Job AD. Research Directions: 1. Selection in early development; Pop gen methods applied to new technologies, i.e. scDNA-seq with D. Shao 2. Study of hypermutability and selection using population cohorts with E. Koch 3. Evolution of Mutagenesis with M. Penenell & @jgschraiber.bsky.social

I rounded up some of the missing heritability discussions from the past few weeks and got the last word in (for now).

What causes bladder cancer initiating mutations? Our paper in Science Advances asks the question: can BK virus infections of normal urothelium lead to the APOBEC3 mutational signatures found in bladder cancers? We found that they can!

Transcription start sites show a strong influx of heritable variants arising in early development. Our new paper is now in Nat. Comms: www.nature.com/articles/s41... It would be interesting to see this effect in the new mosaic-mutation dataset from @r-rahbari.bsky.social and @isaacgs94.bsky.social.

New preprint with @pyjiang.bsky.social and @kelleyharris.bsky.social! The discovery and patterns of the underlying long-standing mild-effect mutator alleles in S. cerevisiae populations www.biorxiv.org/content/10.1...

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.

How is functional variation at large-effect loci maintained in natural populations, even as environments change? In a paper led by @mkarag.bsky.social, we tracked known pesticide resistant alleles in outdoor 𝘋. 𝘮𝘦𝘭𝘢𝘯𝘰𝘨𝘢𝘴𝘵𝘦𝘳 cages & inferred selection and dominance from temporal sequencing data.

New publication alert! Click-code-seq, our DNA-damage sequencing method, is now out! This tool can advance our understanding of aging, cancer and neurodegeneration. Huge thanks to the amazing collaborative team behind this! @sturlalab.bsky.social @ethz.ch

The exciting next instalment of Mutations in Time and Space... Open for registration now

Isaac et al, congratulations on a great work! May I ask two questions: a) did you see effect for TFBS that was described here www.biorxiv.org/content/10.1... and b) is there any way to share mosaic mutations as suppl table?

Nature research paper: Evidence for improved DNA repair in long-lived bowhead whale go.nature.com/4oNJSAG

WEEKEND LISTEN This year, the Trump admin threw everything it had at the nation's oldest and richest university 3 Harvard profs tell the story of what they saw @naxerova.bsky.social @ryanenos.bsky.social & Kit Parker www.wnycstudios.org/podcasts/otm...

New preprint from another part of my PhD! 📝👇 Some mutations arise after fertilisation 🧬, so early they can appear in both a parent’s body and their germ cells. By analysing family trio genomes 👪, we built one of the largest catalogues of these “hidden” inherited variants yet. tinyurl.com/mvns2ytv

I’ll be attending #ASHG25! I’m currently hiring for (i) a Senior Research Scientist or (ii) a Postdoc position in my lab. If you’re interested, please reach out to arrange a time to meet and discuss.

Who wants to chat at #ASHG2025? Also, I have no idea how to navigate this many posters - so if you think I should take a look at yours, let me know!

Age distinguishes selection from causation in cancer genomes https://www.biorxiv.org/content/10.1101/2025.10.06.680730v1

Our paper on clonal expansions in Sperm is out in Nature www.nature.com/articles/s41... If you are interested in working at an intersection of Mendelian genomics/Population genetics/Clonal expansions +Cancer genetics/ and of course mutagenesis, please rich out about postdoc in my lab

Now published! Our paper on: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/n] www.nature.com/articles/s41...

Our latest work is out in Nature today. In this paper, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people www.nature.com/articles/s41...

🚨 New paper alert! Sex and smoking bias in the selection of somatic mutations in human bladder www.nature.com/articles/s41... by @raquelbmi.bsky.social, @ferriol.bsky.social et al (in collaboration with Rosana Risques lab in @uwmedicine.bsky.social)

One week left to apply!

Just an absolutely horrific self own, depleting the US of amazing students from all over the world who contributed to what used to make America great: its diversity, its openness, and its leadership in education.

How fast does a cancer clone expanding after first driver mutation? In our new preprint, we show that you can measure selection during the first cell divisions, using segregating DNA lesions. TL;DR: Founding cells grows fast, producing >1.3 cancer each division. www.biorxiv.org/content/10.1...

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

Some problems have simple solutions. This new “Compact for Academic Excellence in Higher Education” is one. The answer is simply saying no. Simple does not mean easy. But Brown, Dartmouth, MIT, Vanderbilt, Univ of AZ, UPenn, USC, UT Austin & UVA must understand what they’ll lose if they sign on.

Cool idea to detect selection, from excessive variance in distribution of mutations. Could be a mice tool especially for missense mutations, with heterogeneous effects

I’m excited that my department at UT Southwestern (McDermott Center) is recruiting a new colleague in human genetics for a tenure-track faculty role. It’s a great place to do science — please apply or share: www.nature.com/naturecareer...

