On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

Job alert🚨📢! Join us as Director of the SIB Centre for Pathogen Bioinformatics, on a topic where global collaboration is particularly important, in a highly stimulating environment. This is a research infrastructure leadership position. Apply or spread the word! apply.refline.ch/499599/0346/...

Apply for our Master of Science in Physics of Life – training in cutting-edge research at the interface of physics, mathematics, engineering and life sciences. Scholarships available. Application deadline: 30 November. More: www.biozentrum.unibas.ch/education/de... @biozentrum.unibas.ch @unibas.ch

📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU. Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.

Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging www.biozentrum.unibas.ch/open-positio... #biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging

HHMI adopts Plan U journals.plos.org/plosbiology/...

What novel biological dynamics might be hiding under the measurement noise of your time-lapse fluorescence microscopy data? Try our new RealTrace tool to find out! Fantastic work by Bjoern Kscheschinski and others. Tweetorial follows. 1/n www.biorxiv.org/content/10.1...

Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond. Read more: virological.org/t/the-16th-e... 1/7

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Join us for an exciting #BiozentrumDiscovery lecture! Prof. Tami Lieberman from @mit.edu will speak about the dynamic selective landscape of human microbiomes. Her lab studies microbial evolution in real time, with a focus on mutations occurring within individual human microbiomes.

Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover. And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak. #IDsky 🧪 virological.org/t/the-16th-e...

Super excited that our group will be supported by an ERC Starting Grant! In project "InfoFate" we will study how cells use information in dynamical, neighborhood & mechanical signals to make decisions. We'll have PhD and Postdoc positions available, please get in touch if interested!

🗓 Pathoplexus turns ONE! 🎂🎉 In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing. 📰 Read the full update: pathoplexus.org/news/2025-08... 1/10

🤔 Can migrating cells 'remember' their past trajectories? In collab w/ @sgabriele.bsky.social & @kyohalie.bsky.social, we address this question: Confined cells undergo geometry-sensitive morphology switches, and these switches depend on the past migration history! www.nature.com/articles/s41...

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...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

A fascinating SARS-CoV-2 sequence was recently uploaded—collected from a dog in Kazakhstan in July 2022. Usher puts the sequence one nuc mutation from the Wuhan reference (C21846T, S:T95I)—i.e. pre-D614G. Could this sequence somehow have a close connection to the first days of the pandemic? 1/18

The Guardian with a clear take: www.theguardian.com/commentisfre...

I have never seen anything like this in NYC. 5th Ave covered from 42nd St well to the 20s. Nobody prepared for this volume. Volunteers are holding the traffic on all the side streets. No police in sight. #handsoff

🧬 Pathoplexus at GA4GH April Connect At the @broadinstitute.org, experts gathered to discuss the future of genomic data sharing. Alongside Anna Parker (ETH Zurich) & @theo.io (LSHTM), we introduced Pathoplexus.org and Loculus to members of @ga4gh.org. 1/4

Mr. Trump, this statute at the National Museum of African American History and Culture does not "undermine the remarkable achievements of the United States". It does not "fosters a sense of national shame." It does not "advance a corrosive ideology." It is literally what might redeem the USA.

France raises a fascinating hypothetical point: what if the law still exists even if people might get mad at you

From my colleague @cellarchlab.com and his lab at the @biozentrum.unibas.ch I continue to be amazed by what cyro-electron tomography can do...

Photo Umit Bektas. www.nytimes.com/2025/03/24/w...

Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available. More information: www.biozentrum.unibas.ch/education/de... #Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland

5 years ago, I subscribed to Eco di Bergamo and spent a few hours counting obituaries in Feb/March. Most cases in northern Europe at the time were travel returnees that didn't get very sick, but the 7x increase in mortality in Bergamo left no doubt what happens if the virus hits the vulnerable.

Do you remember BA.3—the weakling cousin of BA.1 & BA.2 that seemed to take the worst from each & had weaker ACE2 binding than even the ancestral Wuhan Virus? After three years, BA.3 is back. And it is transmitting. Who saw this coming? 1/13

Current state of EU legislation on crop breeding summed up in one picture. Note that all plants carry the same mutation! One does not need to be a scientist to understand the this legislation makes no sense. #GMOs #CommonSense @testbiotech

At the masters level, together with @knutdrescher.bsky.social @neher.io @mihaelazavolan.bsky.social @davidbrueckner.bsky.social @cellarchlab.com and others, we just started a very exciting Physics of Life masters program. www.biozentrum.unibas.ch/education/de... which has scholarships also.

Great idea. To add to this list, my institute @biozentrum.unibas.ch has a wonderful international PhD fellowship program: www.biozentrum.unibas.ch/phd/internat... Students do rotations and choose their PhD lab. Also great for students with quantitative background.

Wer hätte es ahnen können…

Major cuts planned in SRF science journalism in Switzerland - the public service media. Scientists today launched a petition ‘Facts Instead of Misinformation: For Strong Science Journalism!’ Become one of over 1,800 signatories www.openpetition.eu/ch/petition/...

Thinking the unthinkable: With #CDC webpages going dark & research funding getting slashed, scientists are beginning to fear for the integrity of key databases maintained by the #NIH's National Library of Medicine, databases that are of "incalculable importance." www.statnews.com/2025/02/10/g...

Um die grossen Herausforderungen unserer Zeit (KI, Klimawandel, Pandemien, etc) richtig beurteilen zu können, brauchen wir fundierten Wissenschaftsjournalismus. Es ist ein Fehler, dass #SRF ausgerechnet hier spart. bajour.ch/a/die-srf-sp...

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...

Never forget. Never again. #niewieder

🎺 PhD studentship available at @lshtm.bsky.social and RVC! @influenzal.bsky.social and I are advertising for a project to investigate the unexpected phenomenon that mutagenic antiviral drugs can give rise to viruses with hundreds of mutations which are still viable. 🧵 www.lshtm.ac.uk/study/fees-a...

What do you think are the critical features pathogen genomic data-sharing platforms require to meet the public health need? Please participate in this public consultation!

What is the diversity of antiphage systems out there ? We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families. Leb by E. Mordret. www.biorxiv.org/content/10.1... Interactive UMAP to have fun mdmparis.github.io/antiphage-la...

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...

We are pleased to announce the availability of the human metapneumovirus (hMPV) phylogenetic analysis on Nextstrain and its corresponding Nextclade dataset. Read more on our blog: nextstrain.org/blog/2025-01...

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]🧵

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling