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Edward Marcotte

@edwardmarcotte.bsky.social
1.8K followers 684 following 132 posts

Systems & synthetic biologist, proteomics, bioinformatics; Professor of Molecular Biosciences @ UT Austin; Cofounder, Erisyon

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Reposted by Edward Marcotte
Brett Baker @archaeal.bsky.social · 02/10/2026
Two Assistant Professor Positions in Evolutionary Biology and Mechanistic Processes - including microbes! faculty.utexas.edu/career/191568
faculty.utexas.edu
Faculty Careers - The University of Texas at Austin
Unleash your intellectual power by joining a world-renowned faculty that is solving the world's most urgent problems. At UT Austin, we provide you the freedom to blaze trails, follow your curiosity, e...
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Sjors Scheres @sjorsscheres.bsky.social · 30/09/2026
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. 🥳
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Michael Marty @michaelmarty.bsky.social · 24/09/2026
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...
theanalyticalscientist.com
The Analytical Scientist | 2026
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Richard Sever @richardsever.bsky.social · 20/09/2026
"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...
giorgio.gilest.ro
The Weimar of knowledge – la bottega
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Brett Baker @archaeal.bsky.social · 16/09/2026
www.nature.com/articles/d41...
nature.com
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.
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Roland Hatzenpichler @environmicrobio.bsky.social · 16/09/2026
“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 😂
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Andrew Savinov @biosavinov.bsky.social · 16/09/2026
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)
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Brett Baker @archaeal.bsky.social · 15/09/2026
Two Assistant Professor Positions in Evolutionary Biology and Mechanistic Processes - including microbes! faculty.utexas.edu/career/191568
faculty.utexas.edu
Faculty Careers - The University of Texas at Austin
Unleash your intellectual power by joining a world-renowned faculty that is solving the world's most urgent problems. At UT Austin, we provide you the freedom to blaze trails, follow your curiosity, e...
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Reposted by Edward Marcotte
Buzz Baum @buzzbaum.bsky.social · 11/09/2026
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!
biorxiv.org
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 ...
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Tanmay Bharat @tbharat-lab.bsky.social · 11/09/2026
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.
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Nozomu Yachie @nzmyachie.bsky.social · 04/09/2026
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: 🧵
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Claus Wilke @clauswilke.com · 03/09/2026
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-...
blog.genesmindsmachines.com
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
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Pam Ronald @pcronald.bsky.social · 03/09/2026
www.nature.com/articles/d41.... If you are eligible, vote this fall for candidates that support the US scientific enterprise
nature.com
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.
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Kevin Drew @ksdrew.bsky.social · 01/09/2026
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...
nature.com
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...
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Dan Garisto @dangaristo.bsky.social · 25/08/2026
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:
nature.com
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.
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Weizmann Institute of Science @weizmann.ac.il · 31/08/2026
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
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MRC-LMB Cell Biology Division @cellbiol-mrclmb.bsky.social · 28/08/2026
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.
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Mara Duncan @mcduncanlab.bsky.social · 28/08/2026
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)
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Reese Richardson @reeserichardson.bsky.social · 25/08/2026
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/🧵
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 24/08/2026
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...
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Mia K. Markey @markeymk.bsky.social · 25/08/2026
www.theguardian.com/us-news/2026...
theguardian.com
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’
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Edward Marcotte @edwardmarcotte.bsky.social · 25/08/2026
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.
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Stand Up for Science! @standupforscience.net · 24/08/2026
🚨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...
fight2win.standupforscience.net
Stand up for Science
Stand up for Science
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Edward Marcotte @edwardmarcotte.bsky.social · 19/08/2026
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/...
arstechnica.com
mRNA cancer vaccine succeeded in Phase 3 melanoma trial, Moderna and Merck say
The vaccine reportedly thwarted the cancer's return and spread.
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Mia K. Markey @markeymk.bsky.social · 18/08/2026
www.theguardian.com/us-news/ng-i...
theguardian.com
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
