Senior Associate Scientist

Gayatri R. Tiwari

M.S. Biotechnology

Camarillo, California, USA

•**********@*****.*** • Cell: +1-512-***-**** • US Permanent Resident PROFESSIONAL SUMMARY:

Senior Associate Scientist with over 20 years of extensive experience in molecular biology, computational biology and bioinformatics. Expertise in analyzing complex multi-omic data, including NGS, single-cell RNA-seq, bulk RNA-seq, proteomics, and metabolomics. Proficient in R, Python, and Linux with experience in cloud computing. Strong collaborative, analytical, and communication skills, facilitating interdisciplinary research and biomarker discovery in oncology and immuno- oncology.

PROFESSIONAL EXPERIENCE:

Nov 2020- April 2025-Senior Associate Scientist, Cell Biology, Kite Translational Medicine

(Remote) Kite Pharma, Santa Monica, California

• Analysis of NGS data - RNAseq data, Nanostring data, Olink, Metabolomics, CyTOF and sc-RNA seq data using Seurat and Bioturing and other analysis methods focused on cancer biology.

• Correlative analysis of PK PD data with gene expression data, network analysis using R, Spotfire, Python available tools and packages.

• Pathway & Network Analysis: Perform in-depth analysis of biological pathways and networks using tools (e.g., GSEA, IPA, GO, Reactome, String, Cytoscape) and understand cancer biology, product mechanism of action, and therapy resistance.

• Multi-Omics Data Integration: Conducted end-to-end multi-omic biomarker analysis and apply advanced computational and statistical methods to integrate and analyze large-scale datasets from various 'omics' platforms (e.g., genomics, transcriptomics, proteomics, metabolomics) to derive actionable biological insights in Oncology.

• Optimized computational pipelines for NGS data analysis, including QC, alignment, differential expression, and pathway analysis.

• Collaborated across clinical, process development, research and biostatisticians to manage the timely processing of clinical samples and deliver data.

• Prepared high-quality digital reports and presentations to internal and external collaborators accurately, reporting on scientific results.

• Expertise in biological software (e.g. Benchling LIMS, Rosalind, Ingenuity Pathway analysis

(IPA) etc).

Sep 2009-Nov 2020– Research Scientist Associate

Waggoner Centre of Alcohol and Addiction Research

University of Texas at Austin, Austin, TX

Project 1: Single nuclei transcriptome profiling of the human alcohol-dependent brain Project 2: Standardization of 3’ Tag-seq and Quantseq (Lexogen) samples and data analysis pipeline. Project 3: RNA-seq data analysis projects.

Project 4: Integration of Weighted gene co-expression network analysis (WGCNA) to identify potential blood biomarkers in peripheral rat blood during forced abstinence from cocaine self- administration.

Project 5: Repeated measures time-course analysis comparing gene expression profiling of rat blood during cocaine and methamphetamine self-administration followed by forced abstinence. Project 6: Time and Brain dependent changes due to chronic ethanol exposure on mRNA and miRNA.

2

Project 7: Gene expression analysis of alcoholic human blood samples.

• Isolation and preparation of single nuclei for 10X Genomics sequencing. Data analysis with Cell ranger and available pipelines.

• RNA sequencing and core Next generation sequencing data analysis (Illumina platforms). Experience with standard bioinformatics tools and statistical methods such as, but not limited to STAR, bowtie, bwa, samtools, bedtools, DESeq2 etc.

• Standardized and optimized 3’ Tag-seq and Quantseq (Lexogen) pipelines for high- throughput transcriptomic profiling.

• Applied WGCNA and differential expression analysis to identify potential biomarkers in preclinical and clinical samples.

• Total RNA extraction from human, rat, and mouse brain and blood samples.

• Quality control of RNA- Nanodrop, Bioanalyzer, and Tapestation.

• RNA amplification using commercially available kits.

• Real-time PCR – Gene expression, lincRNA, and microRNA assay.

• Automated liquid handling – Qiagilty and epMotion

• Microarray data analysis using R programming.

• Optimization of synaptoneurosomes isolation from human post-mortem brain samples.

• Writing manuscripts and providing material for grants and scientific journals.

• Submitted sequencing data to NCBI repositories (SRA, GEO) and ensured compliance with data sharing regulations.

