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Anne Kupczok

@annecmg.bsky.social
1.6K followers 594 following 64 posts

Assistant professor at Wageningen University, interested in Comparative Microbial Genomics, Phage genomics, Evolution

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Anne Kupczok @annecmg.bsky.social · 11h
Cool and probably parasitic, do you call this efficient?
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 23h
Version 1.3.2 of PearTree released: github.com/artic-networ... Fixes many of the remaining niggling bugs. WebApp updated at peartree.live
The logo of the PearTree phylogenetic tree viewer app - a partridge in a pear tree.
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Anne Kupczok @annecmg.bsky.social · 10/10/2026
Want to come to the Netherlands 🤣
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Lavisha Parab @lavishaparab.bsky.social · 07/10/2026
hello #phage pholks, any of you already have a protocol for high-through put one-step growth curves? Making any step faster/more convenient is welcome. Thanks!!! Spotting on a big agar plate doesn't save as much time as we lose by reducing the precision/least count and then having to repeat it 😅
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Ursula Oggenfuss @oggenfussursula.bsky.social · 06/10/2026
Are you interested in learning how genomes of weird fungi and protists evolve and are you looking for an exciting PhD opportunity? Jolien van Hooff and I are looking for an enthusiasic PhD candidate at Wageningen University: www.wur.nl/en/vacancy/p... #TEworldwide #Fungi #Protists #Genome
wur.nl
PhD position in genome evolution and architecture in unicellular eukaryotes
Are you fascinated by how eukaryotic genomes evolve? Do you want to look beyond model organisms and point mutations to uncover the complexity of genome evolution?
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Molecular Biology and Evolution @molbioevol.bsky.social · 07/10/2026
@pavelpayne.bsky.social et al. show that bacterial herd immunity can promote homologous recombination, suggesting bacterial immune systems can shape molecular evolution not only by blocking infection but also by regulating genetic exchange 🔗 academic.oup.com/mbe/article/... #societyjournal #evobio
academic.oup.com
Herd immunity underlies homologous recombination in stationary phase bacteria
Abstract. Homologous recombination is ubiquitous across evolution, generating variation through genetic reshuffling. Although bacteria lack meiotic recombi
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 06/10/2026
Hidden but Expanding Sampling Bias Distorts Prokaryotic Genome Collections www.biorxiv.org/content/10.64898/20…
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Alexis Stamatakis @stamatak.bsky.social · 06/10/2026
Applications for the 2027 summer school on Computational Molecular Evolution on Crete are still open at: meetings.embo.org/event/27-com... Strict Application Deadline: November 2
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Shoichi Sakaguchi @sho1.bsky.social · 04/10/2026
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...
rdrp.io
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…
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Pleuni Pennings @pleunipennings.bsky.social · 29/09/2026
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...
abetterscientist.wordpress.com
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…
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Vivek Mutalik @vivekmutalik.bsky.social · 29/09/2026
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
Machine learning workflow for GenoPHI platform
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Iris van Rooij 💭 @irisvanrooij.bsky.social · 29/09/2026
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🧵
Protecting the Ecosystem of Human Knowledge: Five Principles
We must protect and cultivate the ecosystem of human knowledge. AI models can mimic
the appearance of scholarly work, but they are (by construction) unconcerned with truth
— the result is a torrential outpouring of unchecked but convincing-sounding “informa-
tion”. At best, such output is accidentally true, but generally citationless, divorced from
human reasoning and the web of scholarship that it steals from. At worst, it is confidently
wrong. Both outcomes are dangerous to the ecosystem.
Olivia Guest, Iris van Rooij, Marcela Suarez, et al. (2025, n.p.)
Knowledge production is supposed to be safeguarded by (inter)national codes of conduct for research
integrity (ALLEA 2023; KNAW et al. 2018). Such codes forbid, for instance, fabrication of data,
falsification of results, plagiarism, and, generally, distortion of the scientific record. Many argue that
new rules are required to regulate academic AI use, but pre-existing guidelines fit the bill (cf. Tafani
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Gytis Dudas @evogytis.bsky.social · 22/09/2026
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
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Genome Biology and Evolution @genomebiolevol.bsky.social · 17/09/2026
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
academic.oup.com
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
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Ákos T Kovács @evolvedbiofilm.bsky.social · 11/09/2026
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...
academic.oup.com
Validate User
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
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...
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Bas E. Dutilh @bedutilh.bsky.social · 07/09/2026
Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇
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Rafal Mostowy @rafalmostowy.bsky.social · 04/09/2026
🧬 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-...
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Katy Brown @thekatybrown.bsky.social · 07/08/2026
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
royalsociety.org
Endogenous viral elements | Royal Society
Theo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton
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Simon Roux @simrouxvirus.bsky.social · 27/07/2026
Reminder, registration for the Viral EcoGenomics & Applications (VEGA) 26 symposium is open ! See jgi.doe.gov/work-with-us... for more information
jgi.doe.gov
VEGA Symposium | Joint Genome Institute
Berkeley, CA
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Aude Bernheim @audeber.bsky.social · 21/07/2026
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...
sciencedirect.com
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…
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Anne Kupczok @annecmg.bsky.social · 17/07/2026
