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mmolari.bsky.social
Marco Molari
@mmolari.bsky.social
95 followers 110 following 25 posts
PostDoc @ Biozentrum - Basel in the group of Richard Neher Interested in microbial genomics, pangenome graphs & evolution 🧬🦠💻
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Reposted by Marco Molari
zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · 17d
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
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Reposted by Marco Molari
davidbrueckner.bsky.social
David Brückner @davidbrueckner.bsky.social · 27d
We're looking for highly motivated candidates for PhD positions in the physics of living systems.

Our group uses theoretical physics to understand how cells collectively self-organize.

If you're interested, get in touch & check out the Biozentrum PhD Fellowship program, deadline October 12th!
biozentrum.unibas.ch
Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 4
Apply now for the prestigious and independent #BiozentrumPhDFellowships. Great science. Unique rotation-based selection of research group and other incentives. The summer call is open until October 12, 2025. bit.ly/4caiqqX @biozentrum.unibas.ch @unibas.ch #fellowship #PhD#Switzerland
Biozentrum PhD Fellowships
Share your passion for life sciences. If you are talented and highly motivated, want to broaden your horizons and are interested in a wide range of research topics, apply for one of the sought after B...
bit.ly
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Reposted by Marco Molari
epcrocha.bsky.social
Eduardo Rocha @epcrocha.bsky.social · Sep 8
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...
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Reposted by Marco Molari
neher.io
Richard Neher @neher.io · Aug 23
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.

We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.

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www.biorxiv.org/content/10.1...
The Actinobacteriophage Database | Home
phagesdb.org
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Reposted by Marco Molari
firefoxx66.bsky.social
Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

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An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
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Reposted by Marco Molari
dhdegroot.bsky.social
Daan de Groot @dhdegroot.bsky.social · May 9
Bonsai is out! Finally, we can visually explore high-dimensional data in a distortion-free way. Try it out! It works from scRNA-seq data (bonsai.unibas.ch/bonsai-scout...) up to football statistics (bonsai.unibas.ch/bonsai-scout...). 
Ever wondered why low-dimensional embeddings like t-SNE
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Reposted by Marco Molari
nytimes.com
The New York Times @nytimes.com · Mar 10
Agencies within the Trump administration have flagged hundreds of words to limit or avoid, according to a compilation of government documents. These terms appeared in government memos, in official and unofficial agency guidance and in other documents. www.nytimes.com/interactive/...
A card reads: "These Words Are Disappearing in the New Trump Administration." A long list of words follows, including: biologically female; biologically male; BIPOC; Black; breastfeed + people; clean energy; climate crisis; climate science; commercial sex worker; community diversity; community equity; confirmation bias; cultural competence; cultural differences; cultural heritage; cultural sensitivity; culturally appropriate; culturally responsive; DEI; equity; feminism; genders.
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Reposted by Marco Molari
epcrocha.bsky.social
Eduardo Rocha @epcrocha.bsky.social · Jan 27
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
Transformation, Recombination and horizontal transfer
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Reposted by Marco Molari
neher.io
Richard Neher @neher.io · Jan 11
Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:

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www.biorxiv.org/content/10.1...
The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure
RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...
www.biorxiv.org
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 7
Thank you Will! 🙏 Coming from you who know the tool means a lot. Always inspiring to see it used!
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 7
Thank you so much! 🙏 Very very honored!
mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
Thank you! 🙏 That’s so nice to hear!
mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
Thank you Alice! 🙏
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[20/N]
We are curious to check in follow-up works whether these rates and patterns are specific to ST131, or are more general and can be found in other sequence types or even microbial species.

Hope you'll find the work interesting! Let us know if you have any observations or comments!
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[19/N]
To explain the total structural diversity of the dataset, more than 2000 distinct structural variations must have happened in its short evolutionary history, corresponding to an average rate of one every 3 mutations on the core-genome. This is a remarkably high rate!
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[18/N]
Most of the IS integrations disrupt genes, and such structural gains would be interpreted as loss events in gene-based analyses. However, this happens less than expected by chance, indicating that roughly 2/3 of these integrations have already been removed by purifying selection.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[17/N]
In binary junctions the vast majority of events are gains, often corresponding to an insertion sequence (IS) or prophage integrating in an otherwise conserved region of the genome. This corresponds to a rough rate of one of these events every 20 mutations on the core-genome.
Most events are gain events, associated to the movement of an Insertion sequence.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[16/N]
For binary junctions we can go even further: they can be associated with gain or loss events.
In particular singleton junctions correspond to events on terminal branches of the tree, while non-singleton junctions can in principle be associated also to events on internal branches.
By comparing presence / absence of sequence with the phylogenetic tree, we can associate junction with gain/loss events.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[15/N]
By looking at the content of the junctions, we find that the two peaks in binary junctions are explained by the movement of insertion sequences and prophages respectively, while hotspots are very flexible regions, rich in mobile genetic elements and defense systems.
In the previous scatter-plot we highlight junctions containing insertion sequences, prophages and defense systems. Insertion sequences are present in the majority of junctions, and in particular they explain the high number of 1 kbp junctions. Prophages are present in many hotspots, and also explain the enrichment in 30 kbp junctions. Defense systems are mainly present in hotspots.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[14/N]
On the other end of the spectrum we find hotspots, regions with tens to hundreds of different distinct paths, and a total accessory genome content of tens to hundreds of kbp in length.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[13/N]
If we scatter-plot these two quantities for all of the 519 junctions in the dataset, we find that the majority are binary, i.e. they contain only two possible distinct paths, of which one is often empty. Their length distribution is bimodal, with a peak around 1 kbp and another around 30 kbp.
scatter-plot of number of different paths and total accessory length for all junctions in the dataset. It shows an enrichment in binary junctions of length 700 bp and 30-40 kbp.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[12/N]
We look at the local graph between two adjacent core blocks, that we call a junction graph. In this graph the diversity can be quantified in terms of number of distinct paths and total accessory sequence content.
the portion of graph between two subsequent core-blocks is called a junction graph. One can quantify the number of different paths and the amount of accessory sequence in the junction.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[11/N]
Next we investigate the structural diversity in the accessory genome. The fact that the order of core-genes is mostly conserved provides a well-defined frame of reference in which to study accessory variation.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[10/N]
However, the fact that synteny is largely conserved across big evolutionary distances, and the fact that many of these changes happen on terminal branches of the tree, indicate that these changes are likely removed by purifying selection.
Phylogenetic tree with marks on the leaves that show core-genome rearrangements. Most of the events occur on terminal branches, possibly as a consequence of purifying selection.
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mmolari.bsky.social
Marco Molari @mmolari.bsky.social · Jan 6
[9/N]
This suggests that changes in synteny are relatively frequent, occurring at a rough rate of one every ~250 clonally-inherited mutations on the (filtered) core-genome.
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