Juan Manuel Trinidad Barnech
@jtrinidad13.bsky.social
PhD. Bioinformatic. Evolutionary biologist. Kinetoplastid research.
Reposted by Juan Manuel Trinidad Barnech
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Juan Manuel Trinidad Barnech
FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
Communications Biology - FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and...
www.nature.com
August 15, 2025 at 12:05 AM
FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
@gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social
@csic.es www.nature.com/articles/s42...
Reposted by Juan Manuel Trinidad Barnech
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Reposted by Juan Manuel Trinidad Barnech
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
Reposted by Juan Manuel Trinidad Barnech
New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...
A general substitution matrix for structural phylogenetics.
Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the
academic.oup.com
June 11, 2025 at 2:01 PM
New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...
Reposted by Juan Manuel Trinidad Barnech
InterPro just got one of its biggest updates ever.
Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD).
See it all at www.ebi.ac.uk/interpro
🖥️🧬
@interprodb.bsky.social
Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD).
See it all at www.ebi.ac.uk/interpro
🖥️🧬
@interprodb.bsky.social
June 12, 2025 at 3:27 PM
InterPro just got one of its biggest updates ever.
Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD).
See it all at www.ebi.ac.uk/interpro
🖥️🧬
@interprodb.bsky.social
Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD).
See it all at www.ebi.ac.uk/interpro
🖥️🧬
@interprodb.bsky.social
Excited to share the results of my PhD! Using advanced protein structure comparisons, we uncovered remote homologs and revealed essential eukaryotic genes “lost” in kinetoplastids – what I like to call the “missing gears.”
Discover more: journals.plos.org/plospathogen...
Discover more: journals.plos.org/plospathogen...
Expanding kinetoplastid genome annotation through protein structure comparison
Kinetoplastids are a group of parasites that cause severe diseases in the poorest regions of the world. Despite the increasing amount of genomic information available on these parasites, predicting th...
journals.plos.org
May 5, 2025 at 2:06 PM
Excited to share the results of my PhD! Using advanced protein structure comparisons, we uncovered remote homologs and revealed essential eukaryotic genes “lost” in kinetoplastids – what I like to call the “missing gears.”
Discover more: journals.plos.org/plospathogen...
Discover more: journals.plos.org/plospathogen...
Reposted by Juan Manuel Trinidad Barnech
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 by Juan Manuel Trinidad Barnech
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) 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 12, 2025 at 4:39 PM
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
Reposted by Juan Manuel Trinidad Barnech
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
Reposted by Juan Manuel Trinidad Barnech
Polarization has become a serious threat to shared reality, democracy, and even health
"Thousands of people were dying needlessly because they didn’t trust medical advice, or their government, or mainstream media”
Reducing partisan animosity is doable, but tricky:
www.pnas.org/doi/epub/10....
"Thousands of people were dying needlessly because they didn’t trust medical advice, or their government, or mainstream media”
Reducing partisan animosity is doable, but tricky:
www.pnas.org/doi/epub/10....
January 27, 2025 at 2:12 PM
Polarization has become a serious threat to shared reality, democracy, and even health
"Thousands of people were dying needlessly because they didn’t trust medical advice, or their government, or mainstream media”
Reducing partisan animosity is doable, but tricky:
www.pnas.org/doi/epub/10....
"Thousands of people were dying needlessly because they didn’t trust medical advice, or their government, or mainstream media”
Reducing partisan animosity is doable, but tricky:
www.pnas.org/doi/epub/10....
Reposted by Juan Manuel Trinidad Barnech
📜 Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis
🧑🔬 Federico A. Vignale, Andrea Hernandez Garcia, Todd J. Barkman, Adrian G. Turjanski, et al.
📔 @elife.bsky.social
🔗 elifesciences.org/articles/104...
#️⃣ #PlantSciene #PlantMetabolism
🧑🔬 Federico A. Vignale, Andrea Hernandez Garcia, Todd J. Barkman, Adrian G. Turjanski, et al.
📔 @elife.bsky.social
🔗 elifesciences.org/articles/104...
#️⃣ #PlantSciene #PlantMetabolism
Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis
DNA sequencing of the yerba mate (Ilex paraguariensis) genome reveals convergent genomic changes, biochemical pathways, mutations, and substrate-binding orientations responsible for caffeine biosynthe...
elifesciences.org
January 27, 2025 at 8:15 AM
📜 Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis
🧑🔬 Federico A. Vignale, Andrea Hernandez Garcia, Todd J. Barkman, Adrian G. Turjanski, et al.
📔 @elife.bsky.social
🔗 elifesciences.org/articles/104...
#️⃣ #PlantSciene #PlantMetabolism
🧑🔬 Federico A. Vignale, Andrea Hernandez Garcia, Todd J. Barkman, Adrian G. Turjanski, et al.
📔 @elife.bsky.social
🔗 elifesciences.org/articles/104...
#️⃣ #PlantSciene #PlantMetabolism
Reposted by Juan Manuel Trinidad Barnech
This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
Highly multiplexed spatial transcriptomics in bacteria
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...
www.science.org
January 24, 2025 at 4:30 AM
This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫
Reposted by Juan Manuel Trinidad Barnech
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