Not all cichlid sex chromosome turnover happens at lightning speed!

What is the PhD actually for? A response to Prachee’s “Free the PhD”, and a critique of my own work

What is the PhD actually for, especially now that AI can do increasingly more of what we train scientists to do? compbiologist.substack.com/p/what-is-th...

A response to @pracheeac.bsky.social's thought-provoking essay "Free the PhD".

Delighted to share our latest research from the 23andMe Research Team, just published in @nature.com !
We looked at data from >27,000 participants to uncover how human genetics influences weight loss efficacy and side effects of GLP-1 medications like semaglutide. A short thread 🧵👇

Few people are aware of how much progress has been made against cancers.

Leukemia is probably the most striking example.

Before the 1970s, most children affected by leukemia would soon die from it.

Now, most children in rich countries survive.
ourworldindata.org/childhood-le...

ERK inhibits Capicua repressor function via multisite phosphorylation Highlighted Article: Multisite phosphorylation is important in the regulation of the Capicua (Cic) repressor by ERK, in part because multiple phosphosites contribute to Cic protein degradation.

I am excited to share that our paper on ERK-mediated Capicua (Cic) phosphorylation was published in its final form at @jcellsci.bsky.social ! A short 🧵 1/5
journals.biologists.com/jcs/article/...

OK Kids, our ERK story is finally heading out into the world. After 9 years of having funding, losing funding, losing staff, getting funding, gaining staff...it's ready!

We discovered a novel stage of what is an otherwise extensively studied process: how cells respond to extracellular signals. 1/n

"genAI can be used to create podcasts from a paper to teach st-"

Let me stop you right there. Before you feed somebody's paper to a slop machine, invite that somebody to talk to your students about their paper. We're right here. We academics won't shut up about our work, man. 🧪

Killifish community:

Spectral multiplexing is typically limited to 4-5 channels. Our new preprint introduces a framework that utilizes DNA barcoding and signal tuning to enable robust spectral unmixing and ground-truth benchmarking to achieve 15-plex subcellular profiling without cycling
www.biorxiv.org/content/10.6...

Graphics stating Apply to be a Preprint Editor

Preprint Editors – Development's next step into the preprint landscape

In this Editorial, @reinierprosee.bsky.social, @amjeve.uk and @jamesbriscoe.bsky.social announce a call for Preprint Editors in Development. Apply by 30 March.

doi.org/10.1242/dev....

Adapted from Axelsson et al. 2013 Fig 2c: Histogram showing the distribution of diploid amylase copy number in wolf (n=35, blue) and dog (n=136, red). Dogs carry more copies of the starch-digesting gene AMY2B than wolves. Additional copies make dogs better than wolves at digesting starchy foods like grains & vegetables.

Dogs evolved to eat your leftovers! Comparing dog & wolf genomes revealed dogs have up to 30 EXTRA copies of the amylase gene (AMY2B) that helps digest starch. This is a key genomic signature of living alongside humans & table scraps for thousands of years 🐕 www.nature.com/articles/nat... #2026MMM

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

Very happy to see this out. 👏 @yinanwan.bsky.social
Bogdan Bintu and team.
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...

Redefining cellular reprogramming with advanced genomic technologies - Nature Reviews Genetics Morris discusses how single-cell genomics and computational tools expose failure points in reprogramming and guide protocols that improve the fidelity, maturity and purity of engineered cells, advanci...

Excellent review by S. Morris in @NatureRevGenet on cellular reprogramming 🧬 How single-cell genomics & molecular recording tools are revealing why engineered cells still fall short — and how to fix it. A must-read for anyone in cell biology & regenerative medicine

www.nature.com/articles/s41...

If you're looking to build or deepen your knowledge in statistical genetics, the ISG Workshop (June 1–11) covers the full range: biometrics, GWAS, polygenic scores, causal inference, and more. Open to all levels, virtual, and international: www.colorado.edu/ibg/workshop...

