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Deepali L. Kundnani

Postdoctoral Researcher, Biomedical AI

University of New Mexico Comprehensive Cancer Center, Albuquerque, NM · dkundnani@salud.unm.edu · dkundnani.bio · Google Scholar · github.com/DKundnani

Education

Ph.D. in Bioinformatics Aug 2019 – Jul 2025

Georgia Institute of Technology · Atlanta, GA

Minor in Machine Learning · GPA 4.00 / 4.00.
Thesis: distribution and features of ribomes, the genome-wide embedment of ribonucleotides in eukaryotic genomes.
Mark Borodovsky Prize for Excellence in Bioinformatics.

M.S. Molecular Biotechnology Aug 2013 – May 2015

University of Houston – Clear Lake · Houston, TX

GPA 3.88 / 4.00 · Jones NAS merit scholarship.
Independent research: yeast two-hybrid screen of an asthma-patient lung cDNA library for iNOS interactions.
Capstone: high-yield monoclonal antibody production in CHO cells.

B.E. Biotechnology Aug 2008 – May 2012

Thadomal Shahani Engineering College · University of Mumbai, India

Third Prize, IEEE national technical paper presentation.
Thesis: stem cell therapy and wound care for diabetic foot complications.

Experience

Postdoctoral Researcher Apr 2026 – Present

University of New Mexico Comprehensive Cancer Center · Albuquerque, NM

Developing interpretable AI/ML models integrating EHR, genomics, and multi-omics data for cancer risk prediction.
Building longitudinal EHR phenotypes, linking clinical variables with large-scale genomic cohorts.
Contributing to foundation-model research for variant interpretation and tumour genome classification.
Collaborating across clinical oncology, statistical genetics, and genetic counselling.

AI Strategic Project Advisor, STEM Research Apr – Jul 2026

Turing · Remote

Advised a high-priority programme spanning 200+ subject matter experts, tied to $1M+ revenue.
Consulted on delivery planning and execution of custom dataset generation for frontier LLM clients.
Oversaw hiring, onboarding, and weekly targets to hold quality and sign-off timelines.

AI Evaluation Team Lead, STEM Scientific Coding Dec 2025 – Mar 2026

Turing · Remote

Led and trained teams of 10–30 SMEs across bioinformatics, computer science, and machine learning.
Built a cross-domain STEM expert team from scratch across physics, chemistry, maths, biology, and scientific coding.
Designed rubrics, failure-mode taxonomies, SOPs, QA systems, and SME calibration workflows.
Contributed to proofs-of-concept, pilots, and large-scale multimodal HLE data generation.
Built reviewer guidelines, trainer materials, unit-testing protocols, and single-ground-truth factor analysis.

Bioinformatics Subject Matter Expert & Reviewer Nov 2025

Turing · Remote

Analysed LLM transcripts to identify model breakage patterns in bioinformatics reasoning.

Graduate Research and Teaching Assistant Aug 2019 – Jul 2025

Georgia Institute of Technology, Storici Lab · Atlanta, GA

Storici Lab · Aug 2020 – Jul 2025
Led research on a novel epigenetic layer in the human genome, analysing multi-omics data to uncover regulatory roles.
Published novel sequence motifs in a neuro-immune genetic disorder tied to DNA replication and repair.
Analysed enzyme expression and copy number across CCLE and TCGA in 33+ cancer types, producing an R package for multi-omics integration.
Contributed the preliminary analysis behind a $1M grant.
Conceptualised ribose-seq normalisation and ribonucleotide enriched zones (REZ).
New data-cleaning protocols for ribose-seq NGS libraries, doubling pattern-recognition accuracy.
Co-founded the Molecular BioMedical (MBM) Cancer student committee.
Mentored 4+ early-career bioinformaticians; trained 15+ students in Linux, Python, and R.
Presented at 8+ national and international conferences.
Rotational student · Aug 2019 – Jul 2020
Identified differentially methylated regions in 900+ HIV+ patients (Yale VACS); modelled survival with kNN and SVM.
Led genome assembly and comparative genomics teams tracing foodborne outbreak sources from CDC data.
Differential expression and pathway analysis in lung cancer lines across wild-type and multiple p53 mutants.
Lectured and graded courses for 20–250 students.

