Yunha Hwang
@microyunha.bsky.social
๐ค 1323
๐ฅ 1119
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Building genomic intelligence @ Tatta Bio
pinned post!
Proteinโprotein interactions (PPIs) are key to discovering and interpreting new biological functions. Weโre excited to introduce ๐ญ๐๐๐๐๐ท๐ท๐ฐ: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.
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about 1 month ago
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Yunha Hwang
Tatta Bio
2 days ago
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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Yunha Hwang
Tatta Bio
3 days ago
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...
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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!
https://forms.gle/iBQrpYnLeiF1VE8c8
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My group at MIT is seeking a research scientist with a strong *experimental* background to lead and help shape the labโs experimental infrastructure, supporting efforts to advance AI-driven enzyme discovery and characterization. See the full JD here:
acrobat.adobe.com/id/urn:aaid:...
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Adobe Acrobat
https://acrobat.adobe.com/id/urn:aaid:sc:us:0fa4c365-ce1d-4b4f-8bc1-e0c3bb9b8901
11 days ago
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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
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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...
https://engineering.mit.edu/novo-nordisk
17 days ago
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We thought a lot about how to deploy ๐ญ๐๐๐๐๐ท๐ท๐ฐ, and we are very proud of this implementation that integrates annotation+context+CoSearch+agent with FlashPPI on SeqHub!
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about 1 month ago
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Step-by-step how to run FlashPPI on your favorite genomes!
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about 1 month ago
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Yunha Hwang
Andre Cornman
about 1 month ago
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. 1/๐งต
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Proteinโprotein interactions (PPIs) are key to discovering and interpreting new biological functions. Weโre excited to introduce ๐ญ๐๐๐๐๐ท๐ท๐ฐ: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.
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about 1 month ago
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reposted by
Yunha Hwang
Tatta Bio
about 2 months ago
Weโd love to join your lab meeting! Weโve 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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Yunha Hwang
Tatta Bio
about 2 months ago
Weโre 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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First,
@tattabio.bsky.social
is now on Bluesky!๐ and second, we launched mult-sequence CoSearch on SeqHub!
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about 2 months ago
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reposted by
Yunha Hwang
Lizzy Wilbanks
5 months ago
This. Is. So. Cool. ๐คฏ
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Yunha Hwang
ISCB News
5 months ago
Released today from Tatta Bio: SeqHub! A place to explore, annotate, and share sequence data with functional insights.ย 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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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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5 months ago
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reposted by
Yunha Hwang
Axel Visel
7 months ago
Ready to explore New Lineages of Life with
@jgi.doe.gov
? ๐งฌ๐ฆ 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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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:
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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.
https://tattabio.substack.com/p/todays-sequence-data-infrastructure
10 months ago
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reposted by
Yunha Hwang
Florian Trigodet
11 months ago
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 ๐งต
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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...
https://www.biorxiv.org/content/10.1101/2025.04.22.649783v2
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Itโs official! ๐ Iโm 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.
11 months ago
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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!
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Job Board | Notion
Overview
https://www.tatta.bio/careers
about 1 year ago
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Can LLM agents discover novel protein functions? Introducing Gaia Agent ๐ ๐ค: 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
over 1 year ago
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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
over 1 year ago
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Excited to be at
#NeurIPS
this week.
@ancornman1.bsky.social
will give a spotlight talk at the
@workshopmlsb.bsky.social
on gLM2/OMG! Please reach out if you want to chat about gLM2/OMG/Gaia and our latest projects๐
www.biorxiv.org/content/10.1...
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The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling
Biological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraini...
https://www.biorxiv.org/content/10.1101/2024.08.14.607850v2
over 1 year ago
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reposted by
Yunha Hwang
Mitja M. Zdouc
over 1 year ago
Are you working on natural products? Weโve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8)
academic.oup.com/nar/advance-...
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MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1115/7919508?searchresult=1
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reposted by
Yunha Hwang
Amy Lu
over 1 year ago
1/๐งฌ Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
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reposted by
Yunha Hwang
Martin Steinegger ๐บ๐ฆ
over 1 year ago
Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. ๐
bfvd.foldseek.com
๐พ
bfvd.steineggerlab.workers.dev
๐
academic.oup.com/nar/advance-...
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Hello ๐ฆ
#protein
/
#microbio
/
#BioML
community! We are excited to release Gaia๐, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on
gaia.tatta.bio
over 1 year ago
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