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Tim Dallman @tdallman.bsky.social · 19d

Please join us for the next @who.int IPSN Webinar on the Utility of Pathogen Genomics focussing this time on metagenomics as a tool to detect emerging threats. 25/09/25 at 13:00 CET

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Reposted by Tim Dallman

Willem van Schaik @wvschaik.bsky.social · Jul 25

Just a few days left to apply for PhD positions in the Health Protection Research Unit - Public Health Genomics @imibirmingham.bsky.social.

preview-uob.cloud.contensis.com/research/cen...

I am offering two projects (on Clostridioides difficile & metagenomics of wastewater and freshwater).

PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham

PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches

preview-uob.cloud.contensis.com

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Tim Dallman @tdallman.bsky.social · Jul 1

who.zoom.us/webinar/regi...

Welcome! You are invited to join a webinar: WHO EPI-WIN Webinar: The Utility of Pathogen Genomics: Spotlight TB. After registering, you will receive a confirmation email about joining the webinar.

who.zoom.us

Tim Dallman @tdallman.bsky.social · Jul 1

Please register for the latest @who.int

IPSN EPI-WIN webinar on current and future perspectives of genomic surveillance of TB - tomorrow - 02:07:25 @ 13:00 CEST

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Tim Dallman @tdallman.bsky.social · Apr 16

Reminder to join the latest @who.int IPSN EPI-WIN webinar on current and future perspectives of genomic surveillance of mpox - today @ 13:00 CET

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Reposted by Tim Dallman

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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Reposted by Tim Dallman

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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Tim Dallman @tdallman.bsky.social · Jan 17

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!

silargi.bsky.social @silargi.bsky.social · Jan 17

Does your team deposit and access pathogen genomic data via data-sharing platforms for public health use? Participate in WHO's online consultation on the critical features of pathogen genomic data-sharing platforms to meet public health needs.

All info here: www.who.int/news-room/ar...

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Reposted by Tim Dallman

Richard Neher @neher.io · Jan 11

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...

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 ...

www.biorxiv.org

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Reposted by Tim Dallman

Noémie Lefrancq @noemielefrancq.bsky.social · Jan 2

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

Learning the fitness dynamics of pathogens from phylogenies - Nature

Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…

buff.ly

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Reposted by Tim Dallman

Tim Dallman @tdallman.bsky.social · Dec 4

Please join us at 13:00 CET December 12th for the next edition of the IPSN webinar series 'Pathogen Genomics in Health Emergencies' to hear how genomics can contribute to the understanding of Cholera outbreaks. Register here:

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Reposted by Tim Dallman

Treasa Ní Creabhín @treasac.bsky.social · Nov 29

Applied Bioinformatics & Public Health Microbiology (21-23 May 2025) is open for registrations!
Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social
@ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social

Bluesky

anharrison.bsky.social

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Tim Dallman @tdallman.bsky.social · Dec 4

Please join us at 13:00 CET December 12th for the next edition of the IPSN webinar series 'Pathogen Genomics in Health Emergencies' to hear how genomics can contribute to the understanding of Cholera outbreaks. Register here:

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Tim Dallman @tdallman.bsky.social · Nov 23

Great to have you here Anderson!

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Tim Dallman @tdallman.bsky.social · Nov 23

Thanks for all your input Peter!

Tim Dallman @tdallman.bsky.social · Aug 22

Please join us to hear how genomics is helping in response to the multiple outbreaks of Dengue from the
@who
hosted International Pathogen Surveillance Network. Register here: echo.zoom.us/webinar/regi...

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Tim Dallman @tdallman.bsky.social · Feb 29

Come join the group in Utrecht! I have a post-doc position to fill to work on using microbial genomics and metagenomics to build machine learning models to better understand the spread of pathogens and dissemination of resistance www.uu.nl/en/organisat...

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Tim Dallman @tdallman.bsky.social · Nov 17

Excited to announce the funding of the Health Holland project ‘Predict and Prevent’ working on the integration of pan-genomics, population dynamics and clinical outcomes to elucidate emerging pathogen threats using machine learning.

www.health-holland.com/project/2023...

Predict and Prevent Emerging Pathogen Threats

Predicting which pathogen variants warrant intention for intervention is critical for a proportional and optimal public health response. ‘Predict and Prevent’ will leverage the power of routine in...

www.health-holland.com

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Tim Dallman @tdallman.bsky.social · Sep 9

That’s awful, not sure I know of a larger daycare STEC outbreak

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