@noahreid.bsky.social
Computational Biology Core at the University of Connecticut. Genomics, bioinformatics, evolution. Also nature, natural history. A little too into birding. https://scholar.google.com/citations?user=IbPpB9sAAAAJ&h
this is satire, right?
"after the late Thag Simmons", 12yo responds.
Watching netflix's The Dinosaurs with the family. A stegosaurus segment starts. They show the tail. My 12yo, who has been pickling his brain with The Far Side comics for several years looks at me and goes "the Thagomizer". Then Morgan Freeman says "it's called the Thagomizer". 🤯
We are offering a workshop on single-cell RNA-seq! Spaces are available!
Join us March 24–26 for a Virtual Single Cell RNA-seq Workshop! 🧬
🕙 10 AM – 2 PM ET
💻 MS Teams + recordings
🧑💻 No prior bioinformatics experience needed!
Register: bioinformatics.uconn.edu/cbc-workshops/
#RNAseq #Bioinformatics #Workshop
I like how typos in manuscripts are no longer considered evidence of sloppiness, and have turned instead into luxury signals of hand-crafted writing by a human master wordsmith who keeps to the traditional ways
New story on the Avian Hybrids blog!
A colorful mess: Widespread exchange of pigmentation genes across the Parulidae phylogeny
avianhybrids.wordpress.com/2026/03/11/a...
Based on the PLoS Biology paper by Kevin Bennett and his colleagues | #ornithology
Would have been epic to have a guano island warlord in Fury Road.
Didn't Vance say it?
“Fire every single midlevel bureaucrat, every civil servant in the administrative state, replace them with our people
Schrodinger's war?
"At no point in your rambling, incoherent response were you even close to anything that could be considered a rational thought. Everyone in this room is now dumber for having listened to it. I award you no points, and may God have mercy on your soul."
I am now grasping the rationale for this and it makes sense, but also, remembering a multitude of getter/setter functions for various packages has long been a problem for me.
The first time I got familiar with this is this epic rant from Aaron Lun on the Seurat R package to analyse single cell RNAseq data: github.com/LTLA/scRNAse...
We have an RNA-seq workshop including de novo transcriptome assembly/annotation coming up. Ideal for organisms without reference genomes.
Interesting, but also giving "it is illegal to repair your own automobile" vibes.
There's the data I want! obj@obj@obj@list$params
Wait is it bad to do this?
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
I believe there is. I don't have a custom R profile because customization scares me a little from a code sharing perspective, but this might push me to make one.
I have been an R user for my entire scientific life. I did not realize that the `$` accessor did partial matching so that `iris$Sp` will return the column for `iris$Species`.
It just drove me crazy for 20 minutes because I was making a typo that made one column name a partial match for another.
Thanks to micro-CT and www.antscan.info, you can now explore high resolution, 3D ant images from anywhere in the world. Fantastic work from Julian Katzke, Francisco Hita Garcia, @economo.bsky.social, Thomas van de Kamp and colleagues just dropped: www.nature.com/articles/s41...
The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.
NSF Update (Awards through 2/27/26)
Directorates to follow
1/10
The growing number of sequenced #genomes provides a positive feedback loop, in which database searches become more effective and shared sequence patterns emerge more clearly www.nature.com/articles/s41... #biodiversity #genomics
“The forces we are up against have made peace with mass death. They are treasonous to this world and its human and non-human inhabitants.”
At this rate I just hope we get WWIII out of the way before my kids are draft age.
For people who still care about this sort of thing, here's James Madison writing from 1793 (6 years after the delegates in Philadelphia signed the Constitution) about why the power to make war was vested in the legislature.
press-pubs.uchicago.edu/founders/doc...
theonion.com/this-war-wil...