Retweets appreciated 🙏

📢 Save the Date!
The 12th Aquatic Models for Human Disease Conference (AQMHD)
🗓 October 17–21, 2026
📍 Marine Biological Laboratory, Woods Hole, MA

Theme- Diving Deeper into Disease Biology: Emerging Models in Human Health

#AQMHD #ModelOrganism #MBL #DiseaseBiology

Molecular Complexity Constrained Early Amino Acid Recruitment into the Genetic Code Abstract. Previously proposed chronologies of amino acid incorporation into the genetic code rely on consensus rankings derived from prebiotic synthesis ex

Hashmi et al. reconstructed a complexity-based amino acid chronology, integrating 16 molecular complexity metrics, suggesting that molecular complexity constraints influenced substitution patterns during genetic code evolution.

🔗 doi.org/10.1093/gbe/evag012

#genome #evolution

I use the silver morph fox coat as a teaching example of selection against a recessive allele as these silver morphs are homozygotes for a pigmentation allele. They were prized by hunters and so they were selected against over time
See Figure 2 of Allendorf and Hard
www.pnas.org/doi/10.1073/...

The molecular evolution of vertebrate organs Nature Ecology & Evolution - This Review discusses recent advances in the molecular evolution of vertebrate organs, including rates of evolution of organs and cell types, molecular mechanisms...

Our internal organs are evolutionary marvels. New technologies are transforming our understanding of the evolution of vertebrate organs. You can find more by reading here:
rdcu.be/e5EgU
#EvoBio #EvoDevo 🐟🦎🐢🦇🐊🦜

Gotta admit, I’m somewhat heartened by this recent post (not WHAT it is reporting but that it IS reporting):

grants.nih.gov/news-events/...

Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio Aguilar-Gómez et al. use exome sequencing of 347 strawberry poison frogs to uncover the genetic basis of color variation. They identify that kit, ttc39b, and bco1 underlie blue-red, yellow-red, and gr...

The last chapter of my PhD is finally out !!!! In the same species, on neighboring islands, we see radically different warning colors emerge. Evolution in action:
Selection-driven color variation in the aposematic strawberry poison frog, Oophaga pumilio: Current Biology www.cell.com/current-biol...

Regeneration of fins and limbs relies on a shared cellular playbook The findings strengthen the case that regeneration is an old trait, offering insights into how complex tissues rebuild themselves.

www.sciencenews.org/article/rege... @josanesousa.bsky.social @gabrielalima19.bsky.social @perezlouise.bsky.social @patyschneider22.bsky.social

Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites Abstract. The evolution of sociality involves shifts in physiology and behavior, most notably the emergence of a reproductive division of labor. Within soc

Ploessl & Jones compared transcription factor binding motifs in 42 bee species, covering multiple independent gains and losses of sociality; findings demonstrate an expansion of TF motifs in lineages which have gained sociality.

🔗 doi.org/10.1093/gbe/evag003

#genome #evolution

Thanks @patyschneider22.bsky.social for a wonderful visit to @michiganstateu.bsky.social and a great talk in our #EEB seminar series! Check out her lab’s recent preprint on the four-eyed fish retina: www.biorxiv.org/content/10.1...

#EndlessFishMostBeautiful

Desert primroses & sand verbena illuminated by the setting sun.

Anza Borrego Desert State Park is absolutely amazing rn. #Bloomscrolling

Rethinking ADHD as ‘hypercuriosity’ What if ADHD isn’t a deficit of attention, but an intensified curiosity? A new study explores how reframing ADHD could transform education

Yes! What if we treated extremely normal human variation as something other than a "disorder"???

www.positive.news/society/yout...

NIGMS will have council meeting tomorrow. You can watch the open session here. nigms.nih.gov/node/145911

Google DeepMind unleashes new AI to investigate DNA’s ‘dark matter’ DeepMind’s AlphaGenome AI model could help solve the problem of predicting how variations in noncoding DNA shape gene expression

Google DeepMind unleashes new AI to investigate DNA’s ‘dark matter’ www.scientificamerican.com/article/goog...

More on the dark genome www.crick.ac.uk/news/2025-10...

Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis Researchers identified anoctamin-2 (ANO2) as a frequent autoimmune target in multiple sclerosis, with T cell responses against ANO2 occurring in over half of patients. These ANO2-specific T cells shar...

Epstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!!
🧪🧠Cell www.cell.com/cell/fulltex...

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

Fun! Link to original research: www.sciencedirect.com/science/arti...