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Marco Molari

@mmolari.bsky.social
113 followers 117 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
SIB Swiss Institute of Bioinformatics @sib.swiss · 15/06/2026
Welcome Eneida Hatcher from the NIH! Her extensive experience will strengthen Switzerland's leadership in pathogen tracking and epidemic preparedness, including through flagship global project the Pathogen Data Network (PDN). @dessimoz.bsky.social @tanjastadler.bsky.social
sib.swiss
Eneida Hatcher joins SIB as Centre for Pathogen Bioinformatics director
Genomic surveillance expert Eneida Hatcher joins SIB today as director of the Centre for Pathogen Bioinformatics. Coming from the US National Institutes of Health (NIH), she brings over a decade of ex...
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Reposted by Marco Molari
Dr Emma Hodcroft @firefoxx66.bsky.social · 07/11/2025
I want to spell this out in case the implications aren't clear: This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited. The file allowed this. Cut that - cut off all tools the public & others were using.
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Reposted by Marco Molari
Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
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. Thread 1/n
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David Brückner @davidbrueckner.bsky.social · 15/09/2025
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!
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Eduardo Rocha @epcrocha.bsky.social · 08/09/2025
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...
pasteur.fr
Pasteur-Paris University International doctoral program​ (PPU)
OverviewIn 2009, the Institut Pasteur, the world leading biomedical research institute founded by Louis Pasteur in 1887, inaugurated the Pasteur Paris-University (PPU) international doctoral program i...
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Reposted by Marco Molari
Richard Neher @neher.io · 23/08/2025
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. [1/6] www.biorxiv.org/content/10.1...
phagesdb.org
The Actinobacteriophage Database | Home
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Reposted by Marco Molari
Dr Emma Hodcroft @firefoxx66.bsky.social · 25/07/2025
📢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! 1/5
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
Daan de Groot @dhdegroot.bsky.social · 09/05/2025
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
bonsai.unibas.ch
First select a node by clicking in the tree, then click the below buttons to indicate if that node is the ancestor or a downstream node of the subtree.
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Reposted by Marco Molari
The New York Times @nytimes.com · 10/03/2025
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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Eduardo Rocha @epcrocha.bsky.social · 27/01/2025
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
Richard Neher @neher.io · 11/01/2025
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: [1/N] www.biorxiv.org/content/10.1...
biorxiv.org
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 ...
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Marco Molari @mmolari.bsky.social · 07/01/2025
Thank you Will! 🙏 Coming from you who know the tool means a lot. Always inspiring to see it used!
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Marco Molari @mmolari.bsky.social · 07/01/2025
Thank you so much! 🙏 Very very honored!
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Marco Molari @mmolari.bsky.social · 06/01/2025
Thank you! 🙏 That’s so nice to hear!
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Marco Molari @mmolari.bsky.social · 06/01/2025
Thank you Alice! 🙏
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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[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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Marco Molari @mmolari.bsky.social · 06/01/2025
[8/N] Using the graph we can survey all possible changes of synteny in the dataset. Out of 222 isolates, we find only 26 with any change in synteny. Most of these changes are inversions, often around the origin or terminus of replication.
schematic representation of all observed changes in order of genes in the core genome for the dataset considered.
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Marco Molari @mmolari.bsky.social · 06/01/2025
[7/N] Core-genome synteny, i.e. the order of core genes, has been shown to be strongly conserved across large evolutionary distances. But what happens on short timescales?
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Marco Molari @mmolari.bsky.social · 06/01/2025
[6/N] Once selected the dataset we tackle a second challenge: detecting structural changes. For this we encode all genomes in a pangenome graph. The fundamental units of this representation are blocks, encoding alignments of homologous sequences, and paths, encoding genomes as sequences of blocks.
Schematic representation for a pangenome graph. Edges in the graph represent alignments of homologous portions of the sequences in different genomes. Each genome is a particular walk through the graph.
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Marco Molari @mmolari.bsky.social · 06/01/2025
[5/N] Thanks to its recent evolution, we can filter out the effects of recombination from the core-genome alignment of this dataset, and recover a reliable phylogeny.
A core-genome phylogenetic tree for our ST131 dataset.
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Marco Molari @mmolari.bsky.social · 06/01/2025
[4/N] To solve this problem we focus on a recently-diverged Sequence Type (ST): E. coli ST131. Estimated to have originated around 1900, this multidrug-resistant ST reached global distribution under antibiotic pressure. We download n=222 complete genomes from RefSeq.
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Marco Molari @mmolari.bsky.social · 06/01/2025
[3/N] Horizontal Gene Transfer, i.e. the exchange of genetic material from one individual to the next, is at the origin of many of these changes. This process however also complicates phylogenetic inference, invalidating the hypothesis of exclusively vertical inheritance.
schematic representation of a phylogenetic tree, with horizontal exchange of genes between different branches of the tree.
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Marco Molari @mmolari.bsky.social · 06/01/2025
[2/N] We were motivated by this puzzling observation: microbial genomes can be extremely similar in the core genome, while still differing by large portions of accessory genome. Therefore we ask: 1) how does this diversity accumulate? 2) at what rate do genomes undergo large structural changes?
Two microbial genomes can be extremely similar on the portions that can be aligned, with less than one mutation every 10000 basepairs, while still retaining a lot of accessory diversity, for example having one non-shared gene every 10.
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Marco Molari @mmolari.bsky.social · 06/01/2025
Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉 academic.oup.com/mbe/advance-... Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬 A summary thread [1/N]🧵
academic.oup.com
Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes
Abstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics
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Marco Molari @mmolari.bsky.social · 22/12/2024
Grazie Alice! Buone Feste!!!
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Reposted by Marco Molari
Dr Emma Hodcroft @firefoxx66.bsky.social · 11/12/2024
It's a huge honour to have been named by Nature as "One to Watch" in 2025 for @pathoplexus.org ! 🙏 I'm proud to see Pathoplexus continuing to draw attention - but this is truly a team effort and only possible thanks to all the amazing people involved! 🙌 swisstph.ch/en/news/news... 1/2
swisstph.ch
Swiss TPH Researcher Emma Hodcroft Named by Nature as 1 of 3 People To Watch in 2025
Emma Hodcroft, group leader at Swiss TPH and assistant professor at the University of Basel, was named one of three people to watch in shaping science in 2025 by the renowned...
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Reposted by Marco Molari
Dr Emma Hodcroft @firefoxx66.bsky.social · 28/11/2024
It's an incredible honour to have received this #OpenData prize from Swiss Academies of Arts & Sciences for @pathoplexus.org! Though not everyone in Pathoplexus could be there in person, it was a fantastic & thought-provoking event, & I'm so glad were part of it! #OpenScience #OpenSource
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