Not that long ago, in vivo mouse enhancer design was a dream. Today, it's a reality! Using transfer deep learning to design de novo synthetic embryonic enhancers active in the heart, limb, and CNS. Great collab with @alex-stark.bsky.social lab! @ucibiosci.bsky.social @impvienna.bsky.social

Within a pitcher plant, bacteria break down prey to feed the plant. As the leaf ages, bacteria become less diverse, but more efficient at degrading insects. It appears that species that are strong degraders are weak competitors. Read now ahead of print! www.journals.uchicago.edu/doi/10.1086/...

Biologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated). #iteachbio 🧪 #Evolution

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social, @natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

Interesting article on the evolution of views of Stephen Jay Gould in relation to punctuated equilibria. www.cambridge.org/core/journal... 🧪 #Paleobio #EvoBio

Excited to share the final version of our study on Nematostella cell type regulatory programs. Part of our @erc.europa.eu StG project, this was a challenging 5-year effort extraodinarily led by @aelek.bsky.social and @martaig.bsky.social. www.nature.com/articles/s41...

Happy to announce the publication of our foray into studying what happens to the transcriptomes of nuclei when cells fuse to form a syncytium. More to follow in the coming few years. One really wonderful thing about the Company of Biologists is that's it's free to publish there for my university!

All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.

"Range extender mediates long-distance enhancer activity" by @evgenykvon.bsky.social 's team, led by @gracebower.bsky.social is one of my papers of the year. Discovery of a new class of cis-regulatory elements that modulate the regulatory activity and reach of enhancers. doi.org/10.1038/s415...

Hey all, I reached out to the PO of my NIGMS MIRA to ask if the gov't shut down, and rescheduling of study sections, might allow for some accommodation to the standard rule that PIs cannot resubmit a MIRA while their MIRA (or other RPG) is under review (waiting in scores or summary statements) 🧪

Check out our preprint investigating host use in sympatric Caenorhabditis nematodes! We found three Caenorhabditis species in a local community are associated with different invert taxa, and document a strong association between one species and invasive nitidulid beetles. doi.org/10.64898/202...

Very excited to share this work led by Austin Link, a graduate student in our lab. We have discovered a novel, fig-associated microbe that promotes reproductive success via variable life history mechanisms in two nematode species. www.biorxiv.org/content/10.6...

The Golden Age of Caenorhabditis ecology is right now.

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes www.biorxiv.org/content/10.6...

Live thread of the NSF biology virtual office hour: 🧵

NSF bio hour - NSF BIO lost 40% of its staff 😑

Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA? Well, wonder no more! (Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social) "No molecular evidence for Muller's ratchet in mitochondrial genomes" www.biorxiv.org/content/10.6...

Engineering the auxin-inducible degron system for tunable in vivo control of organismal physiology www.nature.com/articles/s41...

Abundant Recurrent Mitochondrial Mutations and Widespread Mitonuclear Epistasis in Caenorhabditis elegans academic.oup.com/mbe/article/...

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

How did I miss this one??! Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation journals.plos.org/plosgenetics...

1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size! www.biorxiv.org/content/10.6...

It's in print! My opinionated dive into the definition of "coevolution" is officially out in the December issue of @journal-evo.bsky.social doi.org/10.1093/evol...

I taught Genetics again this year. We need to include discussion of the problematic history of our field, especially as the claims of eugenics are once again centered in our political discourse. Last year I wrote this piece, explaining my reasoning and approach 🧪 1/n www.cell.com/trends/genet...

😀 Nictation behavior in nematodes link.springer.com/article/10.1...

**How distributed is the brain-wide network that is recruited for cognition?** That goes to the top of the list! #neuroskyence doi.org/10.1038/s415...

IMO it’s weird and probably irresponsible to teach bioinformatics without some nod to the group dynamics that shaped (otherwise inexplicable) things like the GFF file format or the Gene Ontology. Not to mention why tools back then had names like BLAST and FASTA,but now are named after cuddly animals

Since AI slop is again all over Scientific Reports, a thread on the economics of grey-zone publishing. Why does slop keep getting published? What does it mean for science? How can we stop this? Background readings: Understand the strain: tinyurl.com/2b6wxx5r Stop the drain: tinyurl.com/3jfscscy

#Throwback 🧪 COMMENT | Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics KS Lee, X Su & T Huan

The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts. We have been mapping mRNA modifications for over a decade. => Characterizing their functions -- especially on translation -- is a research frontier.

New must-read review article for all lovers of #centrioles and #centrosomes 😍👇

Paper alert! Mechanical conditions preventing live cell extrusion during primary neurulation in amniotes. @sabr-bio.bsky.social article published as pre-proof in @cellsdev.bsky.social! doi.org/10.1016/j.cd...

How to keep in step when your (protein) partner speeds up… Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection. Congrats to whole team! www.science.org/doi/10.1126/...

(1/3) Imagine reconstructing a history over a billion years in the making. New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process. www.nature.com/articles/s41...

Read this inspiring perspectives coauthored by the Worm Resource directors and worm Nobel Laureates! 4 Nobel Prizes and how they were enabled by major NIH-supported research resources (the Caenorhabditis Genetics Center, WormBase, and WormAtlas) www.pnas.org/doi/10.1073/...

Real age prediction from the transcriptome with RAPToR www.nature.com/articles/s41...

Latest work out today in @currentbiology.bsky.social We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬 To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain). 🔗 tinyurl.com/2vyuevpy

MLT-11 is necessary for C. elegans embryogenesis and conserved sequences play distinct roles in cuticle structure www.biorxiv.org/content/10.1...

Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis www.nature.com/articles/s41...

We are hiring! The School of Biological Sciences at the University of Oklahoma is seeking an Assistant Professor studying the Neurobiology of Pain. Applications are due Nov. 21. Please share with colleagues! apply.interfolio.com/175314

Apply!! Applications are due tomorrow!!!

Re-posting this! Applications are due Friday!

Divergent organelle allocation in the evolution of sperm gigantism revealed from subcellular quantification of nematode sperm with electron microscopy academic.oup.com/evolut/advan...

TE dynamics across high-quality #genome assemblies of 75 bee species to quantify their diversity in an evolutionary context link.springer.com/article/10.1...

I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A

Diplolaimelloides woaabi sp. n. (Nematoda: Monhysteridae): A Novel Species of Free-Living Nematode from the Great Salt Lake, Utah reference-global.com/article/10.2...

I wrote this insight for eLife. A friend said, "Why would you want to step on that rake?". Well, I guess that's just who I am. Enjoy. elifesciences.org/articles/109...

this looks very interesting with numerous implications for nuclear biology and gene expression. Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions: Cell www.cell.com/cell/fulltex...

Transposon Regulation in the Caenorhabditis elegans Germline and Soma www.biorxiv.org/content/10.1...