Anne Kupczok
@annecmg.bsky.social
Assistant professor at Wageningen University, interested in Comparative Microbial Genomics, Phage genomics, Evolution
Reposted by Anne Kupczok
Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/
Bonus: beautiful seascape and friendly spirit!
Bonus: beautiful seascape and friendly spirit!
EBAME workshop
EBAME - Computational Microbial Ecogenomics Workshop
maignienlab.gitlab.io
February 16, 2026 at 10:03 AM
Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/
Bonus: beautiful seascape and friendly spirit!
Bonus: beautiful seascape and friendly spirit!
Reposted by Anne Kupczok
Last seats available! 🚨
Join our #ComparativeGenomics course with @sedlazeck.bsky.social & @Ingo Ebersberger and learn how to analyse, compare, and interpret genomes using modern bioinformatics approaches. Don’t miss it—registration is closing soon!
@nanoporetech.com @pacbio.bsky.social
Join our #ComparativeGenomics course with @sedlazeck.bsky.social & @Ingo Ebersberger and learn how to analyse, compare, and interpret genomes using modern bioinformatics approaches. Don’t miss it—registration is closing soon!
@nanoporetech.com @pacbio.bsky.social
Join our online #ComparativeGenomics course with Ingo & @sedlazeck.bsky.social , 23-27 Feb 2026! Learn genome assembly, variant detection (SNVs & SVs), and functional impact analysis with hands-on sessions.
www.physalia-courses.org/courses-work...
#Bioinformatics #Genomics
www.physalia-courses.org/courses-work...
#Bioinformatics #Genomics
February 11, 2026 at 12:16 PM
Last seats available! 🚨
Join our #ComparativeGenomics course with @sedlazeck.bsky.social & @Ingo Ebersberger and learn how to analyse, compare, and interpret genomes using modern bioinformatics approaches. Don’t miss it—registration is closing soon!
@nanoporetech.com @pacbio.bsky.social
Join our #ComparativeGenomics course with @sedlazeck.bsky.social & @Ingo Ebersberger and learn how to analyse, compare, and interpret genomes using modern bioinformatics approaches. Don’t miss it—registration is closing soon!
@nanoporetech.com @pacbio.bsky.social
Reposted by Anne Kupczok
Hooray 🎉 from virologists! :)
The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
www.ebi.ac.uk
February 17, 2026 at 4:41 PM
Hooray 🎉 from virologists! :)
Reposted by Anne Kupczok
Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 16, 2026 at 4:43 PM
Our latest preprint: Together with the team of Jan Löwe, @danieltamarit.bsky.social and many others we discovered and characterized several Asgard tubulin genes and propose that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Anne Kupczok
If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you
jobs.ncsu.edu/postings/226...
jobs.ncsu.edu/postings/226...
Postdoctoral Research Scholar
The Callahan Lab at NC State University (https://callahanlab.cvm.ncsu.edu/team/) is seeking a postdoctoral scholar to study the transfer of DNA between bacteria (horizontal gene transfer;HGT) by virus...
jobs.ncsu.edu
February 15, 2026 at 5:35 PM
If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you
jobs.ncsu.edu/postings/226...
jobs.ncsu.edu/postings/226...
Reposted by Anne Kupczok
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
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
February 14, 2026 at 6:02 AM
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
with Adam Strange, Jumpei Ito, and @systemsvirology.bsky.social
academic.oup.com/nargab/artic...
details below...
#NARGAB
Reposted by Anne Kupczok
what can be better than global RNA virome and Dolja?
Nothing for me.. :)
Join RNA virus club (by @rdrpsummit.bsky.social ) already tomorrow:
Thu, Feb 12, 11:00 AM Pacific Time (US 🇺🇸, Canada🇨🇦)
(or 7pm London time 🇬🇧)
for an hour with one and only Prof. Valerian Dolja (Oregon State University)
Nothing for me.. :)
Join RNA virus club (by @rdrpsummit.bsky.social ) already tomorrow:
Thu, Feb 12, 11:00 AM Pacific Time (US 🇺🇸, Canada🇨🇦)
(or 7pm London time 🇬🇧)
for an hour with one and only Prof. Valerian Dolja (Oregon State University)
February 11, 2026 at 8:58 PM
what can be better than global RNA virome and Dolja?
