Edward Marcotte
@edwardmarcotte.bsky.social
Systems & synthetic biologist, proteomics, bioinformatics; Professor of Molecular Biosciences @ UT Austin; Cofounder, Erisyon
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
Here is a link to the website: pubchef.org Hope you all enjoy surfing chemical space!
PubCheF Explorer
pubchef.org
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 · 3d agoCan 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
Cilia alert! Last year Juyeon Hong described a new domain in 9+2 cilia called the EDT, the extreme distal tip. Now, she's found a new protein required for its assembly, but only in non-mammalian vertebrates. A cool evo-cell / protein evolution story in @cellreports.bsky.social tinyurl.com/2xvdskx6
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
biorxiv.org
Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX
Ensembles of in silico structures enable T cell peptide-MHC binding prediction
Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...
biorxiv.org
Always nice to see some of our work featured in the PDB's Molecule of the Month: pdb101.rcsb.org/motm/319
PDB101: Molecule of the Month: Hantavirus
Family of rodent-borne viruses that can cause severe illness in humans
pdb101.rcsb.org
Thrilled to share our collab led by Grace Hibshman with the Shipman lab! Type IX retron-Kva2 structure reveals phage detection via an HTH fold, not a primary sequence. We computationally designed triggers that program bacteria cell death, pointing toward designer antimicrobials.
Let's learn a lesson from the nearly 500K of us who mobilized to comment on the OMB rules. We can leave the sidelines, take action and it can make a difference. After 15 months of inaction, our scientific societies finally woke up and mobilized members. It doesn't stop there 1/n
Zero-shot predictions of mutational effects seem to work well in benchmarks but frequently fail in targeted protein engineering campaigns. Why is that? blog.genesmindsmachines.com/p/how-useful...
How useful are zero-shot predictions of mutational effects?
Zero-shot predictions are great, except for when it matters
blog.genesmindsmachines.com
There are many comments up on the OMB rule but there are now many that claim to be in favor of the rule and they are well written and anonymous- claiming to be tenured professors worried about waste fraud and abuse. We need as many real, unique comments as possible that show how bad this rule is
Bethany Brookshire@beebrookshire.bsky.social · last mo.There's an OMB rule change that would require political oversight of scientific grants, and could pull any that don't "reflect presidential priorities" Another country has tried this before! It was the USSR and it was called Lysenkoism. By @thsaey.bsky.social www.sciencenews.org/article/omb-...
🚨 HEADS UP: If you haven't submitted a comment on the OMB proposal yet, there's still time - but it's running out! There are only 3 days left to push back against Russell Vought's attempt to give political appointees unprecedented control over federal research funding. Take Action: zurl.co/J92d9
Tired of AI-generated figures? I asked our talented scientific illustrator Manon Zuurmond to draw some of the instruments and lab equipment we missed in NIH's otherwise fantastic BioArt resource. First batch now available as CC BY. Free for everyone to use in publications: github.com/Center-for-P...
Well reported piece from @beebrookshire.bsky.social at the Verge on the proposed OMB grant making regulations and the likely consequences. [Gift link] www.theverge.com/science/9576... 1/4
The war against ‘woke’ could end US science as we know it
“Everyone will be affected, not just scientists. Every community in the country.“
theverge.com
Critical reasons to comment on the OMB rule, especially asking to extend the comment time for such a complex ruling with far reaching implications
Pam Ronald@pcronald.bsky.social · 2mo ago
www.regulations.gov/commenton/OM... Submit your comment here. Read this short piece by lawyer Claudia Polsky to see why science needs you and all your friends and colleagues to write. It’s fast and easy and it will make a difference.
Regulations.gov
regulations.gov
Bethany Brookshire@beebrookshire.bsky.social · 2mo agoYou may have heard about the OMB rule change that will put politics over federal grants. However bad you think it is? It's probably worse. Thanks to @theverge.com for letting me report this one out. There is still time to comment. bit.ly/4v2X4nQ
I've gone ahead and posted my comment on the OMB rule as an example of a hyper-focused comment that looks at one portion of the OMB rule. Here, I've tackled a part of the Rule I know a lot about (international research and national security) and cross-walked with a project I've worked on a lot.
What a Focused OMB Rule Comment Could Look Like — Stand Up for Science Foundation
Cole Donovan, Director of Policy at the SUFS Foundation, breaks down how OMB’s grant rule will undermine U.S. research, weaken international collaboration, and threaten American scientific leadership.
standupforscience.foundation
Thanks, @olibclarke.bsky.social! Identifying this complex is good news for our job security as experimentalists... As of today, we still can’t predict the full assembly with AlphaFold. So here is an #open_challenge: if anyone can recover the whole complex computationally, I’d love to hear from them!
Oli Clarke@olibclarke.bsky.social · 2mo agoAmazing stuff, what a structure! Elegant work😍
🔬 Your tax dollars once paid a physicist whose own colleagues told him he was wasting the university's money. In 1951, Charles Townes sat on a D.C. park bench and worked out, on the back of an envelope, how to force molecules to release coherent radiation. 🧵 1/5
This is a tremendous piece by Judy Stone at @forbes.com. This new OMB rule is going to hurt communities from coast to coast. Federal grants are not just about research! www.forbes.com/sites/judyst...
How The OMB Rule Could Hurt You And Your Town
The OMB proposal threatens scientific research and ALL federal funding for states, cities, and nonprofits. It politicizes ALL funding. Call your reps and write an objection.
forbes.com
1/7 New preprint: we found that Chlamydomonas carries a giant and unexpectedly elaborate chloroplast RNA polymerase with 12 previously unknown subunits, overturning the idea that the complexity of this organellar enzyme emerged during plant terrestrialization! www.biorxiv.org/content/10.6...
The structure of a 2-MDa chloroplast RNA polymerase reveals unexpected evolutionary complexity
Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyano...
biorxiv.org
Come join the new Novo Nordisk Foundation Center for Protein Design as a group leader Cool science in a great scientific environment in wonderful and very family friendly Copenhagen There are two positions that can either be at TT assistant or associate prof level employment.ku.dk/tenure-track...
Tenure-track Assistant Professor or Associate Professor of De novo Protein Design
The Novo Nordisk Foundation Center for Protein Design at the University of Copenhagen seeks to appoint two new group leaders in de novo protein design from 1 February 2027 or as soon as possible thereafter. These positions will be at the Assistant or Associate Professor level and associated with the Department of Biology (Faculty of Science) or the Department of Drug Design and Pharmacology (Faculty of Health and Medical Sciences).
employment.ku.dk
We’re delighted to welcome @computingcaitie.bsky.social to the FMI next year! Her work will bring an interdisciplinary perspective spanning structural biology, quantitative imaging and computational analysis to our institute, opening exciting new ways to study ciliary structure and dynamics.
Caitie McCafferty@computingcaitie.bsky.social · 2mo agoHappy to finally share that I will be starting my independent group at the @fmiscience.bsky.social in Feb 2027 in a vibrant new environment. We will use integrative in situ structural cell biology methods to investigate ciliary structure and dynamics in several model (and non-model 👀) systems!!
Two of the most important biomedical breakthroughs came from science of the Gila lizard venom (GLP-1s) and yogurt (CRISPR genome editing). "The system that turned that lizard into a medicine is now being dismantled." gift link nytimes.com/2026/06/20/o...
