@kausthubh.bsky.social
(he/him) PhD student at EMBL Heidelberg | phylogenetics | evolutionary cell biology | Views personal
Pinned
I attended the exciting symposium organized by @floravincent.bsky.social @mwdorr.bsky.social, @nicoledubilier.bsky.social, @gautamdey.bsky.social & Susanna Coelho
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
Reposted
Just uploaded our new preprint to @ecoevorxiv.bsky.social
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
November 26, 2025 at 3:06 PM
Just uploaded our new preprint to @ecoevorxiv.bsky.social
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Multinucleate life really is everywhere...from deep sea forams to slime molds, intracellular parasites, and beyond. 🚀
We explore how scaling, ecology, & evolution intersect when many nuclei share a single cytoplasm.
doi.org/10.32942/X2M...
Reposted
Curious about how this story came to be (we never planned to study centromeres!)? Here’s a glimpse behind the scenes of how a naive method to count chromosomes unlocked the rules behind centromere evolution.
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
Counting Chromosomes: The Simple Idea That Unlocked the Rules Behind Centromere Evolution
tinyurl.com
November 26, 2025 at 4:27 PM
Curious about how this story came to be (we never planned to study centromeres!)? Here’s a glimpse behind the scenes of how a naive method to count chromosomes unlocked the rules behind centromere evolution.
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
P.S. There are cartoons!
👉 tinyurl.com/4rz4ve6u
Reposted
PCAn, our point centromere annotation tool 🔍 was also updated! Try it out with your own genome assemblies and let us know what you think!
👉 github.com/JHelsen/point-centromere-detection
👉 github.com/JHelsen/point-centromere-detection
GitHub - JHelsen/point-centromere-detection: This repository contains all the instructions and code required to perform the analyses used in this study - https://www.biorxiv.org/content/10.1101/2025.0...
This repository contains all the instructions and code required to perform the analyses used in this study - https://www.biorxiv.org/content/10.1101/2025.01.16.633479v1 - JHelsen/point-centromere-d...
github.com
November 26, 2025 at 4:24 PM
PCAn, our point centromere annotation tool 🔍 was also updated! Try it out with your own genome assemblies and let us know what you think!
👉 github.com/JHelsen/point-centromere-detection
👉 github.com/JHelsen/point-centromere-detection
Reposted
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
November 26, 2025 at 4:21 PM
How do new centromeres evolve while staying compatible with the division machinery?
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore.
👉 doi.org/10.1038/s41586-025-09779-1
Reposted
(1/3) Imagine reconstructing a history over a billion years in the making.
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
November 26, 2025 at 4:06 PM
(1/3) Imagine reconstructing a history over a billion years in the making.
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
New research from EMBL and @Stanford shows how centromeres retain their function despite their rapid rate of change, and the evolutionary constraints that govern this process.
www.nature.com/articles/s41...
Reposted
(3/3) The researchers found that the cell’s division machinery acts as a critical filter, allowing only those centromere variants that are compatible with effective attachment to survive and spread.
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
Progressive coevolution of the yeast centromere and kinetochore | Nature
www.nature.com
November 26, 2025 at 4:06 PM
(3/3) The researchers found that the cell’s division machinery acts as a critical filter, allowing only those centromere variants that are compatible with effective attachment to survive and spread.
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
@gautamdey.bsky.social @helsenjana.bsky.social @gsherloc.bsky.social @kausthubh.bsky.social
Reposted
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
Reposted
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
November 26, 2025 at 2:05 PM
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
Reposted
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Reposted
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
Reposted
🚨 Imagine a bacterium that refuses to follow the textbook:
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.
August 20, 2025 at 10:34 AM
🚨 Imagine a bacterium that refuses to follow the textbook:
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.
Reposted
Want to acquire #ExM images like this and help us understand the true extent of cytoskeletal diversity across the tree of life? This position might be for you!
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
With @dudinlab.bsky.social
@embl.org @biology-unige.bsky.social @moorefound.bsky.social
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
With @dudinlab.bsky.social
@embl.org @biology-unige.bsky.social @moorefound.bsky.social
August 7, 2025 at 6:12 PM
Want to acquire #ExM images like this and help us understand the true extent of cytoskeletal diversity across the tree of life? This position might be for you!
