Our adventures into #proteinfolding: GuideFlip designs flexible molecular interactions by discrete flow matching to design sequence & structure together! Grateful for funding by Love Tito's (@titosvodka.bsky.social) and the @ukri.org. 🥳

Kai Yi@kaiyi94.bsky.social · 2d ago

1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.

Honored to be on the 40 under 40 list from the @analyticalsci.bsky.social with a few friends @nmriley.bsky.social @mingxunwang.bsky.social @daniel-petras.bsky.social theanalyticalscientist.com/power-list/2...

"All corners of academia will soon be flooded with AI-generated research....Maths and CS go first because their entire output is symbol manipulation...Biology comes later not because biologists are cleverer but because the rate-limiting step is physical" giorgio.gilest.ro/the-weimar-o...

www.nature.com/articles/d41...

These bizarre, much-coveted microbes are revealing the origins of complex life

Researchers are racing to culture a menagerie of exotic organisms and finding lots of surprises along the way.

nature.com

“Over two days in June, Emily Aguilar-Pine drove 2,500 kilometres from Bozeman, Montana, to Austin, Texas, with one of microbiology’s most coveted organisms in the back of her mother’s SUV.” Find out what she grabbed from my lab in the article 😂

Brett Baker@archaeal.bsky.social · 2w ago

www.nature.com/articles/d41...

Thrilled to announce that the Savinov lab is now live at UT Austin @utaustin.bsky.social! Our lab employs massively parallel experimental and AI methods to discover and design protein fragments as universal regulators of protein interactions in health and disease. www.savinovlab.com (1/n)

Two Assistant Professor Positions in Evolutionary Biology and Mechanistic Processes - including microbes! faculty.utexas.edu/career/191568

The brilliant Kris Kuo, with help from Fabian and the Werner lab, has identified a key driver of cyclic gene expression in Sulfolobus, which has a cell cycle but no CDK/cyclins. Amazingly, TFB2 has a cyclin box that regulates its degradation as cells exit division. Another reason to love archaea!

A TFIIB paralog drives cyclic transcription to orchestrate the archaeal cell cycle

Cyclic transcription is a hallmark of the cell cycle. While transcriptional waves in eukaryotes are driven by oscillations in cyclin-dependent kinase (CDK) activity, many archaea have an ordered cell ...

biorxiv.org

Exciting work by @florianmayer.bsky.social, @buzzbaum.bsky.social and colleagues. Archaea with more than one membrane! cryo-FIB-SEM volume imaging from Andriko von Kügelgen and @zhexinwang.bsky.social.

Florian Mayer@florianmayer.bsky.social · 3w ago

Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6... Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social @tbharat-lab.bsky.social

Maybe it’s time to say goodbye to UMAP and other low-dimensional embeddings (at least in many single-cell analyses). We developed MILK to encode single-cell populations into tree representations at unprecedented scales. www.biorxiv.org/content/10.6... Here’s what MILK is: 🧵

The reason Claude did well at binder design is because the prompt hardcoded that it should use ESMFold2 for scoring, and apparently ESMFold2 is really good. It's also only a few months old so not widely used yet. AI in biology keeps disappointing. blog.genesmindsmachines.com/p/anthropic-...

Anthropic has not solved the peptide-binder design problem, but maybe bi[o]hub has

The protein design field is getting pushed forward by human experts in protein design, who would have thought

blog.genesmindsmachines.com

www.nature.com/articles/d41.... If you are eligible, vote this fall for candidates that support the US scientific enterprise

Exclusive: NSF set to issue lowest number of new grants in four decades

The US science-funding agency is withholding $1 billion of its budget so that the money can go to a special White House project.

nature.com

We are excited that our work describing DirectContacts2, a wiring diagram of human physical protein interactions, is published in @natcomms.nature.com . www.nature.com/articles/s41...

DirectContacts2: a wiring diagram of human physical protein interactions - Nature Communications

Knowledge of the physical interactions of proteins provides mechanistic understanding of their function. Here, the authors develop a machine learning classifier through the integration of 25,000 prote...

nature.com

In May it was big news when 100+ suspicious images were found in Thermo Fisher's catalog. Now, that number has expanded dramatically to 18,000+, thanks to some arduous searching by @reeserichardson.bsky.social. My reporting on the massive trove and its implications for antibody reliability:

More than 18,000 questionable images found in antibody catalogues of 15 companies

Science sleuth’s findings raise questions for researchers working to improve the reliability of commercial antibodies.

nature.com

We, the Weizmann Institute of Science community, deeply mourn the passing of Prof. Ada Yonath - Nobel Laureate and a Model of Scientific Perseverance. May her memory be a blessing. bit.ly/ada-yonath-eng

Great tribute to the discovery by Barbara Pearce of clathrin, the first protein found to act in membrane traffic, along with her mentoring and support of the pioneers (many of whom were other women) who revealed the workings of this key player in cellular function.

