Sign in

Tatta Bio

@tattabio.bsky.social
208 followers 908 following 117 posts

Building genomic intelligence Metagenomic datasets, genomic language models, SeqHub Our research: tatta.bio Analyze your sequences on seqhub.org

PostsRepliesMedia
Tatta Bio @tattabio.bsky.social · 23/09/2026
In our preprint released last Friday, we show that evolutionary sequence information learned by our genomic language model, gLM2, can be used to design complex, multi-domain enzymes and expand their chemistry beyond their natural repertoire. 🧵 Preprint: www.biorxiv.org/content/10.6...
biorxiv.org
Generative Design of New-to-nature Biosynthetic Assembly Lines with Genomic Language Modeling
Reprogramming biosynthetic assembly lines can extend biosynthesis beyond the chemical space explored by nature. However, this remains difficult because assembly-line function depends on coordinated in...
143
Tatta Bio @tattabio.bsky.social · 18/09/2026
We're excited to share our new preprint! In collaboration with the @keaslinglab.bsky.social at UC Berkeley, we made gLM2 generative and used it to redesign a chimeric Type I polyketide synthase in the context of the full biosynthetic assembly line. 🧵 Preprint: www.biorxiv.org/content/10.6...
196
Tatta Bio @tattabio.bsky.social · 16/09/2026
Alongside our launch of SAE features (patterns gLM2 identifies in intergenic regions), we've expanded SeqHub search to incorporate them. CoSearch previously let you search up to 5 proteins co-occurring across genomes. It now also searches SAE features, Rfams, and Pfams in the same query with logic.
120
Tatta Bio @tattabio.bsky.social · 15/09/2026
Microbial intergenic regions encode much of the regulatory and functional logic of the genome, but they remain systematically difficult to discover and annotate. We trained a sparse autoencoder on gLM2 to identify recurring patterns across hundreds of millions of microbial intergenic regions... 🧵
1183
Tatta Bio @tattabio.bsky.social · 10/09/2026
SeqHub is now integrated into UniProt, surfacing genomic context directly on prokaryotic protein entries. The panel (in the Sequence section of UniProt) shows similar proteins to the current entry, each displayed with neighboring genes from its source genome. Blog: seqhub.org/blog/seqhub-...
seqhub.org
SeqHub Genomic Neighborhoods Now Integrated in UniProt - SeqHub
UniProt entries for prokaryotic proteins now show a genomic context panel powered by SeqHub, surfacing functionally similar proteins and their genomic neighborhoods directly on the entry page.
160
Tatta Bio @tattabio.bsky.social · 04/09/2026
UniProt is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.
13811
Tatta Bio @tattabio.bsky.social · 25/08/2026
Explore the intergenic space for promoters, terminators, and other regulatory elements using SeqHub's DNA view. Click into any region of a contig to view and copy the nucleotide sequence directly.
000
Tatta Bio @tattabio.bsky.social · 13/08/2026
You can now explore DNA in SeqHub. Click into any gene or intergenic region within a contig to retrieve and copy nucleotides.
033
Tatta Bio @tattabio.bsky.social · 10/08/2026
One day until our SeqHub webinar. Tomorrow at 11am ET we'll cover what's new, including non-coding RNA annotations and protein-protein interaction predictions in search, plus time for your questions. Sign up: docs.google.com/forms/d/e/1F... Can't make it? DM us to find time to chat.
000
Tatta Bio @tattabio.bsky.social · 06/08/2026
SeqHub protein searches now show which regions of a predicted structure are tied to specific biological functions or evolutionary patterns, powered by @biohub.org's SAE features. 🧵
1177
Tatta Bio @tattabio.bsky.social · 05/08/2026
SeqHub's Diversity Search widens your results to surface distant homologs that other search algorithms rank low or miss entirely. When you find a hit with low sequence identity, you can run a structural alignment within SeqHub to validate it before committing time to the candidate.
020
Tatta Bio @tattabio.bsky.social · 30/07/2026
SeqHub has an updated interface and new features! Join a live walkthrough on August 11 at 11am ET to see SeqHub in action, whether you're just getting started or want to catch up on what's changed since our last update. Sign up: docs.google.com/forms/d/e/1F...
000
Tatta Bio @tattabio.bsky.social · 29/07/2026
Retrieving gene neighborhoods is still one of the harder parts of working with sequence data, often needing large downloads and manual parsing of genomic locations. The SeqHub API returns functional annotations and surrounding genes for a query protein in one call, with locations already resolved.
