People

Faculty

Rui Kuang 

Associate Professor of Computer Science and Engineering

  • Research interests: network-based learning, string kernels, semi-supervised learning and multi-task learning in bioinformatics; cancer genomics; phenome-genome association analysis; protein remote homology detection
  • Education: PhD, Computer Science, Columbia University (2006); MS, Computer Science, Temple University (2002); BS, Computer Science, Nankai University (1999).
Lab members

Wei Zhang

Research Associate

  • Research interests: network-based learning, mRNA 3’UTR shortening, isoform quantification, drug sensitivity prediction
  • Education: PhD and MS, Computer Science, University of Minnesota Twin Cities (2015 & 2011); BS, Computer Science, Hebei University of Technology (2009).
Huanan Zhang

Huanan Zhang

PhD Student (Computer Science and Engineering)

  • Research interests: transfer learning, matrix decompositions for Copy Number Variation detection, population and phylogenetic study
  • Education: MS, Computer Science, Nankai University (2010); BS, Computer Science, Nankai University (2007)
Dave Roe

David Roe

PhD Student (Biomedical Informatics and Computational Biology)

  • Research interests: immunogenetics, machine learning, HLA, KIR, cancer therapies, genetic associations
  • Education: MBS, University of Minnesota (2007); BS, Computer Science, North Dakota State University (1994).
  • Professional: Bioinformatics Scientist at the National Marrow Donor Program

Raphael Petegrosso

PhD Student (Computer Science and Engineering)

  • Research interests: isoform quantification, network-based learning, semi-supervised learning, phenome-genome association analysis
  • Education: BS, Computer Engineering, University of São Paulo (2008)

Nishitha Paidimukkala

PhD Student (Biomedical Informatics and Computational Biology)

  • Research interests: RNA- seq analysis, Hair follicle Stem cells, Mouse genomics.
  • Education: MS in Biology, University of Minnesota, Bachelors Degree in Biotechnology

Catherine Lee

PhD Student (Molecular, Cellular, Developmental Biology, and Genetics)

  • Research interests: single-cell RNA-sequencing, recessive dystrophic epidermolysis bullosa, stem cells.
  • Education: MS, BICB, University of Minnesota-Twin Cities (2015); MS, Stem Cell Biology, University of Minnesota-Twin Cities (2013); BA University of California-Berkeley (2009)
    .

Zhuliu Li 

PhD Student (Computer Science and Engineering)

  • Research interests: statistical learning, semi-supervised learning, network-based learning, and the applications in biological network.
  • Education: BS, Electric Engineering, Xidian Universiy (2014); MS, Electric and Computer Engineering, University of Minnesota-Twin Cities (2016).
Alumni
  • Wei Zhang, PhD in Computer Science, 2015. Thesis: Computational Analysis of Transcript Interactions and Variants in Cancer
  • Ze Tian, PhD in Computer Science, 2012. Thesis: Learning with Kernels and Graphs to Understand Cancer DNA Copy Number Variations
  • TaeHyun Hwang, PhD in Computer Science, 2011. Thesis: Network-based Learning Algorithms for Understanding Human Disease
  • Changjin Hong, PostDoc, 2008-2010
  • Raghav Pavan Srivatsav (co-advised with Julie Jacko), M.S., Computer Science/Health Informatics, 2012, Project: An Endof-life Decision Making Tool for Ovarian Cancer Patients Entering Hospice, 2012
  • Seshamahadev Kanchinadham, M.S., Computer Science/Health Informatics, 2012, Project: A Webtool for Biomarker Discovery from Multiple Gene Expression Datasets
  • Spencer Dille, M.S., Computer Science/Health Informatics, 2012, Project: Java Application for Sparse Latent Graph Component Learning with Genomic Data
  • Yixin Chen (co-advised with Lynda Ellis), M.S., Health Informatics, 2011, Thesis: Gene Expression Analysis of the Dedifferentiation of Primary Rat Hepatocyte
  • Baryun Hwang, M.S., Computer Science, 2009, Thesis: Finding Consistent Biomarkers from Independent Microarray Gene Expression.
  • Thanh Le, B.S., 2012
  • Xiang Yao, B.S., 2012
  • Mila Gorodetsky, B.S., 2010, Thesis: A Constrained Label Propagation for Biomarker Discovery in Genetic Data.
  • Zhixian Yang, Visiting Scholar 2015, China University of Civil Aviation
  • Meng Lu, Visiting PHD student 2015, Texas A&M University
  • Tao Li, Visiting scholar 2014, Nankai University
  • Maoqiang Xie, Visiting scholar 2010-2011, Nankai University
  • Gengzhi Li, Visiting scholar 2008-2009, Beijing Industrial University