August 22, 2025 at 12:20 PM
Talking about structure-based protein annotations in weid critters (or „Why we shouldn’t say ‘structural homolog’!”). Thanks for having me @strphy.bsky.social #StrPhy #StrPhy26 #StructuralPhylogenetics
February 16, 2026 at 11:50 PM
Talking about structure-based protein annotations in weid critters (or „Why we shouldn’t say ‘structural homolog’!”). Thanks for having me @strphy.bsky.social #StrPhy #StrPhy26 #StructuralPhylogenetics
Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
February 7, 2026 at 2:53 AM
Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base
doi.org
January 14, 2026 at 11:07 AM
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
#Evolution #Science #StrPhy
On Confidence Assessment in Structure-Aware Alignments
doi.org/10.1093/gbe/...
The program is now live. An excellent global lineup of speakers - AUS, NZ, Korea, India, Laos, UK, Switzerland, France, Finland, Germany, Hungary, Japan, Uruguay, Mexico and USA. Browse abstracts. Just 3 weeks left. Super excited.
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
The program for the SMBE Australasian Protein Structural Phylogenetics Meeting 2026 is now out! Abstract book coming soon.
@official-smbe.bsky.social @proteinmechanic.bsky.social
biosig.lab.uq.edu.au/strphy26/pro...
@official-smbe.bsky.social @proteinmechanic.bsky.social
biosig.lab.uq.edu.au/strphy26/pro...
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
January 26, 2026 at 9:36 AM
The program is now live. An excellent global lineup of speakers - AUS, NZ, Korea, India, Laos, UK, Switzerland, France, Finland, Germany, Hungary, Japan, Uruguay, Mexico and USA. Browse abstracts. Just 3 weeks left. Super excited.
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
#StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
Wrapping up an incredible final day at the APSPM meeting! Huge thanks to the organizers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social Jordan Douglas and all the speakers for the brilliant talks and rich discussions. Beautiful Brisbane!
#StrPhy #StrPhy26 #StructuralPhylogenetics
#StrPhy #StrPhy26 #StructuralPhylogenetics
February 18, 2026 at 11:50 AM
Wrapping up an incredible final day at the APSPM meeting! Huge thanks to the organizers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social Jordan Douglas and all the speakers for the brilliant talks and rich discussions. Beautiful Brisbane!
#StrPhy #StrPhy26 #StructuralPhylogenetics
#StrPhy #StrPhy26 #StructuralPhylogenetics
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
October 9, 2025 at 4:04 AM
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
Looking forward to working together in the future and further develop #StructuralPhylogenetics in viruses @spyroslytras.bsky.social
#StrPhy26 #StrPhy
#StrPhy26 #StrPhy
What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics!
Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!
Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!
February 20, 2026 at 7:16 PM
Looking forward to working together in the future and further develop #StructuralPhylogenetics in viruses @spyroslytras.bsky.social
#StrPhy26 #StrPhy
#StrPhy26 #StrPhy
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
October 15, 2025 at 2:05 AM
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
APSPM2026 - What can we learn from ancient protein history?
@joannamasel.bsky.social will open with her research tracing how the genetic code first evolved and the surprising origin of tryptophan.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
@joannamasel.bsky.social will open with her research tracing how the genetic code first evolved and the surprising origin of tryptophan.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
February 17, 2026 at 9:06 PM
APSPM2026 - What can we learn from ancient protein history?
@joannamasel.bsky.social will open with her research tracing how the genetic code first evolved and the surprising origin of tryptophan.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
@joannamasel.bsky.social will open with her research tracing how the genetic code first evolved and the surprising origin of tryptophan.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
A new tool for structural phylogenetics: Folddisco makes connecting structural conservation to evolutionary signal beyond the twilight zone of protein sequence similarity a tractable problem. #StrPhy
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe.
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
June 9, 2026 at 12:26 AM
A new tool for structural phylogenetics: Folddisco makes connecting structural conservation to evolutionary signal beyond the twilight zone of protein sequence similarity a tractable problem. #StrPhy
APSPM2026 - Today's session starts with @claudiaalcar.bsky.social
Charting the protein universe: Deep evolutionary signals in sequence structure space (remote).
She'll present her work on exploring how protein folds emerged and diversified over billions of years.
#StrPhy26 #StrPhy
Charting the protein universe: Deep evolutionary signals in sequence structure space (remote).
She'll present her work on exploring how protein folds emerged and diversified over billions of years.
#StrPhy26 #StrPhy
February 16, 2026 at 10:30 PM
APSPM2026 - Today's session starts with @claudiaalcar.bsky.social
Charting the protein universe: Deep evolutionary signals in sequence structure space (remote).
She'll present her work on exploring how protein folds emerged and diversified over billions of years.
#StrPhy26 #StrPhy
Charting the protein universe: Deep evolutionary signals in sequence structure space (remote).
She'll present her work on exploring how protein folds emerged and diversified over billions of years.
#StrPhy26 #StrPhy
Abstract submissions are open for #APSPM2026!
🗓️ Deadline: Nov 28, 2026
📍 Brisbane + online
🎓 Travel grants for students & ECRs
Join us to explore how protein structures and AI are reshaping evolutionary biology.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
🗓️ Deadline: Nov 28, 2026
📍 Brisbane + online
🎓 Travel grants for students & ECRs
Join us to explore how protein structures and AI are reshaping evolutionary biology.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 24, 2025 at 4:06 AM
Abstract submissions are open for #APSPM2026!
