Director of AI Research Solutions at Florida State University (FSU)
I bridge the gap between cutting-edge AI and R1 scientific discovery. I focus on developing high-level strategy and support structures that empower domain experts to harness AI as a transformative force in their research.
I believe that putting AI tools directly into the hands of content experts is critical to ensure the ethical and accelerated advancement of science.
Expertise & Background
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Interdisciplinary Focus: 14+ years as a researcher at the intersection of Computational Biology, Biochemistry, and Biomedical Engineering.
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AI/ML & Data Science: Well-versed in regression modeling, deep learning, and AI foundation model engineering. I specialize in building robust analysis pipelines for complex datasets.
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Educational Leadership: Extensive experience in teaching and training, focusing on making high-level computational methods accessible to researchers across disciplines.
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Academic Background: Ph.D. in Biological Chemistry & M.S. in Bioinformatics (University of Michigan) | B.S. in Biomedical Engineering (The Ohio State University).
This README is intended to be a table of contents for my github repositories.
These are a series of snakemake for processing illumina sequencing data. Each is general purpose with a simple sample sheet as the expected input. Each was designed with the smaller genome sizes of bacteria in mind.
| Pipeline | Description |
|---|---|
| Strandedseq_pipeline | Snakemake pipeline for analyzing bacterial illumina sequencing where strand matters. I.e. RNA-seq, NET-seq |
| ChIPseq_pipeline | Snakemake pipeline for analyzing bacterial ChIP-seq data |
| Bacterial_reseq | Snakemake pipeline for analyzing bacterial whole-genome sequencing using breseq |
| HiC_pipeline | Snakemake pipeline for analyzing bacterial Hi-C data. Currently private. |
Here are repositories with code that is associated with a publication that I have contributed to.
| Repo | Description |
|---|---|
| ShapeME | Mutual information-based tool for finding DNA-shape based binding motifs https://doi.org/10.1101/2025.01.28.635290 |
| Shen_H-NS_2022 | Bayesian model for analyzing E. coli H-NS footprinting data https://doi.org/10.1016/j.isci.2022.104429 |
| 2018_Lrp_ChIP | Custom ChIP-seq workflow to analyze E. coli Lrp gene regulation https://doi.org/10.1128/jb.00411-18 |
| 2018_genomeProfiling | Utilities to calculate windowed summaries of features to predict positional transcription of a reporter in E. coli https://doi.org/10.1016/j.cels.2019.02.004 |
Here are some extensions for working with quarto
| Extension | Description |
|---|---|
| front-van | Journal extension for writing Frontiers-in articles in quarto |
Here are some repositories I have made contributions to.
| Repo | Description |
|---|---|
| MultiQC | Added support for some pairtools Hi-C reports |
| pyGenomeTracks | Added ability to specify an alpha for genome tracks |
Here are some utility tools and scripts I have developed.
| Repo | Description |
|---|---|
| pytools3 | A series of utility scripts and classes for dealing with genomic data |
| CMARRT_python | A python re-implementation of CMARRT peak caller https://pmc.ncbi.nlm.nih.gov/articles/PMC2862456/ |
Here are some repositories associated with workshops, teaching, or personal development in my own continued education.
| Repo | Description |
|---|---|
| UWMadisonMLM25 | Repo for the 2025 UW-Madison Machine Learning Challenge predicting changes in protein function due to changes in sequence |
| R4DSNotes | Personal notes on the excellent R for Data Science book https://r4ds.had.co.nz/ |
| 2019-05-23-shapiro | Software carpentry workshop at University of Michigan where I was a lead instructor |
| SICP | Personal notes on the Structure and Interpretation of Computer Programs book https://web.mit.edu/6.001/6.037/sicp.pdf |