Lab Members

.Group pictures

The Omics Group Meeting in Fall 2019 (from left: Shang, Ankit, Dr.Dai, Derek, Jingting, Ulises, Daiqing, Alex, and Isuru)

Current members

    Derek Reiman (BioE)
    Ph.D Candidate
    Shang Gao (BioE)
    Ph.D Candidate (co-advised with Prof. Rehman, Dept. Pharmacology)

    Daiqing Chen (BioE)
    MS student
    Ryan Morley (BioE)
    Undergraduate student


    GPIP Undergraduate interns (Summer 2020)
    Ben Deschand (CS)
    Tuyen Mai (BioE)
    Ulises Sosa (Undergraduate, BioE, Fall 2019- Spring 2020)
    Research project: A Machine Learning Toolbox for Prediction of Host Phenotype Using Microbiome Data
    Jingting XU (Ph.D. in Bioinformatics, 2019)
    PhD Thesis Title:
    Computational Analysis of DNA Methylation and Gene Regulation
    First Employment: Clinical Data Scientist, Gilead Sciences, CA.
    Ahmed Metwally (Ph.D. in Bioinformatics, 2018), co-advised with Profs. Finn and Perkins, Dept. Medicine.
    PhD Thesis Title:
    Computational Methods on Longitudinal Microbiome Analysis: IdentiĀ€cation, Modeling, and Classification
    First Employment: Postdoc Research Fellow, Genetics, Stanford University
    Lingge Feng (M.Sc. in Bioinformatics, 2017)
    Research Project: Prediction of the microRNA-gene targets.
    OPT training
    Peter Larsen (Ph.D. in Bioinformatics, 2017)
    PhD Thesis Title:
    Modeling Host-Microbiome Interactions
    First Employment: Assistant Computational Biologist, Biosciences Division, Argonne National Laboratory.
    Xiao Long (M.Sc. in Bioinformatics, 2015)
    MS Research Project: Select highly correlated splicing sites from RNA-seq and DNA methylations data.
    PhD candidate in Computer and Information Sciences, Drexel University, 2018-
    Hong Hu (PhD in Bioinformatics, 2015)
    PhD Thesis Title:
    Identification of Transcriptional Regulatory Elements: Novel Machine Learning Approaches.
    First Employment: Bioinformatician, Center for Research Informatics (CRI) at UIC
    Amira Kefi (M.Sc. in Bioinformatics, 2014)
    Master Thesis Title:
    A Statistical Framework For Geneset Enrichment Analysis Based on DNA Methylation and Gene Expression.
    Ph.D. candidate in Bioengineering, UIC
    Bhavisha Modi (M.Sc. in Bioinformatics, 2013)
    Master Thesis Title:
    Identification of microRNA Functional Targets based on microRNA and mRNA Co-expression Network Analysis.
    Damian Roqueiro (Ph.D. in Bioinformatics, 2013)
    PhD 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)
    PhD 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
    Wenbo Mu (M.Sc. 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.
    Joel Fontanarosa (MD/PhD, Ph.D. in Bioinformatics, 2013)
    PhD 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)
    PhD Thesis Title:
    Exploring Topology of Genetic Networks for Better Reconstruction.
    First Employment: Verizon
    Zhengdeng Lei (Ph.D. in Bioinformatics, 2007)
    Ph.D Thesis Title: Genome-wide Computational Prediction of Protein Localizations.
    First Employment: Bioinformatician, Department of High-Throughput Screening Core Facility, Memorial Sloan-Kettering Cancer Center.
    Deepa Vijayraghavan ( Bioinformatics, 2007)
    Master Thesis Title: Study of Bayesiang Regression and
    Ranking Feature Selection Methods on Cancer Classification Problems.

    First Employment: Microsoft.
    Peter Larsen (M.Sc. in Bioinformatics, 2006)
    Master Thesis Title: Identifying Gene Interaction Networks from Time Course Microarray Data and Gene Ontology Annotation.
    First Employment: the Biosciences Division, Argonne National Laboratory.
    Alice Diec (M.Sc. in Bioinformatics, 2005)
    Master Thesis Title: Multi-class Classification Methods for Applications in Bioinformatics: Comprehensive Study.
    First Employment: Bioinformatician, the Genome Sequencing Center, Washington University.
    Munawer Baig (M.Sc. in CS, 2004)
    Master Project Title: Identification of Patterns in DNA sequences.