Nothing for me.. :)
Join RNA virus club (by @rdrpsummit.bsky.social ) already tomorrow:
Thu, Feb 12, 11:00 AM Pacific Time (US 🇺🇸, Canada🇨🇦)
(or 7pm London time 🇬🇧)
for an hour with one and only Prof. Valerian Dolja (Oregon State University)
Nothing for me.. :)
Join RNA virus club (by @rdrpsummit.bsky.social ) already tomorrow:
Thu, Feb 12, 11:00 AM Pacific Time (US 🇺🇸, Canada🇨🇦)
(or 7pm London time 🇬🇧)
for an hour with one and only Prof. Valerian Dolja (Oregon State University)
Reposted by Anne Kupczok
We are excited to share that @jeremyjbarr.bsky.social will be joining us as speaker at the 2026 International SPP 2330 Symposium.
We look forward to meeting you in Berlin!
📅 October 5 – 7, 2026
📍 Harnack House, Berlin
🌐 More information is available at lnkd.in/eeSphFER
We look forward to meeting you in Berlin!
📅 October 5 – 7, 2026
📍 Harnack House, Berlin
🌐 More information is available at lnkd.in/eeSphFER
February 9, 2026 at 10:33 AM
We are excited to share that @jeremyjbarr.bsky.social will be joining us as speaker at the 2026 International SPP 2330 Symposium.
We look forward to meeting you in Berlin!
📅 October 5 – 7, 2026
📍 Harnack House, Berlin
🌐 More information is available at lnkd.in/eeSphFER
We look forward to meeting you in Berlin!
📅 October 5 – 7, 2026
📍 Harnack House, Berlin
🌐 More information is available at lnkd.in/eeSphFER
Reposted by Anne Kupczok
At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
www.biorxiv.org
February 7, 2026 at 10:08 AM
At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
Reposted by Anne Kupczok
One week to go and some seats available. If you're interested, please sign up. Very relevant documentary.
At Tuesday February 10 @17.00 DocuScience at @w-u-r.bsky.social
Suzette Bousema's documentary Dead Zones about oxygen-depleted areas in sea + discussion with the audience, Suzette and myself.
Free to attend, but registration needed (documentary+discussion will be English)
www.wur.nl/en/activity/...
Suzette Bousema's documentary Dead Zones about oxygen-depleted areas in sea + discussion with the audience, Suzette and myself.
Free to attend, but registration needed (documentary+discussion will be English)
www.wur.nl/en/activity/...
DocuScience: Dead Zones
Dead Zones is een documentaire over zuurstofloze gebieden in zee, veroorzaakt door overwoekering van micro algen, gevoed door menselijke afvalstromen. Microbioloog Detmer Sipkema zal de film inleiden ...
www.wur.nl
February 3, 2026 at 2:10 PM
One week to go and some seats available. If you're interested, please sign up. Very relevant documentary.
Reposted by Anne Kupczok
PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...
jobs.uni-jena.de/jobposting/c...
PhD student bioinformatics: Phage genomic modules: data mining, visualisation, and databasing
jobs.uni-jena.de
January 12, 2026 at 11:41 AM
PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...
jobs.uni-jena.de/jobposting/c...
Reposted by Anne Kupczok
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...
📄 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...
www.science.org
January 30, 2026 at 6:11 AM
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...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Anne Kupczok
The abstract submission deadline for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org has been extended until February 6
February 2, 2026 at 6:01 AM
The abstract submission deadline for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org has been extended until February 6
Reposted by Anne Kupczok
Can plant pathogens boost vector fitness?
Together with @hassansalem.bsky.social, we review how phytopathogens can spread further by moonlighting as insect symbionts 🪲 More on this nifty lifestyle in @annualreviews.bsky.social!
www.annualreviews.org/content/jour...
Together with @hassansalem.bsky.social, we review how phytopathogens can spread further by moonlighting as insect symbionts 🪲 More on this nifty lifestyle in @annualreviews.bsky.social!
www.annualreviews.org/content/jour...
Plant Pathogens Moonlighting as Beneficial Insect Symbionts
Herbivorous insects can shape the epidemiology of disease in plants by vectoring numerous phytopathogens. While the consequences of infection are often well-characterized in the host plant, the extent...
www.annualreviews.org
February 2, 2026 at 7:48 AM
Can plant pathogens boost vector fitness?
Together with @hassansalem.bsky.social, we review how phytopathogens can spread further by moonlighting as insect symbionts 🪲 More on this nifty lifestyle in @annualreviews.bsky.social!
www.annualreviews.org/content/jour...