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Clay Kosonocky @kosonocky.bsky.social · 18/08/2026
Here is a link to the website: pubchef.org Hope you all enjoy surfing chemical space!
pubchef.org
PubCheF Explorer
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Clay Kosonocky @kosonocky.bsky.social · 18/08/2026
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! 🧵
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Clay Kosonocky @kosonocky.bsky.social · 17/08/2026
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!
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elizabethginexi.bsky.social @elizabethginexi.bsky.social · 15/08/2026
A great description of what is happening to peer review at NIH. www.forbes.com/sites/brucel...
forbes.com
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.
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Chris Sullivan @sullivanlab.bsky.social · 15/08/2026
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...
biorxiv.org
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...
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Reposted by Edward Marcotte
Russ Poldrack @russpoldrack.org · 14/08/2026
This was a really fun interview with Russ Altman for the Future of Everything podcast. www.youtube.com/watch?v=xLZQ...
youtube.com
The future of neuroimaging
YouTube video by Stanford University School of Engineering
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John Wallingford @jbwallingford.bsky.social · 04/08/2026
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
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Ben Lehner @benlehner.bsky.social · 03/08/2026
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...
biorxiv.org
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...
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Quaid Morris @quaidmorris.bsky.social · 21/07/2026
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
biorxiv.org
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...
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Jason McLellan @mclellanlab.bsky.social · 20/07/2026
Always nice to see some of our work featured in the PDB's Molecule of the Month: pdb101.rcsb.org/motm/319
pdb101.rcsb.org
PDB101: Molecule of the Month: Hantavirus
Family of rodent-borne viruses that can cause severe illness in humans
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Nogales Lab @nogaleslab.bsky.social · 20/07/2026
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.
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 14/07/2026
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
496,769 comments received
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Claus Wilke @clauswilke.com · 13/07/2026
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...
blog.genesmindsmachines.com
How useful are zero-shot predictions of mutational effects?
Zero-shot predictions are great, except for when it matters
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Craig Kaplan @triggerloop.bsky.social · 11/07/2026
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
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Stand Up for Science! @standupforscience.net · 10/07/2026
🚨 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
Graphic from Stand Up for Science urging action on a federal funding proposal. Large text reads: "3 Days Left" and "Help Us Stop Vought From Destroying American Science." A portrait of Russell Vought appears beside the U.S. Capitol. A banner along the bottom reads: "Submit a comment on the OMB proposal | Link in bio to take action." The Stand Up for Science logo appears in the top left.
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Magnus Palmblad @magnuspalmblad.bsky.social · 07/07/2026
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...
Drawings of various laboratory equipment (liquid chromatography system, mass spectrometers and a centrifuge).
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Jeremy Berg @jeremymberg.bsky.social · 29/06/2026
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
theverge.com
The war against ‘woke’ could end US science as we know it
“Everyone will be affected, not just scientists. Every community in the country.“
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Edward Marcotte @edwardmarcotte.bsky.social · 29/06/2026
Critical reasons to comment on the OMB rule, especially asking to extend the comment time for such a complex ruling with far reaching implications
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Pam Ronald @pcronald.bsky.social · 29/06/2026
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
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Cole Donovan @colesci.bsky.social · 28/06/2026
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.
standupforscience.foundation
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.
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Silvia Ramundo @sramundo.bsky.social · 27/06/2026
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!
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TK (Takashi DY) Kozai @bioniclab.bsky.social · 26/06/2026
🔬 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
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Mia K. Markey @markeymk.bsky.social · 25/06/2026
Please share widely aimbe.org/advocate/omb...
aimbe.org
Action Alert: OMB Proposed Rule Resources - AIMBE
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Gregg Gonsalves @gregggonsalves.bsky.social · 25/06/2026
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...
forbes.com
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.
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Silvia Ramundo @sramundo.bsky.social · 24/06/2026
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...
biorxiv.org
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...
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