I am a Bioinformatician (Scientist III) in the Cancer Informatics Shared Resource (CISR) at the Carbone Cancer Center at the University of Wisconsin-Madison. I received my Ph.D. in Biological Chemistry and M.S. in Bioinformatics from the University of Michigan and my B.S. in Biomedical Engineering from the Ohio State University.
I am broadly interested in the molecular mechanisms of gene regulation that underlie how cancer cells respond to treatment, how bacteria develop antibiotic resistance, and how immune cells respond to their environment.
A couple things about me:
- I have over 10 years of experience as an interdisciplinary researcher with training in computational biology, biochemistry, and biomedical engineering.
- I have extensive experience with many -Omics methodologies including bulk and scRNA-seq, ChIP-seq, and Hi-C.
- I am well-versed in computational and statistical methods including regression modeling, machine learning, and analysis pipeline development.
- I have a wide-breadth of biology expertise working with experimental systems from bacteria to humans and at scales from the molecular to the systems-level.
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 |