Korin Eckstrom

I am currently a Bioinformatics Programmer & Analyst at Genentech in the Early Research & Development arm. My work is focused on improving data utility and cloud computing, providing bioinformatics & engineering support to scientists and analysts across clinical trials and multi-modal data types for actionable insights within the drug dicovery pipeline.

Primarily focused on whole exome sequencing and ctDNA/cfDNA assays, I develop workflows (Nextflow/Snakemake/WDL) that streamline & distill high-dimensional data in order to provide analysis-ready objects to stakeholders while maintaining end-to-end provenance of metadata. My team is responsible for the processing of thousands of clincial trial samples and preparing these outputs in a format that is readily available to downstream teams, including tertiary analyses such as AI/ML modeling. Currently working towards the migration of HPC & slurm managed workflows to AWS, focusing on efficiency and cost without sacrificing data quality and accessibility. To aid users in accessing data stored in s3, I’ve also developed functions for common tasks that can be drop-in replacements to existing code in order to make the transition to cloud-based analysis feel familiar. I also work closely with teams responsible for data cataloging to ensure findability of resources across the organization.

During my time working for the Vermont Integrative Genomics Resource Bioinformatics core, I worked on a wide array of NGS workflows and applications. These included metagenomics, single-cell RNA sequencing, assembly of novel genomes, RNAseq and more. From vaccine trials to field research, this core facility provided support to projects across Vermont and other regions. See more on my publications page. I was also a co-instructor for MMG231 (Bioinformatics & Data Analysis) & MMG232 (Advanced Bioinformatics), focusing on the fundamentals of HPC computing, basic Unix, and metagenomics.

My graduate research focused on applying omics assays to issues within the field of animal & farm health, such as bovine vaccine design and antimicrobial resistance on poultry farms. Through a One Health and ecological perspective, I worked to leverage high throughput techniques such as shotgun metagenomics to address gaps within our agricultural system and provide feedback for ongoing management practices.

I am passionate about open access software and data reproducibility, especially data FAIR-ness from experimental design to final publication. Initially starting as a bench scientist, I am skilled in both computational and wet lab procedures, bridging the gap between the design and execution of complex NGS experiments with a clear understanding of the complexities of both settings. I strive to provide stakeholders with metadata rich and user-friendly deliverables in order to improve data reuse and reproducibility, meeting the needs of users at every skill level while maintaining the data lifecycle from start to finish.