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Lab Members

.Group pictures

Principal Investigator

Ph.D. Students

  • Mehrdad Zandigohar (2020-, Bioinformatics)
  • Yongchao Huang (2020-, Bioinformatics, co-advised with Prof. Penalver Bernabe)
  • Brando Lucas (2021-, Bioinformatics)
  • Tina Khajeh (2022-, Bioinformatics)
  • Jeff Kim (2023-, MSTP/BME)
    Affiliated member

  • Julianne Jorgensen (2021-, MSTP/BME, co-advised with Prof. Brain Layden)

MS Students with thesis research

  • Palak Agrawal (2022-, Bioinformatics)

Undergrad students

  • Alannah Rodrigues Agrawal (2022-, BME, Honor’s College Capstone Research)


  • Shang Gao (Ph.D. in Bioinformatics, August 2022, Co-advised with Prof. Jalees Rehman)
    Thesis Title: Machine learning on the integration analysis of multi-omics data
    First Employment: Genetec
  • Derek Reiman (Ph.D. in Bioinformatics, Fall 2021)
    Thesis Title: Deep Learning Frameworks for Multi-omics Analyses of the Microbiome in Disease Studies
    First Employment: Research Assistant Professor, Toyota Technological Institute at Chicago (TTIC)
  • Jingting XU (Ph.D. in Bioinformatics, Fall 2019)
    Thesis Title: Computational Analysis of DNA Methylation and Gene Regulation
    First Employment: Clinical Data Scientist, Gilead Sciences, CA
  • Ahmed Metwally (Ph.D. in Bioinformatics, Fall 2018. Co-advised with Profs. Finn and Perkins, Dept. Medicine)
    Thesis Title: Computational Methods on Longitudinal Microbiome Analysis: Identification, Modeling, and Classification
    First Employment: Postdoc Research Fellow, Genetics, Stanford University
  • Peter Larsen (Ph.D. in Bioinformatics, 2017)
    Thesis Title: Modeling Host-Microbiome Interactions
    First Employment: Assistant Computational Biologist, Biosciences Division, Argonne National Laboratory
  • Hong Hu (Ph.D. in Bioinformatics, 2015)
    Thesis Title: Identification of Transcriptional Regulatory Elements: Novel Machine Learning Approaches
    First Employment: Bioinformatician, Center for Research Informatics (CRI) at UIC
  • Damian Roqueiro (Ph.D. in Bioinformatics, 2013)
    Thesis Title: Computational Methods to Study Gene Regulation Using Genomic, Epigenomic and Chromosome Conformation Data
    First Employment: Postdoc at the Max Planck Institute for Intelligent Systems, Tubingen, Germany
  • Lei Huang (Ph.D. in Bioinformatics, 2013)
    Thesis Title: Integrated Bioinformatics Approach for Better Understanding of Estrogen Receptor Mechanisms in Breast Cancer
    First Employment: Bioinformatician, Center for Research Informatics, University of Chicago
  • Joel Fontanarosa (MD/Ph.D., Ph.D. in Bioinformatics, 2013)
    Thesis Title: Integrative Analysis Strategies for Discovering Genetic Associations with Common Diseases
    First Employment: Resident, Northwestern University Feinberg School of Medicine
  • Guanrao Chen (Ph.D. in CS, 2008)
    Thesis Title: Exploring Topology of Genetic Networks for Better Reconstruction
    First Employment: Verizon
  • Zhengdeng Lei (Ph.D. in Bioinformatics, 2007)
    Thesis Title: Genome-wide Computational Prediction of Protein Localizations
    First Employment: Bioinformatician, Department of High-Throughput Screening Core Facility, Memorial Sloan-Kettering Cancer Center


  • Kaustubh Kishor Pachpor (MS in Bioinformatics, June 30, 2023. Co-advised with Prof. Brian Layden)
    Thesis Title: MOMMI-MP: A Comprehensive Database for Integrated Analysis of Metabolic and Microbiome Profiling of Mouse Pregnancy
    First Employment
  • Daiqing Chen (M.S. in Bioinformatics, May 2021)
    Research project: Using machine learning to predict rapid decline of kidney function in sickle cell anemia
    First Employment: Research Technician, University of Chicago
  • Lingge Feng (M.S. in Bioinformatics, 2017)
    Research Project: Prediction of microRNA-gene Targets
  • Xiao Long (M.S. in Bioinformatics, 2015)
    Research Project: Select highly correlated splicing sites from RNA-seq and DNA methylations data.
    PhD Candidate in Computer and Information Sciences, Drexel University, 2018-
  • Amira Kefi (M.S. in Bioinformatics, 2014)
    Thesis Title: A Statistical Framework For Geneset Enrichment Analysis Based on DNA Methylation and Gene Expression
  • Bhavisha Modi (M.S. in Bioinformatics, 2013)
    Thesis Title: Identification of microRNA Functional Targets based on microRNA and mRNA Co-expression Network Analysis
  • Wenbo Mu (M.S. in Bioinformatics, 2013)
    Master Thesis Title: A Local Genetic Algorithm for the Identification of Condition-Specific microRNA-Gene Modules
    First Employment: Bioinformatics Analyst, Ambry Genetics, CA
  • Deepa Vijayraghavan (M.S. in Bioinformatics, 2007)
    Thesis Title: Study of Bayesian Regression and Ranking Feature Selection Methods on Cancer Classification Problems
    First Employment: Microsoft
  • Peter Larsen (M.S. in Bioinformatics, 2006)
    Thesis Title: Identifying Gene Interaction Networks from Time Course Microarray Data and Gene Ontology Annotation
  • Alice Diec (M.S. in Bioinformatics, 2005)
    Thesis Title: Multi-class Classification Methods for Applications in Bioinformatics: Comprehensive Study
    First Employment: Bioinformatician, the Genome Sequencing Center, Washington University
  • Munawer Baig (M.S. in CS, 2004)
    Research Project: Identification of Patterns in DNA sequences


  • Ayaan Siddiqui (BME, GPIP intern 2023)
  • Pradyun Shrestha (CS, GPIP intern 2023)
  • Matt Heffernan (CS, GPIP intern 2021)
  • Hafsa Hussain (BioE, GPIP intern 2021)
  • Ryan Morley (B.S. in Bioengineering, May 2021)
    Research project: MicrobiomeBioinformaticsUsing the QIIME 2 Pipeline
  • Ben Deschand (CS, GPIP intern 2020)
  • Tuyen Mai (BioE, GPIP intern 2020)
  • Ulises Sosa (B.S. in Bioengineering, Fall 2019- Spring 2020)
    Research project: A Machine Learning Toolbox for Prediction of Host Phenotype Using Microbiome Data