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Philadelphia, PA • Software Engineer • Bioinformatics Graduate Student

Grant Merrigan
Building software and data tools for genomics, biomedical research, and computational biology.

I'm a software developer and bioinformatics graduate student interested in research software engineering, computational genomics, and biomedical machine learning. My work combines full-stack development, data pipelines, and biological data analysis — from comparative genomics platforms to single-cell RNA-seq modeling.

PythonC# & .NETReactSQLAWSscRNA-seqBioinformaticsMachine Learning
Bioinformatics pipeline development
Research software engineering
Full-stack application development
Biomedical data analysis

Current focus

  • • PSM student in Bioinformatics & Biological Data Science at Temple University
  • • Graduate Researcher in Temple's Kulathinal Lab of Evolutionary Genomics & Bioinformatics
  • • Building computational workflows for duplicate gene functionalization and comparative genomics
  • • Interested in bioinformatics software, biomedical ML, genomics platforms, and healthtech engineering
ResumeGitHub
Open to full-time roles

Selected Work

Research software, bioinformatics pipelines, and full-stack applications.

Research Software

PhyloDIVaS

Genome-scale dN/dS analysis platform

A full-stack bioinformatics platform for running comparative genomics analyses across species. PhyloDIVaS automates ortholog detection, codon alignment, and selection testing by connecting NCBI genomic data with a multi-tool pipeline using OrthoFinder, MAFFT, and HyPhy-BUSTED.

ReactASP.NET CoreOrthoFinderMAFFTHyPhy-BUSTEDNCBI APIsBioinformaticsAWS

My contribution

Architected backend services in ASP.NET Core for NCBI API integration, async job orchestration, and scientific file processing. Built a React frontend for gene search, pipeline submission, phylogenetic visualization, and downloadable FASTA/scientific outputs.

Details

Computational Biology

Graph-Based ML Model for Immunotherapy Response Prediction

Single-cell RNA-seq + biomedical machine learning

An exploratory predictive modeling project studying whether malignant-cell heterogeneity from pre-treatment single-cell RNA-seq data can help predict immune checkpoint blockade response across multiple cancer types. The workflow uses patient-level aggregation, graph-based features, and statistical evaluation of outcome-associated tumor heterogeneity.

PythonScanpyAnnDatascikit-learnPCA/UMAPinfercnvpyscRNA-seqMachine Learning

My contribution

Developed the modeling workflow from scRNA-seq preprocessing through malignant-cell filtering, dimensionality reduction, graph-based feature engineering, patient-level aggregation, and model evaluation using ROC-AUC, statistical testing, and outcome-stratified visualizations.

Paper

Evolutionary Genomics

Duplicate Gene Functionalization Research

Evolutionary genomics across primates and Drosophila

A computational genomics research project studying how duplicated genes diverge in expression and function across evolutionary lineages. The work involves orthology inference, expression matrix harmonization, duplicate retention classification, and pipeline development for analyzing conservation, specialization, neofunctionalization, and subfunctionalization.

PythonROrthoFinderCDROMCLOUDGene ExpressionEvolutionary GenomicsData Harmonization

My contribution

Built reproducible preprocessing workflows for protein/gene ID mapping, longest-isoform filtering, orthogroup analysis, expression matrix preparation, and duplicate classification inputs. Focused on connecting fragmented bioinformatics tools into a cleaner comparative genomics workflow.

Poster

Systems / Bioinformatics Tooling

FASTA Compression CLI

Custom nucleotide compression tooling

A C-based command-line tool that compresses nucleotide FASTA files using a custom bit-packing format, achieving up to 3× size reduction on genomic sequence datasets.

CFASTACompressionLow-Level ProgrammingBioinformatics Tooling

My contribution

Implemented a custom 2-bit nucleotide encoding algorithm, optimized file I/O with buffering strategies, and added validation/error handling for malformed FASTA sequences.

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Full-Stack Application

Travel Planner

CIS-3342 Term Project: Vacation Package Builder

A full-stack ASP.NET Core MVC travel booking application that lets users browse destinations, view hotels, and book vacation packages, backed by SQL Server stored procedures, authentication, 2FA, and automated weekly recommendation emails.

.NETASP.NET Core MVCMicrosoft SQL ServerStored ProceduresFull Stack

My contribution

Developed stored procedures for booking workflows, implemented ASP.NET Identity with 2FA email verification, and built an automated email recommendation service.

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Research Interests

I'm interested in using software engineering and data science to answer biological questions, especially where research depends on reproducible pipelines, scalable data processing, and clear communication of complex results.

Computational Genomics

Building workflows for orthology inference, gene duplication analysis, expression divergence, and comparative genomics.

Single-Cell & Biomedical ML

Using patient-level modeling, graph-based features, and single-cell RNA-seq data to study tumor heterogeneity and treatment response.

Research Software Engineering

Designing tools that make computational biology workflows more reproducible, usable, and easier to connect across datasets and platforms.

About

I'm a Temple University Information Science & Technology graduate and current PSM student in Bioinformatics & Biological Data Science. My background combines professional software engineering experience with computational biology research, giving me a practical perspective on how to build tools that are technically reliable and useful for scientific work.

I've worked across full-stack development, database-backed applications, cloud deployment, bioinformatics pipelines, single-cell analysis, and evolutionary genomics. I'm especially interested in roles where I can bridge software engineering and life sciences — including bioinformatics software, healthtech engineering, biomedical data science, and research software development.

Let's Connect

Open to software engineering, bioinformatics, research software, and healthtech roles.

Email MeResumeLinkedInGitHub