CV

Research Informatics Data Scientist

Fred Hutch

• Build WDL workflow and Docker resources to be used across Fred Hutch
• Develop an LLM-based tool to write WDL workflows using a locally hosted model
• Meet one-on-one with reserachers in Data House Calls to support individual needs

Bioinformatician

University of Washington

Studied immune responses to tuberculosis (TB) in the Seshadri Lab, part of the Seattle TB Research Advancement Center.

• Utilized R and Bioconductor packages (e.g. Seurat) for analyzing multi-modal single-cell immune repertoire profiling data, including 10X with CITE-seq and TCR-seq.
• Employed methods such as differential gene expression (DGE), gene set enrichment analysis (GSEA), and cell-cell communication inference for single-cell gene expression data analysis.
• Ran bioinformatics pipelines using custom WDL scripts and Docker containers (e.g. for running Cell Ranger on Google Cloud instances).
• Developed custom visualizations including volcano plots, PCA plots, Circos plots, and alluvial plots.
• Established standard workflows for bioinformatics analyses and trained lab members.
• Contributed to scientific manuscripts, presentations, quarterly reports, and grant applications.
• Managed lab AWS and GitHub accounts, built custom reference genomes, and uploaded data to bioinformatics databases (SRA, GEO).

Bioinformatics Graduate Research Assistant

San Diego State University

Developed bioinformatics tools to study clinical Mycobacterium tuberculosis genomes in the Valafar Lab.

• Built and maintained a SQLite database for storing genomic variant data from 400 clinical Mycobacterium tuberculosis genomes.
• Improved Python software for annotating whole Mycobacterium tuberculosis genomes and performing variant calling.
• Used standard bioinformatics tools and databases such as BCFtools, STAR, VEP, and Mycobrowser.
• Implemented and developed bioinformatics pipelines for processing Illumina and PacBio next-generation sequencing data.
• Participated in grant writing, internal manuscript review, and journal club.

Teaching Assistant

San Diego State University

• Independently taught ‘BIOL 211L Fundamentals of Microbiology’ to 30 students.

Clinical Research Coordinator

UC San Diego Health Moores Cancer Center

• Coordinated a phase I CAR-T trial for Multiple Myeloma.
• Coordinated early phase trials for Acute Lymphoblastic Leukemia.
• Entered data into iMedidata RAVE, DataLabs, InForm, ClinTrak, and other EDCs.

Clinical Research Coordinator II

Benaroya Research Institute at Virginia Mason

• Coordinated phase IB/II trials.
• Coordinated Institutional Biosafety Committee reviewed studies.

Clinical Research Coordinator I

Benaroya Research Institute at Virginia Mason

• Coordinated phase III-IV immunotherapy and small molecule oncology trials.
• Collected and processed blood, tissue, and urine samples.
• Consented patients, scheduled visits, ordered labs and tests.

Research Assistant

Benaroya Research Institute at Virginia Mason

• Collected, processed, and shipped blood and tissue samples to central laboratories.
• Played a major role in the foundation and management of a blood and fresh tissue repository.

Undergraduate Research Associate

Kaeberlein Lab, University of Washington

• Studied the effects of caffeine on lifespan in yeast (S. cerevisiae) and nematodes (C. elegans).
• Used RNAi, PCR, fluorescence microscopy, and microbiology lab techniques.
• Developed novel assay to study movement of caffeinated nematodes.
• Assisted with manuscript writing.

Master of Science

San Diego State University

Bioinformatics

Bachelor of Science

University of Washington

Biology, General

Graduate Equity Fellowship

San Diego State University

BCG vaccination induces antibacterial effector functions among Vδ1/3 T cells that are associated with protection against tuberculosis

IFN-gamma-GranzymeB+ Natural killer cells are induced by IV BCG vaccination and associated with protection against tuberculosis in rhesus macaques

Automated Discovery of Patterns in T-Cell Receptor Physicochemical Signatures

Probing Dermal Immunity to Mycobacteria through a Controlled Human Infection Model

PBHoover and Hybran: Tools for studying genomic features in Mycobacterium tuberculosis

Hybran: Hybrid Reference Transfer and ab initio Prokaryotic Genome Annotation

Caffeine extends life span, improves healthspan, and delays age-associated pathology in Caenorhabditis elegans