Xing-Xing Shen
@xingxingshen.bsky.social
Evolutionary biology, Phylogenetics, Comparative genomics, Structural genomics, Collaboratives, Insects. Lab website: https://shenxlab.com/
Reposted by Xing-Xing Shen
Democratizing protein language model training, sharing and collaboration www.nature.com/articles/s4...
November 4, 2025 at 3:15 PM
Democratizing protein language model training, sharing and collaboration www.nature.com/articles/s4...
Reposted by Xing-Xing Shen
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Labs in bacterial immunity
docs.google.com
November 4, 2025 at 3:06 PM
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Reposted by Xing-Xing Shen
"We are like butterflies who flutter for a day and think it is forever."
- Carl Sagan, Cosmos
- Carl Sagan, Cosmos
May 10, 2025 at 6:30 PM
"We are like butterflies who flutter for a day and think it is forever."
- Carl Sagan, Cosmos
- Carl Sagan, Cosmos
Reposted by Xing-Xing Shen
Visit our posters at #RECOMB2025 for:
Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis
Metagenomics: Classification & Metabuli App
GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery
& get Marv stickers!
Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis
Metagenomics: Classification & Metabuli App
GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery
& get Marv stickers!
April 25, 2025 at 7:46 AM
Visit our posters at #RECOMB2025 for:
Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis
Metagenomics: Classification & Metabuli App
GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery
& get Marv stickers!
Structural: MSAs, Virus DB, Core Genes, Motif Discovery, Multimer Clustering & Search, pLM Foldseek, Environmental analysis
Metagenomics: Classification & Metabuli App
GPU-based & RNA search, Proteome clustering, Novel Ribozyme discovery
& get Marv stickers!
Reposted by Xing-Xing Shen
Today @yewonhan.bsky.social will give a flash talk about our metagenomic large-scale protein structure clustering and analysis at #RECOMB2025.
Today (April 29) 1 p.m. at Global Lounge in “The Commons”
Today (April 29) 1 p.m. at Global Lounge in “The Commons”
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...
April 29, 2025 at 1:08 AM
Today @yewonhan.bsky.social will give a flash talk about our metagenomic large-scale protein structure clustering and analysis at #RECOMB2025.
Today (April 29) 1 p.m. at Global Lounge in “The Commons”
Today (April 29) 1 p.m. at Global Lounge in “The Commons”
Reposted by Xing-Xing Shen
So nice to see this out! Congratulations Kelsey, @lauraeme.bsky.social , @andrewjroger.bsky.social and colleagues! www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
www.nature.com
March 13, 2025 at 10:42 AM
So nice to see this out! Congratulations Kelsey, @lauraeme.bsky.social , @andrewjroger.bsky.social and colleagues! www.nature.com/articles/s41...
Reposted by Xing-Xing Shen
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Structure-guided discovery of viral proteins that inhibit host immunity
Large-scale, structure-guided computational pipeline sifts through millions of phage
proteins to identify those that bind and antagonize host immune proteins. Detected
proteins are shown to inhibit no...
www.cell.com
January 23, 2025 at 4:12 PM
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Reposted by Xing-Xing Shen
A critical evaluation of deep-learning based phylogenetic inference programs using simulated data sets https://pubmed.ncbi.nlm.nih.gov/39824436/
January 19, 2025 at 3:45 AM
A critical evaluation of deep-learning based phylogenetic inference programs using simulated data sets https://pubmed.ncbi.nlm.nih.gov/39824436/
Reposted by Xing-Xing Shen
An #AI model created to design proteins simulates 500 million years of protein evolution in developing a previously unknown bright fluorescent protein.
Learn more in a new Science study: https://scim.ag/40l2z3J
Learn more in a new Science study: https://scim.ag/40l2z3J
January 17, 2025 at 3:07 PM
An #AI model created to design proteins simulates 500 million years of protein evolution in developing a previously unknown bright fluorescent protein.
Learn more in a new Science study: https://scim.ag/40l2z3J
Learn more in a new Science study: https://scim.ag/40l2z3J
Reposted by Xing-Xing Shen
The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out!
🌐 search.foldseek.com
🌐 search.foldseek.com
January 17, 2025 at 12:33 PM
The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out!
🌐 search.foldseek.com
🌐 search.foldseek.com
Reposted by Xing-Xing Shen
FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social
January 3, 2025 at 2:14 PM
FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social
Reposted by Xing-Xing Shen
Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 13, 2025 at 9:09 AM
Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Xing-Xing Shen
A reminder that we have two open PhD projects on Bayesian phylogenetics in the lab:
One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan)
And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)
One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan)
And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)
January 6, 2025 at 7:42 PM
A reminder that we have two open PhD projects on Bayesian phylogenetics in the lab:
One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan)
And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)
One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan)
And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)
Reposted by Xing-Xing Shen
Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG
December 5, 2024 at 5:09 PM
Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG
Reposted by Xing-Xing Shen
On the 4th day of #Fishmas, my true love gave to me: The Troyer et al. 2022 Tetraodontiformes phylogenetic tree!!
www.pnas.org/doi/full/10....
www.pnas.org/doi/full/10....
December 29, 2024 at 12:16 AM
On the 4th day of #Fishmas, my true love gave to me: The Troyer et al. 2022 Tetraodontiformes phylogenetic tree!!
www.pnas.org/doi/full/10....
www.pnas.org/doi/full/10....
Reposted by Xing-Xing Shen
I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪
December 28, 2024 at 9:00 PM
I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪
Reposted by Xing-Xing Shen
Bumblebee, Bombus spec. The wild bees of the genus Bombus, also called bumblebees, can be easily identified by the ocelli between the compound eyes. These are arranged almost in a straight line next to each other and not in a triangle like in other bees genera.
December 29, 2024 at 7:32 AM
Bumblebee, Bombus spec. The wild bees of the genus Bombus, also called bumblebees, can be easily identified by the ocelli between the compound eyes. These are arranged almost in a straight line next to each other and not in a triangle like in other bees genera.
Reposted by Xing-Xing Shen
What did the Last Eukaryotic Common Ancestor (#LECA) look like? Consensus View in #PLOSBiology; massive authorship including @AncestralState, @lauraeme.bsky.social, John Archbald, @andrewjroger.bsky.social, @dackslabecb.bsky.social, Jeremy Wideman. plos.io/4g0alq4
November 25, 2024 at 7:29 PM
What did the Last Eukaryotic Common Ancestor (#LECA) look like? Consensus View in #PLOSBiology; massive authorship including @AncestralState, @lauraeme.bsky.social, John Archbald, @andrewjroger.bsky.social, @dackslabecb.bsky.social, Jeremy Wideman. plos.io/4g0alq4
Reposted by Xing-Xing Shen
This looks interesting! Anyone tried it on amino acid alignments?
PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites https://pubmed.ncbi.nlm.nih.gov/39650558/
December 11, 2024 at 3:54 PM
This looks interesting! Anyone tried it on amino acid alignments?
Reposted by Xing-Xing Shen
Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
December 23, 2024 at 4:39 PM
Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...