Fabian van Beveren
@fabianvanbeveren.bsky.social
Evolutionary biologist / bioinformatician
#EVOLF
#symbiosis
#algae
#EVOLF
#symbiosis
#algae
Reposted by Fabian van Beveren
Diversity and spread of #cytoplasmicIncompatibility genes among maternally inherited #symbionts
#SymbioSky
doi.org/10.1371/jour...
#SymbioSky
doi.org/10.1371/jour...
Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts
Author summary Cytoplasmic incompatibility (CI) is a reproductive strategy used by certain bacteria to promote their spread within arthropod populations. These bacteria, inherited through the mother, ...
doi.org
September 19, 2025 at 10:00 AM
Diversity and spread of #cytoplasmicIncompatibility genes among maternally inherited #symbionts
#SymbioSky
doi.org/10.1371/jour...
#SymbioSky
doi.org/10.1371/jour...
Reposted by Fabian van Beveren
So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution
Abstract. Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occur
academic.oup.com
August 28, 2025 at 8:08 AM
So excited to see our review on how to detect horizontal gene transfers and their impact on plant functional evolution finally published in @theplantcell.bsky.social!
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
Great teamwork between @lrsv-toulouse.bsky.social and LGDP-Perpignan 😎🥳🌱
academic.oup.com/plcell/advan...
Reposted by Fabian van Beveren
New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
August 26, 2025 at 4:54 PM
New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
Reposted by Fabian van Beveren
I gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.
August 25, 2025 at 12:09 PM
I gave a symposium talk at the European Society for Evolutionary Biology 2025 (#eseb2025) meeting last week and this was my title slide showcasing how I was speaking as an independent scientist because @dalhousieu.bsky.social @dalhousie.bsky.social has locked us out.
Reposted by Fabian van Beveren
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
www.biorxiv.org
July 20, 2025 at 1:04 PM
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
Reposted by Fabian van Beveren
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
July 20, 2025 at 4:58 PM
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
Reposted by Fabian van Beveren
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
July 14, 2025 at 1:45 PM
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Reposted by Fabian van Beveren
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
No, AlphaFold has not completely solved protein folding
Biology is hard. Yes, even for AI.
clauswilke.substack.com
July 12, 2025 at 6:19 PM
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
Reposted by Fabian van Beveren
𝗠𝗶𝗰𝗿𝗼𝗯𝗲 𝘄𝗶𝘁𝗵 𝗯𝗶𝘇𝗮𝗿𝗿𝗲𝗹𝘆 𝘁𝗶𝗻𝘆 𝗴𝗲𝗻𝗼𝗺𝗲 𝗺𝗮𝘆 𝗯𝗲 𝗲𝘃𝗼𝗹𝘃𝗶𝗻𝗴 𝗶𝗻𝘁𝗼 𝗮 𝘃𝗶𝗿𝘂𝘀
or maybe not. a 🧵
roland @environmicrobio.bsky.social and Krzysztof @ktjurdzinski.bsky.social already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky
or maybe not. a 🧵
roland @environmicrobio.bsky.social and Krzysztof @ktjurdzinski.bsky.social already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky
Microbe with bizarrely tiny genome may be evolving into a virus
With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses
www.science.org
June 18, 2025 at 1:14 PM
𝗠𝗶𝗰𝗿𝗼𝗯𝗲 𝘄𝗶𝘁𝗵 𝗯𝗶𝘇𝗮𝗿𝗿𝗲𝗹𝘆 𝘁𝗶𝗻𝘆 𝗴𝗲𝗻𝗼𝗺𝗲 𝗺𝗮𝘆 𝗯𝗲 𝗲𝘃𝗼𝗹𝘃𝗶𝗻𝗴 𝗶𝗻𝘁𝗼 𝗮 𝘃𝗶𝗿𝘂𝘀
or maybe not. a 🧵
roland @environmicrobio.bsky.social and Krzysztof @ktjurdzinski.bsky.social already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky
or maybe not. a 🧵
roland @environmicrobio.bsky.social and Krzysztof @ktjurdzinski.bsky.social already commented, please also read their posts.
www.science.org/content/arti...
#MicroSky #SymbioSky #ProtistsOnSky
Reposted by Fabian van Beveren
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
May 14, 2025 at 2:07 PM
New vacancy in my team!
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.
Please repost and share with talented MSc students in #evobio, bioinformatics or related :)
www.uu.nl/en/organisat...
#MEvoSky #MicroSky
Reposted by Fabian van Beveren
A fantastic resource for fern biology @natplants.nature.com 🔽!
www.nature.com/articles/s41...
Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽
www.biorxiv.org/content/10.1...
www.nature.com/articles/s41...
Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽
www.biorxiv.org/content/10.1...
Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls - Nature Plants
New fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution, providing a comprehensive database that underscores the ancient divergen...
www.nature.com
April 23, 2025 at 10:44 PM
A fantastic resource for fern biology @natplants.nature.com 🔽!
www.nature.com/articles/s41...
Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽
www.biorxiv.org/content/10.1...
www.nature.com/articles/s41...
Taking about ferns, are you interested by their immune system? Have a look at our recent preprint by @baptistebio.bsky.social @jacquet-chris.bsky.social 🔽
www.biorxiv.org/content/10.1...
Reposted by Fabian van Beveren
Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
March 19, 2025 at 8:29 PM
Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Fabian van Beveren
🔗 Preprint alert: www.biorxiv.org/content/10.1...
🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿
Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]
🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿
Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]
Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity
Land plants include angiosperms, bryophytes, lycophytes and ferns, each of which may deploy distinct strategies to resist pathogens. Here, we investigate fern-pathogen interactions by characterizing n...
www.biorxiv.org
March 20, 2025 at 10:35 AM
🔗 Preprint alert: www.biorxiv.org/content/10.1...
🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿
Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]
🧵 New insights into plant immunity: using ferns to understand evolution! 🌱✨🌿
Excited to share my first (but not last) published research at @lrsv-toulouse.bsky.social. A THREAD … [1/9]
Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054
With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social
A thread: (1/5)
doi.org/10.1111/nph.70054
With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social
A thread: (1/5)
Ectomycorrhizal symbiosis evolved independently and by convergent gene duplication in rosid lineages
Click on the article title to read more.
doi.org
March 12, 2025 at 8:17 PM
Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054
With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social
A thread: (1/5)
doi.org/10.1111/nph.70054
With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social
A thread: (1/5)
Reposted by Fabian van Beveren
Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...
Postdoc Comparative genomics and genome architecture in early-diverging fungi and their protist relatives (3-year position)
www.wur.nl
March 5, 2025 at 11:56 AM
Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...
Reposted by Fabian van Beveren
Super interview sur @franceculture.fr de @chloe-beaulieu.bsky.social, sur nos travaux publiés dans @naturegenet.bsky.social !
www.radiofrance.fr/francecultur...
www.radiofrance.fr/francecultur...
Avec sciences : podcast et émission en replay | France Culture
Chaque matin, Alexandra Delbot décrypte en 5 minutes les dernières actualités scientifiques et leurs enjeux.
www.radiofrance.fr
February 24, 2025 at 10:16 AM
Super interview sur @franceculture.fr de @chloe-beaulieu.bsky.social, sur nos travaux publiés dans @naturegenet.bsky.social !
www.radiofrance.fr/francecultur...
www.radiofrance.fr/francecultur...
Reposted by Fabian van Beveren
January 30, 2025 at 3:16 PM