Lightnews — Scholar-powered news

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Jason Williams @jasonwilliamsny.bsky.social · 14d

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.

The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP

jasonjwilliamsny.github.io/grfp2025/

An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program

jasonjwilliamsny.github.io

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Reposted by Meg T (she/her/hers)

Frances Arnold @francesarnold.bsky.social · Jul 22

I'm really proud of this work by Jae Kennemur and Yueming Long. #Enzymes rock, with some help from #directed evolution to do chemistry not known in nature (and really hard for humans, too). @caltechcce.bsky.social
pubs.acs.org/doi/10.1021/...

Enzymatic Stereodivergent Synthesis of Azaspiro[2.y]alkanes

Azaspiro[2.y]alkanes are increasingly valuable scaffolds in pharmaceutical drug discovery; however, an asymmetric catalytic method for their synthesis remains unknown. Here, we present a stereodiverge...

pubs.acs.org

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25d

The posting is unfortunately not super clear on this, but please apply if you want to do BioML research, especially around machine learning for molecular biology and bioengineering!

I get sad if there are no applicants with this profile in the pool!

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 27d

If you're an undergrad and want to intern with me, this is where you need to apply!

Microsoft Research @msftresearch.bsky.social · 27d

The Microsoft Research Undergraduate Internship Program offers 12-week internships in our Redmond, NYC, or New England labs for rising juniors and seniors who are passionate about technology. Apply by October 6: msft.it/6015scgSJ

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Kieran Didi @kdidi.bsky.social · Jul 19

Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!

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Reposted by Meg T (she/her/hers)

Erle Ellis @erleellis.bsky.social · Jul 28

Really nice metastudy of citizen science contributing to ecology & biodiversity research @inaturalist.bsky.social @aibsbiology.bsky.social
👀🔎🍄🧪🌎🌐
iNaturalist accelerates biodiversity research academic.oup.com/bioscience/a...

iNaturalist accelerates biodiversity research

Abstract. Participatory citizen science is expanding, with iNaturalist emerging as one of the most widely used platforms globally. However, its application

academic.oup.com

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Gina El Nesr @ginaelnesr.bsky.social · Jul 28

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jul 25

There's a lot more in the preprint!

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

The Dayhoff Atlas: scaling sequence diversity for improved protein generation

Modern biology is powered by the organization of biological information, a framework pioneered in 1965 by Margaret Dayhoff's Atlas of Protein Sequence and Structure. Databases descended from this comm...

www.biorxiv.org

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jul 25

In 1965, Margaret Dayhoff published the Atlas of Protein Sequence and Structure, which collated the 65 proteins whose amino acid sequences were then known.

Inspired by that Atlas, today we are releasing the Dayhoff Atlas of protein sequence data and protein language models.

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Meg T (she/her/hers) @megthescientist.bsky.social · Jul 21

“Writing compels us to think — not in the chaotic, non-linear way our minds typically wander, but in a structured, intentional manner. By writing it down, we can sort years of research, data and analysis into an actual story, thereby identifying our main message and the influence of our work.”

Gilbert C FAURE @grip54.bsky.social · Jul 21

Writing is thinking | Nature Reviews Bioengineering

On the value of human-generated scientific writing in the age of large-language models.

www.nature.com

Meg T (she/her/hers) @megthescientist.bsky.social · Jul 21

Was looking for it here today as well :(

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Reposted by Meg T (she/her/hers)

Scott McGrath @smcgrath.phd · Jul 19

🧪 The EPA is eliminating its scientific research arm and firing hundreds of scientists.

This move, enabled by a Supreme Court ruling, dismantles the office providing independent research for environmental policies.
#Climate

E.P.A. Says It Will Eliminate Its Scientific Research Arm

www.nytimes.com

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Reposted by Meg T (she/her/hers)

EvolutionaryScale @evolutionaryscale.bsky.social · Jul 8

We're sponsoring the use of ESM3 and EMSC to help researchers engineer improved PETase enzymes in the @AlignBio 2025 Protein Engineering Tournament.

Get started using ESMC to predict protein function and ESM3 to generate new enzymes here: github.com/evolutionary...

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The Align Foundation @alignbio.bsky.social · Jul 8

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🚀 Announcing the 2025 Protein Engineering Tournament.

This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️

#AIforBiology #ClimateTech #ProteinEngineering #OpenScience

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Reposted by Meg T (she/her/hers)

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Dec 3

Three BioML starter packs now!

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
Pack 3: go.bsky.app/NAKYUok

DM if you want to be included (or nominate people who should be!)

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Meg T (she/her/hers) @megthescientist.bsky.social · Jun 30

Pls tell me im living under a rock and we have citation managers compatible with iPads where your writing & highlighting can be automatically transcribed into notes and key words attached to a pdf (vs me manually transcribing over from edits I make in Adobe??) In the age of AI, we have this, right??

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Reposted by Meg T (she/her/hers)

Christian Dallago @machine.learning.bio · Jun 15

With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jun 19

Physics-based design of efficient Kemp eliminases

@lynnkamerlin.bsky.social

www.nature.com/articles/s41...

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jun 25

All all-atom diffusion model of protein sequences.

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

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Reposted by Meg T (she/her/hers)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jun 11

End-to-end differentiable homology search for protein fitness prediction.

@yaringal.bsky.social @deboramarks.bsky.social @pascalnotin.bsky.social

arxiv.org/abs/2506.089...

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Reposted by Meg T (she/her/hers)

Pascal Notin @pascalnotin.bsky.social · Jun 18

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9

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Debora Marks @deboramarks.bsky.social · Jun 18

Which RNAs are functional? Been a long time goal of @deboramarks.bsky.social to start an RNA sequence —> function and structure mapping.

Huge thx to team for pushing on this when - led by Rohit Arora and Murphy Angelo for seeing this thru and Pascal Notin for pulling together!!!

Pascal Notin @pascalnotin.bsky.social · Jun 18

🚨 New paper 🚨 RNA modeling just got its own Gym! 🏋️ Introducing RNAGym, large-scale benchmarks for RNA fitness and structure prediction.
🧵 1/9

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Debora Marks @deboramarks.bsky.social · Jun 18

RNA, RNA, RNA -> RNAGym!
read all about it! biorxiv.org/content/10.110…
Been a long time goal of @deboramarks.bsky.social We tried a million years ago,
sciencedirect.com/science/articl��
Now total refresh led by Rohit Arora and Murphy Angelo and Pascal Notin for pulling together!!

https://biorxiv.org/content/10.110…

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Meg T (she/her/hers) @megthescientist.bsky.social · May 30

Sounds like their new slogan is MPGA— make proteins great again (but without homologs or diverse screens😭)

Reposted by Meg T (she/her/hers)

Patrick Bryant @patrickbryant1.bsky.social · May 25

Happy to release our breakthrough AI-model: RareFold, which predicts and designs proteins with noncanonical AAs. With EvoBindRare, we designed linear & cyclic peptide binders with high affinity & novel binding modes, wet lab validated.

📄 biorxiv.org/content/10.1...
💻 github.com/patrickbryan...

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