100
Tatta Bio @tattabio.bsky.social · 28/07/2026
SeqHub, now in dark mode. Curious about the new UI or want to get up to speed on the latest SeqHub features? Join us for a webinar on August 11 at 11am EST. Sign up link below.
100
Tatta Bio @tattabio.bsky.social · 23/07/2026
We'll be at the AI x Bio Summit today at the NYSE, hosted by Decoding Bio. If you're at the event and curious to learn more about our models or platform, SeqHub, send us a DM or find Steph Flamen on the floor.
000
Tatta Bio @tattabio.bsky.social · 22/07/2026
We just launched a new UI for SeqHub so things might look a little different next time you log in 👀 With your feedback, we rebuilt navigation across the platform, with most tools now accessible from one location.
011
Tatta Bio @tattabio.bsky.social · 09/07/2026
We've arrived at ICML! @microyunha.bsky.social will be speaking at the GenBio Workshop on July 10th at 1:30pm local time: "Genomic Language Modeling for Context-Aware Biological Discovery." Hope to see you there! #ICML2026
010
Tatta Bio @tattabio.bsky.social · 07/07/2026
This week we are at ICML in Seoul, and next week we're headed to Washington, D.C. for ISMB. Our ICML (GenBio Workshop) talk: July 10th at 1:30pm Our ISMB talk: July 15 at 12:30pm We'd love to connect. Send a DM or email team@tatta.bio and we'll find time!
000
Tatta Bio @tattabio.bsky.social · 02/07/2026
In SeqHub, you can now search a protein to find FlashPPI2-predicted interaction partners across all 400 million proteins and 132K microbial genomes in our database (OpenGenome). You can still upload full genomes to find interactions within and between genomes.
020
Tatta Bio @tattabio.bsky.social · 01/07/2026
Two weeks ago, our FlashPPI paper was published in @pnas.org. Today, we introduce our updated model, FlashPPI2. Fine-tuned on new AlphaFold structures, this new model achieves a 17% improvement over FlashPPI on the E. coli protein interaction benchmark. seqhub.org/blog/flashppi2
seqhub.org
FlashPPI2: Enhanced Model, Scaled Across 130,000+ Genomes - SeqHub
FlashPPI2 drives up PPI prediction performance (AUPRC) by 17% while maintaining inference speed at minutes per genome — now deployed across SeqHub's database of over 130,000 microbial genomes.
153
Tatta Bio @tattabio.bsky.social · 25/06/2026
We'll be at ICML in Seoul July 6 - 11! Our Chief Scientist, @microyunha.bsky.social, will be speaking at the GenBio Workshop on July 10 at 1:30pm local time, presenting "Genomic Language Modeling for Context-Aware Biological Discovery." #ICML2026
121
Tatta Bio @tattabio.bsky.social · 23/06/2026
"SeqHub has become an integral part of our workflow...[it's] typically the first place we go to begin understanding what a gene might be doing and to identify its genomic neighbors across bacterial genomes." - Jeremy Rock, Rockefeller University seqhub.org/blog/rock-la...
seqhub.org
How the Rock Lab Uses SeqHub to Accelerate Discovery in Mtb and Mabs - SeqHub
The Rock Lab at Rockefeller University studies Mycobacterium tuberculosis and M. abscessus — two pathogens with large stretches of unannotated genome. SeqHub has become an integral part of their workf...
101
Tatta Bio @tattabio.bsky.social · 17/06/2026
Our FlashPPI paper is out in @pnas.org! FlashPPI is a model for proteome-wide protein-protein interaction prediction. 🔹4x better predictive performance & 2,400x faster than existing sequence-based methods 🔹20,000x faster than leading structure-based approaches. www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
121
Tatta Bio @tattabio.bsky.social · 16/06/2026
Search a protein in SeqHub and relevant literature appears alongside your genomic context results. Using the PaperBLAST database (Price & Arkin 2024), SeqHub retrieves papers, with specific passages highlighted, citing the sequence you searched and closely related ones.
