Jonathan Blake Kirkland

Bioinformatician & software engineer

Currently a PhD Candidate in the Knight Lab @ University of California, San Diego. My research is focused on building attention based models for predicting disease states via the microbiome, alongside large data curation for subject wide meta-analysis.

You'll also find me working on AI infrastructure projects, benchmarking open source LLMs, over-automating my home garden, and occasionally touching grass. See my links in the start menu below.

• Bioinformatics

  • Qiita Python

    Scalable multi-omic study management, processing, and analysis platform for microbiome data — amplicon, metagenomic, metatranscriptomic, metabolomic, and proteomic.

  • duckdb-miint C++

    MIINT — a DuckDB extension bringing columnar analytics to microbiome data. Read alignments, filter, and compute OGU counts in SQL.

  • bwa-rs Rust

    A pure-Rust implementation of BWA-MEM for genomic short-read alignment.

  • pontifficate Python

    Image normalization and immunofluorescence quantification for ECHO-Revolve microscope images.

  • fastq-detangler Python

    Finds paired FASTQ reads across messy directories and puts them back in order.

  • aam Python

    16S deep learning pipeline for predicting Unifrac

• Everything Else

  • wheel-n-deal Python

    Price-tracking service that watches products across e-commerce sites and notifies you when they drop to your target.

  • booking-the-cooks Markdown

    A version-controlled recipe collection.