Traffic@traffic-journal.bsky.social · last mo.

Happy 50th anniversary, Clathrin! onlinelibrary.wiley.com/doi/full/10.... @effc.bsky.social

Lovely recollection of some of the key steps in the discovery of clathrin by three women who defined key aspects of this important protein complex and its function. (CW-discusses a bit of the literal butchery that went into the early discussion)

Traffic@traffic-journal.bsky.social · last mo.

Happy 50th anniversary, Clathrin! onlinelibrary.wiley.com/doi/full/10.... @effc.bsky.social

A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵

Curate a molecule <-> text dataset, train a model, and use it to discover molecules that fight antibiotic resistance by deactivating beta-lactamase enzymes. @kosonocky.bsky.social www.biorxiv.org/content/10.6...

www.theguardian.com/us-news/2026...

Trump’s border wall construction threatens rock art as old as the pyramids: ‘The ancestors are still here’

The president’s border wall plan could damage or destroy ‘the oldest-known books in North America’

theguardian.com

The window for public comments is still open but closes soon (tonight!) for NSF's proposed changes to require approval by political appointees, add restrictions to publishing & communication of research, and ban international collaborations.

Stand Up for Science!@standupforscience.net · last mo.

🚨WARNING🚨 Today is the LAST DAY to leave your public comment on the NSF Proposal. The Proposal implements some of Vought's Science-Destroying OMB Proposal plans in advance: zurl.co/9nywR Leave your public comment TODAY using our guide & tool: fight2win.standupforscience.net/campaign/Pro...

🚨WARNING🚨 Today is the LAST DAY to leave your public comment on the NSF Proposal. The Proposal implements some of Vought's Science-Destroying OMB Proposal plans in advance: zurl.co/9nywR Leave your public comment TODAY using our guide & tool: fight2win.standupforscience.net/campaign/Pro...

Stand up for Science

Stand up for Science

fight2win.standupforscience.net

Exciting news for personalized mRNA cancer vaccines, especially if the phase 3 effect size matches the phase 2 trial (49% reduced death or recurrence), although we have to wait for the official numbers arstechnica.com/health/2026/...

mRNA cancer vaccine succeeded in Phase 3 melanoma trial, Moderna and Merck say

The vaccine reportedly thwarted the cancer's return and spread.

arstechnica.com

www.theguardian.com/us-news/ng-i...

Trump 2.0 has deleted or altered nearly 400 US datasets, endangering public health, education and more

Health data appears to be most affected by administration’s attempt to wipe findings that don’t align with its priorities, tracker shows

theguardian.com

Here is a link to the website: pubchef.org Hope you all enjoy surfing chemical space!

One part of this project I'm very excited about is the website we made to explore the PubCheF-1 predictions over 13.2 million molecules! 🧵

Clay Kosonocky@kosonocky.bsky.social · 2mo ago

Can we use human language to predict novel bioactive molecules that work in vivo? In our new paper, we trained a deep learning model on a dataset derived from PubMed text and used it to discover novel antibiotic co-inhibitors that reduced infection burden, even in mouse models!

Can we use human language to predict novel bioactive molecules that work in vivo? In our new paper, we trained a deep learning model on a dataset derived from PubMed text and used it to discover novel antibiotic co-inhibitors that reduced infection burden, even in mouse models!

A great description of what is happening to peer review at NIH. www.forbes.com/sites/brucel...

NIH Proposes Big Change In How Grant Applications Evaluated

The National Institutes of Health (NIH) is proposing yet another significant change in its grant review process, moving away from numerical scores for applications.

forbes.com

Learning from human and chemical languages to predict biological function Novel LLM AI approach trained on the literature Effective compounds in vivo for antimicrobial resistance Congrats UT Austin researchers Mavridou, Ellington, Wilke, Marcotte & colleagues www.biorxiv.org/content/10.6...

Learning from human and chemical languages to predict biological function

Understanding how molecular structure encodes biological function remains a grand challenge in drug discovery. Here, we present PubCheF-1, a deep learning model that predicts literature-derived biolog...

biorxiv.org

This was a really fun interview with Russ Altman for the Future of Everything podcast. www.youtube.com/watch?v=xLZQ...

The future of neuroimaging

YouTube video by Stanford University School of Engineering

youtube.com