Tatta Bio

If you haven't tried it yet, you can run proteome-wide PPI prediction on your own genome in SeqHub.

BioByte 150: Reconstructing Cellular History, FlashPPI Improves Protein-Protein Predictions, LNPs Allow for Pancreatic Drug Delivery, and a Proof of Concept for Parasites in Drug Discovery Welcome to Decoding Bio’s BioByte: each week our writing collective highlight notable news—from the latest scientific papers to the latest funding rounds—and everything in between.

Thanks to Decoding Bio for covering FlashPPI in BioByte this week! Good write-up if you want the context behind the method: open.substack.com/pub/decoding...

ecoli_k12 by tattabio - SeqHub View and analyze 4,317 sequences on SeqHub

Drill into any interaction and you get a residue-level contact map (not just whether two proteins interact, but where).

Try it on your own genome or start with our sample genome first: seqhub.org/tattabio/eco...

Preprint: www.biorxiv.org/content/10.6...

Within minutes of uploading your genome, you have a full predicted interaction network with proteins grouped into functional sub-networks. The genome browser stays integrated, so you can toggle between the network and your genomic data without losing context.

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:

FlashPPI in SeqHub: Proteome-Scale Protein-Protein Interaction Prediction - SeqHub FlashPPI brings proteome-wide protein-protein interaction prediction to SeqHub — completing full-genome PPI screens in minutes, directly in your browser.

More, high-level context in our blog: seqhub.org/blog/flashpp...
Full technical details in our preprint: www.biorxiv.org/content/10.6...

We’ve made this freely available for non-commercial use in SeqHub, where results are integrated with functional annotations, genomic context, and more.

Protein interaction prediction doesn't scale to full proteomes. It can take days to months to run all pairwise predictions for a single organism. FlashPPI (our new model) works directly from sequences without pairwise comparisons, which can translate to PPI predictions in minutes.

Ha, that would be some serious speed!

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.

3/ Model preprint: www.biorxiv.org/content/10.6...
Sample genome in SeqHub we've run FlashPPI on: seqhub.org/tattabio/eco...

2/ Explore clusters, check out individual interactions, and view contact maps, alongside functional annotations and genomic context in SeqHub.

1/ Upload your genome, click PPI in the tool bar, get a full predicted interaction network in minutes.

🧵 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: 👇

Exciting update today!

Upload your FASTA, CSV, or Genbank file. Generate annotations in seconds. Turn your data into a structured workspace.

SeqHub data tables make it easy to organize annotations, notes, links, and custom metadata as your analysis evolves.

If it would be useful for your lab, you can book a session with us here: calendar.app.google/V65mLVQ4BTWV...

Prefer to coordinate directly? Reach us at team@tatta.bio

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.

Integration of therapeutic cargo into the human genome with programmable type V-K CAST - Nature Communications RNA-guided CRISPR-associated transposases (CAST) are natural systems with broad potential in biotechnology. Here, the authors report compact type V-K CAST discovered from genome-resolved metagenomics ...

Paper cited: www.nature.com/articles/s41...

We used SeqHub's CoSearch to explore CRISPR-associated transposon (CAST) systems and found interesting patterns. By searching for TnsB + Cas12 together (Liu et al., 2025), we compared genomic context and architecture across organisms, making it easier to reason about CAST subtypes.

Understanding protein co-occurrence in genomic context: Introducing CoSearch - SeqHub CoSearch is a new, user-requested analysis in SeqHub that lets you explore where multiple proteins co-occur across genomes. It complements single-protein search and batch annotation by enabling relati...

Learn more about CoSearch: seqhub.org/blog/introdu...

CoSearch complements our single-protein search and batch annotation by adding a relational lens, useful for studying pathways, operons, BGCs, and other protein systems.

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.

Here's what we've been building:

🔬 SeqHub: protein & genome analysis platform (seqhub.org, free for academic use)

🤖 gLM2: genomic language model (github.com/TattaBio/gLM2)

🧬 OMG: metagenomic dataset containing 3.3B protein sequences and 2.8B intergenic sequences (github.com/TattaBio/OMG)

Our co-founders @microyunha.bsky.social and @ancornman1.bsky.social are here as well!

We're Tatta Bio, a scientific non-profit on a mission to make biological sequence data easy to find, understand, and share. We're building SeqHub, a platform for protein/genome analysis, with a focus on microbial research. Excited to connect with the scientific community here!