Andrew Bonney

Hi, I'm Andrew. I’m a computational biologist. 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 worked under Dr. David Spencer for two years at the Washington University School of Medicine, creating interpretable learning models and pipelines to research the epigenetics of acute myeloid leukemia. Today I’m in the Data Science department at the Dana-Farber Cancer Institute in Boston, working with Dr. Nicoletta Cieri to build the algorithms and testing methods for understanding graft-versus-host disease in hematopoietic stem cell transplantation. 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

dafseq-smk

A Snakemake pipeline for DAF-seq (deaminase-assisted footprinting) data. Takes raw sequencing reads to per-haplotype chromatin accessibility tracks ready to load into a genome browser.

Snakemake Python Genomics Epigenomics Pipeline

evo2-cli

A command-line tool for pulling DNA sequence embeddings out of Evo 2, the genomic foundation model. Point it at sequences, get back embedding vectors for downstream ML.

Python CLI Machine Learning Genomics Foundation Models

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