Anne Kupczok
@annecmg.bsky.social
Assistant professor at Wageningen University, interested in Comparative Microbial Genomics, Phage genomics, Evolution
Reposted by Anne Kupczok
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Reposted by Anne Kupczok
A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions https://www.biorxiv.org/content/10.1101/2025.11.01.686033v1
November 3, 2025 at 3:33 AM
A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions https://www.biorxiv.org/content/10.1101/2025.11.01.686033v1
Reposted by Anne Kupczok
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Anne Kupczok
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!
For more information and how to apply, see below 👇
Please RT!
For more information and how to apply, see below 👇
Please RT!
📢 The #HIRI is looking for a #postdoc & a #PhD student to join the research group of @jenshoer.bsky.social. His lab focuses on understanding the molecular mechanisms of #phages with #RNA genomes during infection, host takeover & anti-phage defense. 🧫🦠 More info: www.helmholtz-hiri.de/en/jobs-tale...
Working at HIRI
At the HIRI, we do not just value excellent research. Short distances, an open door policy, and a good working atmosphere—this is what distinguishes us from others. Have a look at our current job…
www.helmholtz-hiri.de
October 17, 2025 at 12:52 PM
Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab!
For more information and how to apply, see below 👇
Please RT!
For more information and how to apply, see below 👇
Please RT!
Reposted by Anne Kupczok
What factors shape viral protein evolution? Fuchs et al. estimate evolutionary rates of numerous herpesvirus proteins and residues, revealing short- and long-term evolutionary constraints.
🔗 doi.org/10.1093/molbev/msaf256
#evobio #molbio #virus
🔗 doi.org/10.1093/molbev/msaf256
#evobio #molbio #virus
Functional and Structural Determinants of Long- and Short-Term Evolution of Herpesvirus Proteins
Abstract. Understanding the factors that shape viral protein evolution is a central question in evolutionary virology. However, these determinants are poor
doi.org
October 31, 2025 at 12:19 PM
What factors shape viral protein evolution? Fuchs et al. estimate evolutionary rates of numerous herpesvirus proteins and residues, revealing short- and long-term evolutionary constraints.
🔗 doi.org/10.1093/molbev/msaf256
#evobio #molbio #virus
🔗 doi.org/10.1093/molbev/msaf256
#evobio #molbio #virus
Reposted by Anne Kupczok
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens
Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...
www.medrxiv.org
October 31, 2025 at 12:19 PM
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Reposted by Anne Kupczok
My paper is out! Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases. doi.org/10.1093/ve/v... 💻🧬 1/5 🧵
October 28, 2025 at 1:27 PM
My paper is out! Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases. doi.org/10.1093/ve/v... 💻🧬 1/5 🧵
Reposted by Anne Kupczok
We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩💻🎓: banklab.github.io/positions/
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
October 28, 2025 at 4:22 PM
We have an open PhD position (application deadline 9 January 2026) in "Theory of fitness landscapes" at @unibe.ch 🤓⛰️📊👩💻🎓: banklab.github.io/positions/
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Please share widely!
#QueerInSTEM #DisabledInSTEM #BlackInSTEM #WomenInSTEM #CarersInSTEM #AcademicSky #HigherED
Reposted by Anne Kupczok
Applications for the Erasmus Mundus Mobility European Master Programme in Evolutionary Biology (MEME) are open. More info at https://www.evobio.eu/. Apply via Uppsala or Groningen. #gradstudent
MEME | Mobility European Master Evolutionary Biology
MEME | Mobility European Master Evolutionary Biology
www.evobio.eu
October 24, 2025 at 12:54 PM
Applications for the Erasmus Mundus Mobility European Master Programme in Evolutionary Biology (MEME) are open. More info at https://www.evobio.eu/. Apply via Uppsala or Groningen. #gradstudent
Reposted by Anne Kupczok
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world
Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio
academic.oup.com
October 21, 2025 at 1:45 PM
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Reposted by Anne Kupczok
🧬 Now published in Bioinformatics Advances: “Advances and challenges in understanding evolution through genome comparison.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223
October 20, 2025 at 10:01 AM
🧬 Now published in Bioinformatics Advances: “Advances and challenges in understanding evolution through genome comparison.”
