Timothy Stephens
I am a computational evolutionary biologist working at the intersection of comparative genomics, evolutionary biology, and data science. My research investigates how genes with unknown function (“dark genes”) originate, diversify, and acquire biological roles. I develop and apply computational approaches to identify evolutionary relationships, interpret poorly characterized genomic sequences, and generate testable hypotheses about gene function.
My work spans coral, algal, amoebal, bacterial, and environmental microbial systems. Across these systems, I combine comparative genomics, phylogenomics, sequence- and structure-based analysis, genome annotation, metagenomics, and multi-omics to address general questions about genomic novelty and biological function.
I also develop research software and reproducible computational workflows, including PhySortR, naive ATLAS, and the Dinoflagellate Annotation Workflow. My broader software projects explore graph-based analysis, multi-agent software development, and secure computational environments.
My research experience includes collaborative project leadership, day-to-day mentoring of graduate and undergraduate researchers, and translational technology development as a co-founder of OceanOmics.
Research themes
Evolutionary origins and functions of dark genes
How do genes with no recognizable function originate? When do they represent genuinely new evolutionary innovations, and when are they highly diverged members of existing gene families? My research combines comparative genomics, phylogenetic inference, and sequence- and structure-based homology detection to investigate these questions.
Comparative and environmental genomics
I develop and apply computational workflows to analyze genomic data across diverse biological systems, from microbial communities and dinoflagellates to photosynthetic amoebae and corals. The biological systems provide evolutionary contrasts; the computational questions and methods are designed to transfer across taxa.
Computational methods and research software
I build and maintain tools for phylogenetic classification, genome annotation, metagenomic analysis, and graph-based data exploration. See the Code and Software page for selected projects and source repositories.
Selected software
- PhySortR — R package for screening and sorting phylogenetic trees.
- Dinoflagellate Annotation Workflow — evidence-integrating gene-prediction workflow for dinoflagellate genomes.
- naive ATLAS — domain-agnostic metagenomic workflow derived from ATLAS.
- Network Analysis Scripts — Python graph-tool utilities.
- MAGS-CodeDev and AgentBox — complementary projects in AI-assisted software engineering and computational infrastructure.
View my publications · View code and software · Download my CV