Lightnews — Scholar-powered news

Reposted by Yunha Hwang

Axel Visel @axelvisel.bsky.social · Aug 25

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 · Aug 25

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

2025 NeLLi Symposium | Joint Genome Institute

Las Vegas, NV Immediately followed by 1.5-day jamboree on November 6-7

jointgeno.me

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Yunha Hwang @microyunha.bsky.social · Jun 2

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

Gaia — Tatta Bio

www.tatta.bio

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Yunha Hwang @microyunha.bsky.social · Jun 2

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

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Reposted by Yunha Hwang

Florian Trigodet @floriantrigodet.bsky.social · Apr 28

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...

www.biorxiv.org

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Yunha Hwang @microyunha.bsky.social · Apr 28

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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Yunha Hwang @microyunha.bsky.social · Apr 28

It’s been an incredible journey building Tatta Bio with @ancornman1.bsky.social to advance AI infrastructure for biology, and I will continue to further our mission as chief scientist.

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Yunha Hwang @microyunha.bsky.social · Apr 28

My lab will couple ML and high throughput experimentation to harness the remarkable functional diversity of microbial genomes. If you are excited about the intersection of AI and microbiology, please get in touch!

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Yunha Hwang @microyunha.bsky.social · Apr 28

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.

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Yunha Hwang @microyunha.bsky.social · Mar 24

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

www.tatta.bio

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Yunha Hwang @microyunha.bsky.social · Dec 18

Our thoughts too! (stay tuned👀) 😉

Yunha Hwang @microyunha.bsky.social · Dec 17

As we improve Gaia Agent, we want to hear your feedback on the agent predictions. If you have suggestions on how we can increase its capabilities, please reach out! This was a major collaborative effort with @cong-ml.bsky.social , @joshuakravitz.com @nishantjha.org @ancornman1.bsky.social @Tatta Bio

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Yunha Hwang @microyunha.bsky.social · Dec 17

We tested Gaia Agent's capabilities with hypothetical genes in Mycobeterium tuberculosis. In our blog, We detail our in silico validation of Gaia Agent-predicted membrane transporter and lanthipeptide biosynthesis loci that were uncharacterized despite decades of Mtb research. Read more:

Gaia Agent: Context-Aware Functional Insights at Scale — Tatta Bio

An AI biologist discovers previously uncharacterized systems in the Mtb genome.

tatta.bio

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Yunha Hwang @microyunha.bsky.social · Dec 17

Like a human biologist, Gaia Agent considers sequence, structure and genomic context to *think* about functions of novel genes, drastically accelerating our ability to predict functions of billions of unannotated proteins across the tree of life.

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Yunha Hwang @microyunha.bsky.social · Dec 17

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

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Yunha Hwang @microyunha.bsky.social · Dec 15

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

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Yunha Hwang @microyunha.bsky.social · Dec 10

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 projects😇

www.biorxiv.org/content/10.1...

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...

www.biorxiv.org

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Reposted by Yunha Hwang

Mitja M. Zdouc @mmzdouc.bsky.social · Dec 10

Are you working on natural products? We’ve 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-...

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

academic.oup.com

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Reposted by Yunha Hwang

Amy Lu @amyxlu.bsky.social · Dec 6

1/🧬 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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Yunha Hwang @microyunha.bsky.social · Nov 23

you can search for eukaryotic sequences too, and you might find interesting homology to microbial proteins! (the current database you search against is microbial)

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Reposted by Yunha Hwang

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Nov 23

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.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...

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Yunha Hwang @microyunha.bsky.social · Nov 22

Great question, translation tables 11 and 4 should be covered, and we have seen translation table 15 being accounted for in some cases. @apcamargo.bsky.social

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Yunha Hwang @microyunha.bsky.social · Nov 21

and we are live on biorxiv! bsky.app/profile/bior...

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Nov 21

Gaia: A Context-Aware Sequence Search and Discovery Tool for Microbial Proteins https://www.biorxiv.org/content/10.1101/2024.11.19.624387v1

Protein sequence similarity search is fundamental to genomics research, but current methods are typi

www.biorxiv.org

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Yunha Hwang @microyunha.bsky.social · Nov 19

Thank you! We are building additional features (e.g. bookmarks, tags, comments), stay tuned for updates!

Yunha Hwang @microyunha.bsky.social · Nov 19

Great suggestion -- noted!

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Yunha Hwang @microyunha.bsky.social · Nov 19

We cluster all protein embeddings across all 100 retrieved contexts, and then the top 5 most frequently occurring clusters are colored!

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