Bioinformatics Engineer & Computational Systems Builder — genomic pipeline development, machine learning for biology, and production infrastructure at the Dana-Farber Cancer Institute.https://andrewbonney.cloud/en-ushttps://andrewbonney.cloud/projects/dafseq-smkhttps://andrewbonney.cloud/projects/dafseq-smkA 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.Tue, 14 Jul 2026 00:00:00 GMTSnakemakePythonGenomicsEpigenomicsPipelinehttps://andrewbonney.cloud/projects/evo2-clihttps://andrewbonney.cloud/projects/evo2-cliA 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.Tue, 14 Jul 2026 00:00:00 GMTPythonCLIMachine LearningGenomicsFoundation Modelshttps://andrewbonney.cloud/projects/bert-sequencehttps://andrewbonney.cloud/projects/bert-sequenceTransformer-based language models applied to biological sequence classification, exploring gene function prediction and regulatory element annotation.Mon, 16 Feb 2026 00:00:00 GMTBERTTransformersNLPPyTorchGenomicshttps://andrewbonney.cloud/projects/deeplabcuthttps://andrewbonney.cloud/projects/deeplabcutMachine learning-based pose estimation system for tracking zebrafish behavior in custom experimental rigs, enabling high-throughput behavioral analysis.Mon, 16 Feb 2026 00:00:00 GMTPythonDeepLabCutComputer VisionPose Estimationhttps://andrewbonney.cloud/projects/epibenchhttps://andrewbonney.cloud/projects/epibenchBenchmarking suite for DNA methylation detection methods. CNN/PyTorch framework for methylation classification from bisulfite sequencing data, benchmarked against traditional statistical approaches.Mon, 16 Feb 2026 00:00:00 GMTBioinformaticsPyTorchMachine LearningGenomicshttps://andrewbonney.cloud/projects/nf-core-scgehttps://andrewbonney.cloud/projects/nf-core-scgeCloud-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.Mon, 16 Feb 2026 00:00:00 GMTNextflowAWS BatchDRAGENnf-coreGenomicshttps://andrewbonney.cloud/projects/stl-bcbhttps://andrewbonney.cloud/projects/stl-bcbA vertically integrated bioinformatics agency serving the St. Louis biotech ecosystem. Infrastructure, analysis, and talent — from a scientist who speaks the language.Mon, 16 Feb 2026 00:00:00 GMTBioinformaticsCommunityWebhttps://andrewbonney.cloud/projects/deflabhttps://andrewbonney.cloud/projects/deflabA translational chemistry laboratory exploring new synthetic methodology in organic chemistry.Web DevelopmentDNSGo