People

Faculty
Rui Kuang
Personal Website

Rui Kuang 

Professor of Computer Science and Engineering

  • Research interests: tensor-based modeling for high-order data and multi-relational graphs; spatial and single-cell transcriptomics; 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).
  • Contact: email – kuang at umn dot edu; telephone – 6126247820
  • Office: Keller Hall 6-187
Lab members (Keller Hall 6-225D)

Tianci Song

PhD Student (Computer Science and Engineering)

  • Research interests: Semi-Supervised Learning, Deep Learning, Statistical Learning and their application in Computational Biology and Bioinformatics.
  • Education: BS, Computer Science, Jilin University (2014); MS, Computer Science, Jilin University (2017).
  • Email: song0309 at umn dot edu

Charles Broadbent

PhD Student (Computer Science)

  • Research interests: Computational Biology and Bioinformatics, Machine Learning.
  • Education: BA, Computer Science, Carleton College (2020).
  • Email: broad123 at umn dot edu

Ethan Kulman

PhD Student (Computer Science)

  • Research interests: Machine Learning, Cancer Genomics, Computational Biology.
  • Education: BS, Health Studies, University of Rhode Island (2015); MS, Computer Science, University of Rhode Island (2020).
  • Email: kulma009 at umn dot edu

Yoshitaka Inoue

PhD Student (Computer Science and NIH Fellowship Program)

  • Research interests: Machine Learning, Mathematical Optimization, Graph Theory, and Biological Networks of transcriptome and metabolome.
  • Education: BS, Biological Science, Kumamoto University (2017); MS, Information Science, Nara Institute of Science and Technology (2019).
  • Email: inoue019 at umn dot edu

Quoc Nguyen

PhD Student (Computer Science)

  • Research interests: Spatial Computational Biology.
  • Education: BS, Computer Science, Carleton College (2023).
  • Email: nguy5647 at umn dot edu

Sharada K Sridhar

PhD Student (Bioinformatics and Computational Biology)

  • Research interests: Machine learning & image processing for solutions in Bioinformatics & Computational Biology.
  • Education: Masters in Electrical Engineering, UMN TC (2017); Bachelor of Technology in Electronics & Communication Engineering, Amrita University, India (2015)
  • Email: kadab004 at umn dot edu
Rotation students and summer interns
Alumni
  • Zhuliu Li, PhD in Computer Science, 2021.  Current Position: Machine Learning Engineer, Linkedin. Thesis: Learning multi-way associations across biological networks
  • David Roe, PhD in Bioinformatics and Computational Biology, 2021.  Current Position: Bioinformatics Scientist (Consulting), Genentech. Thesis: Computational Methods for Sequencing and Interpreting Killer-cell Immunoglobulin-like Receptors (KIRs) at Multiple Resolutions
  • Raphael Petegrosso, PhD in Computer Science, 2019. Current Position: Applied Scientist, Amazon. Thesis: Learning High Order Relations for Network Based Phenome Genome Association Analysis
  • Huanan Zhang, PhD in Computer Science, 2017. Current Position: Applied Researcher, Microsoft. Thesis: Detecting Biomarkers among Subgroups with Structured Latent Features and Multitask Learning methods
  • Wei Zhang (co-advised with Baolin Wu), PhD in Computer Science, 2015. Current Position: Assistant Professor, Computer Science Department, University of Central Florida. Thesis: Computational Analysis of Transcript Interactions and Variants in Cancer
  • Ze Tian, PhD in Computer Science, 2012. Current Position: Senior Applied Researcher, Microsoft. Thesis: Learning with Kernels and Graphs to Understand Cancer DNA Copy Number Variations
  • TaeHyun Hwang, PhD in Computer Science, 2011. Current Position: Florida Department of Health Cancer Chair, Department of Artificial Intelligence and Informatics and Department of Immunology, Mayo Clinic. Thesis: Network-based Learning Algorithms for Understanding Human Disease
  • Yao Gong, PhD in Bioinformatics and Computational Biology (secondary advisor) 2023
  • Nishitha Paidimukkala, PhD in Bioinformatics and Computational Biology (secondary advisor) 2021
  • Kaige Zhang, PostDoc (co-supervised), 2020
  • Changjin Hong, PostDoc, 2008-2010
  • Shrijana Gurung, M.S., Bioinformatics and Computational Biology, 2024. Thesis: Network-guided Clustering of Spatially Co-Expressed Genes: An Exploration of Regularization Losses
  • Manish Keshri, M.S., Data Science, 2019
  • Haoda Chu, M.S., Data Science, 2019
  • Catherine Lee, M.S., Bioinformatics and Computational Biology, 2018
  • Michael Pickett-Leonard, M.S., Bioinformatics and Computational Biology, 2018
  • 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.
  • Thomas Atkins, REU Student, 2022-2023, Thesis: FIST-nD: A tool for n-dimensional spatial transcriptomics data imputation via graph-regularized tensor completion
  • Michael Li, Summer Intern, 2020
  • Elizabeth Ankrah, REU Summer Intern, 2018
  • Maria Elise Kloiber, REU Summer Intern, 2018
  • Molly Srour, REU Summer Intern, 2017
  • 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.
  • Kai Tian, Visiting PhD student 2018-2019, South China Agricultural University
  • 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