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!

New Paper🚀! Our work analysing the Swiss national SARS-CoV-2 wastewater 🚱 monitoring data is now published in PLOS Water 💧 @plos.org journals.plos.org/water/articl... (Julien Riou, @tanjastadler.bsky.social @trj2.bsky.social Christoph Ort et al)

Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

We are excited to announce the Latsis Symposium 2026: The history of epidemics – are there lessons for the future? latsis-epidemics.ethz.ch We have a great lineup of international speakers - true leaders in this field. The symposium is held at ETH Zürich, Switzerland, from the (1/2)

Tanja Stadler @tanjastadler.bsky.social @ethz.ch awarded prestigious #DoronPrize for pioneering work in computational evolution and public health. Big congrats, Tanja! > u.ethz.ch/IxSY8

AI is revolutionising palaeontology | New @NatureRev paper by @ethz.ch & UZH shows how #AI tools are transforming the analysis of complex fossil data and evolutionary patterns – unlocking new insights across deep time > u.ethz.ch/BjDtR @tanjastadler.bsky.social

🗓 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

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!

Vaughan & @tanjastadler.bsky.social develop a method to infer multitype population trajectories and apply it to MERS-CoV, revealing transmission patterns between camels and humans. 🔗 doi.org/10.1093/molbev/msaf130 #evobio #molbio #virus

In this project led by James Munday, we quantified the post-sampling degradation of viral RNA in wastewater. Taking into account this degradation is core towards unbiased quantification of epidemiological dynamics based on wastewater data.

We have a new preprint 📝 *Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates* Now on bioRxiv doi.org/10.1101/2025... with @tanjastadler.bsky.social, trj2.bsky.social, Christoph Ort and others

📢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

Drei aus meiner Sicht zentrale Herausforderungen für die Bildungs-, Forschung- und Innovations-Landschaft der Schweiz: wissenschaftsrat.ch/blog/die-gro...: Blog Beitrag zum 60. Geburtstag des Schweizer Wissenschaftsrat, Happy Birthday!

🗓️ 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

Thank you, @tanjastadler.bsky.social, for your great efforts during the #Covid19 pandemic! Watch the Switzerland-Germany comparison on measures 5 years after the breakout of #SarsCoV2 on @zdfde.bsky.social > www.zdf.de/play/magazin...

I first read the famous 1925 Yule paper at its 80th birthday - during my Master thesis work, and it shaped my research profoundly. It was a pleasure and honour to lead this special 100 anniversary issue celebrating Yule's legacy and phylogenetic models with @noahrosenberg.bsky.social and Mike Steel!

A mathematical theory of evolution: phylogenetic models dating back 100 years—a new #PhilTransB theme issue describes recent developments in models of #evolutionary trees and networks, and in #phylogenetic modeling for applications in biology: https://buff.ly/41r1wkR @tanjastadler.bsky.social

Quantification of developmental processes (here early Danio rerio development) with our novel Bayesian phylogenetic methodology - leveraging single cell lineage tracing data based on CRISPR/Cas9 technology royalsocietypublishing.org/doi/10.1098/... Antoine Zwaans @seidels.bsky.social Marc Manceau

Featured article: The lives of cells, recorded go.nature.com/4g2gRwG by Amjad Askary, Wei Chen, @choijunhong.bsky.social, Lucia Y. Du, @elowitzlab.bsky.social, @james-gagnon.bsky.social, @schierlab.bsky.social, @seidels.bsky.social, @jshendure.bsky.social, @tanjastadler.bsky.social & Martin Tran

Thoughts on how AI can help prepare for the next pandemic - Thanks for having led this work @mugkraemer.bsky.social Joseph L.-H. Tsui Serina Y. Chang, @sjbhatt.bsky.social - it is an honour to be part of it!

SRF - the core Swiss public service journalism stakeholder - plans to majorly cut on science journalism. You can still sign our petition if you think this is problematic openpetition.eu/!sciencejour...

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/...

Starke Kürzungen im SRF Wissenschaftsjournalismus in der Schweiz geplant. WissenschaftlerInnen starteten heute eine Petition "Fakten statt Falschinformationen: Für einen starken Wissenschaftsjournalismus!" Werde eine(r) von bereits über 1'800 UnterzeichnerInnen openpetition.eu/!sciencejour...

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.

📯 #Swiss wastewater dashboard through our #wise project is now updated with historic data within which you can overlay the seasons. #Influenza B is now high, after skipping a year. Check it out here: wise.ethz.ch

Excited to be in Bern today to launch the Center for Pathogen Bioinformatics (CPB) - a great collaboration of SIB, @tanjastadler.bsky.social & Niko Beerenwinkel @ethzurich.bsky.social, @neher.io @unibas.ch & myself @swisstph.ch, to better tackle known & novel pathogens - introduced by SIB director!

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.

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

It is a great honour to have been awarded the Karl-Heinz Hoffmann prize by the Bavarian Academy of Sciences and Humanities www.linkedin.com/posts/bayeri...

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

Read the NY Times article featuring ETH computational biologist Tanja Stadler.

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!

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