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223
Read the full paper here: https://doi.org/10.1093/bioadv/vbaf223
Reposted by Anne Kupczok
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Reposted by Anne Kupczok
Evolution induced state shifts in a long-term microbial community experiment https://www.biorxiv.org/content/10.1101/2025.10.10.680894v1
October 11, 2025 at 12:31 AM
Evolution induced state shifts in a long-term microbial community experiment https://www.biorxiv.org/content/10.1101/2025.10.10.680894v1
Reposted by Anne Kupczok
We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org
Home
meehubs.org
October 7, 2025 at 2:30 PM
We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org
Reposted by Anne Kupczok
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 7, 2025 at 4:11 PM
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
Reposted by Anne Kupczok
Protein Language Models are Accidental Taxonomists https://www.biorxiv.org/content/10.1101/2025.10.07.681002v1
October 8, 2025 at 3:47 AM
Protein Language Models are Accidental Taxonomists https://www.biorxiv.org/content/10.1101/2025.10.07.681002v1
Reposted by Anne Kupczok
@annecmg.bsky.social opens this autumn Microbial Ecology symposium in Utrecht - connected/supported by @biosb.bsky.social
#NIME2025
#NIME2025
October 7, 2025 at 7:41 AM
@annecmg.bsky.social opens this autumn Microbial Ecology symposium in Utrecht - connected/supported by @biosb.bsky.social
#NIME2025
#NIME2025
Reposted by Anne Kupczok
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for
>4,400 viruses, allowing mapping of form and function across the human and animal
virosphere. Viro3D i...
www.embopress.org
September 28, 2025 at 5:39 AM
New exciting resource published!! The Viro3D paper is out, describing our comprehensive database of predicted virus protein structures! 💻🧬
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Work with @ulad-litvin.bsky.social , @grovearmada.bsky.social , Alex Jack, @bljog.bsky.social , @davidlrobertson.bsky.social
www.embopress.org/doi/full/10....
Reposted by Anne Kupczok
New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...
Using cross-species co-expression to predict metabolic interactions in microbiomes
In microbial ecosystems, metabolic interactions are key determinants of species’ relative abundance and activity. Given the immense number of possible interactions in microbial communities, their expe...
www.biorxiv.org
September 22, 2025 at 7:42 AM
New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...
Reposted by Anne Kupczok
We are hiring! On the search for an ambitious post-doc with hot skills in metagenomics, metatranscriptomics and bioinformatics to join our EcoEnergeticS project with
@michaeladippold.bsky.social
Find the ad here: uni-tuebingen.de/zh/266340
@michaeladippold.bsky.social
Find the ad here: uni-tuebingen.de/zh/266340
Opportunities
uni-tuebingen.de
September 17, 2025 at 6:10 AM
We are hiring! On the search for an ambitious post-doc with hot skills in metagenomics, metatranscriptomics and bioinformatics to join our EcoEnergeticS project with
@michaeladippold.bsky.social
Find the ad here: uni-tuebingen.de/zh/266340
@michaeladippold.bsky.social
Find the ad here: uni-tuebingen.de/zh/266340
Reposted by Anne Kupczok
Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today
Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics | mBio
The virus-host arms race is a major component of the evolutionary process in all organisms
that drove the evolution of a broad variety of immune mechanisms. In the last few
years, over 200 distinct an...
journals.asm.org
September 16, 2025 at 10:52 PM
Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today
Reposted by Anne Kupczok
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted by Anne Kupczok
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...
September 8, 2025 at 8:56 AM
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...
Reposted by Anne Kupczok
Only 10 days left to apply:
We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
September 1, 2025 at 5:54 AM
Only 10 days left to apply:
We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv