So excited to finally share my recent work on sex differences in crossing over using mice from diverse genetic backgrounds! www.biorxiv.org/content/10.6...

Now accepted in Genetics! academic.oup.com/genetics/adv... We ask why and when rescaling of forward simulations in population genetics is not accurate. There are some interesting results for people performing simulations with selection.

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

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.

Hi all! We developed CAD-C to map chromatin organization at high res in yeast. It revealed an unexpected tight alignment: nucleosomes covering the same sequence tend to be associated across sister chromatids. www.biorxiv.org/content/10.6... #3DGenome #chromatin #Cohesin #centromere

Population genetics analysis in a phylogenetic framework shows convergent evolution in the genomes of five brood-parasitic species, including selection on genes involved in spermatogenesis, sperm function and nervous system development 🧪 www.nature.com/articles/s41...

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...

"The 3D genome during germline development and meiosis" by Yuka Kitamura & Satoshi Namekawa "Distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis..." FREE till Feb 4 at authors.elsevier.com/a/1mHYpcQbJF...

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Preprint online right before the holidays! Excited to share the first piece of work from the Zhang Lab, led by my absolutely stellar postdoc Michelle Kim! In this work, we ask how admixture, selection and demography shape complex trait genetics and GWAS performance 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...

I wrote about the bizarre case of Herasight, the embryo selection company going all in on eugenics.

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...

So excited to finally be able to share my first paper and the culmination of my PhD work with @felipekteixeira.bsky.social 🪰🔬 www.pnas.org/doi/10.1073/...

I am happy to share that my postdoctoral work in the @gerlichlab.bsky.social at @imbavienna.bsky.social is finally out 🎉! Our study reveals how cohesin guides focused and accurate homology search. Read more 👉 www.science.org/doi/10.1126/... Follow along for key insights and updates! 🧵

@science.org 🧬🔬 A vision of #chromosome organization | Science www.science.org/doi/10.1126/... @vram142.bsky.social et al.

Our latest, led by the inimitable Chris Kay "Dated gene duplications elucidate the evolutionary assembly of eukaryotes" in which we used gene duplications to test hypotheses of eukaryogenesis. TLDR? They're all wrong. With @tweethinking.bsky.social @anya1.bsky.social @ssolo.bsky.social Davide Pisani

I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making! Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃 https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #MolecularEvolution

Our new ancient DNA paper has just been published! We present 28 new genomes from southern Africa - several of them high-coverage whole genomes. Exciting to be moving towards population-level representation of ancient southern African genetic diversity! www.nature.com/articles/s41...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

I am very pleased to see our work, in which we describe a mutational hotspot at transcription start sites in the human germline, out: www.nature.com/articles/s41... Great work from @castellanoed.bsky.social, @vseplyarskiy.bsky.social, Miguel Cortés Guzmán and Clàudia Serrano Colomé!

So excited to see my PhD work finally being published!!! It was such a pleasure working with a great team!!!

Beautiful story on the evolutionary response to fly telomeres battling the genome they protect the ends of! Also, nice to see that the dream data clarity we all imagine when starting a project can actually materialize! www.science.org/doi/10.1126/... @sungyalin.bsky.social @levine-lab.bsky.social

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

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

Excited to share a preprint of my PhD project looking at interactions between SNPs and polygenic scores in the UK Biobank! A thread... 🧵 www.medrxiv.org/content/10.1...

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)

I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...

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/...

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

The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup! Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉. Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.

Next paper published in the @hpgg-pivot.bsky.social special issue on popgen methods and software! Coll Macià & Skov "Best practices and pitfalls in using hmmix for reference-free detection of introgressed sequences" doi.org/10.47248/hpg... Submission for contributions still open to 15 January!

Paper out now: A curated dataset of the great ape genome diversity! rdcu.be/eQLCi

Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...

Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social #TEsky #TEworldwide authors.elsevier.com/c/1m6MC,LqAZ...

Amazing to have a byline with @cbo.bsky.social - read our take on Watson’s ultimate legacy in the Boston Globe. Will be in Sunday’s print edition.

Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals go.nature.com/47UiBWa

SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the @simonsfoundation.org. Details to follow. Please RT.

"Homologous recombination counteracts mismatch repair to promote fertility and genetic diversity" by Ting-Fang Wang (@tingfangwang.bsky.social) & Ji-Long Liao (廖吉隆) "We postulate that counter-actions of MMR and HR contribute to the post-zygotic isolation..." authors.elsevier.com/sd/article/S...

Happy to share Jialin's first publication. She did a great job exploring the transition to land in animals. Co-supervised by the great Jordi Paps and me and in collaboration with Davide Pisani and @phil-donoghue.bsky.social

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

Come join us in beautiful Britanny, France in May 2026 for a workshop that I am organizing with @lucievirevolte.bsky.social and @psudmant.bsky.social on Rapid host adaptations to infections: sites.google.com/berkeley.edu...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia. www.biorxiv.org/content/10.1...

𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n