Archive - Paired Ends

Weekly Recap (March 2025, part 2)

AI agents for biomedical reasoning, species tree inference, a spatial transcriptomics foundation model, biomedical research with LLMs, mapping cells…

Mar 28

uv, part 2: building and publishing packages

Using uv to create, manage, build, and publish a Python package to PyPI

Mar 24

Weekly Recap (March 2025, part 1)

Heritable polygenic editing, self-supervised learning in single-cell genomics, predictive modeling with tabular foundation models, ESM3, pangenome…

Mar 21

GUIs for Local LLMs with RAG

Running local LLMs with Ollama, LMStudio, Open WebUI, and others for private and secure chat, vibe coding, image analysis, and "chat with your…

Mar 14

uv, part 1: running scripts and tools

Over the past year I’ve heard a lot great things about uv, an extremely fast Python package and project manager, written in Rust.

Mar 3

February 2025

Weekly Recap (Feb 2025, part 3)

T2T assembly, DNA language models for variant effect analysis, ortholog inference at scale, a foundation model of transcription across cell types…

Feb 27

Weekly Recap (Feb 2025, part 2)

Predicting RNA-seq coverage from DNA sequence with Borzoi, doing it faster with Flashzoi, phylogenetic inference from structure, prioritization in GWAS…

Feb 20

Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper

Collect metadata and publication details for >200k preprints over a 10 year period, investigate trends, and scrape full text for sentiment analysis

Feb 10

Weekly Recap (Feb 2025, part 1)

Neuropsychiatric PGS don't predict professional categories, pangenome graph-based GWAS, building and using single cell atlases, sketching sketching in…

Feb 7

January 2025

Technical blogging for growth and learning

Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. This post: why blog…

Jan 25

Weekly Recap (Jan 2025 part 3)

Visualizing pathogen dispersal, DNA language model benchmarks for regulatory DNA, polygenic risk prediction with GWAS summary stats, multimodal analysis…

Jan 24

AI in data science education

Listen now | Balancing growth with guidance: teaching data science in the age of AI assistants

Jan 15

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