Research Assistant II Oct 2015 – Jul 2019

MD Anderson Cancer Center, Hanash Lab · Houston, TX

Optimised and validated immunoassays for lung, pancreatic, colon, and ovarian cancer biomarkers.
Developed auto-antibody assays targeting alternative-splicing products and exosomes.
Processed patient blood in a CLIA-certified lab for double-blind early lung and breast cancer trials.
Batch normalisation and missing-data handling for cohorts of 300–7,000+ samples.
Validated novel protein markers in epithelial–mesenchymal transition (EMT).
Managed large-scale DNA vaccine production and in-house antigen/antibody production.
Integrated genomic and transcriptomic data with in-house mass spectrometry.

Laboratory Intern Jan – May 2015

AnshLabs · Houston, TX

Led production of highly sensitive antigens in mammalian cell lines under GMP guidelines; supported ISO and FDA audits.
Screened, purified, and QC’d monoclonal antibodies from hybridoma clones for commercial ovarian cancer ELISA kits.

Graduate Teaching Assistant Sep – Dec 2014

University of Houston – Clear Lake · Houston, TX

Liaison between students and faculty on applied biotechnology projects and course queries.
Trained teaching assistants to set up basic and advanced molecular biology labs.

Research and Teaching Assistant Sep 2012 – Jul 2013

Usha Biotech Ltd. · Hyderabad, India

Tested proprietary vectors including the patented CELL EXPRESS-100™, using an eGFP reporter for stable antibody expression in CHO-K1 cells.
Molecular cloning of custom plasmid vectors and transfection optimisation supporting a patent filing.
Selected transfected pools and clones by fluorescence-activated cell sorting.
Trained students in mammalian cell culture.

Trainee May 2011 – Apr 2012

S. L. Raheja Hospital (a Fortis Associate) · Mumbai, India

Reviewed literature and monitored clinical study and toxicology reports on stem cell therapy for diabetic foot complications.
Screened patients against inclusion criteria and supported biochemical testing.
Developed statistical standards for treatment efficacy from wound-closure measurements.

