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Reposted by Tanja Stadler

D-BSSE, ETH Zurich @bsse.ethz.ch · Aug 26

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

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Reposted by Tanja Stadler

Pathoplexus @pathoplexus.org · Aug 27

🗓 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...

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Biozentrum, University of Basel @biozentrum.unibas.ch · Aug 4

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!

SIB Swiss Institute of Bioinformatics @sib.swiss · Jul 22

💡 The SIB Remarkable Outputs 2024 are out !
This shortlist of the most outstanding works produced by SIB members in 2024 showcase the latest advances in the Swiss bioinformatics field. Attend their presentations at [BC]2!

👉 Discover this shortlist of outstanding works
www.sib.swiss/remarkable-o...

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Reposted by Tanja Stadler

Molecular Biology and Evolution @molbioevol.bsky.social · Jun 17

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

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data

Abstract. Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important to

doi.org

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Tanja Stadler @tanjastadler.bsky.social · Jun 17

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.

James Munday @jdmunday.bsky.social · Jun 9

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

Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates

Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the...

doi.org

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Reposted by Tanja Stadler

James Munday @jdmunday.bsky.social · Jun 9

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

Post-sampling degradation of viral RNA in wastewater impacts the quality of PCR-based concentration estimates

Successful wastewater-based infectious disease surveillance programs depend on regular, reliable molecular detection of nucleic acids in municipal wastewater systems. This process is challenged by the...

doi.org

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Reposted by Tanja Stadler

Pathoplexus @pathoplexus.org · May 22

📢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.

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Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

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Tanja Stadler @tanjastadler.bsky.social · May 14

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!

Die grössten Herausforderungen für die BFI-Landschaft bis 2035

wissenschaftsrat.ch

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Reposted by Tanja Stadler

Pathoplexus @pathoplexus.org · Apr 16

🗓️ 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

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Pathoplexus | Pathoplexus Spring Update

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

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Reposted by Tanja Stadler

D-BSSE, ETH Zurich @bsse.ethz.ch · Mar 24

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...

Corona-Politik: Deutschland vs. Schweiz

Die Corona-Politik in Deutschland und der Schweiz fiel unterschiedlich aus. Welches Land kam mit seinen Maßnahmen besser durch die Pandemie?

www.zdf.de

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Tanja Stadler @tanjastadler.bsky.social · Feb 21

So many great scientists contributed papers to the special issue! To get an overview over the history and state of phylogenetic models and the papers of the issue, you might want to start reading the introduction to the issue doi.org/10.1098/rstb... and then dive into the variety of exciting papers!

"A mathematical theory of evolution": phylogenetic models dating back 100 years | Philosophical Transactions of the Royal Society B: Biological Sciences

Can't sign in? Forgot your password?

doi.org

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Tanja Stadler @tanjastadler.bsky.social · Feb 21

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!

Royal Society Publishing @royalsocietypublishing.org · Feb 21

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

buff.ly

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Reposted by Tanja Stadler

Royal Society Publishing @royalsocietypublishing.org · Feb 21

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

buff.ly

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Tanja Stadler @tanjastadler.bsky.social · Feb 21

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

A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites | Philosophical Transactions of the Royal Society B: Biological Sciences

Analysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. Clustered regularly interspaced short palindromic repeats (CRISPR)-based dynamic lineage tracing relies ...

royalsocietypublishing.org

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Nature Reviews Genetics @natrevgenet.nature.com · Feb 20

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

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Tanja Stadler @tanjastadler.bsky.social · Feb 20

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!

Moritz Kraemer @mugkraemer.bsky.social · Feb 20

AI is poised to accelerate understanding in infectious diseases, but its value needs to be demonstrated through close collaboration between research, industry, society, and policy.

Paper free to read: rdcu.be/eaxEw

Summary here: www.ox.ac.uk/news/2025-02...

Artificial intelligence for modelling infectious disease epidemics

Nature - This Perspective considers the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science.

rdcu.be

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Tanja Stadler @tanjastadler.bsky.social · Feb 12

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...

Fakten statt Falschinformationen: Für einen starken Wissenschaftsjournalismus! - Online-Petition

Offener Brief aus der Wissenschaft an SRF Sehr geehrte Direktion der SRG, sehr geehrte Geschäftsleitung von SRF, sehr geehrte Medien- und Wissenschaftspolitiker:innen Mit grosser Besorgnis haben wir z...

openpetition.eu

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Tanja Stadler @tanjastadler.bsky.social · Feb 10

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/...

Facts Instead of Misinformation: For Strong Science Journalism! - Online-Petition

Open Letter from the Scientific Community to SRF Dear Management of SRG, Dear Executive Board of SRF, Dear Media and Science Policy Makers, We are deeply concerned about SRF’s plans to make significan...

www.openpetition.eu

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Tanja Stadler @tanjastadler.bsky.social · Feb 10

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...

Fakten statt Falschinformationen: Für einen starken Wissenschaftsjournalismus! - Online-Petition

Offener Brief aus der Wissenschaft an SRF Sehr geehrte Direktion der SRG, sehr geehrte Geschäftsleitung von SRF, sehr geehrte Medien- und Wissenschaftspolitiker:innen Mit grosser Besorgnis haben wir z...

openpetition.eu

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Pathoplexus @pathoplexus.org · Feb 5

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-...

Screenshot of the virological post on the Ebolavirus sequence

Screenshot of the sequence on pathoplexus

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Reposted by Tanja Stadler

Andrew Rambaut @arambaut.bsky.social · Feb 3

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.

Near Real-Time Genomic Characterization of the 2025 Sudan Ebolavirus Outbreak in Uganda’s Index Case: Insights into Evolutionary Origins

Introduction Case History: On January 30, 2025, the Ministry of Health declared an outbreak of Sudan Ebola Virus (SUDV) Disease in Kampala, Uganda, following the death of a healthcare worker at Mula...

virological.org

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Tim Julian @trj2.bsky.social · Jan 31

📯 #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

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Reposted by Tanja Stadler

Dr Emma Hodcroft @firefoxx66.bsky.social · Jan 23

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!

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Chaoran Chen @chaoranchen.de · Jan 10

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.

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Pathoplexus @pathoplexus.org · Dec 9

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.

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