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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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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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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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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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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 · 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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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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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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