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Deepali Kundnani

Computational Biologist with a strong foundation in molecular biology and over eight years of experience applying multi-omics approaches to uncover disease-related insights. I specialize in developing customized bioinformatics workflows, utilizing high-performance computing, and implementing advanced statistical techniques to drive innovation and discovery in biomedical research.

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About me

During my Ph.D. journey at GeorgiaTech, my focus has been on discovery and validation of ribonucleotide incorporation in human genome as a novel epigenomics phenomena. I have also discovered unique ribonucleotide embedment features in associated rare genetic disorder mutants, studied enzyme associations in large public datasets and developed tailored software packages. For the same work, I have been awarded Mark Borodovsky Prize for Excellence in Bioinformatics at Georgia Institute of Technology.

Before coming to Georgia Tech, I have developed, optimized and validated multiplex Immuno Assays for protein biomarkers in patient blood samples for early detection of multiple cancers, fortunate to have worked with amazing doctors and scientists at Hanash Lab in MD Anderson Cancer Center. The incredible effort in diagnostics of Lung Cancer Risk Assessment Biomarkers has been recognized by the institution.

Career Highlights

  • Led pioneering research projects in bioinformatics, developing multi-omics association frameworks for linking DNA features to functional outcomes.
  • Secured > $1 million in grants by providing hypothesis based on preliminary analysis.
  • Co-authored 7+ papers in GeorgiaTech and 9+ papers in MD Anderson
  • Proficient in developing and maintaining bioinformatics pipelines, including data modeling, feature selection, and ML-driven survival analysis.
  • Extensive experience create SOPs for CLIA labs and FDA approvals, in clinical trails and working with proprietary materials.
  • Experience mentoring and training students in both molecular biology techniques and computational biology.
Interests
  • Biomarker discovery
  • Precision Medicine
  • Multi-omics Integrated research
  • Clinical Cancer Research
  • Aging associated epigenetic phenomena
  • Immune, brain and gut microbiome traid

Awards and Prizes

Student Government Association Conference Award 2024
Georgia Institute of Technology
Mark Borodovsky Prize for Excellence in Bioinformatics 2023
Georgia Institute of Technology
US National Science Foundation Conference Award 2021
The 26th Annual Meeting of the RNA Society
Performance Excellence Award 2029
University of Texas at MD Anderson Cancer Center
Jones NAS Biological Sciences Scholarship 2014 - 2015
University of Houston – Clear Lake
Third Prize in National Technical Paper Presentation 2010
Institute of Electrical and Electronics Engineers (IEEE) committee in India

