Sign in

Julian Catchen

@jcatchen.bsky.social
940 followers 263 following 28 posts

associate professor, dept. of evolution, ecology, & behavior, UIUC. computational biologist and population genomics practitioner.

PostsRepliesMedia
Reposted by Julian Catchen
Ratna Karatgi @ratnakaratgi.bsky.social · 15/09/2026
New preprint out, where we examined the transcriptomic differences underlying the remarkable fin color diversity in Bluefin killifish, using the genome assembled by @jcatchen.bsky.social and Giovanni Madrigal
1102
Reposted by Julian Catchen
Angel G. Rivera-Colón @arcolon14.bsky.social · 18/08/2026
New version of our Pacific acorn barnacle genome paper is up on bioRxiv! Now titled: Large population sizes shape genome evolution in barnacles www.biorxiv.org/content/10.6...
biorxiv.org
042
Reposted by Julian Catchen
kottke.org @kottke.org · 23/07/2026
“A beloved, useful, free website, run carefully by a competent, honest person for nearly thirty years, was crushed between two features of the new AI economy.” (AI bots and prediction market dipshits.) [stephenfollows.com]
stephenfollows.com
What just happened to TheNumbers.com should worry us all
If you work in or around the film industry, there is a decent chance you have used the work of The Numbers this month, whether you realise it or not.
09056
Reposted by Julian Catchen
c0nc0rdance @c0nc0rdance.bsky.social · 08/07/2026
"The dream of every cell is to become two cells." - François Jacob, paraphrasing Jacques Monod.
"François Jacob (left) and Jacques Monod in the lab at the Institut Pasteur, 1971, New York Times obituary."  Two men in a laboratory, Monod in a white shirt and dark tie, smoking, standing behind Jacob, who is seated at a microscope, looking at a slide collection.

