1/ 🚀 Pathoplexus now supports Bundibugyo virus (BDBV), a species of Ebolavirus. BDBV has been associated with past outbreaks of Ebola in the DR Congo and Uganda, & a case has been reported today during response to the current Ebola outbreak. pathoplexus.org/ebola-bdbv #ebola #bdbv #ebolaoutbreak

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year. Here's what’s new in our latest update 👇🏻 Read the full update: pathoplexus.org/news/2026-03... 📰

> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely. And if you love podcasts: open.spotify.com/episode/0wrp...

“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.” #IDsky 🧪

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%. You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...

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

Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝 A fantastic turnout & wonderful time spent with curious users!

PI's of BSky: If you had to guess, What percentage of 2nd+ year PhD students in your lab have an @orcid.org?

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4

🗓 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

If you would like to find out more about Loculus, you can still register for the Loculus tutorial at the [BC]2 Basel Computational Biology Conference 2025 on 8 September! Registration closes on 1 September. www.bc2.ch/tutorials-wo...

“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases." 🥁That’s what the committee said about this #SIBRemarkableOutputs 2024 👉Discover the output: tinyurl.com/53arz2rz

Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️ Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss‬) in Basel, run by @chaoranchen.de & Anya Parker! 🧬 Register: www.bc2.ch/registration... #bioinformatics #openScience

Loculus, an open-source software for building pathogen sequencing databases, is on the shortlist for #SIBRemarkableOutputs 2024. It’s a joint project by the teams of @neher.io, @tanjastadler.bsky.social and @firefoxx66.bsky.social xx66.bsky.social. Congratulations!

📢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

🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility! 📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update 1/9

You might be wondering why we haven't updated outbreak.info for months. Well, the reason is that GISAID cut our access in January - as they did others. Without telling us. After a ♾️ back and forth, that is now permanent. More on that soon - and why GISAID should not be trusted with critical data.

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV. These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response. 1/4

🤔Interested in building and managing microbial genomic databases? Join the hands-on tutorial on #Loculus & learn how to set up, customize & deploy Loculus for your projects. 🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch 📆8 sept at #BC2Basel 👉 Register: tinyurl.com/5n8w3pwb

🚀 New proof-of-principle: An interactive, searchable MLST hash database... all in your browser! 🔥 Live demo ➡️ lskatz.github.io/mlst-hash-te... A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te... 🧵

Interested in #Bayesian #phylogenetics? 🧬 Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing! 📍Beijing, July 14–18, 2025 📅 Apply by April 25 I'll teach on TiDeTree & cell trees 🔗 taming-the-beast.org/news/Deadlin...

The time is flying by.. Hard to believe that it has already been 7 months since we started Pathoplexus!

🗓️ Pathoplexus has now been around for 7 months! And both we and our users have been busy - so we wanted to share some updates & highlights! 📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update 1/9

I think I may buy a few dozen copies of this book and just hand them out to strangers. bookshop.org/p/books/who-...

The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss

Today I have resigned from my position as a Data Editor at Proceedings B. I believe the journal does great work, but it feels wrong to voluntarily spend my time holding authors to account on behalf of the Royal Society, while the Society refuses to hold its own Fellows to account.

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/...

Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...

First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.

Interested in finding out more about @pathoplexus.org? We're running two Information/Q&A sessions! 22 Jan 15-17.00 CET 4 Feb 16-18.00 CET Come join us & bring your questions, to find out more about using & sharing data with Pathoplexus! 😁 Sign up here: forms.gle/YRRZA1rRtgYy...

We have just received an updated dataset from GISAID for cov-spectrum.org. Many thanks to the GISAID team for fixing the data feed!

Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

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

Our group CBG at ETHZ: We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings […]

GenSpectrum just added a mpox dashboard using data from @pathoplexus.org – see genspectrum.org

@pathoplexus.org now accepting MPXV genomes. I've played around with it's upload interface and it's genuinely so intuitive to use and has a lot of great error catching functionality!

Our Executive Board decided to prioritize adding mpox to Pathoplexus based on feedback from the community. This included a letter from those working on mpox & in areas affected by mpox, asking that the virus be added. Community involvement is a key part of Pathoplexus. 2/7

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

The life of cells, recorded www.nature.com/articles/s41.... We dive into the opportunities of DNA recording for understanding single cell dynamics. Fantastic collaboration with @shendure.bsky.social, @elowitzlab.bsky.social, @james-gagnon.bsky.social, and @schierlab.bsky.social labs.

We are excited to share our new preprint „Bayesian phylodynamic inference of multi-type population trajectories using genomic data“ www.biorxiv.org/content/10.1.... Using BEAST2, you can estimate past population sizes and spillover events between populations based on genetic sequencing data. 1/2

Thank you, Swiss Academies, for awarding @pathoplexus.org with the National ORD prize! To summarize our lightning talk and our fundamental beliefs: (1) It is crucial to make it easy to share and use data which includes having a user-friendly interface, a simple API and good documentation. 1/3

It's wonderful to have initiatives like this to support, recognise, and reward #OpenData work. Congratulations to the other 3 fantastic winners, and to the whole Pathoplexus team, who couldn't all be with us last night! 2/2

We're incredibly honoured to be winners of the Swiss Academies of Arts & Sciences National Prize for Open Research Data 2024! 🎉🎊 "Pathoplexus ensures open access and provides a cutting-edge infrastructure for interactive and programmable data exploration" akademien-schweiz.ch/en/medien/pr... 1/2

Do you want to track virus variants for H5N1, SARS-CoV-2, RSV and the West Nile Virus? Check out our new genspectrum.org @GenSpectrum dashboard - building upon the successful features of cov-spectrum.org!

How can we understand the lives of cells over time? In this review we discuss **why** DNA recording cellular histories matters, **how** to record and reconstruct them (spoiler alert: there will be phylogenies 😉) and **what** biological insights they reveal...

Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5