• Provided bioinformatics expertise for grant applications and peer-reviewed publications. June 2008-Dec 2008 Project Assistant

National Chemical Laboratory (NCL) Plant Tissue Culture Division, Pune, India. Project: Pathway engineering and system biology approach towards the homologous and heterologous expression of high-value phytoceuticals - artemisin. Jan 2008-Mar 2008 Project Assistant

National Chemical Laboratory (NCL) Plant Tissue Culture Division Pune, India. Project: Biotechnological approaches for the improvement of plant species with special reference to pulp and paper.

Oct 2007-Dec 2007 Medical Laboratory Technician

Golwilkar Metropolis Heath Services (India) Private Limited, Pune. Molecular Diagnostics and Microbiology

Jul 2006-Mar 2007- Life Scientist

Randox Laboratories (India) Private Limited, Immunology Division, R&D, Mumbai. Project: Development and Design of Immunoturbidimetric assay kit for detection of a peptide as a disease marker for diagnostic use.

Sep 2004-Mar 2006 - Project Assistant

NATIONAL CHEMICAL LABORATORY, (NCL) Biochemical Engineering Division, Pune, India.

Project: Studies for the development of Affinity membranes for purification and isolation of therapeutic proteins.

TECHNICAL SKILLS:

• Programming Languages: R, Python, Bash

• Operating Systems: Linux, Cloud Computing (AWS, HPC) 3

• Bioinformatics Tools: STAR, Bowtie, BWA, Samtools, DESeq2, Cell Ranger, Seurat, IPA, WGCNA, etc.

• Statistical analysis: Supervised and unsupervised clustering methods for biomarker discovery

• Data Visualization: ggplot2, R packages and Spotfire

• Clinical Biomarker Analysis: Multi-omic integration (RNA-seq, proteomics, metabolomics)

• Regulatory Compliance: Data submission to NCBI repositories (SRA, GEO) LEADERSHIP & PROJECT MANAGEMENT:

• Led cross-functional collaborations between bioinformatics, clinical, and data science teams for biomarker discovery projects.

• Managed data sharing and compliance with institutional and regulatory guidelines.

• Trained and mentored junior scientists in bioinformatics methodologies and best practices.

• Developed documentation for bioinformatics workflows, ensuring reproducibility and efficiency in analysis pipelines.

• Sound knowledge of documentation for Good Laboratory Practice (GLP), which includes preparation of SOP, work instruction sheets, laboratory work files, inventory and purchase documents, maintenance, and validation protocols for instruments.

• Managed lab safety records.

• Managed sample records and inventory.

EDUCATION

2002 – 2004 Master of Science in Biotechnology

Amravati University, India

1999 – 2002 Bachelor of Science in Microbiology

Amravati University, India

PUBLICATIONS

1. Poddar S, Yan J, Tiwari G, Rinchai D, Budka J, Zhang W, Peng W, Salunkhe S, Davis M, Song Q, Beygi S, Miao H, Mattie M, Shen RS, Jacobson CA, Bedognetti D, Filosto S, Neelapu SS. Clinical, tumor and product features associated with outcomes after axicabtagene ciloleucel therapy in follicular lymphoma. J Clin Invest. 2025 Jun 19:e181893. doi: 10.1172/JCI181893. PMID: 40536814.

2. Giulia Cheloni, Dimitra Karagkouni, Yered Pita-Juarez, Daniela Torres, Eleni Kanata, Jessica Liegel, Zachary Avigan, Isabella Saldarriaga, Georges Chedid, Kathrine Rallis, Brodie Miles, Gayatri Tiwari, Jenny Kim, Mike Mattie, Jacalyn Rosenblatt, Ioannis S. Vlachos & David Avigan. Durable response to CAR T is associated with elevated activation and clonotypic expansion of the cytotoxic native T cell repertoire. (2025) Nature Communications.https://doi.org/10.1038/s41467-025-59904-x 3. Yuan Tian, Justin Budka, Frederick L. Locke, Jason R. Westin, Christina To, Gayatri Tiwari, Daqin Mao, Davide Bedognetti, Rhine R. Shen, Jorge Andrade and Simone Filosto. Tumor gene expression signatures associated with outcome in large B−cell lymphoma treated with CD19-directed CAR T−cell therapy (axicabtagene ciloleucel). (2025) Front. Oncol. 15:1519473. doi: 10.3389/fonc.2025.1519473