Journey

Research and Teaching Assistant 2019 - 2025
Georgia Institute of Technology, Atlanta, GA
  • Led pioneering research projects in bioinformatics, developing multi-omics association frameworks for linking DNA features to functional outcomes.
  • Applied strand-specific sequencing analytics to dissect disease-associated mutational effect on replication.
  • leveraged public databases for pan-cancer analyses across 35+ cancer types, linked basic science (ribonucleotide biology) to clinical insights (cancer proliferation, cell cycle)
  • Secured > $1 million in grants by providing hypothesis based on preliminary analysis.
  • Developed novel software packages and maintained, and updated Lab's pipelines.
  • Showcased research findings at international conferences, mentored 4+ students
  • Lectured, created modules and graded courses with students ranging from 20-250
  • Provided hands on training to 15+ students on linux based cloud computing enviroment, python and R scripts
Ph.D in Bioinformatics 2019 - 2025
Georgia Institute of Technology, Atlanta, GA
  • Designed modular frameworks for web-based biomedical applications
  • Data modeling for better feature selection
  • Deployed ML-driven survival analysison longitudinal clinical-genomic datasets
  • Standardized pipelines for real-time outbreak analytics using public health datasets (CDC)
  • Invited and co-hosted well-known cancer researchers to address Georgia Tech community
  • Particapted in Georgia Tech Bioinformatics PhD orientation T-short design panels
  • Founding Student Committee Member, Molecular BioMedical (MBM) Cancer Talk Series
  • Volunteered a a secretary and President at student organizations
Research Assistant II 2015 - 2019
MD Anderson Cancer Center
  • translational cancer research: optimized/validated immune/multiplex assays for multiple cancers and FDA approval.
  • Set up CLIA-certified patient blood sample processing lab for trials.
  • DNA vaccines, propriety antigen and antibody production.
  • Data handling and batch normalizaiton for >100 patient sample protein levels
  • Integrated multiomics data (genomic, transcriptomic, mass spectrometry) to advance biomarker discovery.
Lab Intern Jan 2015 - May 2015
Georgia Institute of Technology, Atlanta, GA
  • Optimized SOPs for antigen production in mammalian cells.
  • Monoclonal antibody screening, purification, and QC for ovarian cancer ELISA kits.
  • Supported FDA audits.
Teaching Assistant Sep 2014 - Dec 2014
University of Houston - Clear Lake
  • Liaison between students and professor for applied biotechnology projects and assignments.
  • Trained other TAs for both basic and advanced molecular biology labs.
M.S. Molecular Biotechnology 2013 - 2015
University of Houston Clear-Lake, Houston, TX
  • Jones NAS Scholarship for merit, 2013-2014 academic year
  • Good GPA, Experience in lab experiments and training.
  • Independent Resarch - Human asthma lung cDNA library screening employing a yeast two-hybrid system to detect protein interaction with iNOS.
  • Capstone - Cloning techniques for high yield productivity of monoclonal antibodies in mammalian cells.
  • Activities and societies: SLICE, Welcome Back Bash, Strictly speaking
Research and Teaching Assistant 2012-2013
Usha Biotech
  • Trained students in Mammaliam Cell culture and Molecular cloning
  • DNA vaccines, propriety antigen and antibody production.
  • Data handling and batch normalizaiton for >100 patient sample protein levels
  • Integrated multiomics data (genomic, transcriptomic, mass spectrometry) to advance biomarker discovery.
Trainee Sep 2011 - Apr 2012
S.L. Raheja Hospital
  • Researched clinical data on stem cell therapy for diabetic foot complications.
  • conducted patient eligibility assessments.
  • developed statistical standards.
B.E. Biotechnology 2008 - 2012
University Mumbai - TSEC
  • Thrid Prize - IEEE Techical Paper Presentation
  • Attended seminars and training for clinical research and molecular biotechnology.
  • Organizing Committee member and speaker for workshops for multiple events.
  • Mendelian genetics, Molecular Cloning, Immunology, Biochemistry, Biotechnology, Protein Enginnering
  • DNA and protein isolations and titration experiments
  • Engineering aspects in general - Applied Phys & Chem
  • Large scale fermentations and Chromatographies

Selected Publications

(2025). Human nuclear ribomes reveal DNA-embedded ribonucleotides as a novel epigenetic layer.in preparation.
(2025). Characterization of a new mutation of mitochondrial ND6 gene in hepatocellular carcinoma and its effects on Complex I.Sci Reports. PDF Code
(2024). Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of Saccharomyces cerevisiae.IScience. PDF Code
(2022). FeatureCorr: An R package to study feature correlations aided with data transformation for sequencing and microarray data.IScience. PDF Code
(2020). NFATc Acts as a Non-Canonical Phenotypic Stability Factor for a Hybrid Epithelial/Mesenchymal Phenotype.Frontiers in Oncology. PDF Impact
(2018). Assessment of Lung Cancer Risk on the Basis of a Biomarker Panel of Circulating Proteins.JAMA Oncology. PDF News

All Publications

Skills

  • Python, R, C++, Java
  • Statistical Analysis
  • Machine Learning, Deep Learning
  • Cloud Computing (AWS)
  • Next Gen and Long read sequence analysis
  • Multi-omics integration and association
  • Workflow Management (SnakeMake)
  • Data visualization

Contact

Feel free to reach incase of questions, collaborative ideas, or just want to say hello!




deepali.kundnani@gatech.edu

(+1) 832-787-2815

855 W Peachtree Street NE, Atlanta, GA 30308