Together with @hassansalem.bsky.social, we review how phytopathogens can spread further by moonlighting as insect symbionts 🪲 More on this nifty lifestyle in @annualreviews.bsky.social!
www.annualreviews.org/content/jour...
Reposted by Anne Kupczok
Very interesting paper. www.science.org/doi/10.1126/...
Bacteriophages mobilize bacterial defense systems via lateral transduction
Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.
www.science.org
January 24, 2026 at 1:24 PM
Very interesting paper. www.science.org/doi/10.1126/...
Reposted by Anne Kupczok
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
January 15, 2026 at 11:19 AM
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Reposted by Anne Kupczok
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/...
January 14, 2026 at 5:10 AM
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/...
Reposted by Anne Kupczok
Save the date, please RT:
Looking forward to an exciting International Symposium @spp2330.bsky.social "New concepts in prokaryotic virus-host interactions".
October 5-7, 2026; Harnack-Haus Berlin (Germany).
@dfg.de @hhu.de @fz-juelich.de
Looking forward to an exciting International Symposium @spp2330.bsky.social "New concepts in prokaryotic virus-host interactions".
October 5-7, 2026; Harnack-Haus Berlin (Germany).
@dfg.de @hhu.de @fz-juelich.de
January 14, 2026 at 2:41 PM
Save the date, please RT:
Looking forward to an exciting International Symposium @spp2330.bsky.social "New concepts in prokaryotic virus-host interactions".
October 5-7, 2026; Harnack-Haus Berlin (Germany).
@dfg.de @hhu.de @fz-juelich.de
Looking forward to an exciting International Symposium @spp2330.bsky.social "New concepts in prokaryotic virus-host interactions".
October 5-7, 2026; Harnack-Haus Berlin (Germany).
@dfg.de @hhu.de @fz-juelich.de
Reposted by Anne Kupczok
#microsky #phagesky #phage
At last! Great to see this one out: journals.plos.org/plospathogen...
Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social
At last! Great to see this one out: journals.plos.org/plospathogen...
Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social
Ecological ubiquity and phylogeny drive nestedness in phages–bacteria networks and shape the bacterial defensome
Author summary Viruses that infect bacteria, known as phages, are part of microbial communities and influence the abundance, diversity, and traits of their hosts. In an agriculture-related context, th...
journals.plos.org
January 12, 2026 at 7:37 PM
#microsky #phagesky #phage
At last! Great to see this one out: journals.plos.org/plospathogen...
Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social
At last! Great to see this one out: journals.plos.org/plospathogen...
Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social
Reposted by Anne Kupczok
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
Reposted by Anne Kupczok
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
January 5, 2026 at 10:45 PM
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Reposted by Anne Kupczok
Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!
High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1
January 5, 2026 at 2:55 PM
Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!
Reposted by Anne Kupczok
@ccasola.bsky.social, V. Luria, @vakirlis.bsky.social & @lizhao.bsky.social discuss advances and open questions in de novo gene emergence and evolution presented at the SMBE Satellite Meeting on De Novo Gene Birth (@official-smbe.bsky.social).
🔗 doi.org/10.1093/gbe/evaf230
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf230
#genome #evolution
De Novo Genes: Current Status and Future Goals
Abstract. The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6
doi.org
December 29, 2025 at 6:27 PM
@ccasola.bsky.social, V. Luria, @vakirlis.bsky.social & @lizhao.bsky.social discuss advances and open questions in de novo gene emergence and evolution presented at the SMBE Satellite Meeting on De Novo Gene Birth (@official-smbe.bsky.social).
🔗 doi.org/10.1093/gbe/evaf230
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf230
#genome #evolution
Reposted by Anne Kupczok
De wetenschap moet investeren in mensen, niet in hype.
'AI-gigafabriek' van 22,5 miljard kan rekenen op kritiek: 'Dit is van de zotte'
Wetenschappers zijn kritisch over het duurste project uit het rapport van Peter Wennink.
nos.nl
December 20, 2025 at 9:22 AM
De wetenschap moet investeren in mensen, niet in hype.
Reposted by Anne Kupczok
Vir2vec: A Genome-Wide Viral Embedding https://www.biorxiv.org/content/10.64898/2025.12.12.693901v1
December 14, 2025 at 5:46 AM
Vir2vec: A Genome-Wide Viral Embedding https://www.biorxiv.org/content/10.64898/2025.12.12.693901v1