Arafat Rahman

Arafat Rahman, Ph.D.

I am a Computational Biologist, specializing in microbial genomics, high-throughput data pipelines, and host-pathogen interactions. Currently a Research Associate at Oregon State University, I build scalable software and do reproducible analysis to decode complex biological systems.

Finished Ph.D. in Genetics, Genomics, and Bioinformatics from the University of California, Riverside (2023). My research was on evolutionary questions of symbiosis in the Sachs lab.

I have also been a Teaching Assistant on different courses, particularly Introduction to Genetics and Evolution multiple times during my PhD.

Photography and hiking are my hobby.

In Bangladesh, I was a Lecturer for two years in the Department of Microbiology at Noakhali Science and Technology University.

An avid learner of computational biology and my learning philosophy is by doing.

Google Scholar

As a Computational Biologist, I specialize in transforming complex biological data into insights by building robust, reproducible softwares and pipelines. My work bridges the gap between high-throughput sequencing and production-grade data engineering.

  • Pipeline Development: Architected and containerized end-to-end genomic workflows using Nextflow, Snakemake, and Docker to ensure reproducibility and scale across compute environments.
  • Software Engineering: Authored and actively maintain production-grade open-source tools, including the Beav annotation pipeline and the PySyntenyViz Python package.
  • Data Analytics: Process massive short- and long-read genomic datasets, optimizing variant calling algorithms and deploying analytical workflows in high-performance computing (HPC) environments.
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My research leverages computational and molecular tools to answer fundamental biological questions about how pathogens evolve and interact with their hosts. Currently a research associate at Oregon State University, I am deeply committed to scientific discovery, securing funding, and training the next generation of researchers.

  • Research Focus: Investigating microbial pangenomics, phylodynamics, and plant-symbiont interactions across diverse agricultural organisms, including Agrobacterium and Rhizobium species.
  • Grants & Funding: Actively engaged in project management and research funding, including the submission of competitive grant proposals such as the USDA NIFA postdoctoral fellowship.
  • Mentorship & Teaching: Dedicated to capacity building and science education. I have trained undergraduate researchers at the bench and computationally, and designed a comprehensive 16-week curriculum on “Comprehensive Bioinformatics for Advanced Microbial Genomics”.
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Technical Stack

Languages & Infrastructure

  • Python, R, Unix
  • Docker, Conda, Pixi
  • Snakemake, Nextflow

NGS

  • Illumina & Nanopore
  • WGS & RNA-Seq
  • Annotation, variant calling, phylogeny

AI (ML/DL)

  • Decision trees, SVM, K-NN
  • Fine tuning foundational models like ESM2
  • PyTorch, FLAX/JAX

Automation & Web-Dev

  • GitHub Actions (CI/CD)
  • Flask, Wordpress REST API
  • Redis

Selected Publications