🗓️ Deadline: Nov 28, 2026
📍 Brisbane + online
🎓 Travel grants for students & ECRs
Join us to explore how protein structures and AI are reshaping evolutionary biology.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
🗓️ Deadline: Nov 28, 2026
📍 Brisbane + online
🎓 Travel grants for students & ECRs
Join us to explore how protein structures and AI are reshaping evolutionary biology.
@official-smbe.bsky.social
#StrPhy26 #StrPhy
Looking forward to sharing this method as a hands-on workshop in the upcoming meeting
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
February 7, 2026 at 3:10 AM
Looking forward to sharing this method as a hands-on workshop in the upcoming meeting
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
For a full list of workshop we have: biosig.lab.uq.edu.au/strphy26/wor...
#StrPhy26 #StrPhy #StructuralPhylogenetics #Evolution #Brisbane
Interested in knowing more about distance-based #phylogenetics? Check out #Structome Playground — a no-code interactive educational resource for exploring distance matrices, neighbour-joining trees, and now the resolution limit in real time.
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
Structome-Playground: Learning Structural Phylogenetics
An interactive lab for understanding how geometric noise affects phylogenetic trees. Master the concepts of distance-based calibration and the Duplicate Monophyly Criterion.
biosig.lab.uq.edu.au
March 26, 2026 at 2:30 PM
Interested in knowing more about distance-based #phylogenetics? Check out #Structome Playground — a no-code interactive educational resource for exploring distance matrices, neighbour-joining trees, and now the resolution limit in real time.
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
biosig.lab.uq.edu.au/structome_pl...
#StrPhy (3/3)
Previously we used molecular simulations for this — rigorous but prohibitive at scale. This new preprint introduces the Duplicate Monophyly Criterion (DMC): a calibrated approximation that doesn't require simulation. More testing needed - but promising!
#StrPhy (2/3)
www.biorxiv.org/content/10.6...
#StrPhy (2/3)
www.biorxiv.org/content/10.6...
www.biorxiv.org
March 26, 2026 at 2:27 PM
Previously we used molecular simulations for this — rigorous but prohibitive at scale. This new preprint introduces the Duplicate Monophyly Criterion (DMC): a calibrated approximation that doesn't require simulation. More testing needed - but promising!
#StrPhy (2/3)
www.biorxiv.org/content/10.6...
#StrPhy (2/3)
www.biorxiv.org/content/10.6...
Distance-based #StructuralPhylogenetics is a powerful approach for exploring deep evolutionary relationships. Tools like those in the #Structome suite make this accessible in web workflows — but there's always been a critical missing piece: confidence estimates for the inferred trees.
#StrPhy (1/3)
#StrPhy (1/3)
March 26, 2026 at 2:21 PM
Distance-based #StructuralPhylogenetics is a powerful approach for exploring deep evolutionary relationships. Tools like those in the #Structome suite make this accessible in web workflows — but there's always been a critical missing piece: confidence estimates for the inferred trees.
#StrPhy (1/3)
#StrPhy (1/3)
Like with the MBE work, DeepRoots introduces a new and much faster way to bootstrap. It achieves this by introducing "Embedding Jitter"—injecting Gaussian noise into the latent space to estimate branch support.
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
February 7, 2026 at 2:56 AM
Like with the MBE work, DeepRoots introduces a new and much faster way to bootstrap. It achieves this by introducing "Embedding Jitter"—injecting Gaussian noise into the latent space to estimate branch support.
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
#Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
The logic behind this is #EmergentLatentBiology #ELB & is now formalized in our new paper in Curr Op in #StructuralBiology arguing that transformers organize biophysics into a "substrate" where biology becomes easily-decodable. www.sciencedirect.com/science/arti...
#Strphy #StructuralPhylogenetics
#Strphy #StructuralPhylogenetics
February 7, 2026 at 2:55 AM
The logic behind this is #EmergentLatentBiology #ELB & is now formalized in our new paper in Curr Op in #StructuralBiology arguing that transformers organize biophysics into a "substrate" where biology becomes easily-decodable. www.sciencedirect.com/science/arti...
#Strphy #StructuralPhylogenetics
#Strphy #StructuralPhylogenetics
Enter Structome-DeepRoots which uses high-dimensional embeddings from protein language models to see evolutionary "roots" invisible to geometry alone. It was turned into a web app (still has a lot of bugs 😅). 🔗 biosig.lab.uq.edu.au/structome_de...
#StructuralBiology #StructuralPhylogenetics #StrPhy
#StructuralBiology #StructuralPhylogenetics #StrPhy
Structome-DeepRoots
Structome-DeepRoots: A web server for phylogenetic inference using a novel, high-dimensional structural embedding method.
biosig.lab.uq.edu.au
February 7, 2026 at 2:54 AM
Enter Structome-DeepRoots which uses high-dimensional embeddings from protein language models to see evolutionary "roots" invisible to geometry alone. It was turned into a web app (still has a lot of bugs 😅). 🔗 biosig.lab.uq.edu.au/structome_de...
#StructuralBiology #StructuralPhylogenetics #StrPhy
#StructuralBiology #StructuralPhylogenetics #StrPhy