Andrew Bonney

Hi, I'm Andrew. I’m a Scientist. I aim to understand the mechanisms of life better utilizing new technology. My journey into compbio started with deep dives into philosophy, which convinced me of the necessity to understand biology through information systems. I work in a research laboratory at the Washington University School of Medicine under Dr. David Spencer, where I create machine learning models and algorithms to research the epigenetics of acute myeloid leukemia. I am motivated by the challenge of doing things nobody has done before; where there is no template to model your work on. My ultimate goal is to spend my life uncovering amazing mysteries on the frontier of biology.

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Projects

Research & Tools

EpiBench

Benchmarking suite for DNA methylation detection methods. CNN/PyTorch framework for methylation classification from bisulfite sequencing data, benchmarked against traditional statistical approaches.

Bioinformatics PyTorch Machine Learning Genomics

nf-core/scge Pipeline

Cloud-native tumor-normal sequencing pipeline for the NIH Common Fund's Somatic Cell Genome Editing program. Built with Nextflow DSL2 and DRAGEN hardware acceleration on AWS.

Nextflow AWS Batch DRAGEN nf-core Genomics

DeepLabCut Imaging Pipeline

Machine learning-based pose estimation system for tracking zebrafish behavior in custom experimental rigs, enabling high-throughput behavioral analysis.

Python DeepLabCut Computer Vision Pose Estimation

BERT for Sequence Classification

Transformer-based language models applied to biological sequence classification, exploring gene function prediction and regulatory element annotation.

BERT Transformers NLP PyTorch Genomics

Digital Deployments

Biointal — Bioinformatics Agency

A vertically integrated bioinformatics agency serving the St. Louis biotech ecosystem. Infrastructure, analysis, and talent — from a scientist who speaks the language.

Bioinformatics Community Web