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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 50m

I almost forgot I wrote a short review in 2019 saying this. genomemedicine.biomedcentral.com/articles/10.... The new supplementary notes have useful maths and historical references though.

Somatic mutation and clonal expansions in human tissues - Genome Medicine

Recent sequencing studies on healthy skin and esophagus have found that, as we age, these tissues become colonized by mutant clones of cells carrying driver mutations in traditional cancer genes. This comment summarizes these findings and discusses their possible implications for our understanding of cancer, ageing, and other diseases.

genomemedicine.biomedcentral.com

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Tami Lieberman @contaminatedsci.bsky.social · 48m

!!! Sorry I missed this!!

Reposted by Tami Lieberman

Eric Turkheimer @ent3c.bsky.social · 2h

Blog post: Ancestry and Education
Indirect, direct, confounded and quasi-causal.

I write about a preprint by Wang et al, in which they look for associations with genetic ancestry in an admixed Mexican population. They found genetic effects for height and Type-II diabetes, but not for education.

Ancestry and Education

Indirect, direct, confounded and quasi-causal

ericturkheimer.substack.com

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Tami Lieberman @contaminatedsci.bsky.social · 1h

Long time admirer if your work.

Thanks so much for putting these notes into the world. I think a separate article with these same points (maybe even not expanded much) would be highly impactful-- especially coming from someone like you.

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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 2h

...or (2) the observation of driver mutations in normal tissues "proves" that non-mutational factors are needed to explain cancer (epigenetics, promotion, etc). Of course, many other factors are important, but ... [2/4]

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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 2h

A short thread. For years, I have been surprised by how much confusion our discovery of clones carrying cancer-driver mutations in normal tissues has caused in the cancer community. Typical questions like: (1) if you see these mutations in normal cells, are they really cancer drivers?... [1/4]

Inigo Martincorena @imartincorena.bsky.social · 1d

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

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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 2h

In our latest paper, I wrote 2 supplementary notes (5 and 6) to briefly recap classical models, starting with Armitage&Doll and moving onto models with different types of clonal expansions. Some readers may find them of interest. [4/4] static-content.springer.com/esm/art%3A10...

static-content.springer.com

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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 2h

...the observation of large numbers of clones with driver mutations in normal tissues is perfectly consistent with (and indeed predicted by) multistage models of carcinogenesis dating from the 1950s. In the constant rush for new data, we seem to have forgotten invaluable lessons hidden in them [3/4]

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Asaf Levy @asaflevylab.bsky.social · 6h

Very well deserved prize for Prof. Vorholt, one of my favorite productive and humble scientists! and what a great meating it was!

Julia Frunzke @frunzkelab.bsky.social · 5d

Just returning from a fantastic symposium celebrating my former postdoc mentor, Julia Vorholt, on receiving the Novonesis Biotechnology Prize! Huge congratulations to Julia — and to the Novo Nordisk Foundation on an outstanding choice!

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Reposted by Tami Lieberman

Vaughn Cooper @vscooper.micropopbio.org · 20h

Holy moly

Cameron Thrash @jcamthrash.bsky.social · 1d

Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope www.nature.com/articles/s41... #jcampubs

Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope - Nature Communications

Loretan and colleagues present a low-cost smartphone-based microscope capable of detecting single-molecule fluorescence. This approach opens doors to personalised and widely distributed applications in diagnostics, biosensing, and science education.

www.nature.com

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Reposted by Tami Lieberman

Matthew Neville @mattneville.bsky.social · 1d

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

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Reposted by Tami Lieberman

Laura Helmuth @laurahelmuth.bsky.social · 1d

Six of the nine Nobel Prize winners this year work in the U.S.
Three of the six were born outside the U.S., which is the pattern most years. No country has benefited more from welcoming immigrants from around the world.
www.nobelprize.org

The official website of the Nobel Prize - NobelPrize.org

The Nobel Prize rewards science, humanism and peace efforts. This is one of the central concepts in the will of Alfred Nobel, and it also permeates the outreach activities that have been developed for...

www.nobelprize.org

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Tami Lieberman @contaminatedsci.bsky.social · 1d

We did not explicitly do that, but our assumption of varying local selective pressures is quite similar to some types of frequency dependent selection.

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Tami Lieberman @contaminatedsci.bsky.social · 1d

I believe that similar signatures have been found in mammals. academic.oup.com/mbe/article/...

Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

Abstract. Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged

academic.oup.com

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Tami Lieberman @contaminatedsci.bsky.social · 1d

Indeed it may be the same claim. We were cautious to restrict ourselves to species for which we have the most evidence, but perhaps this is generalizable.

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Tami Lieberman @contaminatedsci.bsky.social · 1d

Yes, thats our hypothesis. Its comes from observations of frequent in-person adaptive evolution involving stop codons in key genes (potentially phage receptors).

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Tami Lieberman @contaminatedsci.bsky.social · 1d

We've made a related but different claim in bacteria:
elifesciences.org/articles/93146

Reversions mask the contribution of adaptive evolution in microbiomes

The timescale dependence of dN/dS in bacteria is better explained by adaptive than purifying dynamics, suggesting comparative genomics can underestimate past adaptation.

elifesciences.org

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Reposted by Tami Lieberman

C. Brandon Ogbunu @cbo.bsky.social · 1d

www.pnas.org/doi/10.1073/...

In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS

Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...

www.pnas.org

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Reposted by Tami Lieberman

Claus Wilke @clauswilke.com · 2d

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Reposted by Tami Lieberman

Ryan Flynn @raflynn5.bsky.social · 2d

We found that csDNA is not restricted to cultured cells, but in health donors, B cells and monocytes had clear csDNA accumulation while T cells and NK cells did not.

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Reposted by Tami Lieberman

Ryan Flynn @raflynn5.bsky.social · 2d

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells

The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...

www.biorxiv.org

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Tami Lieberman @contaminatedsci.bsky.social · 2d

The response from the senator was quite bad-- talking only about policy and paperwork, when there was the opportunity to refute her claims about caring for the state and talk about freedoms.

Reposted by Tami Lieberman

Erik Bakkeren @erikbakkeren.bsky.social · 2d

Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️

MEEhubs @meehubs.bsky.social · 2d

We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org

Home

meehubs.org

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Reposted by Tami Lieberman

Maddy Seale @maddyseale.bsky.social · 2d

Wonderful to see this beautiful image on the cover of Science this week highlighting a paper that uses high resolution imaging to show the spatial patterns of bacterial attraction to glutamine from roots.
Paper here: www.science.org/doi/10.1126/...
Perspective here: www.science.org/doi/10.1126/...

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Dave Baltrus 🦦 @surtlab.bsky.social · 2d

Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination

academic.oup.com/g3journal/ad...

Genomic correlates of tailocin sensitivity in Pseudomonas syringae

Abstract. Phage-derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular enviro

academic.oup.com

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