NIH budget, AI, R, Bluesky & Science, state of biotech, AI in higher ed, R packages Top 40, structural variation, statistical power, Python documentary, Manhattan Project, tidymodels, ...

Biobank-scale relatedness estimation, SNP calling and phasing with long RNA-seq reads, predicting expression-altering promoter mutations with DL, cross-species filtering for comparative genomics, ...

RAND corp AIxBio report, AI accelerating: GPT-4b for stem cell reprogramming; AI is slowing down; UVA SDS on Bluesky; LLMs and education; Python needs R's CRAN;

Developing an R package using the OpenAI Codex agent in Positron

Using R and the GitHub API to get licensing information for GitHub repos for sequencing-related companies, one-shot with GPT-5.

Best AI for R, the weight of a cell, R+MCP, AI is a mass delusion event, AI hiring freezes, Quarto+Positron, biology moonshots, Julia for R users, AI hallucination, nf-core advisories...

Genome annotation, viral genome clustering, metagenomic diagnostics, SV analysis on ONT reads, functional prediction, gene loss, DNA damage/repair, CRISPR metagenomics, LLM lit review, ...

ChatGPT can be (mis)used to conduct scientific peer review with a predetermined outcome.

Closing my browser tabs: papers, blogs, news stories, YouTube videos, tutorials, etc.

This week’s recap highlights analysis of human de novo mutation rates from a four-generation pedigree reference, how LLMs internalize scientific literature and citation practices, the py_ped_sim forward pedigree and genetic simulator for complex family pedigree analysis, and a review on predicting gene expression from DNA sequence using deep learning models like Enformer and Borzoi.

I recently wrote a piece about leaving academia for biotech. I left academia for industry in 2019. I spent four years at a consulting firm before joining Colossal Biosciences. This week I’m returning to the University of Virginia School of Data Science as a tenured associate professor and dean of research. The transition from academia to industry can be tricky, but it’s also increasingly common.