4. Frederick L. Locke, Simone Filosto, Justin Chou, Saran Vardhanabhuti, Regis Perbost, Peter Dreger, Brian T. Hill, Catherine Lee, Pier L. Zinzani, Nicolaus Kröger, Armando López- Guillermo, Hildegard Greinix, Wangshu Zhang, Gayatri Tiwari, Justin Budka, Francesco M. Marincola, Christina To, Mike Mattie, Marco Schupp, Paul Cheng, Adrian Bot, Rhine Shen, Davide Bedognetti, Harry Miao & Jérôme Galon. Impact of tumor microenvironment on efficacy of anti-CD19 CAR T cell therapy or chemotherapy and transplant in large B cell lymphoma. Nature Medicine (2024). https://doi.org/10.1038/s41591-023-02754-1 4

5. Simone Filosto, Gayatri Tiwari, Justin Szu-Ting Chou. Impact of Tumor Microenvironment on efficacy of Immunotherapy. US Patent 2024/0309428 A1 2024. 6. S Adhikary, AI Bot, JS Chou, S Qinghua, K Speth, GR Tiwari. Predicting adverse events from immunotherapy. US Patent App. 18/168,791

7. Grantham EK, Tiwari GR, Ponomareva O, Harris RA, Lopez MF, Becker HC, Mayfield RD. Transcriptome changes in the nucleus of the solitary tract induced by repeated stress, alcohol dependence, or stress-induced drinking in dependent mice. Neuropharmacology. 2024 Jan 1;242:109768. Doi https://doi.org/10.3390/cells12131695. Epub 2023 Oct 20. PubMed PMID: 37865137; PubMed Central PMCID: PMC10688594. 8. Zhu L, Brown MA, Sims RJ, Tiwari GR, Nie H, Mayfield RD, Tucker HO. Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation. Cells. 2023; 12(13):1695. https://doi.org/10.3390/cells12131695 9. Eric Brenner, Gayatri R. Tiwari, Yunlong Liu, Amy Brock, R. Dayne Mayfield. (2020) Single cell transcriptome profiling of the human alcohol-dependent brain. Human Molecular Genetics. https://doi.org/10.1093/hmg/ddaa038

10. Rajani Maiya, Matthew B. Pomrenze, Thi Tran, Andrea Beckham, Gayatri R. Tiwari, R. Dayne Mayfield, Robert O. Messing (2020). Differential Regulation of Alcohol Consumption and Reward by the Transcriptional Cofactor LMO4. Molecular Psychiatry. 10.1038/s41380- 020-0706-8

11. Sean P. Farris, Gayatri R. Tiwari, Olga Ponomareva, Marcelo F. Lopez, R. Dayne Mayfield, Howard C. Becker (2020). Transcriptome Analysis in Dependent Mice Following Repeated Cycles of Forced Swim Stress and Chronic Intermittent Consumption of Alcohol. Brain Sci. 2020, 10(5), 275; 10.3390/brainsci10050275

12. R. Dayne Mayfield, Li Zhu, Tyler A Smith, Gayatri R. Tiwari, Haley Tucker (2020) The SMYD1 methyltransferase and the skNAC transcription factor contribute to neurodegenerative diseases. Brain, Behavior, & Immunity - Health,100129. https://doi.org/10.1016/j.bbih.2020.100129.

13. Osterndorff-Kahanek EA, Tiwari GR, Lopez MF, Becker HC, Harris RA, Mayfield RD

(2018) Long-term ethanol exposure: Temporal pattern of microRNA expression and associated mRNA gene networks in mouse brain. PLoS ONE 13(1): e0190841. 14. Most, Dana & A. Salem, Nihal & Tiwari, Gayatri & A. Blednov, Yuri & Mayfield, Roy & Harris, Robert. (2018). Silencing synaptic MicroRNA 411 reduces voluntary alcohol consumption in mice. Addiction Biology. 10.1111/adb.12625. 15. Osterndorff-Kahanek EA, Becker HC, Lopez MF, Farris SP, Tiwari GR, Nunez YO, et al.

(2015) Chronic Ethanol Exposure Produces Time and Brain Region-Dependent Changes in Gene Coexpression Networks. PLoS ONE 10(3):e0121522 16. Adikane HV, Iyer GJ. (2013) Chemical modification of ethyl cellulose-based highly porous membrane for the purification of immunoglobulin G., Appl Biochem Biotechnol., 169(3):1026-38.

17. Lewohl JM, Nunez YO, Dodd PR, Tiwari GR, Harris RA, Mayfield RD. (2011) Up- regulation of MicroRNAs in Brain of Human Alcoholics, Alcoholism: Clinical and Experimental Research, 35, 1928–1937.

18. Tiwari GR, Fox RG, Stutz SJ, Cunningham KA, Mayfield RD. Gene co-expression networks in the blood are differentially altered during forced abstinence from cocaine self- administration in rats. (Unpublished)

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