French biologists François Jacob and Jacques Monod were pioneering scientists at the Pasteur Institute who revolutionized molecular biology by discovering how cells regulate gene expression. For their groundbreaking work on the lac operon, they were jointly awarded the 1965 Nobel Prize in Physiology or Medicine.
1410613
Reposted by Julian Catchen
Katharina Hoff @katharinahoff.bsky.social · 11/04/2026
1/ BRAKER4 hatched! The Earth BioGenome Project is on track to sequence ~1.5M eukaryotic species. Every one needs a structural annotation. No Perl monolith was going to survive that. So we rewrote BRAKER from the ground up. github.com/Gaius-August...
16839
Julian Catchen @jcatchen.bsky.social · 18/11/2025
I am recruiting graduate students to my genomics-focused lab in EEB at Illinois Urbana-Champaign. Please spread the word if you know any students with an interest in a computational focus to genomics research! evol.mcmaster.ca/brian/evoldi...
evol.mcmaster.ca
https://evol.mcmaster.ca/brian/evoldir/GradStudentPositions//UIllinois.EEB.Genomics
The Catchen Lab (https://catchenlab.life.illinois.edu/), in the Department of Evolution, Ecology, and Behavior at the University of Illinois at Urbana-Champaign is recruiting graduate students to join...
01533
Julian Catchen @jcatchen.bsky.social · 26/08/2025
Our EEB department at the University of Illinois at Urbana-Champaign is hiring an assistant professor in evo-devo. See go.illinois.edu/EEBAsstProf for details. Please share!
03662
Julian Catchen @jcatchen.bsky.social · 19/06/2025
“Aware of my inability to detect AI use with certainty, I implored the students: please don’t use AI. It’s terrible for you. It’s terrible for me, a dystopian experience of spending weeks giving detailed constructive feedback to a machine.” www.forkingpaths.co/p/the-death-...
forkingpaths.co
The Death of the Student Essay—and the Future of Cognition
One professor's reflections on the end of an era, as AI tools such as ChatGPT have murdered the student essay (RIP). Here's why that threatens the future of human cognition—and how to save ourselves.
020
Julian Catchen @jcatchen.bsky.social · 08/05/2025
Finals start tomorrow here at UIUC. You may have seen the NYMag article outlining how pervasive AI has become in student course work, how it's degrading the learning experience. I wrestled with it all semester in my own course. But OpenAI knows the effects, and they known exactly what they are doing
Electronic sign in a UIUC campus building advertising free ChatGPT use during finals
074
Reposted by Julian Catchen
Mark Follman @markfollman.bsky.social · 13/03/2025
We will greatly miss our friend and longtime colleague Kevin Drum, as will all who knew him and his tremendous body of work. I had the privilege of editing Kevin for a spell, and I learned a lot from that, too. A top-notch thinker and writer, and a true mensch. www.motherjones.com/media/2025/0...
motherjones.com
Goodbye, Kevin Drum
"Take care of Donald Trump for me."
532444
Reposted by Julian Catchen
Josh Marshall @joshtpm.bsky.social · 11/03/2025
Remembering Kevin Drum talkingpointsmemo.com/edblog/remem...
talkingpointsmemo.com
Remembering Kevin Drum
Kevin Drum died on Friday. Many of you knew Kevin’s blog. For...
5753897
Reposted by Julian Catchen
Steven L. Johnson @stevenljohnson.org · 10/03/2025
Just learned political blogger Kevin Drum, who I've read daily since his CalPundit days 20+ yrs ago, has died. Along with Friday cat photos, his most enduring legacy may be bringing attention to the links between childhood lead exposure and early adult crime. I will miss his old-school blogging
en.wikipedia.org
Kevin Drum - Wikipedia
1366
Reposted by Julian Catchen
Josh Marshall @joshtpm.bsky.social · 06/03/2025
Everybody (me included) is getting bogged down on the details of events at NIH et al. Fatal mistake. The big picture is Musk/Trump are trying to shut down all gov-funded Medical/Disease research in the US. Have to understand that to have any hope of stopping it. talkingpointsmemo.com/edblog/act-now
talkingpointsmemo.com
Act Now
I may do a longer, maybe several longer versions of this post....
29691241
Reposted by Julian Catchen
Jeremy Yoder says no war @jbyoder.org · 02/03/2025
And, my @sciencehomecoming.bsky.social-inspired op-ed is online at LNP/Lancaster Online — in print, it's alongside a piece from two geoscientists with local roots on the front page of the Sunday Perspectives section lancasteronline.com/opinion/colu...
lancasteronline.com
Plant biologist who went from Manheim to the Mojave makes case for federal funding for science [column]
If there’s a single origin to my scientific career, it’s the moment Charlie Longenecker introduced me to chicory.
517753
Julian Catchen @jcatchen.bsky.social · 16/01/2025
If you want to search and/or visualize how a set of long reads lay down on a reference genome -- whether to check a gene annotation, for assembly error, or another reason, Gio Madrigal's Klumpy can help you do it. Excited to see it on the cover! (and online: catchenlab.life.illinois.edu/klumpy/)
Molecular Ecology Resources journal cover image of the Klumpy algorithm.
0238
Julian Catchen @jcatchen.bsky.social · 10/01/2025
Happy to see our latest work out in G3 @genetics-gsa.bsky.social. This is the fourth notothenioid genome our group has assembled so far -- a highly cold-specialized fish with a large complement of antifreeze proteins and an interesting set of chromosomal fusions/rearrangements.