Huge paper: DREAM complex ⬆️ somatic mutation rate, helping explain 10–100× higher mut rates vs germline. www.biorxiv.org/content/10.1... connects variability in mutation rate across tissues to DREAM. Though about similar things myself after this paper www.nature.com/articles/s41....

🚨 New preprint out! We reconstructed parental haplotypes in >440k individuals (UK & Estonian biobanks) to estimate assortative mating directly in the parental generation. This reveals intensified assortment in recent generations. www.biorxiv.org/content/10.1...

Sex differences in transcription-associated mutagenesis in the human germline https://www.biorxiv.org/content/10.1101/2025.09.18.677082v1

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University. If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch. faculty-emory.icims.com/jobs/151181/...

Sonya is an incredible college. Not ideal circumstances, but you can turn it into new opportunities

A deep dive into the destruction of US cancer research by @jonathanmahler.bsky.social “It’s an absolutely unmitigated disaster,” a former top official at NIH told him. “It will take decades to recover from this, if we ever do.” Gift link: nyti.ms/48iH3Cr

SINGER, our ARG inference method, is finally published and freely available online: doi.org/10.1038/s415... It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...

After our study on RNU4-2 and RNU5B-1 published in May (Nava et al, Nature Genetics 2025), I am excited to share our new preprint reporting dominant and recessive variants in RNU2-2 as a frequent cause of developmental and epileptic encephalopathy (DEE). 📄 www.medrxiv.org/content/10.1...

In these dark times, it comes as a rare pleasure to highlight @natanaels.bsky.social ‬ & @marcdemanuel.bsky.social's work on germline and somatic mutations in humans. 1/n www.biorxiv.org/cgi/content/...

New paper led by @yadirapga.bsky.social! Opossums have babies at 6-months of age, but are still highly male-biased in their mutations academic.oup.com/genetics/adv...

I wrote an op-ed on the world-class STEM research ecosystem in the United States, and how this ecosystem is now under attack on multiple fronts by the current administration: newsletter.ofthebrave.org/p/im-an-awar...

Dive into the step-by-step choreography of transcription-coupled DNA repair. In our new review published in Nature Cell Biology, we explore what we know and what’s next in this exciting field of research! www.nature.com/articles/s41...

I NEED to tell you the story of Tae Heung “William” Kim. He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease. He's a *legal permanent resident* of the United States. And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.

Today is my last day at the @uoe-igc.bsky.social in Edinburgh, as I'm starting my own lab in Munich as part of the German Cancer Consortium (DKTK), DKFZ and the LMU. I'll continue to focus on DNA damage and mutagenesis to determine their role in somatic evolution and disease.

I still can’t believe that all NIH grants to my colleagues at Harvard and Harvard Medical School have been nullified. And that, as a nation, we’re somehow okay with this illegal, arbitrary, and petty act. Just think of the consequences: scientists, students, and patients will all suffer.

New paper by Luke O'Connor @lukeoconnor.bsky.social and Guy Sella @gs2747.bsky.social

Introducing 2 new papers from my lab on somatic mutations in liver disease. The 1st is about a mutated gene that leads to improved clone fitness and organismal health (CIDEB). The 2nd is about a mutated gene that leads to improved clone fitness but worse overall health (TBX3). 1/8

Delighted to share our latest on longitudinal methylation dynamics preceding cancer. Epigenetic signs of AML appear in blood DECADES before Dx. 👉 Early cancer detection 👉 Methylation drivers 👉 Epimutation rates 👉 CpG lineage tracing www.biorxiv.org/content/10.1...

The cells in our bodies constantly acquire mutations. But what are the patterns of mutations across tissues? How do mutations in normal cells lead to cancer and disease? These are questions we will tackle within the Somatic Mosaicism across Human Tissues (SMaHT) Network, now described in @nature.com

🚨 Looking for postdocs! I'm starting my lab at UT Southwestern this September. If you're interested in: 🧬 Somatic & germline mutagenesis 🐭 Evolution of mutation processes 🧠 Adjacent areas like Mendelian genomics & population genetics—please consider joining. Formal ad coming soon. DM me!

Are you ready for the 2nd half of 2025? Social DNAing is ready. Check out the speaker list and schedule! Sign up at www.cancer.columbia.edu/research/pro...

Social media grump Kamila has finally made it onto Bluesky! Please check out my new perspective on metastasis evolution in @natrevcancer.nature.com if you need a reprieve from the news. I tried my best to develop some new conceptual thoughts here, you be the judge whether I succeeded.

If you’ve ever wondered about the statistical significance of differences among mutational signature profiles, check out our new Aggregate Mutation Spectrum Distance (AMSD) preprint co-led by Sam Hart and @alisonfeder.bsky.social with @nalcala.bsky.social www.biorxiv.org/cgi/content/...