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Reposted by Tami Lieberman

Tiffany Lowe-Power 🌱🦠 @tlowepower.bsky.social · 21h

onlinelibrary.wiley.com/doi/full/10....

Remember -- it's easy to speculate that trait X imposes a fitness cost (but that's basically the biologist's version of drunk-uncle-whinging). Attacking with the T6SS doesn't impose a fitness cost.

Constitutive expression of the Type VI Secretion System carries no measurable fitness cost in Vibrio cholerae

The T6SS is a bacterial protein secretion system that is many multi-megadaltons in size, highly complex, and has a very conservative developmental regulation; all prior work has assumed that the T6SS...

onlinelibrary.wiley.com

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Tami Lieberman @contaminatedsci.bsky.social · 23h

We are recruiting new faculty in IMES at MIT!

IMES (Institute for Medical Engineering and Science) is the MIT home of the famous HST program. As faculty are also appointed in a department at MIT, we have diverse research programs, all focused on human health.

faculty-searches.mit.edu/imes-search/

MIT Faculty Searches MIT INSTITUTE FOR MEDICAL ENGINEERING AND SCIENCE FACULTY SEARCH

faculty-searches.mit.edu

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Reposted by Tami Lieberman

EvolDir @evoldir.bsky.social · 1d

Registration and abstract submission for the Probabilistic Modeling in Genomics Conference in Berkeley, March 2026, is open. Keynotes by Sally Otto and Jonathan Pritchard. Details: https://probgen2026.github.io/registration.html #conference

Registration - ProbGen 2026

probgen2026.github.io

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Reposted by Tami Lieberman

Emmanuele Severi @emmseveri.bsky.social · 1d

www.biorxiv.org/content/10.1...

#microsky #phagesky #phage

Phages communicate across species to shape microbial ecosystems

Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

www.biorxiv.org

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Reposted by Tami Lieberman

Frédérique Le Roux @fredoleroux.bsky.social · 2d

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community

Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

www.biorxiv.org

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Reposted by Tami Lieberman

Mark Peifer (He, him) @peiferlabunc.bsky.social · 3d

I'm very excited to announce that UNC Biology has 6 faculty positions open this year! The first is for an Asst Professor who studies organismal resilience using an integrative approach 1/n
unc.peopleadmin.com/postings/307...

Poster with QR code linking to the position

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Reposted by Tami Lieberman

Anne Carpenter @drannecarpenter.bsky.social · 5d

This means that we can screen for potential novel drugs for schizophrenia and bipolar disorder in easily-grown skin cells, using mitochondria as a simple readout. In fact, a team at NIH’s NCATS is working on this now! Stay tuned.

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Reposted by Tami Lieberman

Rachel M. Wheatley @rachelmwheatley.bsky.social · 5d

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The Lancet Microbe @lancetmicrobe.bsky.social · 6d

New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA

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Reposted by Tami Lieberman

Jason Furman @jasonfurman.bsky.social · 5d

The other day a student asked me about the prevalence of insider trading in prediction markets. I now have an answer.

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Reposted by Tami Lieberman

Inigo Martincorena @imartincorena.bsky.social · 6d

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 · 6d

!!! Sorry I missed this!!

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Reposted by Tami Lieberman

Eric Turkheimer @ent3c.bsky.social · 6d

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 · 6d

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 · 6d

...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 · 6d

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 · 7d

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 · 6d

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 · 6d

...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 · 6d

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 · 11d

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 · 6d

Holy moly

Cameron Thrash @jcamthrash.bsky.social · 7d

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 · 7d

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 · 7d

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 · 7d

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 · 7d

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 · 7d

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 · 7d

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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