Warming nest boxes by 2°C during great tit nestling development accelerated telomere shortening and reduced post-fledging survival, likely via increased metabolic demand rather than oxidative stress. https://www.biorxiv.org/content/10.1101/2021.12.21.473625

A tribe of weevils has cracked a rare evolutionary puzzle: shifting hosts between parasitic and non-parasitic plants across distantly related families. Phylogenomic analysis reveals how plant-plant parasitism creates unique opportun... https://www.biorxiv.org/content/10.1101/2024.04.03.587887

This week in preprints: just one, but it's a fascinating look at how enhancers cluster in 3D space at transcriptional condensates.

A new algorithm called BOUQUET maps which genes interact with transcriptional condensates by integrating 3D genome topology and protein binding data. The approach identifies "3D-super-enhancers"—exceptionally protein-rich regulatory... https://www.biorxiv.org/content/10.1101/2024.02.01.578210

Google Trends for "contaminados" and "contaminados in english"

This week in preprints: 3 papers spanning human brain genomics, phylogenetic methods, and cancer evolution. Some nice methodological advances across scales.

Researchers developed SVCFit, a tool that tracks how prostate cancer evolves under treatment by analyzing large chromosomal rearrangements often missed by standard approaches. https://www.biorxiv.org/content/10.1101/2025.02.01.636056

Researchers built a massive atlas of 13.3 million predicted protein structures from 824 insect species, revealing that structural analysis detects remote evolutionary relationships invisible to sequence-based methods.

Researchers found three previously unknown whole-genome duplications in yeast, challenging the long-held view that such events are rare in fungi. The work reveals these ancient duplications occurred 100-200 million years ago.

Excited to announce our latest publication in reporting evidence for three (3!) new whole genome duplications (WGDs) in yeasts. Scientists have often wondered why WGD is so rare in fungi, it turns out we may just not have been looking hard enough! 🧪 🍄 🧬 www.sciencedirect.com/science/arti...

Researchers tested ASTRAL species tree inference with realistic gene tree dependence from recombination. Gene trees on chromosomes aren't independent, but full independence isn't needed for accuracy. https://www.biorxiv.org/content/10.1101/2024.06.06.597697

Researchers mapped sex differences in the human hypothalamus at single-cell resolution, revealing how specific neuron types contribute to sex-biased psychiatric and metabolic disorders. https://www.biorxiv.org/content/10.1101/2024.12.07.627362

This week in preprints: 3 papers exploring the genome's hidden corners and catalytic machinery. From dark matter DNA to long noncoding RNAs to vitamin B12 enzymes doing their dance.

Researchers captured crystal structures of methionine synthase in action, revealing that five-coordinate, His-off methylcobalamin drives homocysteine methylation—not the expected six-coordinate form. https://www.biorxiv.org/content/10.1101/2024.08.29.610163

Ancient hybridization drove plum diversification across tropical and temperate zones—a rare biome transition in woody plants. Machine learning quantified leaf traits tied to this success spanning 50 million years. https://www.biorxiv.org/content/10.1101/2023.09.13.557598

One thing I keep thinking about from this morning's preprint: if these lncRNAs are "poorly expressed in bulk RNA-Seq" but show functional signals, what does that tell us about tissue heterogeneity vs. true rarity? Would love to hear from single-cell folks on this.

GENCODE doubled human gene annotations through targeted long-read sequencing of lncRNAs across matched tissues. 17,931 new human genes added—the largest expansion since the genome was first sequenced. https://www.biorxiv.org/content/10.1101/2024.10.29.620654

166 poorly characterized human transcription factors mapped in living cells. Half bind known regulatory regions. The other half—"Dark TFs"—each recognize unique repeat sequences in closed chromatin. https://www.biorxiv.org/content/10.1101/2024.11.11.622123

A new algorithm can jointly analyze tens of millions of genetic variants at once in whole genome sequence data. Applied to human height in UK Biobank, it reveals rare variants and achieves 46% prediction accuracy. https://www.biorxiv.org/content/10.1101/2023.09.14.557703

Without a shadow of a doubt, I've had the opportunity to grow so much at Berkeley -- and I have grown. Dear Universe, thank you

Art that is human-made feels like a beautiful act of resistance against AI. Lux by Rosalia is a great example I anticipate we will see more and more of this — and human-made, much like hand-made goods, will come at a premium

Wikipedia reminds me that millions of strangers collectively built one of the greatest knowledge resources in history -- and it is free. Faith in humanity stays strong

I hope everyone is having a restful and happy holiday 😊

Things are coming up roses

Fluorescent microscopy is beautiful🔬✨ People who are pushing the envelope will not only uncover new biology, but captivate (and entice!) new generations of brilliant minds to love biology the same way we do

I'm taking recommendations for the type of content you'd like to see on my Substack. I feature weekly newsletters about what is happening in BioAI (eg, research advances) and what is happening in Biotech (eg, acquisitions, mergers) Please feel free to DM me if there's something you'd like to see!

