Kalpana Pillai

• Individualized Therapies:
• Led the design, verification and validation of WES and RNA Seq workflows to support mRNA vaccine production process.
• Developed and implemented a novel targeted sequencing workflow that consolidated separate WES and RNA Seq into a unified platform. Key contribution was able to demonstrate that FFPE alone are sufficient for neoantigen prediction leading to significant reductions in TAT and cost
• Cell and Gene Therapy:
• Provided pre-IND bioanalytical support for a wide range of cell and individualized therapy products. Implementation of high throughput qPCR based assays for validation of signature genes (150) to monitor end to end stem cell differentiation process. Pioneered the first WGS using long read seq technology to assess the genomic integrity of the cell therapy products and supported the development of analysis pipeline with cross -functional team. Analytical assays to support process understanding in various stages of stem cell differentiation.
• Reviewing of genomics technical portions for regulatory submission.
• Collaborating with AI/ML team for the integration of various analytical/ process parameters to assess the key predictors for the successful manufacturing of the DP.
• Managing CRO/ CDMOS for WGS and Bulk RNA seq needs for the cell therapy program.
• Introduced high throughput cost effective Single cell sequencing method and received 'Raising Star' award.

• Designed innovative scalable SEC based EV isolation system optimized for recovery from cell culture media.
• Developed EV sub-population enrichment strategies using specific surface markers (LICAM for neuronal EVs isolation)
• Established a rapid miRNA detection method from crude EV extracts, minimizing processing time.

Skills: Antibody Array, ELISA, small RNA sequencing, Size exclusion chromatography

• Isolated exosomal RNA from diverse biofluids; and performed RNA QC to ensure integrity and suitability for downstream analysis.
• Evaluated and optimized RNA isolation methods, small RNA-seq library prep kits, and Illumina sequencing platforms improving reproducibility and data quality.
• Designed and validated primers for the biomarkers identified via NGS pipeline for biomarker discovery.
• Directed and managed 300+ RNA-Seq projects (over 1000 clinical samples), overseeing experimental design, platform selection, partial library prep, sequencing, troubleshooting and data analysis.
• Maintained accurate project documentation, case logs, and tracking metrics, ensuring accuracy and compliance with quality standards.
• Provided training and technical guidance to global customers and junior scientist on RNA Seq data analysis using proprietary pipeline.

Skills: Project Management, People Leader, Budgeting, SME, CDMO management, Business Development.

• Evaluated methods for the isolation of exosome RNA from variety of biofluids for NGS analysis.
• Performed QC measures to screen the samples for library prep.
• Provided scientific and technical support to the customers on a broad range of products in the area of exosome research, gene expression tools, gene expression regulation, non-coding RNAs, and genome engineering products.
• Developed content, and presented scientific and technical webinars and seminars for academic and industrial partners. Launched presale support program for worldwide distributors.
• Organized and led exosome hands-on training workshop, presented SBI products portfolio for exosome researchers.
• Collaborated with R&D, product development and marketing teams to understand customers’ needs and requirements to improve current products portfolio.
• Collaborated with production team to troubleshoot existing products and to establish quality control metrics.
• Established and led collaborations with academic labs to evaluate new products (alpha testing, beta testing).
• Streamlined SOPs with quality control and production team.

Skills: Genetic engineering, Lentiviral, minicircle production, piggybac and CRISPR/Cas9 Systems.

• Developed a course curriculum for the Applied Health Education program.
• Taught Anatomy and Physiology, Systems Biology, Advanced Biochemistry and Molecular Biology courses

• Designed and executed cellular and molecular biology studies to investigate the role of exosomes in placental development and preeclampsia, uncovering mechanistic insights into maternal-fetal communication.
• Identified the exosomal miRNAs, critical for maternal- fetus signaling during normal pregnancy and in preeclampsia.
• Worked with Instrumentation group and informatic group to optimize the liquid handling system (Tecan) for automation.
• Investigated the therapeutic potential of modified heparins (LMWH) for the prevention preeclampsia in clinical trial samples and matched tissues; developed novel cell-based assays to evaluate angiogenesis and therapeutic response.
• Established a time-lapse microscopy-based cell tracking method to assess angiogenic processes, enabling dynamic analysis of cell behavior in vitro.
• Presented research at international conferences and won best presentation awards.
• PIs: Dr. John Kingdom and Dr. Jeff Wrana

Skills: placental explant culture, angiogenesis, analytical UC, NTA, IF, tube formation assay, cell based assays, sequencing.

• Designed and executed experiments to explore the role of miRNA in CAF.
• Developed a panel of RT-qPCR sensitive assays to quantify mouse contamination in the primary cells from xenografts to achieve higher sequencing coverage and to improve downstream genetic analysis.
• Performed PTEN methylation analysis on FFPE tumor samples via bisulfite conversion followed by gene specific PCR amplification, followed by SEQUENOM analysis.
• Designed and executed Copy Number Variation Analysis using Microarrays to identify genomic alterations in CAF.
• Validated 11 gene prognostic signatures in CAF-NF samples and NSCLC cell lines, characterized their function using cell attachment and gel contraction assays.
• Investigated miRNA-mRNA interactions to define mechanisms of gene regulation in NSCLC, demonstrating their role in tumor biology and therapeutic targeting.
• Studied prognostic signature genes for therapeutic applications, evaluating drug treaments (estradiol, raloxifene, fulvestrant) targeting ESR2 using shRNA lentiviral clones.
• Designed stimulation assays to identify the CAF specific signaling pathways in NSCLC.
• Supervised and mentored 2 graduate students and presented research findings at international conferences.
• PIs: Dr. Ming Sound Tsao and Dr. Igor Jurisica

skills: qPCR, WB, ELISA, primary cell culture, speroid culture, genome engineering, microscopy, cell based assays- Incucyte, xCelligenece, IHC, flow cytometry.

• Evaluated the association of Copy Number Variations in serum samples derived from Autism Spectrum Disorder using Microarray platform and the CNV analysis was performed using Golden Helix.
• Targets were validated in patient samples using TaqMan assays.
• Mentor: Dr. Lakshmi Muthuswamy