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
With @dudinlab.bsky.social
@embl.org @biology-unige.bsky.social @moorefound.bsky.social
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
With @dudinlab.bsky.social
@embl.org @biology-unige.bsky.social @moorefound.bsky.social
Reposted
9. TL;DR + link dump
WitChi is:
✔ Fast
✔ Interpretable
✔ Tree- and model-free
✔ Benchmark-validated
Designed to fix compositional bias at phylogenomic scale.
With: @kassipan.bsky.social, @danieltamarit.bsky.social, @ettema.bsky.social
💻 github.com/stephkoest/w...
📄 www.biorxiv.org/content/10.1...
WitChi is:
✔ Fast
✔ Interpretable
✔ Tree- and model-free
✔ Benchmark-validated
Designed to fix compositional bias at phylogenomic scale.
With: @kassipan.bsky.social, @danieltamarit.bsky.social, @ettema.bsky.social
💻 github.com/stephkoest/w...
📄 www.biorxiv.org/content/10.1...
GitHub - stephkoest/witchi: A compositional bias testing and pruning tool for multiple sequence alignments
A compositional bias testing and pruning tool for multiple sequence alignments - stephkoest/witchi
github.com
July 20, 2025 at 1:04 PM
9. TL;DR + link dump
WitChi is:
✔ Fast
✔ Interpretable
✔ Tree- and model-free
✔ Benchmark-validated
Designed to fix compositional bias at phylogenomic scale.
With: @kassipan.bsky.social, @danieltamarit.bsky.social, @ettema.bsky.social
💻 github.com/stephkoest/w...
📄 www.biorxiv.org/content/10.1...
WitChi is:
✔ Fast
✔ Interpretable
✔ Tree- and model-free
✔ Benchmark-validated
Designed to fix compositional bias at phylogenomic scale.
With: @kassipan.bsky.social, @danieltamarit.bsky.social, @ettema.bsky.social
💻 github.com/stephkoest/w...
📄 www.biorxiv.org/content/10.1...
Reposted
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
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
June 3, 2025 at 6:55 AM
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
I attended the exciting symposium organized by @floravincent.bsky.social @mwdorr.bsky.social, @nicoledubilier.bsky.social, @gautamdey.bsky.social & Susanna Coelho
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
May 15, 2025 at 10:05 AM
I attended the exciting symposium organized by @floravincent.bsky.social @mwdorr.bsky.social, @nicoledubilier.bsky.social, @gautamdey.bsky.social & Susanna Coelho
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
LOTs of takeaways from the Symposium (from biology to climate change)
🚨Here are a few important ones in my listicle below 👇
Reposted
With rapid changes in our environment and climate, there's an urgent need to better understand living systems and their interactions, going beyond the few well-established ‘model’ organisms. A recent EMBO | EMBL Symposium explored how we might do that.
Learn more: www.embl.org/news/science...
Learn more: www.embl.org/news/science...
May 15, 2025 at 9:05 AM
With rapid changes in our environment and climate, there's an urgent need to better understand living systems and their interactions, going beyond the few well-established ‘model’ organisms. A recent EMBO | EMBL Symposium explored how we might do that.
Learn more: www.embl.org/news/science...
Learn more: www.embl.org/news/science...
Reposted
Our next extraordinary biologist for this week is Gautam Dey, who co-organised the 2023 @dev-journal.bsky.social and 2024 @jcellsci.bsky.social Journal Meetings. Gautam’s research group at @embl.org, Germany, frequently contributes to @prelights.bsky.social. #100biologists @gautamdey.bsky.social
April 24, 2025 at 3:42 PM
Our next extraordinary biologist for this week is Gautam Dey, who co-organised the 2023 @dev-journal.bsky.social and 2024 @jcellsci.bsky.social Journal Meetings. Gautam’s research group at @embl.org, Germany, frequently contributes to @prelights.bsky.social. #100biologists @gautamdey.bsky.social
Reposted
Hanh Vu @hanhtkvu.bsky.social, Group Leader at the @embl.org DB unit presenting the diversity of size, pattern and colour of Life #EESWildModels #planarians #DevBio
April 11, 2025 at 9:04 AM
Hanh Vu @hanhtkvu.bsky.social, Group Leader at the @embl.org DB unit presenting the diversity of size, pattern and colour of Life #EESWildModels #planarians #DevBio
Reposted
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
ecoevorxiv.org
April 10, 2025 at 2:13 PM
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
Reposted
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
April 11, 2025 at 9:04 AM
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
Reposted
I had a wild time presenting my coral work for the first time at EMBO/EMBL #EESWildModels.
