/s41698-017-0029-7

  • Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong. Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies. BMB Reports, 2017. doi:10.5483/BMBRep.2017.50.4.019

  • 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]

  • Other manuscript

  • 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, Rui Kuang, and Baolin Wu. Model Based Clustering Analysis of 16S rRNA Sequence. [Paper]

  • Thesis

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

  • Internship

    me     Millennium: The Takeda Oncology Company

    Teaching Assistant@UMN

  • 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