020
Tatta Bio @tattabio.bsky.social · 09/06/2026
Last semester in MB 360: Scientific Inquiry in Microbiology at the Bench, a course designed by Dr. Carlos Goller and Camila Loyola, student teams extracted DNA, sequenced with Nanopore and Illumina, assembled genomes, and used SeqHub to annotate what they had assembled. seqhub.org/blog/nc-stat...
seqhub.org
How an NC State Microbiology Course Used SeqHub to Turn Student Sequencing Data into Published Genomes - SeqHub
Dr. Carlos Goller and TA Camila Loyola built NC State's MB 360 around hands-on genome sequencing and annotation. Students extracted DNA, assembled Delftia genomes, and used SeqHub to annotate and publ...
110
Tatta Bio @tattabio.bsky.social · 05/06/2026
ASM Microbe starts today. We're at booth 2324, next to the Applied and Environmental Microbiology Hub. Come find Andre, Yunha, and Steph if you're curious to learn more, provide feedback, or just say hello!
220
Tatta Bio @tattabio.bsky.social · 02/06/2026
Our Chief Scientist @microyunha.bsky.social is speaking at FOG tomorrow! Catch her talk on Genomic Language Modeling for Sequence Analysis and Management in the Age of AI at 12:30pm at the Biopharma Data Management Stage.
020
Tatta Bio @tattabio.bsky.social · 01/06/2026
The SeqHub API (beta) is free for non-commercial use. You can start querying today, and for throughput beyond the current beta limits, reach out at team@tatta.bio. We look forward to hearing your feedback! Docs: docs.seqhub.org/introduction
020
Tatta Bio @tattabio.bsky.social · 28/05/2026
We'd love to connect at ASM Microbe in D.C.! Stop by booth 2324 to learn more about our research or talk through how SeqHub could support your work.
220
Tatta Bio @tattabio.bsky.social · 27/05/2026
With the SeqHub API (now in beta), you can infer function for hypothetical proteins, identify gene clusters, and reconstruct putative pathways in uncharacterized organisms. Each query pulls from 130,000+ microbial genomes. Request a token from your Dashboard. Docs: docs.seqhub.org/introduction
docs.seqhub.org
SeqHub API - Zudoku
The SeqHub API gives you programmatic access to protein search and annotation tools built on top of Tatta Bio's genomic language models.
000
Tatta Bio @tattabio.bsky.social · 26/05/2026
Programmatic access to SeqHub has been one of the more common user requests. Today we're launching the SeqHub API in beta. Functional annotations for your protein and its genomic neighbors, derived from genomic language model embeddings. Free for non-commercial use. seqhub.org/blog/seqhub-...
seqhub.org
The SeqHub API Is Now in Beta - SeqHub
The SeqHub API is now in public beta. Submit protein sequences programmatically and get back gLM2-powered functional annotations and genomic context — free for non-commercial use.
100
Tatta Bio @tattabio.bsky.social · 21/05/2026
Taxonomy-specific search is now live in SeqHub. By popular request: filter by species, genus, family, or order before running your search, and get more results for the organisms you care about. Works with CoSearch and Diversity Search too.
020
Tatta Bio @tattabio.bsky.social · 14/05/2026
Collaboration in SeqHub: PIs reviewing annotations in-platform instead of through file handoffs, grad students and postdocs building shared datasets and crediting co-authors when they publish, and a class contributing to shared data under a faculty co-author. seqhub.org/blog/working...
seqhub.org
Working Together in SeqHub - SeqHub
Collaboration is now live on SeqHub. Share datasets with labmates, assign read or write access, and add co-authors so everyone who contributed gets credited.
000
Tatta Bio @tattabio.bsky.social · 07/05/2026
Mechanistic insights in host-virus biology often start with identifying which proteins are interacting across that boundary. SeqHub supports cross-proteome protein-protein interaction prediction. Upload any two genome FASTAs and get back a predicted interaction network spanning both.
110
Tatta Bio @tattabio.bsky.social · 06/05/2026
SeqHub can surface protein hits that wouldn't show up in a standard search, through embedding-based retrieval, CoSearch (co-occurrence search), and diversity control. Each targets a different gap in what alignment-based tools return. seqhub.org/blog/why-seq...
seqhub.org
Why SeqHub Search Finds Biology Other Tools Miss - SeqHub
SeqHub uses embedding-based search, diversity control, and co-occurrence search to surface protein connections that BLAST and profile-based tools miss — especially for hypothetical proteins and underr...
100
Tatta Bio @tattabio.bsky.social · 05/05/2026
Non-coding RNA is now annotated automatically in the SeqHub genome viewer. Upload a genome and Rfam annotations surface directly on the gene map alongside your coding sequences. Rfam annotations are now available across search and genome upload.
