Resume

Andrew Bonney

Bioinformatics Engineer & Computational Systems Builder. Full skills inventory and work history below.

Technical Skills

89 capabilities

Proficiency: ■ Advanced ■ Proficient ■ Familiar

Languages

Python R Bash SQL TypeScript Go Rust C++ Java

Workflow & Cloud

Nextflow DSL2 Docker Singularity AWS (Batch, S3, EC2) Git/GitHub Linux/HPC Admin Slurm/PBS VPS Administration Nginx Systemd Quarto Palantir Foundry LSF Snakemake Galaxy

Bioinformatics

SAMtools BEDtools STAR BWA Bowtie2 GATK Bismark MACS Peakachu HOMER FastQC MultiQC Seurat DESeq2 EdgeR Bioconductor BioPython DRAGEN Cell Ranger Monocle Juicer Cooler deepTools fastp MuSE delly BioPerl

Data Science & AI

PyTorch Scikit-Learn Pandas NumPy Matplotlib Seaborn ggplot2 Computer Vision (CNNs) TensorFlow Hugging Face Explainable AI (SHAP, Captum) Molecular Dynamics

AI & LLM Systems

Ollama FastAPI Anthropic Claude API Persistent Memory (RAG) Self-Hosted LLM Deployment OpenAI API LangChain Vector Databases Prompt Engineering LLM Fine-Tuning

Laboratory Techniques

DNA Extraction qPCR CGE (Capillary Gel Electrophoresis) GC-MS HPLC ELISA Cell Culture UV/Vis Spectroscopy Immunofluorescence

Regulatory & QC

ISO 9001 FDA Validation (21 CFR Part 11) GLP/GMP Data Integrity & Audit Trails LIMS ICH Guidelines CAPA / SOP Development

Experience

7 entries

Washington University School of Medicine — Spencer Lab

Bioinformatics Research Assistant

Aug 2024 — Present

Engineering reproducible Nextflow pipelines for multi-omic datasets (RNA-seq, WGBS, Hi-C) in AML research. Developing CNN/PyTorch frameworks for DNA methylation prediction. Orchestrating petabyte-scale ETL on AWS Batch/S3.

Nextflow PyTorch AWS Hi-C WGBS

Pfizer

Analytical R&D Data Scientist

May 2024 — Aug 2024

Developed computer vision algorithms for high-content microscopy data. Automated a long cell-based QC assay for a gene therapy program by integrating Integra automated pipetting robots with reproducible R/Python CV scripts, increasing throughput by 300% and reducing analysis error rates by 40%.

Computer Vision Python R Microscopy

Saint Louis University

M.S. Bioinformatics & Computational Biology

Dec 2022 — Dec 2024

GPA: 3.97/4.00. Graduate research in deep learning for structural RNA classification, molecular dynamics simulations of drug-receptor interactions, and benchmarking methylation detection pipelines.

Neural Networks Molecular Dynamics Benchmarking

ThermoFisher Scientific

Scientist II — Biochemistry & Instrumental Analysis

Jul 2021 — Jan 2024

Technical Lead for analytical biochemistry assays. Built Python parsers for automated instrument data ingestion (CGE, PCR). Maintained 99.8% data accuracy across 200+ monthly samples.

Python Analytical Chemistry Automation

Firmenich

QC Scientist — Analytical Chemistry

May 2021 — Aug 2021

Processed and verified high-volume GC-MS spectral data for 150+ compounds under strict data integrity standards.

GC-MS Quality Control

Bayer

Genetic QA Lab Technician

Aug 2020 — May 2021

High-throughput DNA extractions using Biomek automation systems, processing 500+ samples weekly in an ISO 9001 compliant quality lab.

DNA Extraction Automation ISO 9001

University of Missouri–Kansas City

B.S. Biology

Aug 2015 — May 2019

Undergraduate studies in biological sciences with emphasis on molecular biology and genetics.

Biology Genetics