Brian Thompson Email & Phone Number

San Diego, Ca, Us

San Diego, California, United States

Lead data scientist for the analysis of large and diverse translational datasets from clinical trials investigating oncolytic virus and tumor infiltrating lymphocyte adoptive cell therapy (TIL ACT). Experienced with writing well-documented and reproducible code, SOPs and constructing databases.

Conducting my postdoctoral research on melanoma and immunotherapies in the SciOmics Laboratory: • Writing pipelines (e.g., shell scripts, R) for the analysis of ATAC-, ChIP-, bulk RNA-seq and scRNA-seq data. • Developed a pseudoalignment-based RNA-seq data analysis pipeline. • Analyzing publicly available scRNA-seq datasets from tumor infiltrating lymphocytes with Seurat for the presence of a novel CD4+ population. • Conducted analysis of ATAC- and RNA-seq data from a multitude of clinical trials, including those with a paired design. • Analyzing CITE-seq datasets from healthy donor and melanoma patient PBMCs.• Design, direct (a team of 3 researchers) and analyze flow cytometry and other molecular experiments on human primary T cells. • Investigating novel human T cell phenotypes induced by the pleiotropic cytokine IL-10.• Designing and leading investigations of syngeneic mouse models of melanoma. • Performed the first detailed multiomic analysis of TIL ACT product generated from human melanoma patients (first author manuscript in preparation). Technical Experience:• Advanced analysis of NGS data (i.e., ATAC-seq, bulk/single-cell RNA-seq, ChIP-seq, data integration). • Expertise with bioinformatic programs and techniques (i.e., GSEA, Ingenuity Pathway Analysis, IGV). • Computational biology and data analysis (e.g., R, shell scripting, SQL). • Advanced molecular biology and cell culture techniques (multiparameter flow cytometry, primary human PBMC and T cell, T cell killing assays).• Advanced NGS techniques (i.e., CITE-seq).Awards: • Azure Life Sciences Research Reagents Funding Initiative, BD Biosciences.

Conducted graduate research in the laboratory of Dr. Vasilis Vasiliou at the Yale School of Public Health: • Crafted an interdisciplinary research program that involved labs from around the United States, which lead to over 5 first author publications and more than 10 total publications. • Designed, executed and analyzed molecular experiments, including but not limited to Western blotting, qPCR and histology, to characterize a novel mouse model of impaired lens development. • Devised and performed in vitro experiments to confirm in vivo findings. • Conducted amongst the first RNA-seq analysis of the developing lens in a mouse model of microphthalmia, which lead to the unexpected discovery that oxidative stress may impaired PAX6 function and induce of inflammation of lens cells.• Was pioneering the use of CUT&RUN to study the developing mouse lens. • Closely mentored 1 MPH student. • Taught lab members the basics of RNA-seq data analysis with the Galaxy web platform.• 1 of 10 Americans selected to participate in the Association for Research in Vision and Ophthalmology Science Communication Training Fellowship Program. Technical Experience: • Mouse models for the study of eye development (e.g., Cre-Lox).• Advanced cell culture techniques (e.g., viral transductions, transfections, human iPSCs).• Modern molecular biology techniques (e.g., Electron microscopy, western blotting, qPCR).• RNA-sequencing including sample collection, data analysis and interpretation.Awards: • North American Travel Grant and Furst Award Winner, American College of Toxicology• Knights Templar Eye Foundation Travel Grant, The Association for Research in Vision and Ophthalmology• NRSA T32 Fellowship

Dr. Hoh Lab

Conducted research in the laboratory of Dr. Josephine Hoh at the Yale School of Public Health: • Developed novel mouse models, via selective breeding, for the investigation of Parkinson’s-like phenotypes. • Characterized these mouse models with basic molecular techniques.• Two publications including one first author. • Mentored 5 visiting summer students. Technical Experience: • Basics of mouse husbandry (e.g., mouse identification, sample collection, dissections, genotyping, PCR).• Histological techniques (i.e., cryosectioning, immunofluorescence, histochemical staining and in situ).• Modern molecular biology techniques (e.g., Molecular cloning, western blotting, qPCR).

• Assisted in the development of a curriculum for a new genetics course for the Biochemistry Department. • Participated in the diagnosing and implementation of Dracos Dragon Game (Concord Consortium).• Identified ways to incorporate bioinformatics research methods into course curriculum.• Supervisor: Dr. Molly Fitzgerald-Hayes

Work in a team to maintain the appearance and the health of the fields, complete basic mechanic tasks, and other tasks per request of the first selectman.

Doctor Of Philosophy - Phd, Environmental Health Sciences

Bachelor Of Science (Bs), Biochemistry

General Chemistry