010
Tatta Bio @tattabio.bsky.social · 23/04/2026
SeqHub now generates a UMAP from your uploaded protein family, so you can find clusters, better navigate your dataset, and prioritize candidates for validation. Just select a protein in your data table to launch it.
010
Tatta Bio @tattabio.bsky.social · 21/04/2026
We're offering free 1:1 SeqHub training sessions, tailored to your research. New to the platform or already using it, book a time and we'll walk through what's most relevant to your work. calendar.app.google/KLFsKvszMMko...
000
Tatta Bio @tattabio.bsky.social · 15/04/2026
Add collaborators to share data you've curated in SeqHub! Invited collaborators can... - View functional annotations - Add their own annotations and experimental results - Work with the SeqHub Agent - Run FlashPPI against the data No longer need to download and send files back and forth.
010
Tatta Bio @tattabio.bsky.social · 14/04/2026
We'll be at the MIT Microbiome Symposium this Friday, April 17! If you're interested in learning more about our research at Tatta Bio or want to see how SeqHub can support your work, come find us at our table or set up time to chat (DM or email us at team@tatta.bio).
100
Tatta Bio @tattabio.bsky.social · 13/04/2026
Collaboration is now live on SeqHub. 🔹 Add labmates to your datasets so you can build upon the same annotations and data with additional research findings. 🔹 Add co-authors to public datasets to credit everyone who contributed to the work.
020
Tatta Bio @tattabio.bsky.social · 09/04/2026
Registration is open for our April 15 webinar on protein-protein interaction prediction with FlashPPI. The session will cover how the model works (high-level) and how you can access it in SeqHub. Experimental and computational folks welcome! Sign up: forms.gle/iBQrpYnLeiF1...
forms.gle
SeqHub FlashPPI Walk-Through Webinar Registration
Register to attend the live FlashPPI-focused walk-through of the SeqHub Platform. We'll send you an invite to this email once you submit the form. See you soon!
000
Tatta Bio @tattabio.bsky.social · 08/04/2026
You can now run a multiple sequence alignment directly on your SeqHub search results. Once the alignment runs, conserved regions are mapped onto the 3D structure of your query protein. Explore results in SeqHub or download as an a3m file.
062
Tatta Bio @tattabio.bsky.social · 07/04/2026
We're thrilled to welcome @alexbateman1.bsky.social to the SeqHub Advisory Board! Alex has played a central role in building core global resources for protein science, including UniProt. He has been a longtime leader in developing standards and infrastructure that underpin modern protein analysis.
131
Tatta Bio @tattabio.bsky.social · 02/04/2026
Most protein-protein interaction tools work on protein pairs. FlashPPI runs at proteome scale and now across two proteomes at once. Upload any two datasets (full genomes, partial genomes, or custom protein sets) and get back a predicted interaction network spanning both.
042
Tatta Bio @tattabio.bsky.social · 01/04/2026
We're hosting a live walkthrough of FlashPPI in SeqHub on April 15 at 11am EST. We'll briefly discuss our protein-protein interaction model then walk through how you can use it in SeqHub. Register here: forms.gle/iBQrpYnLeiF1...
forms.gle
SeqHub Platform Walk-Through Webinar Registration
Register to attend the live FlashPPI-focused walk-through of the SeqHub Platform. We'll send you an invite to this email once you submit the form. See you soon!
001
Tatta Bio @tattabio.bsky.social · 31/03/2026
SeqHub now surfaces Rfam annotations directly in the genomic neighborhood view: family name, accession, length, and a link out to the Rfam entry.
121
Tatta Bio @tattabio.bsky.social · 30/03/2026
SeqHub now detects non-coding RNAs in genomic context. Non-coding RNAs are annotated directly in the genomic neighborhood view, giving a more complete picture of operon structure without having to cross-reference external annotation tools.
000
Tatta Bio @tattabio.bsky.social · 25/03/2026
Sequence and structural alignment in SeqHub just got easier. Click any similar sequence from your results, you'll get prompted to run an alignment, and then you'll get identity score, coverage, TM-score, and RMSD. Shout out to the users who flagged this one!
011
Tatta Bio @tattabio.bsky.social · 17/03/2026
FlashPPI predicts protein-protein interactions from sequence. CoSearch finds where those proteins co-occur across genomic contexts. When co-occurrence holds up, it helps you build confidence in what FlashPPI predicted.
110