iiinova — where your digital self keeps evolving

Reposted by Yunha Hwang

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...

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Yunha Hwang @microyunha.bsky.social · 15/09/2026

Microbial genomes have been extensively mined for new proteins, but the noncoding sequences between genes remain largely unexplored despite encoding important regulatory and functional information. In our new work, we asked whether gLM2 could help systematically discover these intergenic features.

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Yunha Hwang @microyunha.bsky.social · 04/09/2026

This one is really special to me! As someone who probably spends more time on UniProt than on Google, I’m incredibly proud that SeqHub search is now integrated with UniProt, bringing together UniProt’s rich protein annotations with SeqHub’s view of native genomic context across diverse microbes!

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Reposted by Yunha Hwang

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.

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Reposted by Yunha Hwang

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. 🧵

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Reposted by Yunha Hwang

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.

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Yunha Hwang @microyunha.bsky.social · 02/07/2026

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!🪄

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Reposted by Yunha Hwang

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.

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Reposted by Yunha Hwang

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

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Reposted by Yunha Hwang

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...

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Yunha Hwang @microyunha.bsky.social · 17/06/2026

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

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Yunha Hwang @microyunha.bsky.social · 26/05/2026

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

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Yunha Hwang @microyunha.bsky.social · 08/04/2026

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

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Yunha Hwang @microyunha.bsky.social · 07/04/2026

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.

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Reposted by Yunha Hwang

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.

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Reposted by Yunha Hwang

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!

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Yunha Hwang @microyunha.bsky.social · 24/03/2026

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:...

acrobat.adobe.com

Adobe Acrobat

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Yunha Hwang @microyunha.bsky.social · 18/03/2026

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

engineering.mit.edu

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...

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Yunha Hwang @microyunha.bsky.social · 05/03/2026

Thanks for the idea, we briefly checked this and for E.coli test set predictions, we get ~80% of the high confidence interactions to be more than 5 genes away from each other, so a large fraction is non-syntenic!

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Yunha Hwang @microyunha.bsky.social · 05/03/2026

For wirus-microbe -- yes (we have examples in paper)!, for microbe-host, we haven't fully evaluated how this would work for eukaryotic proteomes.

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Yunha Hwang @microyunha.bsky.social · 05/03/2026

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!

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Yunha Hwang @microyunha.bsky.social · 04/03/2026

Thanks for pointing this out! We will add an option to download the network!

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

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

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Reposted by Yunha Hwang

Andre Cornman @ancornman1.bsky.social · 03/03/2026

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/🧵

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

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

biorxiv.org

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

For a typical microbial genome, all-vs-all PPI prediction with AF3 would take hundreds of GPU-years. With FlashPPI, we can scale molecular interaction prediction across diverse, non-model microbial genomes, unlocking truly scalable discovery. We deployed FlashPPI on Seqhub.org, give it a spin!

seqhub.org

SeqHub - The Home for Biological Sequences

SeqHub is a platform for exploring, annotating, and sharing biological sequences.

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

3. Online hard negative mining improves sensitivity. We use joint optimization to let the model propose hard negatives for contact prediction during training. This results in even more sensitive and robust performance.

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

2. Learning how proteins interact matters It's not enough to learn that 2 proteins interact, learning *how* they interact at residue level is critical for performance.

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

Some fun highlights on what we learned along the way: 1. Reframing PPI prediction as retrieval Instead of asking “Do A and B interact?”, we ask: Which proteins does A interact with in this genome? This shift in framing enables linear-time scaling and ultrafast performance.

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

For technical details, check out @ancornman1’s excellent breakdown of the model. bsky.app/profile/anco...

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Yunha Hwang @microyunha.bsky.social · 03/03/2026

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.

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Reposted by Yunha Hwang

Tatta Bio @tattabio.bsky.social · 12/02/2026

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.

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Reposted by Yunha Hwang

Tatta Bio @tattabio.bsky.social · 10/02/2026

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.

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Yunha Hwang @microyunha.bsky.social · 04/02/2026

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

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Reposted by Yunha Hwang

Lizzy Wilbanks @lizzywilbanks.bsky.social · 05/11/2025

This. Is. So. Cool. 🤯

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Yunha Hwang @microyunha.bsky.social · 30/10/2025

Hi Roland, our servers are in the US, we explicitly state in our docs that we do not train models on private data, and the data is private to you only - unless intentionally made public (for publication/data sharing purposes)!

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Yunha Hwang @microyunha.bsky.social · 29/10/2025

thanks for the feedback! We are working on making more of the platform exportable as figures😊

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Reposted by Yunha Hwang

ISCB News @iscb.bsky.social · 28/10/2025

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.

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Yunha Hwang @microyunha.bsky.social · 28/10/2025

Annotations are mapped using embedding-based search, making it faster than most alignment-based search. HMM prediction speed-up comes from some optimization and parallelization :)

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Yunha Hwang @microyunha.bsky.social · 28/10/2025

Thank you! and PaperBLAST team deserves a shoutout for the sequence-paper linkages

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Yunha Hwang @microyunha.bsky.social · 28/10/2025

Currently, SeqHub is optimized for microbial protein and genome analysis. As we expand beyond microbial data, we'd love your feedback to help shape what comes next. I'm deeply grateful to our team at Tatta Bio, and to our collaborators and funders, for making this vision a reality. 🔗 seqhub.org

seqhub.org

SeqHub

SeqHub is a platform for exploring, annotating, and sharing biological sequences.

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Yunha Hwang @microyunha.bsky.social · 28/10/2025

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.

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Reposted by Yunha Hwang

Axel Visel @axelvisel.bsky.social · 25/08/2025

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

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Yunha Hwang @microyunha.bsky.social · 02/06/2025

We are building this infrastructure for the scientific community, and we invite feedback and collaboration from researchers at every stage. We are grateful to the Moore Foundation for their generous support in making this project possible. Stay tuned for more updates! www.tatta.bio/gaia

tatta.bio

Gaia — Tatta Bio

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Yunha Hwang @microyunha.bsky.social · 02/06/2025

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:

tattabio.substack.com

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.

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Reposted by Yunha Hwang

Florian Trigodet @floriantrigodet.bsky.social · 28/04/2025

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 🧵

biorxiv.org

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...

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Yunha Hwang @microyunha.bsky.social · 28/04/2025

I am so grateful for all the support I received from my mentors, colleagues and collaborators over the years: @pgirguis.bsky.social, @sokrypton.org, @simrouxvirus.bsky.social, @alexjprobst.bsky.social, @annedekas.bsky.social

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