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Hello, I'm

Walsh Quigley

Bioinformatics Engineer

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About Me

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Experience

Bioinformatics Engineer
University of Pennsylvania

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Education

B.S. Computer Science
Western Washington University

My name is Walsh Quigley. I hold a bachelor's degree in Computer Science from Western Washington University, and I currently work as a Bioinformatics Engineer at the University of Pennsylvania. Most of my time goes to building the pipelines a base editing lab depends on, and to getting them running on the compute cluster so the bench scientists can run their own analyses without waiting on me. During times that I'm not writing code, I try to spend time rock climbing in the gym or convincing friends to come with me in search of the cheapest ski mountain within a 3 hour drive.

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Experience

Bioinformatics Engineer

October 2025 - Present

University of Pennsylvania, Department of Cell and Molecular Biology

Philadelphia, Pennsylvania

  • Built an automated FASTQ-to-report pipeline wrapping CRISPResso2, parsing allele-level output for adenine base editing and nuclease experiments and classifying edits as on-target, tolerated, or non-tolerated.
  • Developed a ONE-seq fragment library design pipeline that enumerates genome-wide off-target candidates for a given protospacer/PAM across configurable mismatch and bulge tolerances. Deduplicates hits and outputs a ranked candidate list for wet-lab validation.
  • Developing an automated primer design tool in partnership with bench scientists, generating primers for protospacers annotated in GenBank files and returning a re-annotated file for direct visualization in SnapGene.
  • Deployed and maintained collaborator-provided analysis pipelines on Penn's LSF cluster, enabling lab members to submit jobs independently.

Research Assistant

December 2022 - December 2023

Western Washington University, Department of Computer Science

Bellingham, Washington

  • Led a three-person team building an iOS application in React Native for a neurodivergent research lab, replacing next-day recall surveys with real-time participant self-report of moods and triggers.
  • Translated a faculty lead's high-level outline into a deployed application used for active data collection, implementing the front end and the front-end-to-backend integration layer.
  • Coordinated junior developers and worked directly with the research lead through iterative review, extending the app with daily surveys capturing mood, affect, and recurring thoughts.
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Skills

Languages

Python R Bash / Zsh JavaScript

Bioinformatics

CRISPResso2 Biopython FASTQ / GenBank Processing Base Editing Quantification Off-Target Analysis (ONE-seq) Primer Design SnapGene

Data & Visualization

pandas matplotlib plotly seaborn

Infrastructure

Linux HPC Cluster Computing (LSF) conda Git / GitHub

Testing

pytest Unit Testing Regression Testing Known-Truth Validation
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