CV

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Contact Information

Name Chathura J. Gunasekara, Ph.D.
Professional Title Computational Scientist · Bioinformatics · ML/AI
Email cjgunase@gmail.com
Location Houston, Texas

Professional Summary

Computational scientist with 10+ years of experience designing and deploying production-grade genomics pipelines, machine learning models, and AI-driven research tools.

Experience

  • 2020 - present

    Houston, TX

    Bioinformatics Programmer / Analyst II
    Children's Nutrition Research Center, Baylor College of Medicine
    • Architected and deployed Python-based Whole Genome Bisulfite Sequencing analysis pipelines processing 60 TB of sequencing data across 2 human cohorts
    • Developed and validated ML classifiers for epigenetic biomarker discovery, achieving 80% accuracy in schizophrenia case-control classification (Translational Psychiatry 2021)
    • Co-developed the Agilent SureSelect Baylor Human CoRSIV Panel (launched April 2023), enabling cost-effective population-scale DNA methylation profiling
    • Built data pipelines integrating genomic, clinical, and metadata sources for multi-cohort population studies
  • 2019 - 2020

    Houston, TX

    Bioinformatics Analyst I
    Baylor College of Medicine
    • Developed population-scale epigenomics workflows (Genome Biology 2019, 2023)
    • Built distributed computing workflows on LSF/SLURM HPC clusters for terabyte-scale sequencing datasets
    • Designed reproducible bioinformatics environments using Conda, Docker, and Git CI/CD
  • 2017 - 2019

    Houston, TX

    Post-Doctoral Fellow
    Baylor College of Medicine
    • Developed the first algorithm to screen for systemic epigenetic variants in the human genome
  • 2013 - 2017

    Houghton, MI

    Graduate Researcher — Computational Science & Engineering
    Michigan Technological University
    • Developed ML algorithms for genomic feature discovery and gene regulatory network analysis
    • Built and benchmarked statistical models for large-scale biological datasets

Education

  • 2013 - 2017

    Houghton, MI

    Ph.D.
    Michigan Technological University
    Computational Science and Engineering
    • Thesis: Development Of Bioinformatics Tools and Algorithms for Identifying Pathway Regulators, Inferring Gene Regulatory Relationships and Visualizing Gene Expression Data
  • 2006 - 2010

    Sri Lanka

    B.S.
    University of Colombo
    Computational Physics

Awards

  • 2023
    Dr. Dennis M. Bier Award for Best Pediatric Nutrition Research Publication
    Baylor College of Medicine
  • 2019
    New Investigator Award
    Environmental Mutagenesis and Genomic Society (EMGS)

Publications

  • 2025
    Mouse metastable epialleles are extremely rare
    Nucleic Acids Research

    PMID: 40694849

  • 2023
    Systemic interindividual epigenetic variation in humans is associated with transposable elements and under strong genetic control
    Genome Biology

    PMID: 36631879

  • 2021
    A machine learning case-control classifier for schizophrenia based on DNA methylation in blood
    Translational Psychiatry

    PMID: 34341337

  • 2019
    A genomic atlas of systemic interindividual epigenetic variation in humans
    Genome Biology

    PMID: 31155008

Skills

Genomics & Epigenomics: DNA Methylation (WGBS), Multi-omics Integration, Population-scale Studies, Epigenetic Biomarker Discovery
Machine Learning & AI: scikit-learn, PyTorch, LLMs, RAG, NLP, Statistical Modeling
Data Engineering: Python, R, SQL, Apache Spark, HPC/HTC, Docker, Nextflow, AWS, GCP, Kubernetes, CI/CD