Lab Members

Principal Investigator

• Yang Dai (PhD) Professor

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)

Undergrad students

• Anna Gerasimenko (2024-, BME)
• Yissr Almasri  (2024-, BME)

Alumni

PhD

• 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

Master

• Palak Agrawal (MS in Bioinformatics, July 11, 2024)
  Thesis Title Exploring Microbial Mediation Effect in Acute Pancreatitis: A Path to Understanding Disease Mechanism.
• 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
• 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

Undergraduate

• Alannah Rodrigues (BME, undergraduate research, Honors College, 2024)
  Research project: Predict transcription factor activity from analysis of single cell RNA-seq and ATAC-seq generated from macrophages and monocytes in skin wounds from mice.
• 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