Thanks a lot for the invite. It was great to discuss with you and your group. I enjoyed my first time in Tübingen 🤩
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Rafal Mostowy @rafalmostowy.bsky.social · 15/07/2026
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
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Anne Kupczok @annecmg.bsky.social · 13/07/2026
wheretopublish.github.io
wheretopublish.github.io
Where to Publish?
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Anne Kupczok @annecmg.bsky.social · 10/07/2026
New paper from the group - a tool for RNA virus discovery 🥳
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Georgios (Yorgos) Marinos @maringos.bsky.social · 05/07/2026
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...
doi.org
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...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 04/07/2026
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation www.biorxiv.org/content/10.64898/20…
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Anne Kupczok @annecmg.bsky.social · 04/07/2026
All the trains on this route have been changed. And you typically get a email. However if you booked via university then some admin person might have gotten it 😬
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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026
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...
In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline
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Andrew Carroll @acarroll.bsky.social · 01/07/2026
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...
andrewcarroll.github.io
The Best of Both Worlds - Assessing MiniBWA
Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...
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moicoll.bsky.social @moicoll.bsky.social · 29/06/2026
Interactive schedule for SMBE2026. Enjoy the conference! #SMBE2026 github.com/MoiColl/SMBE...
github.com
GitHub - MoiColl/SMBE2026_schedule: Interactive SMBE2026 schedule
Interactive SMBE2026 schedule. Contribute to MoiColl/SMBE2026_schedule development by creating an account on GitHub.
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Sarah Bagby @scbagby.bsky.social · 29/06/2026
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
Screenshot of an email header with subject line "Crazy ideas"
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Marc Robinson-Rechavi @marcrr.bsky.social · 24/06/2026
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 🤞)
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Anne Kupczok @annecmg.bsky.social · 18/06/2026
Yeah!
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Feargal Ryan @feargalr.bsky.social · 15/06/2026
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.com
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
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NL Institute of Ecology NIOO-KNAW @niooknaw.bsky.social · 05/06/2026
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...
nioo.knaw.nl
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...
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026
🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
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Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026
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
science.org
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.
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Genome Biology and Evolution @genomebiolevol.bsky.social · 28/05/2026
@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
GBE | Genus-wide Homologous Recombination of Tail Fibers Maintains Tailocin Diversity in Pectobacterium
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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
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...
npr.org
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.
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
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! 🙏
uu.nl
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Lavisha Parab @lavishaparab.bsky.social · 20/05/2026
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)
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Ellinor Alseth @ellinoralseth.bsky.social · 13/05/2026
When is an antiphage mechanism an evolved defence adaptation? This question has been on my mind for so long, because despite the field’s rapid progress there is currently no widely agreed framework in place to answer it. So @brownlab.bsky.social and I wrote this, and I'm happy to share the preprint!
ecoevorxiv.org
The bacterial immune system: identifying evolved defense adaptations
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Lavisha Parab @lavishaparab.bsky.social · 08/05/2026
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
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Vaughn Cooper @vscooper.micropopbio.org · 17/04/2026
The deadline for the @meehubs.bsky.social Microbial Ecology and Evolution distributed-network conference is Sunday April 17.😅 Great folks organizing and presenting, details here: meehubs2026.oa-event.com
meehubs2026.oa-event.com
Home
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 16/04/2026
1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere Work led by the indomitable @sheilaroitman.bsky.social‬ #plantscience #microbiome #holobiont www.biorxiv.org/content/10.6...
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Asher Leeks @asherleeks.bsky.social · 14/04/2026
The Social Lives of Viruses is coming to Vancouver, Canada, from 4th-8th August 2026! This is a free meeting dedicated to all aspects of virus-virus interactions & evolution. To apply: socialviruses.zoology.ubc.ca @sociovirology.bsky.social #socialviruses #evosky #lovevirology #virosky
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Ella Sieradzki @sieravirus.bsky.social · 09/04/2026
Deadline is April 20th! Let’s get those viruses
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Rob Edwards @linsalrob.bsky.social · 08/04/2026
Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome github.com/shandley/awe...
The awesome virome logo of a phage above a strand of DNA
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Holly Dunsworth @dunsworth.bsky.social · 31/03/2026
I'm reviewing Sapiens, one page at a time! It's a little bit fact-checking and a little-bit soul-searching combined into a lot of feelings... ecodevoevo.blogspot.com/2026/03/sapi...
ecodevoevo.blogspot.com
"Sapiens": One page at a time
I've been co-teaching a course for several years in which we read Sapiens . I think I've read it eight times, now. That explains the gumband...
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