Publications

2026 Kundnani, D. L., Lee, Y., Yang, T., Warner, T. P., Martinez-Figueroa, F., Channagiri, T., Xu, P., … & Storici, F. Human nuclear ribomes reveal DNA-embedded ribonucleotides as epigenetic modulators. Cell
2026 Niu, X., Kundnani, D. L., Dicome, M., Tafoya, L., Song, L., Mamedov, M. R., Liu, X. S. & Sahu, A. Tumor γδ T-cell abundance is associated with favorable cancer treatment outcomes. bioRxiv (preprint)
2025 Moalic, Y., Reveil, M., Kundnani, D. L., Balachander, S., Yang, T., … Storici, F. & Henneke, G. Genome-wide ribonucleotide detection in Archaea. Nucleic Acids Research
2025 Bazzani, V., Kundnani, D. L., Redin, M. E., Agostini, F., Corso, A., … Storici, F. & Vascotto, C. Characterization of a new mutation of the mitochondrial ND6 gene in hepatocellular carcinoma. Scientific Reports
2024 Kundnani, D. L., Yang, T., Gombolay, A., Mukherjee, K., Newnam, G., Meers, C., … & Storici, F. Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutières syndrome ortholog mutants of S. cerevisiae. iScience
2024 Yang, J., Sun, M., Ran, Z., Yang, T., Kundnani, D. L., Storici, F. & Xu, P. rNMPID: a database for riboNucleoside MonoPhosphates in DNA. Bioinformatics Advances
2023 Xu, P., Yang, T., Kundnani, D. L., Sun, M., Marsili, S., Gombolay, A. L., … Storici, F. Light-strand bias and enriched zones of embedded ribonucleotides in the human mitochondrial genome. Nucleic Acids Research
2021 Kundnani, D. & Storici, F. FeatureCorr: an R package to study feature correlations for sequencing and microarray data. Software Impacts
2021 Marsili, S., Tichon, A., Kundnani, D. & Storici, F. Gene co-expression analysis of human RNASEH2A reveals networks in DNA replication, damage response, and cell cycle. Biology
2020 Ostrin, E. J., Bantis, L. E., Wilson, D. O., Patel, N., Wang, R., Kundnani, D., … & Hanash, S. M. Contribution of a blood-based protein biomarker panel to the classification of indeterminate pulmonary nodules. Journal of Thoracic Oncology
2020 Subbalakshmi, A. R., Kundnani, D., Biswas, K., Ghosh, A., Hanash, S. M., Tripathi, S. C. & Jolly, M. K. NFATc acts as a non-canonical phenotypic stability factor for a hybrid epithelial/mesenchymal phenotype. Frontiers in Oncology
2020 Capello, M., Fahrmann, J. F., Rios Perez, M. V., Vykoukal, J. V., Irajizad, E., … & Hanash, S. M. CES2 expression in pancreatic adenocarcinoma is predictive of response to irinotecan and is associated with type 2 diabetes. JCO Precision Oncology
2020 Kobayashi, M., Katayama, H., Irajizad, E., Vykoukal, J. V., Fahrmann, J. F., Kundnani, D. L., … & Hanash, S. M. Proteome profiling uncovers an autoimmune response signature reflecting ovarian cancer pathogenesis. Cancers
2019 Capello, M., Vykoukal, J. V., Katayama, H., Bantis, L. E., Wang, H., Kundnani, D. L., … & Hanash, S. M. Exosomes harbor B cell targets in pancreatic adenocarcinoma and exert decoy function against complement-mediated cytotoxicity. Nature Communications
2018 Jia, D., George, J. T., Tripathi, S. C., Kundnani, D. L., Lu, M., Hanash, S. M., … & Levine, H. Testing the gene expression classification of the EMT spectrum. Physical Biology
2018 Guida, F., Sun, N., Bantis, L. E., Muller, D. C., Li, P., Taguchi, A., … & Hanash, S. M. Assessment of lung cancer risk on the basis of a biomarker panel of circulating proteins. JAMA Oncology
2018 Fahrmann, J. F., Bantis, L. E., Capello, M., Scelo, G., Dennison, J. B., … & Hanash, S. M. A plasma-derived protein-metabolite multiplexed panel for early-stage pancreatic cancer. JNCI
2016 Capello, M., Bantis, L. E., Scelo, G., Zhao, Y., Li, P., Dhillon, D. S., … & Hanash, S. M. Sequential validation of blood-based protein biomarker candidates for early-stage pancreatic cancer. JNCI

Conference presentations

2024Aicardi-Goutières syndrome: an RNase H2C mutation mimics the ribonucleotide patterns of an RNase H2B PIP-box mutation. Georgia Tech School of Biological Sciences retreat. Full funding
2024Aicardi-Goutières syndrome: RNase H2C mutation mimics RNase H2B PIP-box patterns. FASEB Conference, Florida. Travel funding
2024Aicardi-Goutières syndrome: RNase H2C mutation mimics RNase H2B PIP-box patterns. MCBIOS Conference, Georgia. Full funding
2024Aicardi-Goutières syndrome: RNase H2C mutation mimics RNase H2B PIP-box patterns. Bio-IT World Conference & Expo, Boston. Funded by Combinatics Inc.
2024CellKb: cell-type markers for annotation and discovery in scRNA-seq datasets. Bio-IT World Conference & Expo, Boston. For Combinatics Inc.
2023CellKb: cell-type markers for annotation and discovery in scRNA-seq datasets. Bio-IT World Conference & Expo, Boston. For Combinatics Inc.
2023Ribonucleotide incorporation in AGS-orthologous mutants of yeast RNase H2 subunits. Bio-IT World Conference & Expo, Boston. Funded by Combinatics Inc.
2022Effect of AGS-orthologous mutations on ribonucleotide incorporation in S. cerevisiae. RNASEH Conference, Maryland
2022Expression correlation of RNASEH2A in cancer datasets. Global Virtual Congress on Cancer Research & Drug Development
2021Expression correlation and copy number alteration prevalence of human RNASEH2A in cancer. 26th Annual Meeting of the RNA Society. NSF Conference Award
2011Genetic algorithms. IEEE-EMBS National Technical Paper Presentation, Mumbai. Third Prize
2009Water purification systems. BIOZEAL, Mumbai