030
Reposted by Julian Catchen
Daniel Bolnick @danielbolnick.bsky.social · 10/12/2024
We know that immune genes often show stronger signatures of selection than the genomic average. But what about immune cell types? In a new preprint www.biorxiv.org/content/10.1... we merge single-cell RNAseq (defining stickleback cell types) and population genomic measures of selection...
13610
Reposted by Julian Catchen
Bluesky @bsky.app · 03/12/2024
Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪
456294874996
Reposted by Julian Catchen
Jay 🦋 @jay.bsky.team · 19/11/2024
Bluesky now has over 20M people!! 🎉 We've been adding over a million users per day for the last few days. To celebrate, here are 20 fun facts about Bluesky:
307013027716061
Reposted by Julian Catchen
Milton Tan @mtanichthys.bsky.social · 15/11/2024
Just a quick reminder that PhD applications to work on this funded project are due Dec 1. If you're interested please feel free to reach out to me by e-mail.
067
Julian Catchen @jcatchen.bsky.social · 05/11/2024
This post by Tim Lee on his AI Substack is really good. It describes how 3 trends converged to create the AI boom: the (re)discovery of neural networks, the creation of the 1st massive training dataset, and CUDA, which allowed GPUs to be generalized to train models open.substack.com/pub/understa...
open.substack.com
Why the deep learning boom caught almost everyone by surprise
"You’ve taken this idea way too far," a mentor told Prof. Fei-Fei Li.
021
Reposted by Julian Catchen
Will Ratcliff @wcratcliff.bsky.social · 26/10/2024
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
27682324
Julian Catchen @jcatchen.bsky.social · 18/07/2024
Happy to release Stacks v2.67 today. This release updates process_radtags to make it easier to use SRA data and to filter poly-G (error) runs coming from Nextseq/Novaseq machines + bugfixes. We also added a genotype depth filter to populations #RADseq catchenlab.life.illinois.edu/stacks/
catchenlab.life.illinois.edu
Stacks
052
Reposted by Julian Catchen
Rachel Moran @rachelmoran.bsky.social · 05/04/2024
Please share! My lab will be hiring 2-3 postdocs over the coming months to study the genetic basis of behavioral traits in darters using brain transcriptomics & population genomics. First ad is posted here: tamus.wd1.myworkdayjobs.com/TAMU_Externa... #behavior #popgen #evolution #neuroethology
01624
Julian Catchen @jcatchen.bsky.social · 27/03/2024
If you are interested in the recent attempts to regulate Apple in Europe with the DMA, this is a really interesting (and long) piece by Steven Sinofsky, a major software engineer at Microsoft during its antitrust days (and after). hardcoresoftware.learningbyshipping.com/p/215-buildi...
hardcoresoftware.learningbyshipping.com
Building Under Regulation [215.]
An essay on the EU Digital Markets Act and Apple’s Update on apps distributed in the European Union (and some personal history)
000
Julian Catchen @jcatchen.bsky.social · 16/02/2024
If you have a sequence that you love – a gene family, transposable element, regulatory feature – you probably spend a lot of time looking for it in different sets of sequence. If so, you might find our latest preprint and software tool, Klumpy, useful. www.biorxiv.org/content/10.1...
biorxiv.org
Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
121
Julian Catchen @jcatchen.bsky.social · 30/10/2023
Interesting paper from J Pritchard's lab: "GWAS variants differ from eQTL variants along many axes…GWAS hits are biased toward more constrained genes…with complex regulatory landscapes…eQTLs show strong promoter bias largely absent from GWAS hits"
nature.com
Systematic differences in discovery of genetic effects on gene expression and complex traits - Natur...
This study seeks to explain the poor overlap of genome-wide association study and cis-expression quantitative trait locus variants using a model of differential selective constraint, suggesting that t...
042
Reposted by Julian Catchen
Thomas Desvignes @notothentoma.bsky.social · 26/10/2023
Ever wondered whether adapting to icy, oxygen-rich #Antarctic waters influenced #hemoglobin gene #evolution in #notothenioid fishes? And how white-blooded #icefish lost their hemoglobin genes? Our new MS is for you! A quick 🧵on our finding in @MolBioEvol! #Marinelife tinyurl.com/5n7ym3jp
1258
Julian Catchen @jcatchen.bsky.social · 24/10/2023
I have been having a lot of fun revising private allele analysis in #Stacks from #RADseq data. What are private alleles? Given SNPs in a set of populations, a private allele is found only in a specific population. 1/n
Chromosome genome scan showing private alleles from two species in a hybrid populationZoomed in 1Mbp region showing private alleles having introgressed into hybrid populations (dark blue vertical lines)
1145
Julian Catchen @jcatchen.bsky.social · 25/09/2023
Next week! Please join us: The Practice of RADseq: Population Genomics Analysis with Stacks, October 2-6, 2023 The course will focus on de novo (with parameter optimization) and reference analyses of RAD data, with new modules on PCR duplicates/allele dropout and private allele analysis
prstatistics.com
ONLINE COURSE – The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) This cou...
041