A highlight of my career was when one of my thesis chapters was highlighted on the #SciShow by @hankgreen.bsky.social. I was in my 2nd or 3rd year of my PhD

I'm way too into keyboards 😆

Did the first animal look like a sponge or a comb jelly? The debate continues. Check out the article from MCB's Nicole King and postdoc Jacob Steenwyk @jlsteenwyk.bsky.social: news.berkeley.edu/2025/11/19/d...

There's been an uptick in visitors to my website jlsteenwyk.com. If there is a type of content that you would find helpful (e.g., more bioinformatics tutorials, etc), please let me know! My website has many purposes including serving as a resource for the community!

Prompt: "Can you rotate the clade encompassing A, B, C and D" 1st image is the original, the 2nd image is after 'rotation' They are the same. The LLM was unable to rotate the clade. Frontier Labs, we can get this right - I feel very strongly about our ability to do so! bsky.app/profile/jlst...

Wow - what a location! This looks awesome! bsky.app/profile/erik...

Companies building frontier LLMs, please let me help you teach your models how to interpret evolution These are *so* wrong, but I know we can get it right. prompt: "create an image of a phylogenetic tree with the following topology (((A,B),(C,D)),E);"

Hey folks, we (the School of Life Sciences at Arizona State University) are looking for an Assistant Teaching Professor in microbiology and immunology. Please pass this on to anyone you think might be interested, or check it out if you are interested yourself! apply.interfolio.com/176994

"Project Prometheus aims to build AI systems for engineering and manufacturing across several industries, including computers, automobiles, and spacecraft" www.eweek.com/news/jeff-be...

Over a century ago, Hannah Höch gifted us with the Dada piece titled "Cut with the Kitchen Knife Dada Through the Last Weimar Beer-Belly Cultural Epoch of Germany" (1919-20). imo, this collage shreds meaning, mocks certainty, and still feels more honest than most timelines today. Awesome piece

today has been a wonderful day of rot

Perhaps I should clarify that I speak for myself and can't speak on behalf of my social media-free advisor. So please consider this my personal stance :) bsky.app/profile/jlst...

Cherry chip #mushrooms 🍒🍄 This reddish-orange #mushroom gets its name from a #cherry-like coloration🔴 and for being found in #wood chips🌳 Awesome find in the backyard!

Folks have been super kind regarding this manuscript It is such a contentious topic that I wondered if letting this project go beyond the four walls of the lab was a personal/emotional mistake But no - it wasn't People are chill. People are nice. This community rules 🤘 bsky.app/profile/jlst...

Today is the last day to register! Please consider doing so - it is going to be a fun one! Register here: evomics.org/apply-worksh... bsky.app/profile/jlst...

I decided to join in on the fun and write a popular science-y article about the recent manuscript. It is available on the @genomelybio.bsky.social Substack Subscribe for free :D genomely.substack.com/p/what-was-t... bsky.app/profile/jlst...

I really appreciated this popular science article covering our recent manuscript — big shout-out to @jakecurrie.bsky.social, thank you so much for taking the time to share your writing! nautil.us/fierce-debat... bsky.app/profile/jlst...

The number of free subscriptions to @genomelybio.bsky.social substack has been steadily growing. Super thankful folks find my BioAI and biotech development weeklys helpful. Looking forward to writing more deep dives in the future. Appreciate you :) open.substack.com/pub/genomely...

Tomorrow registration closes for the #Phylogenomics and Evolutionary #Genomics workshop in the beautiful Czech Republic! The #faculty are world-class -- this isn't one to miss! Register today and learn both the fundamentals and advanced techniques in the field! evomics.org/apply-worksh...

Whoa - we've seen a big bump in the number of registrants! After some communication among the organizers, we've decided to continue accepting registrations. Registration closes tomorrow, so please register today! evomics.org/apply-worksh... bsky.app/profile/jlst...

I just finished my 2nd reading of this perspective. It is so great. The article captures a great deal about the sponge/ctenophore and is measured in its assessment of what the true tree is. I absolutely share this position bsky.app/profile/jlst...

tbh, I've really been in my feels about this lately My family situation means leaving the West Coast, even California, will be hard Snagging a job out here is tough. Rejections have largely been due to fit -- or so I'm told But, I'll keep trying while I still can :) bsky.app/profile/jlst...

This may be my last major contribution in academia, I will be content with/ what I've done, & I will always miss the people I've met along the way You all have been & continue to be a major source of inspiration, not only for how I conduct science, but for my personhood🫶 bsky.app/profile/jlst...