A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers. buff.ly/K7CGFLV

Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.

1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.

Boring, field-specific answer. This SMART-PTA technology, which allows genotype + phenotype in hundreds of somatic cells, will lead to an expansion of population genetics for somatic cells as a field. www.biorxiv.org/content/10.1...

This story is absolutely wild. Did you know that avocados change sex over the course of a day? And that it's controlled by a single ancient balanced polymorphism? This is flat our crazy

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

Number 7 in our year-end countdown of most popular @royalsocietypublishing.org papers takes a look at a twist in avian biology: up to 6% of individuals in five wild bird species naturally switch sex, a discovery that could reshape conservation strategies. https://bit.ly/4qihFCL

Our new preprint is out: www.biorxiv.org/content/10.6... We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!

I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here: elinck.org/popgen_conge...

Good coverage in the @economist.com about the investigation of Denisovan ancestry and possible connections to the Yunxian Homo erectus group. (paywall) www.economist.com/science-and-...

It has been a remarkable year of discoveries. From ancient Pompeii, to the medieval Avars, to the American Southwest. Plus some advances in 3D organization of ancient genomes and an ancient disease with unexpected roots. And lots about Denisovans! www.johnhawks.net/p/top-10-dis...

Come learn with us! #REU!

"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD. (...) These results suggest that TAD boundary architecture and gene activity are largely uncoupled"

The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31 probgen2026.github.io

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Seven feel-good science stories to round up 2025. All too often we forget to celebrate the positives 🧪 #AcademicSky www.nature.com/articles/d41...

Well well. The standard model for how frequencies of recessive disease genes are established doesn't work. And that seems to be because recessive variants are visible to selection due to pleiotropy. (But still we teach Mendelian genetics...) www.biorxiv.org/content/10.6...

Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

These people are nuts. NCAR developed the GPS dropsonde, which revolutionized the understanding of TC structure, improved forecasts, and validated remote sensing platforms, as documented in over 400 peer-reviewed publications in the last 25 years. And that’s just one of NCAR’s countless advances.

Congratulations to the winners of the 2025 Genomic History Inference Strategies Tournament challenges! Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...

New preprint from our lab: ‘Retroviral insertions contributed to the divergence of human and chimpanzee brains’. Very proud of this piece which took almost a decade to finish. www.biorxiv.org/content/10.6...

Everytime I read something like this it makes me so angry. The fact that a society has been letting this happen for so long and so often that there are now regularly people who live through a second mass shooting before even finishing their education is the most shocking indictment of US politics

Our latest preprint revisits the classic model of mutation-selection balance. Do human recessive genes fit Haldane's 100-year old model? This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io www.biorxiv.org/content/10.6...

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

How did DNA changes that alter protein structures impact evolution on the branch that led to modern humans? As we demonstrate today in Science Advances, biobanking initiatives offer ways to directly assess biological effects of rare archaic variants in living people, & (re)evaluate their roles. 🧬🧪

🚨New paper out! In our @MolCellNews paper, we solve a piece of the puzzle of how our genome folds. We found the two specific molecular "brakes" in the CTCF protein that stop DNA loop extrusion. One of the final pieces of my PhD! tinyurl.com/29uuc5by

Thank you Alex! Excited to see our paper published in @nature.com ! Huge thanks to @jeffspence.github.io , @tkyzeng.bsky.social , @emmamarydann.bsky.social, @nikhilmilind.dev, @marsonlab.bsky.social, @jkpritch.bsky.social, and all the members of the Pritchard and Marson labs for your enormous help!

1/4 Thrilled to be sharing new work published today in Nature describing the third wave of results from the PGC Cross-Disorder Group. This reflects a massive group effort to examine shared and unique genetic signal across >1 million cases for 14 psychiatric disorders. www.nature.com/articles/s41...

NEW: multiple (senior) postdoctoral fellow roles in Mo Lotfollahi's group at @sangerinstitute.bsky.social There are many research focus areas available, including Open Targets translational AI projects Apply now: sanger.wd103.myworkdayjobs.com/en-US/Wellco...

Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too! preprint (with videos!) + thread 🧵 Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking www.biorxiv.org/content/10.6... 1/9

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...

'Introducing a lottery before peer review in the research funding application process can boost women’s chance of success by almost a quarter, a new study has found, with its authors saying that the approach can also reduce costs and make applying for funding less labour-intensive.' 1/2

We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1.... This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen. 1/7

Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions www.pnas.org/doi/10.1073/...

please share this postdoc job alert! come join the budding Biodiversity Cell Atlas initiative as a postdoc or senior postdoc at @sangerinstitute.bsky.social working closely with @arnausebe.bsky.social and me to make progress on what we cover in this paper www.nature.com/articles/s41...

Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...

Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods Xenium CosMx 1k MERSCOPE Tissue Microarray 17 tumor+16 normal tissue Transcript count vs Reference RNAseq Segmentation accuracy Cell type annotation #NatComms 2025 www.nature.com/articles/s41...

The most precious commodity you have is your attention. You don’t have to waste it on poor-faith debates or arguments with strangers if you don’t think they’ll be productive. You can prioritize the things that matter to you and make your life richer.

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social www.cell.com/cell/fulltex... Key findings in a thread (1/6):

How do new centromeres evolve while staying compatible with the division machinery? Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore. 👉 doi.org/10.1038/s41586-025-09779-1

The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)

This is a remarkable open access resource for genomic work on living great apes. www.nature.com/articles/s41...

📣📣📣 Excited for our lab's latest preprint, led by Chief Ben-Eghan! www.medrxiv.org/content/10.1... tl;dr We identify protein vQTLs in multiple ancestries then use MVMR to show independent effects of mean & variance on disease, suggesting targeting protein variance could have therapeutic potential.

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

To celebrate the publication of the paper about GHIST 2024, the 2025 Genomic History Inference Strategies Tournament has been extended to December 1st, 2025. Read about the 2024 competition in Molecular Biology and Evolution: doi.org/10.1093/molb... And join the 2025 competition at ghist.bio!

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...