Join our RNA Virus Journal Club this Thursday! Dr. Uri Neri urineri.bsky.social presents RolyPoly, a modular toolkit for RNA virus identification and characterization. Thu 8 Oct Paris 09:00 Jerusalem 10:00 Tokyo 16:00 Your local time and Zoom link: rdrp.io/journal-club...

RolyPoly - simplifying RNA virus identification and characterization | rdrp.io

Virus analysis requires many different tools for different steps. While many effective software options exist for automating these, they usually follow an end…

rdrp.io

I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...

Postdoc position on drug resistance evolution in Montpellier, France

I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…

abetterscientist.wordpress.com

Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va

Avery Noonan@averynoonan.bsky.social · 11mo ago

We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing. www.biorxiv.org/content/10.1...

Dear @erc.europa.eu , we DO already have common standards & frameworks. 'AI' likes to pose itself as 'special' but we do not need to reinvent the wheel. We already have established codes of conduct for research integrity. We just need to apply them. See below + more resources in thread🧵

European Research Council (ERC)@erc.europa.eu · 6d ago

There is a need to agree on common standards & frameworks for AI models used across all aspects of research evaluation. These should ensure & encourage trust, confidentiality, & transparency, & should be defined through collaborative discussions between research funding and performing organisations.

baltic v1.0.0 is live! Get it via pip or clone from Github repo. Now with documentation (baltic.readthedocs.io) & a gallery of tutorials & examples (phylo-baltic.github.io/baltic-gallery, still WIP). Huge thanks to @barney-potter.bsky.social for all the initiative & help along the way. #ViroSky

Chen et al. show that a substantial fraction of predicted orphan genes lacks expression support, and they exhibit distinct sequence and evolutionary signatures from expressed orphans. 🔗 academic.oup.com/gbe/article/... #societyjournal #genome #evolution

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome

Abstract. Orphan genes (OGs)—genes lacking detectable homologs outside a species—are widespread in microbial genomes and are thought to contribute to their

academic.oup.com

Characterization of syntons across bacterial genomes using non-redundant genomic contexts @femsjournals.bsky.social microLife by @alexhv.bsky.social, Jean Cury, and @audeber.bsky.social academic.oup.com/microlife/ad...

Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...

Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇

Kuesel Lab@kuesellab.bsky.social · 4w ago

We're hiring! Join the Aquatic Geomicrobiology group as a PhD researcher to explore virus–host interactions and host range evolution in soil and groundwater using cultivation experiments, viral tagging & metagenomics. 🦠🧬 📍Jena | 🗓️ Apply by Oct 1, 2026 jobs.uni-jena.de/jobposting/2...

🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...

Me, @emma-harding.bsky.social, @rtarlinton.bsky.social and @royalsociety.org are organising a meeting on endogenous viral elements! 8-9 Feb 2027, Birmingham UK. 2 whole days of EVEs! Many amazing researchers already agreed to speak. Invites: shorturl.at/jp9sh Provisional schedule: shorturl.at/8O5KV

Endogenous viral elements | Royal Society

Theo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton

royalsociety.org

Reminder, registration for the Viral EcoGenomics & Applications (VEGA) 26 symposium is open ! See jgi.doe.gov/work-with-us... for more information

VEGA Symposium | Joint Genome Institute

Berkeley, CA

jgi.doe.gov

Simon Roux@simrouxvirus.bsky.social · 4mo ago

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...

A family of lanthipeptides with anti-phage function

Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…

sciencedirect.com

PhD opening in my lab @jagiellonskiuni.bsky.social: using AI to predict how phage enzymes break down bacterial capsules — joint work with ML group GMUM and Zuzanna Drulis-Kawa's phage lab (Wrocław), spanning genomics, AI & evolution. mostowylab.com/job-phd-ai-d... Deadline: 15 August 2026

New paper from the group - a tool for RNA virus discovery 🥳

Dimitris Karapliafis@dkarap.bsky.social · 3mo ago

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

Happy to share our new paper in Gut Microbes 🧬 Samer Alban and I developed EcoGS, a genome-scale metabolic modelling tool for predicting ecological interactions between microbes. As first author, I thank Samer, @kaletalab.bsky.social, and all co-authors for the teamwork! doi.org/10.1080/1949...

Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome

Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exc...

doi.org

Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation https://www.biorxiv.org/content/10.64898/2026.07.03.736256v1

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Interactive schedule for SMBE2026. Enjoy the conference! #SMBE2026 github.com/MoiColl/SMBE...

GitHub - MoiColl/SMBE2026_schedule: Interactive SMBE2026 schedule

Interactive SMBE2026 schedule. Contribute to MoiColl/SMBE2026_schedule development by creating an account on GitHub.

github.com

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

If you're going to #SMBE2026 @official-smbe.bsky.social Copenhagen by train, share your plans and experience on #NoFlySMBE. Let's make #NoFlyAcademics normal and visible! I'm going Lausanne-Basel, night train 😴 Basel-Hamburg, and finally Hamburg-Copenhagen. Easy! (I hope 🤞)

Marc Robinson-Rechavi@marcrr.bsky.social · 6mo ago

Are you going to #SMBE2026 Copenhagen by train, or are you hesitating? Let's share experiences and give ideas to those who think to fly from Western or Central Europe with the hashtag #NoFlySMBE. If you're coming from 🇨🇭, there are night trains from Zürich or Basel to Hamburg. ✅🚆 ❌✈️

I’ve been maintaining a list of shotgun #metagenomics tools and resources which I got Claude to turn into a GitHub repo. It has 300+ entries. Please share and tell me if I’ve missed anything! github.com/feargalr/Met... #microbiota #bioinformatics #microbiome #genomics

GitHub - feargalr/Metagenomics-tools-atlas: An inventory of tools and resources for short-read shotgun metagenomics.

An inventory of tools and resources for short-read shotgun metagenomics. - feargalr/Metagenomics-tools-atlas

github.com

We are looking for a PhD candidate who will study the biogeography of above- and belowground fungi associated with several Scalesia species. We aim to develop an integrated view of diversity and distribution of three components of the fungal microbiome. Apply by 26 June: nioo.knaw.nl/en/vacancies...

PhD: Biogeography of plant-associated fungi on the Galapagos islands

In this project, you will investigate the biogeography of above- and belowground fungi associated with several Scalesia species. We aim to develop an integrated view of diversity and distribution of t...

nioo.knaw.nl

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.

science.org

@lakhanp01.bsky.social @annecmg.bsky.social et al. characterized the genomic diversity of a tailocin and discovered that diversity is maintained through exchange of the tail fiber locus DNA across Pectobacterium, a pathogen causing soft rot. 🔗 doi.org/10.1093/gbe/evag106 #genome #evolution

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Researchers say the Trump administration is finding new ways to punish science

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

npr.org

I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏

Hi #microbiomesky and #mevosky and also #phagesky maybe? Some of us want a microbiome journal club to catch up on microbiology/evolution related microbiome research. Monthly@15:00 CET/09:00 EST/18:30 IST or so Please text my LMU email address if you're interested (not typing it here to avoid spam)

Lavisha Parab@lavishaparab.bsky.social · 5mo ago

Does anyone know of an online microbiome journal club? I'm interested in joining one. More along the lines of evolution and microbiology than immunology or human effects #mevosky #microbiomesky