Lightnews — Scholar-powered news

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 10h

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

4 8

Reposted by Vladimir (Vova) Seplyarskiy

Matthew Neville @mattneville.bsky.social · 11h

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...

Sperm sequencing reveals extensive positive selection in the male germline - Nature

A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.

www.nature.com

3 36 56

Reposted by Vladimir (Vova) Seplyarskiy

Inigo Martincorena @imartincorena.bsky.social · 11h

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...

Somatic mutation and selection at population scale - Nature

A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many genes.

www.nature.com

3 20 44

Reposted by Vladimir (Vova) Seplyarskiy

Nuria Lopez-Bigas @nlbigas.bsky.social · 11h

🚨 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)

Sex and smoking bias in the selection of somatic mutations in human bladder - Nature

Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.

www.nature.com

2 14 40

Reposted by Vladimir (Vova) Seplyarskiy

Peter Ly @peterlylab.bsky.social · 15h

One week left to apply!

Children's Research Institute at UT Southwestern @cri-utsw.bsky.social · 23d

🔬 APPLY NOW: Seeking faculty scientists in #stemcells #TissueRegeneration #metabolism & #cancerbiology.

You ready for #relentlessdiscovery at our collaborative Institute? Learn more at cri.utsw.edu/careers & apply before Oct. 15. 🤜💥🤛

#jobs #faculty #facultyjobs #ScienceJobs 🧪

3 2

Reposted by Vladimir (Vova) Seplyarskiy

Joshua G. Schraiber @jgschraiber.bsky.social · 2d

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.

The New York Times @nytimes.com · 2d

The number of international students arriving in the U.S. in August fell by 19% this year compared with last year — the largest decline on record outside of the pandemic.

Nearly 20 Percent Fewer International Students Traveled to the U.S. in August

The data shows the steepest decline in August international student arrivals since the pandemic.

nyti.ms

13 22

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

Thank you Martin!

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

Maha and Masha carried this study, Shamil supervised it and Elli helped with cancer genomics angle of the paper

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

Finally, using data from MIke's paper on lesion segregation in normal blood, we show that persistent lesions mark branches under positive selection.

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

Even more striking, we detected two branching points only three cell divisions apart (and developed a trick to measure that), aligned with two chemotherapy cycles.

In other words, the tree literally connects cell divisions to treatment pulses, informing about frequency of cell divisions.

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

With help from Mike Chapman, we re-analyzed single-cell DNA data from the blood of a chemotherapy-treated AML patient.

This phylogenetic tree let us watch clonal expansions unfold almost in real time, capturing how lesions mark the first few divisions of a growing clone.

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

Than we focused on metastatic tumors from Hartwig collection. And using patterns of multiallelic mutations identified samples with signatures of lesion segregation. We also found that metastasis with lesion segregation pattern grow very rapidly

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

We started with data generated in lesion-segregation study and with help of refined methodology and new theory estimated selection for tumors in mice.

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

First we were inspired by series of works on lesion segregation by @mstaylor.bsky.social Duncan Odom and @s-j-aitken.bsky.social groups, that shows how to use lesions to measure time between pulse of mutagen and tumor MRCA (we call it LAD). We developed theory to measure selection from LADs

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 3d

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...

Segregating DNA lesions point to high selective advantage of tumor initiating cells

The complications with identifying cells at the origin of cancer and tracking their early divisions impede studies of cancer initiation. Recently, it was shown that some DNA lesions generated by a pul...

www.biorxiv.org

2 9

Reposted by Vladimir (Vova) Seplyarskiy

Ana Ignatieva @anaignatieva.bsky.social · 5d

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)

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies

Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla

academic.oup.com

4 37 60

Reposted by Vladimir (Vova) Seplyarskiy

Liz Neeley @lizneeley.bsky.social · 6d

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.

2 190 490

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 7d

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

bioRxiv Genetics @biorxiv-genetic.bsky.social · 10d

Mutation bias in driver genes reveals the distribution of effects of oncogenic mutations https://www.biorxiv.org/content/10.1101/2025.09.25.678277v1

1

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 11d

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...

Tenure-Track Faculty Position in Human Genetics - Dallas, Texas (US) job with The University of Texas Southwestern Medical Center (UT Southwestern Medical Center) | 12845141

Tenure-Track Faculty Position in Human Genetics

www.nature.com

2

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 12d

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....

| bioRxiv

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

Reposted by Vladimir (Vova) Seplyarskiy

Robin Hofmeister @rjhfmstr.bsky.social · 12d

🚨 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...

1 17 30

Reposted by Vladimir (Vova) Seplyarskiy

bioRxiv Genetics @biorxiv-genetic.bsky.social · 18d

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

4 5

Reposted by Vladimir (Vova) Seplyarskiy

Georgii "Yegor" Bazykin @gbazykin.bsky.social · 20d

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/...

Careers | Emory University | Atlanta GA

faculty-emory.icims.com

27 14

Vladimir (Vova) Seplyarskiy @vseplyarskiy.bsky.social · 21d

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

Sofya Garushyants @garushyants.bsky.social · 23d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Reposted by Vladimir (Vova) Seplyarskiy

Carl Zimmer @carlzimmer.com · 24d

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

nyti.ms

12 220 400