Archive - Paired Ends

Closing my tabs (Sep 12, 2025)

AI in academia, $1B NSF cut, AI+biosecurity, bacterial DNA from mammoth bones, understanding LLMs and their math, bioacoustics for conservation…

Sep 12 •

70 years of AI hype

Quoting from Olivia Guest et al. (2025) "Against the Uncritical Adoption of AI Technologies in Academia."

Sep 11 •

Single-cell analysis and infectious disease forecasting: Google's new AI scientist

In Google's new paper, "An AI system to help scientists write expert-level empirical software" an AI supposedly "invents" new methods in bioinformatics…

Sep 10 •

Make your development environment portable and reproducible

Dotfiles, VM setup scripts, R "verse" packages, and dev containers

Sep 9 •

Closing my tabs (Sep 5 2025)

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

Sep 5 •

Weekly Recap (Sep 2025 part 1)

Biobank-scale relatedness estimation, SNP calling and phasing with long RNA-seq reads, predicting expression-altering promoter mutations with DL…

Sep 2 •

August 2025

Closing my tabs (Aug 29, 2025)

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…

Aug 29 •

Using OpenAI Codex in Positron

Developing an R package using the OpenAI Codex agent in Positron

Aug 28 •

GitHub Repositories for Sequencing Companies

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

Aug 26 •

Closing my tabs (Aug 22, 2025)

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…

Aug 22 •

Weekly Recap (Aug 2025, part 4)

Genome annotation, viral genome clustering, metagenomic diagnostics, SV analysis on ONT reads, functional prediction, gene loss, DNA damage/repair…

Aug 21

Prejudicial Peer Review with AI

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

Aug 19 •

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