Computational genomics · Large language models · Reproducible research
Reproducible AI-Driven Approaches to Molecular and Evolutionary Genomics
We combine molecular genetics, computational genomics, and protein language models to investigate how biological sequences relate to function. Our work turns complex data into reproducible analyses and questions that can be tested.
Led by Rodolfo Aramayo, PhD
Associate Professor of Biology · Texas A&M University
Research you can explore¶
Ongoing research · MutScan
What do protein models tell us about variation?
Across 15 disease-associated proteins, we examine what model scores measure, how evidence sources overlap, and which conclusions need further biological support.
Explore the model audit →Peer-reviewed · Computational genomics
Genomes as a basis for biological discovery
Genome assembly and comparative analysis of Myxococcus and Spiroplasma provide public resources for studying microbial function and evolution.
Read the genomics studies →Released software · 2026
Reproducibility through manuscript preparation
One maintained LaTeX manuscript source produces four publication profiles. The versioned release pairs reusable code with build and dependency documentation.
Explore the software release →From a biological question to the next test¶
Frame the question
Use biological mechanism and the literature to define a testable problem.
Establish the evidence
Examine experimental design, sequence quality, annotations, and reference data.
Build and challenge
Run reproducible analyses, compare baselines, and investigate failure cases.
Define the next test
Separate supported conclusions from hypotheses that need additional evidence.
Rodolfo uses Claude and other LLM assistants in scientific software development, analysis, and writing, with checks against code, source data, and biological reasoning. See how this works in MutScan.
People & projects
A laboratory working across biological scales
Graduate and undergraduate researchers contribute distinct questions and methods to a shared program in proteins, genomes, and reproducible science.
Meet our researchersRecent from the lab¶
- Fall 2026Teaching scientific reasoning through practice
Digital Biology and Molecular Cell Biology connect computational skills, biological mechanisms, and careful use of AI. Explore teaching & mentorship →
- Manuscript Multi-Target LaTeX Template
A public software release for reproducible manuscript preparation. Zenodo release · Code & documentation
- Comparative genomics of Spiroplasma
Our co-authored study examines toxin repertoires and metabolic capacities in three Drosophila-associated strains. Read the publication →