Massive thanks to @embl.org @events.embl.org and the organisers for putting this together. It was a real pleasure to interact with so many weird and wonderful creatures...
...and their model organisms (!!)
Massive thanks to @embl.org @events.embl.org and the organisers for putting this together. It was a real pleasure to interact with so many weird and wonderful creatures...
...and their model organisms (!!)
April 11, 2025 at 1:11 PM
I had a wild time presenting my coral work for the first time at EMBO/EMBL #EESWildModels.
Massive thanks to @embl.org @events.embl.org and the organisers for putting this together. It was a real pleasure to interact with so many weird and wonderful creatures...
...and their model organisms (!!)
Massive thanks to @embl.org @events.embl.org and the organisers for putting this together. It was a real pleasure to interact with so many weird and wonderful creatures...
...and their model organisms (!!)
Reposted
Science by day, beats by night 🧬🎶
Sunset skies, science minds, and the EMBL DJ Club bringing the groove to the rooftop. Thanks to everyone who came out and made it such a special evening 🎧🌇 #EESWildModels
But the symposium isn't over yet! Time for the last talk of the day and poster prizes reveal 👀
Sunset skies, science minds, and the EMBL DJ Club bringing the groove to the rooftop. Thanks to everyone who came out and made it such a special evening 🎧🌇 #EESWildModels
But the symposium isn't over yet! Time for the last talk of the day and poster prizes reveal 👀
April 11, 2025 at 10:05 AM
Science by day, beats by night 🧬🎶
Sunset skies, science minds, and the EMBL DJ Club bringing the groove to the rooftop. Thanks to everyone who came out and made it such a special evening 🎧🌇 #EESWildModels
But the symposium isn't over yet! Time for the last talk of the day and poster prizes reveal 👀
Sunset skies, science minds, and the EMBL DJ Club bringing the groove to the rooftop. Thanks to everyone who came out and made it such a special evening 🎧🌇 #EESWildModels
But the symposium isn't over yet! Time for the last talk of the day and poster prizes reveal 👀
Reposted
That’s a wrap on the EMBO | EMBL Symposium: 'Wild frontiers of model organisms'! 🐠🌍🔍
Thanks to our scientific organisers and to all who shared their science and energy. Congrats to our poster prize winners—exceptional work! 👏 #EESWildModels
Let’s keep exploring the unknown and see you next time!
Thanks to our scientific organisers and to all who shared their science and energy. Congrats to our poster prize winners—exceptional work! 👏 #EESWildModels
Let’s keep exploring the unknown and see you next time!
April 11, 2025 at 2:20 PM
That’s a wrap on the EMBO | EMBL Symposium: 'Wild frontiers of model organisms'! 🐠🌍🔍
Thanks to our scientific organisers and to all who shared their science and energy. Congrats to our poster prize winners—exceptional work! 👏 #EESWildModels
Let’s keep exploring the unknown and see you next time!
Thanks to our scientific organisers and to all who shared their science and energy. Congrats to our poster prize winners—exceptional work! 👏 #EESWildModels
Let’s keep exploring the unknown and see you next time!
Reposted
Join us in Catalonia to discuss chromatin evolution across the tree of life and from all angles (metabolism, synthetic chromatin, you name it!) meetings.embo.org/event/24-evo...
EvoChromo: Evolutionary approaches to research in chromatin
Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…
meetings.embo.org
April 11, 2025 at 1:45 PM
Join us in Catalonia to discuss chromatin evolution across the tree of life and from all angles (metabolism, synthetic chromatin, you name it!) meetings.embo.org/event/24-evo...