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.

With pre-calculated FlashPPI2 interactions in SeqHub, you can immediately discover predicted physical interaction partners in the native genomic context AND examine how conserved these patterns are across diverse organisms. Give your favorite protein a try, and let us know what you find!🪄

Tatta Bio@tattabio.bsky.social · last mo.

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.

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

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

"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...

Excited to share the latest version of FlashPPI published with @pnas.org ! And stay tuned for updates soon…👀

Tatta Bio@tattabio.bsky.social · 2mo ago

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/...

SeqHub API Beta now live - genomic neighborhood retrieval and functional annotation just became instantaneous🤗

Tatta Bio@tattabio.bsky.social · 2mo ago

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 MSA live, integrated with structure vis! Another user requested feature🤝

Tatta Bio@tattabio.bsky.social · 4mo ago

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.

We’re incredibly grateful to have Alex Bateman on our advisory board. Biology today would look very different without UniProt. Scientific data infrastructure is the bedrock of innovation, and we’re excited to learn from Alex’s experience helping building such a foundational resource.

Tatta Bio@tattabio.bsky.social · 4mo ago

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.

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.

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...

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!

forms.gle

My group at MIT is seeking a research scientist with a strong *experimental* background to lead and help shape the lab’s experimental infrastructure, supporting efforts to advance AI-driven enzyme discovery and characterization. See the full JD here: acrobat.adobe.com/id/urn:aaid:...

Applications for MIT Novo-Nordisk AI postdoc fellowships are due Apr 15. Focus area lists AI and Biology topics, apply to work on this exciting field with amazing peers! engineering.mit.edu/novo-nordisk

Novo Nordisk Fellowship

Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...

engineering.mit.edu

We thought a lot about how to deploy 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰, and we are very proud of this implementation that integrates annotation+context+CoSearch+agent with FlashPPI on SeqHub!

Tatta Bio@tattabio.bsky.social · 5mo ago

FlashPPI is our new proteome-wide protein-protein interaction prediction model. If you haven't had a chance to try FlashPPI yet, here's what the end-to-end flow looks like in SeqHub:

Step-by-step how to run FlashPPI on your favorite genomes!

Tatta Bio@tattabio.bsky.social · 5mo ago

🧵 FlashPPI (new model) is live in SeqHub. Proteome-wide PPI prediction in minutes, 2,400x faster than the next best sequence-based method, 4x better predictive performance. How it works: 👇

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required. We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions. We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

We’d love to join your lab meeting! We’ve been meeting with research groups to share how scientists are using SeqHub for sequence and genome analysis, and the conversations have been highly interactive and grounded in real workflows. Booking info below.

We’re excited to welcome Daniela Bourges-Waldegg to the SeqHub Advisory Board! Daniela is EVP + Chief Digital & Technology Officer at @addgene.bsky.social. She will help shape our approach to building researcher-centered digital infrastructure with an eye toward long-term scientific impact.

First, @tattabio.bsky.social is now on Bluesky!💙 and second, we launched mult-sequence CoSearch on SeqHub!

Tatta Bio@tattabio.bsky.social · 6mo ago

Many questions in biology aren’t about individual proteins...they’re about how proteins behave together. This week we launched CoSearch in SeqHub: a user-requested analysis that lets you explore where multiple proteins co-occur across 132,000 microbial genomes, in seconds.

This. Is. So. Cool. 🤯

Yunha Hwang@microyunha.bsky.social · 9mo ago

We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.

Released today from Tatta Bio: SeqHub! A place to explore, annotate, and share sequence data with functional insights.  Over 1,000 scientists worldwide have already used SeqHub to annotate more than 550,000 proteins, uncovering new insights and accelerating discovery.

We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.

Ready to explore New Lineages of Life with @jgi.doe.gov ? 🧬🦠 Registration for our 2025 NeLLi Symposium is now open. For the first time in collaboration with @unlv.edu Mark the date: November 6-7 in Las Vegas, NV

Joint Genome Institute@jgi.doe.gov · 12mo ago

You can now register for the November NeLLi Symposium! Join us in November for talks focused on the most recent expansions of the Tree of Life, and the latest discoveries toward the evolution of cellular complexity and microbial symbiosis.  Learn more: jointgeno.me/NeLLi @nigelmouncey.bsky.social

At Tatta Bio, we have been thinking deeply about the sequence-to-function problem. We believe that before AI can power functional prediction, we first need to rethink how we curate, manage, and share sequence data. Here, we share our initial ideas on what we are building next:

Today's sequence data infrastructure is set up for failure in the age of AI.

Building an open and collaborative sequence platform for both Human and AI scientists.

tattabio.substack.com

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

Assemblies of long-read metagenomes suffer from diverse errors

Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

biorxiv.org

It’s official! 🎉 I’m thrilled to announce that I will be joining MIT as an assistant professor in a shared appointment between Biology, EECS and Schwarzman College of Computing this fall.

Tatta Bio is growing! We are hiring *two positions* in Business Development and Software Engineering to lead the development of AI-enabled scientific software for open science and biological sequence interpretation. Please check out the job postings at www.tatta.bio/careers and share widely!

Job Board | Notion

Overview

tatta.bio

Can LLM agents discover novel protein functions? Introducing Gaia Agent 🌎 🤖: an AI biologist capable of reasoning across genomic contexts to predict functions of proteins! Gaia Agent is now integrated with Gaia Search at gaia.tatta.bio

If you are at #NeurIPS2024 don't miss @ancornman1.bsky.social's talk on OMG/gLM2 at 9AM! @workshopmlsb.bsky.social East meeting room 11,12