Ashwini Sunkavalli
Boston,MA
Summary
Quantitative molecular biologist with extensive experience in university and hospital-based research laboratories. Skilled in integrating rigorous wet-lab experimentation with transcriptomic and network-informed data analysis to study transcriptional regulation and stress responses. Experienced in designing multifactor RNA sequencing experiments, performing statistical analysis in R, and translating complex datasets into biologically testable hypotheses.
Overview
15
15
years of professional experience
Work History
Graduate Researcher
Tufts University School of Medicine
01.2016 - 01.2025
- Conducted an integrated wet-lab and quantitative transcriptomic study investigating transcriptional regulation and stress adaptation in Neisseria gonorrhoeae.
- Designed and executed multifactor, time-resolved RNA sequencing experiments under iron-replete and iron-depleted conditions
- Performed RNA sequencing differential expression and temporal analysis across growth phases
- Applied gene co-expression and network-informed analyses to identify regulators coordinating iron homeostasis, oxidative stress, and metabolic adaptation
- Interpreted coordinated transcriptional programs at the module and operon level
- Linked transcriptomic structure to phenotype using growth curves, colony-forming unit viability assays, oxidative stress tolerance assays, and epithelial cell invasion assays
Research Associate II
University of Massachusetts Medical School
01.2014 - 01.2016
- Investigated Influenza A virus replication, RNA biology, and viral fitness under antiviral pressure
- Performed viral mutagenesis, plaque assays, strand-specific quantitative polymerase chain reaction assays, and replication kinetics analyses
- Designed primers and quantitative assays to distinguish viral RNA species during infection
- Contributed to experimental design and data interpretation in virology and RNA biology projects
Lead Research Technician – Cancer Genomics
Dana-Farber Cancer Institute
01.2010 - 01.2014
- Supported large-scale whole-exome and whole-genome sequencing projects in cancer genomics
- Managed high-throughput next-generation sequencing workflows including library preparation, normalization, and quality control
- Contributed to studies published in Nature Genetics, JAMA Oncology, and The Lancet Oncology
- Trained staff and collaborators on sequencing workflows and quality standards
Education
Master of Science (MS) - Genetics, Molecular & Cell Biology
Master of Science (MS) - Biotechnology
Bachelor of Science - Biotechnology
Master of Science - Cell And Molecular Biology
Skills
Laboratory Research Techniques
DNA/RNA isolation and quality control; strand-specific RNA sequencing library preparation
Polymerase chain reaction and primer design; quantitative polymerase chain reaction–based quantification
Bacterial growth, viability, and oxidative stress assays
Mammalian cell culture and viral infection assays; multiplicity of infection optimization
Epithelial cell adherence and invasion assays
Transcriptomics & Quantitative Analysis
RNA sequencing differential expression and time-course analysis
Network-informed interpretation of coordinated gene expression
Identification of regulatory structure using gene co-expression patterns
Module-level and pathway-level analysis (KEGG, GO)
Operon-level analysis and cis-regulatory motif discovery (MEME Suite)
R for statistical and transcriptomic analysis, network analysis (DESeq2, ggplot2)
Network visualization and analysis tools (igraph, Gephi)
High-performance computing environments
PEER-REVIEWED PUBLICATIONS
- Wang A, Fairhurst AM, Liu K, Wakeland B, Barnes S, Malladi VS, Viswanathan K, Arana C, Dozmorov I, Singhar A, Du Y, Imam M, Moses A, Chen C, Sunkavalli A, Casco J, Rakheja D, Li QZ, Mohan C, Clayberger C, Wakeland EK, Khan S. KLF13 promotes systemic lupus erythematosus pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes. Communications Biology. 2024. doi:10.1038/s42003-024-07099-0.
- Sunkavalli A, McClure R, Genco CA. Molecular regulatory mechanisms drive emergent pathogenetic properties of Neisseria gonorrhoeae. Microorganisms. 2022;10(5):922. doi:10.3390/microorganisms10050922.
- Papadopoulos G, Berland R, Sunkavalli A, Coats SR, Darveau RP, Attardo CAG. Microbial lipid A remodeling controls cross-presentation efficiency and CD8 T-cell priming by modulating dendritic cell function. Infection and Immunity. 2021. doi:10.1128/IAI.00335-20.
- McClure RS, Sunkavalli A, Balzano PM, Massari P, Cho C, Nauseef WM, Apicella MA, Genco CA. Global network analysis of Neisseria gonorrhoeae identifies coordination between pathways, processes, and regulators expressed during human infection. mSystems. 2020;5(1):e00729-19. doi:10.1128/mSystems.00729-19.
- Campbell JD, Lathan C, Sholl L, Ducar M, Vega M, Sunkavalli A, Lin L, Hanna M, Schubert L, Osarogiagbon R, Van Hummelen P, Meyerson M, MacConaill L. Comparison of prevalence and types of mutations in lung cancers among Black and White populations. JAMA Oncology. 2017;3(6):801–809. doi:10.1001/jamaoncol.2016.6108.
- Pastor-Garcia A, González-Barca E, Colomo L, Domingo-Domenech E, Sunkavalli A, et al. Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma. The Lancet Oncology. 2015. doi:10.1016/S1470-2045(15)00169-2.
- Brastianos PK, Taylor-Weiner A, Manley PE, Jones RT, Dias-Santagata D, Thorner AR, Sunkavalli A, et al. Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas. Nature Genetics. 2014. doi:10.1038/ng.2868.
- Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Ozduman K, Avşar T, Li J, Murray PB, Henegariu O, Sunkavalli A, et al. Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. Nature Genetics. 2013. doi:10.1038/ng.2526.
Timeline
Graduate Researcher - Tufts University School of Medicine
01.2016 - 01.2025
Research Associate II - University of Massachusetts Medical School
01.2014 - 01.2016
Lead Research Technician – Cancer Genomics - Dana-Farber Cancer Institute
01.2010 - 01.2014
Tufts University School of Medicine - Master of Science (MS), Genetics, Molecular & Cell Biology
University of Texas at Dallas - Master of Science (MS), Biotechnology
SRM University - Bachelor of Science, Biotechnology
Tufts University - Master of Science, Cell And Molecular Biology