Invited talks and lectures

2025Bioinformatics, Ribose-Map, and the PACE cloud computing server. Research Project Laboratory (BIOL-4590), Georgia Tech
2024Distribution of ribonucleotides embedded in the nuclear genome of multiple human cell types. MBM Seminar Series, Georgia Tech
2024Distinct features of ribonucleotides in AGS-ortholog mutants in yeast. MBM Seminar Series, Georgia Tech
2023The role of RNA in DNA repair and modification. RNA Biology and Biotechnology (BIOL-4560/8560), Georgia Tech
2023Bioinformatics and an introduction to the Ribose-Map toolkit. Research Project Laboratory (BIOL-4590), Georgia Tech
2020Data preprocessing and dimensionality reduction in biomedical and clinical settings. Biostatistics (APPH-6225), Georgia Tech
2019DNA sequencing and phylogenetic analysis. Genetics Lab (BIOL-2345), Georgia Tech
2010Time management. Management course, University of Mumbai

Awards

2024Student Government Association Conference Award. Georgia Institute of Technology
2023–24Bio-IT World Conference Registration Funds. Combinatics Inc.
2023Mark Borodovsky Prize for Excellence in Bioinformatics. Georgia Institute of Technology
2021US National Science Foundation Conference Award. 26th Annual Meeting of the RNA Society
2019Performance Excellence Award. UT MD Anderson Cancer Center
2014–15Jones NAS Biological Sciences Scholarship. University of Houston – Clear Lake
2010Third Prize, National Technical Paper Presentation. IEEE, India
2008Top Student Honour, National Standard Examination. Top 10% nationally, India

Leadership and service

2022–25SKY at Georgia Tech: President, then Advisor Raised >$20,000; well-being programmes reaching 1,000+ students.
2021–24Research mentor, 5 B.S./M.S. bioinformatics students Now at Mayo Clinic, Penn State, Moderna, and UT Southwestern.
2022–24Founding committee member, MBM Cancer Talk Series Georgia Tech's molecular biomedical seminar series.
2021Grant writing, Storici Lab Contributed to a $1M award from the W. M. Keck Foundation.
2023Emerging Leaders Advisory Board Advised Georgia Tech's VP of Student Engagement.
2020–22Asha for Education, Atlanta: Secretary Ran a half marathon raising funds for children's education in India.

Skills

Languages & toolsPython, R, SQL, C++, Java, Bash, Git, Snakemake

AI & machine learningPyTorch, Interpretable ML, Foundation models, LLM evaluation, Variational autoencoders, scanpy, Survival analysis (kNN, SVM), Deep learning

Sequencing analysisNext-generation sequencing, Long-read sequencing, ribose-seq, Single-cell RNA-seq, Genome assembly, Comparative genomics

Data & infrastructureMulti-omics integration, EHR phenotyping, High-performance computing, Cloud computing (AWS), Batch normalisation, Data visualisation

LaboratoryMultiplex immunoassays, Molecular cloning, Mammalian cell culture, ELISA development, FACS, CLIA/FDA-compliant SOPs

CertificationsAWS Generative AI (2025), SQL for Data Science, CLIA, MD Anderson (2018), R Programming, Coursera (2017), Data Scientist Toolbox (2016), ISO 9001:2008 (2015)