I work across transcriptomics, functional genomics, and single-cell analysis. My research includes bulk RNA-seq, microarrays, differential expression, functional enrichment, protein–protein interaction networks, and HPC-based single-cell and single-nucleus RNA-seq. I often work with crops, filamentous fungi, and yeasts that lack ready-made Bioconductor annotation, including Fusarium graminearum in wheat and barley.

I turn these methods into reproducible, local-first scientific software in R and Python. My projects span no-code expression analysis, transposable-element annotation and primer design, leakage-safe multi-omics benchmarking, and knowledge tools for researchers. I care about interface design, typography, and visual craft as much as technical correctness.

I am also interested in epistemology and the methodology and history of science: how knowledge is justified, how methods earn trust, and how software can preserve the evidence behind a result.

• Languages & application development: R · Python · TypeScript · JavaScript · Rust · Bash · PySide6 / Qt · Tauri · Svelte · React · WebGPU
• Transcriptomics & machine learning: Bioconductor · DESeq2 · limma · edgeR · Seurat · Scanpy · scvi-tools · PyTorch · scikit-learn
• Sequencing & genomics: STAR / STARsolo · HISAT2 · Salmon / alevin · fastp · FastQC / MultiQC · SAMtools · featureCounts · HMMER · RepeatMasker · Dfam · Primer3 · minimap2
• Networks, annotation & visualization: STRING · GO · KEGG · g:Profiler · clusterProfiler · Reactome · Ensembl · eggNOG · igraph · ggraph · ggplot2 · Plotly
• Reproducibility & quality assurance: Snakemake · conda / mamba · renv · Docker · WSL2 · GitHub Actions · pytest · Vitest · Playwright

Arf — a local-first second brain for scientists and coders: plain-Markdown notes with [[wikilinks]], LaTeX and syntax-highlighted code, a knowledge graph, and on-device embeddings (MiniLM) that surface related but unlinked notes. Native desktop app for Windows, macOS, and Linux. Download.

Litehouse (live) — a browser-only scholarly literature-review tool: it retrieves works from open APIs (OpenAlex, Crossref, Europe PMC, DataCite), then writes an evidence-locked, cited synthesis with a local WebGPU model (Qwen3), attaches SHA-256 integrity receipts, and exports a classic Computer Modern LaTeX report. No server and no install — retrieval, the model, and rendering all run in the browser.

BulkSeq Studio — a cross-platform, no-code desktop app for reproducible bulk RNA-seq and microarray analysis: STAR / HISAT2 / Salmon alignment, DESeq2 / limma, GO / KEGG / g:Profiler enrichment, and STRING interaction networks, with first-class support for crops and fungi that lack a Bioconductor OrgDb.

TEagle — a native desktop app for transposable-element annotation and TE-aware PCR primer design: evidence-traceable structural and protein-domain (HMMER) classification, an interactive genome viewer, Primer3 design checked by pair-aware in-silico PCR, and a local whole-genome off-target scan (RepeatMasker / Dfam and minimap2 run through a managed WSL backend) — with every result sealed by content-addressed provenance (database and tool versions plus checksums) so it reproduces exactly. Windows, no command line. Download.

omicau — a reproducible, leakage-safe multi-omics data-audit CLI: format-agnostic ingestion and alignment, SHA-256 data provenance, missingness-bias and batch-effect diagnostics, group-aware cross-validated classical and PyTorch masked-pooling fusion benchmarks with leakage-safe feature attribution, and a dual clinical/research dashboard. Built for the Build with Claude: Life Sciences hackathon (Anthropic × Gladstone Institutes, Jul 7–13 2026).