AI-Enabled Biological Design and the Risks of Synthetic Biology
Chapter 3 of the National Academies report on AIxBio: Biosecurity implications for what AI can and can't do in biology today....
Reading RNA modifications directly with nanopore sequencing
New RNA sequencing tools enable direct detection of multiple RNA modifications from nanopore data, simplifying epitranscriptome analysis with a single modification-aware basecalling model......
One immune variable predicts poor outcomes across tumor types and species
Using RNA sequencing, researchers identify a conserved pro-tumor neutrophil state marked by CCL3 expression, revealing how specific immune cell programs support cancer growth across tumor types......
Weekly Recap (February 6, 2026)
Positron + Jupyter, Claude Opus 4.6, Vicki Boykis at AMLC, Emily Riederer, Wes McKinney, Codex, CC for science, R updates (R Data Scientist, R Works, R Weekly, R-Ladies, rOpenSci), AlphaGenome, ......
State of the Blog
<p>ChatGPT came out in November 2022 and it has completely changed the Internet. In my post Learning about ChatGPT via ChatGPT I had prompted: "Will ChatGPT replace Google?" to which the model back th...
ULMnet – inferring physical cell-cell communication networks from scRNAseq data using univariate linear models
A new RNA sequencing–based method uses multiplets in scRNAseq data to infer physical cell-cell interactions, revealing tissue......
Understanding what’s going on inside of cells: the dimensionality of gene expression
Researchers at the University of Miami Miller School of Medicine research provided strong evidence that a new platform is a viable, accurate approach to mapping cell development.Dr. Leor Weinberger, c...
Using enadownloader to download fastqs from the ENA
<p>I wanted to download fastq files for a long list of SRR accessions from the <a href="https://www.ebi.ac.uk/ena/browser/home">ENA</a> today.</p><p>I realised I could use the <a href="https://av...
Ten simple rules for teaching data science
A new paper from Tiffany Timbers (UBC) and Mine Çetinkaya-Rundel (Duke), and lessons I learned from my time with Software Carpentry...
Making assemblies for Oxford Nanopore sequence data using Dragonflye
<p>I've been making genome assemblies for some Oxford Nanopore Technology (ONT) sequencing data using the <a href="https://github.com/rpetit3/dragonflye">Dragonflye</a> package by Rober...