www.keystonesymposia.org/conferences/...

Global Virome in Health and Disease: From Individuals to Ecosystems | Keystone Symposia

Join us at the Keystone Symposia on Global Virome in Health and Disease: From Individuals to Ecosystems, February 2027, in Geneva, with field leaders!

keystonesymposia.org

Get excited :) PhyloSpec is coming! A shared standard + modelling language for phylogenetic models. Write a model once, run it across engines like BEAST X, BEAST 2.8 & RevBayes. Easy and reproducible. Built by @tochsner.bsky.social & collaborators (ETH Zürich, Auckland, LMU). phylospec.com

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

Very excited to share our paper (and first for my PhD) on RdRpCATCH in NAR Genomics and Bioinformatics! doi.org/10.1093/narg... Co-authors: @urineri.bsky.social, @ingrida.bsky.social, Justine Charon, @sho1.bsky.social, @xinhou.bsky.social, Dick de Ridder, Mark P. Zwart, and @annecmg.bsky.social

RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models

Abstract. Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RN

doi.org

Inaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...

Predicting viral evolution with AI

Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...

pasteur.fr

Please share 🚨 We have a postdoc position open on avian influenza virus tracking and genomics across natural to develop an early-warning system to protect human and animal health hrwebapp.qub.ac.uk/tlive_webrec...

Until Friday, Australia was the only continent free from HPAI H5N1. Sadly, this is not the case - a 2344b confirmation in a Brown Skua, and a suspected case in a Northern Giant Petrel which turned up in WA. 👉 www.abc.net.au/news/2026-06... (1/x)

Super stoked to share that our Opinion article is now online at @cp-trendsgenetics.bsky.social!!! With "our" I mean: @teuneverts.bsky.social, @sdellicour.bsky.social and myself!! Here is a link to our piece: authors.elsevier.com/a/1nFgD_3rsx...

New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵 #StructuralPhylogenetics #Evolution #Protein

🦇 🦇 🦇

Cell - a Cell Press journal@cp-cell.bsky.social · 3mo ago

Now online! Virological characteristics of SARS-CoV-2-related coronaviruses dynamically circulating in Southeast Asia

New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest

Ten years after the release of version 1.0, we are happy to announce version 2.0 of the toolbox “seraphim”, our R package for studying phylogenetically informed movements in molecular epidemiology studies - 1/4

Applications are open for the 2026 Metagenomic Virus Discovery Workshop! The Centre for Epidemic Response and Innovation, Stellenbosch University is hosting a 5 day hands-on workshop run by experts in the field from around the world Find out more at our website mvdworkshop.com

We found a viral Trojan Horse: a virus can hide inside another virus.This one surprised us: deltaviruses don’t just borrow a helper virus. They can travel inside it. A literal Trojan Horse “virus-in-a-virus” route into cells. 🤯 Kudos to 1st author @viroscope.bsky.social and co-authors !

Deltaviruses spread through a viral Trojan Horse

Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…

sciencedirect.com

Wonderful to host @jonathonmifsud.bsky.social at UQ today for the SCMB Seminar Series. An excellent journey using protein structural information to study viral evolution across deep time, including new insights into the evolutionary history of Flaviviridae (RIP) and viral membrane fusion mechanisms.

APSPM brought together researchers from around the world to explore protein evolution from different angles. Structural approaches are reshaping evolutionary inference and the community is growing. Huge thanks to participants and @official-smbe.bsky.social for making this meeting a success. #StryPhy

Plus got to do some advertising for the new lab 👀 👀 #strphy26

What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics! Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!

Caroline Puente-Lelievre@cpuentelelievre.bsky.social · 6mo ago

Great to chair the session on Virus Evolution at APSPM2026. Thank you to all the speakers for sharing their cool research with us 🦠 Mihnea Bostina, Cinthy Jimenez Silva, @spyroslytras.bsky.social @jonathonmifsud.bsky.social #StryPhy26

Our discovery of novel viruses in invasive camelids in Australia leads us to propose a simple idea: RNA viruses may repeatedly evolve functional modules at the 5′ end of their genomes. #Virology #RNAvirus #VirusEvolution #Picornavirus #VirusDiscovery doi.org/10.64898/202...

Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖 with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social academic.oup.com/nargab/artic... details below... #NARGAB

Inferring context-specific site variation with evotuned protein language models

Abstract. Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancem

academic.oup.com

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

Multiple protein structure alignment at scale with FoldMason

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

science.org

The program for the SMBE Australasian Protein Structural Phylogenetics Meeting 2026 is now out! Abstract book coming soon. @official-smbe.bsky.social @proteinmechanic.bsky.social biosig.lab.uq.edu.au/strphy26/pro...

APSPM 2026: Structural Phylogenetics Meeting

A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.

biosig.lab.uq.edu.au

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

mirdita.org

An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era. #Evolution #Science #StrPhy On Confidence Assessment in Structure-Aware Alignments doi.org/10.1093/gbe/...

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments

Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base

doi.org

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Protein structure-informed bacteriophage genome annotation with Phold

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

academic.oup.com

George Bouras@gbouras13.bsky.social · 12mo ago

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Foraging ecology drives viral community structure in New Zealand's aquatic birds www.biorxiv.org/content/10.6...

Foraging ecology drives viral community structure in New Zealand's aquatic birds

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain...

biorxiv.org

Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring! Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷

I'm excited to introduce our new workflow for detecting endogenous viral elements - HI-FEVER. 🖥️🧬 academic.oup.com/bioinformati... 🧵 Big thanks to @ariskatzourakis.bsky.social, @humanceae.bsky.social, José Gabriel and Cormac for bringing this from conception to fruition!

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements

AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

academic.oup.com

Join us tomorrow! Joana Pereira is talking about AI-powered classification and discovery across the protein universe. @joanampereira.bsky.social 5PM CET, link in the post and in our bio.

Protein Structure Evolution (ProSE) Seminar@proteinstructure.bsky.social · 9mo ago

The next ProSE Seminar will be given by Joana Pereira @joanampereira.bsky.social (VIB, KU Leuven) 🗓️ November 11th, 5pm CET Registration is now open: tinyurl.com/prose-seminar2 Please share!

🧬 Thrilled to share our latest paper in @natmicrobiol.nature.com 📄 A collaboration to give the Flaviviridae (home to Zika, Dengue & HCV) a much-needed taxonomic re-think. Our at-scale AI structure prediction gave a complementary perspective on viral evolution. www.nature.com/articles/s41...

Taxonomic expansion and reorganization of Flaviviridae - Nature Microbiology

Analysis of RNA polymerase hallmark gene phylogenies supported by protein structure relationships of flaviviruses and ‘flavi-like’ viruses underpins the taxonomic expansion and reorganization of Flavi...

nature.com