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Fernán Agüero

@ferag.bsky.social
423 followers 837 following 83 posts

Biologist | UNSAM-CONICET | Bioinformatics | Cheminformatics | Genomics | Drug discovery | Diagnostics | Neglected Tropical Diseases | Argentina 🇦🇷

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Reposted by Fernán Agüero
STCmicrobeblog @stcmicrobeblog.bsky.social · 19h
"groundbreaking discoveries don't always come from animal models!" (or 𝘌. 𝘤𝘰𝘭𝘪, for that matter)
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Reposted by Fernán Agüero
EMBL @embl.org · 22h
Last call to apply! 📢 Read our PhD students' experiences and learn why the EMBL International PhD Programme is a great opportunity. Launch your scientific career with us. Apply now! bit.ly/4x9Edss
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EMBL-EBI Training @training.ebi.embl.org · 21h
Join our webinar on 21 October to learn about the methods of in situ cryo electron tomography (cryoET) and how they can be applied to specifically look at host-pathogen interactions inside the host cell with a focus on apicomplexan parasites and gram-negative bacteria. www.ebi.ac.uk/training/eve...
EMBL-EBI Training. Using in situ cryoET to investigate intracellular host-
pathogen interactions. 21 October 2026. 14:30-15:30 UK time. Leonie Anton. University of Bern (currently). Joining EMBL in 2027.
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C&EN (Chemical & Engineering News) @cenmag.bsky.social · 20h
The 2026 #NobelPrize in Physiology or Medicine has been awarded to @deisseroth.bsky.social, Peter Hegemann and Georg Nagel for discoveries leading to optogenetics, which makes it possible to switch on, or off, the activity of individual nerve cells in a living brain. This story will be updated! 🧪
cen.acs.org
Optogenetics researchers win Nobel Prize in Physiology or Medicine
Karl Deisseroth, Peter Hegemann and George Nagel receive the prize for their work on light-gated ion channels and optogenetics
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EMBL @embl.org · 20h
EMBL congratulates Karl Deisseroth, Peter Hegemann, and Georg Nagel on winning the 2026 #NobelPrize in Physiology or Medicine for their discoveries concerning light-gated ion channels and optogenetics.
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James Balamuta @coatless.bsky.social · 04/10/2026
webrarian is a new R package. It turns a folder of R scripts and data into a static website where R runs in the visitor's browser, with no compute server and nothing to install. blog.thecoatlessprofessor.com/posts/introd... #rstats #webr #webassembly
A card for the R package webrarian. Large text reads "A folder in. A website out." On the left, a small card lists a folder named lab-01 holding lab.R, setup.R and a data folder. A red arrow points from it to a browser window that shows a scatterplot of car weight against miles per gallon with brick-red points. The address coatless-wasm.github.io/webrarian is on the card.
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Richard Sever @richardsever.bsky.social · 28/09/2026
Noise/useless science rather than AI slop is a current challenge: "If medical schools and universities don't want the literature to be overwhelmed with garbage, they should stop giving every applicant ... an incentive to publish a lot of crap." www.medpagetoday.com/special-repo...
medpagetoday.com
Is AI Flooding Medical Journals With 'Meaningless' Research?
'It's not fraudulent, and it's not really slop,' one expert says
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EMBL-EBI Training @training.ebi.embl.org · 28/09/2026
In this webinar, we will consider the strategies that parasites deploy to evade immune detection, including antigenic variation as well as surface proteins which suppress immune cells and immune effectors, and discuss the approaches used to study those mechanisms: www.ebi.ac.uk/training/eve... 🧬🖥️📊
EMBL-EBI Training. How do parasites evade immune clearance? A structural perspective. 14 October 2026. 14:30-15:30 UK time. Matt Higgins. University of Oxford.
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Michael Hiller @hillermich.bsky.social · 23/09/2026
Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...
nature.com
Reference genomes and fossils revise bat family phylogeny and biogeography - Nature
An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.
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Trends in Parasitology @cp-trendsparasitol.bsky.social · 04/09/2026
What’s in a name? Discovering Leishmania
dlvr.it
What’s in a name? Discovering Leishmania
2 June 2026 marked the centenary of the death of Sir William Boog Leishman, the Scottish physician after whom Leishmania was named. However, he was not the first to describe the parasite. In this article, we recount this discovery and explain the etymological conventions that ensured Leishman’s name was preserved in scientific history.
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Pat Walters @wpwalters.bsky.social · 04/09/2026
M6 Mac Mini as the prize for the Marimo Cheminformatics notebook competition!
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Daniel Gorelick @danielgorelick.bsky.social · 04/09/2026
During these times of antibody crisis, when ThermoFisher, Abcam, etc are losing our trust, I turn to onlygoodantibodies.co.uk and the good folks @oga-community.bsky.social
onlygoodantibodies.co.uk
Only Good Antibodies — Free Antibody Characterisation Database
A free, searchable database of knockout-controlled antibody characterisation data covering 155 genes and 1620 antibodies. Includes a free e-learning Academy.
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Nobel Prize @nobelprize.org · 24/08/2026
We've arrived on Bluesky! We hope you will follow along as we share inspiring, motivational and exciting content about the achievements and individuals that have been awarded a Nobel Prize. Stay tuned.
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 25/08/2026
🚀 New updates improve metalloprotein data across the PDB Archive. ~15,500 PDB entries and ~900 metal-containing CCDs now feature more complete chemical descriptions and metal coordination annotations. ⬇️More ⬇️ www.wwpdb.org/news/news?ye... #PDB
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 17/08/2026
🌟Use Shortlinks to Transition to the PDB Beta Archive Shortlinks make it easier to download data using extended PDB IDs without coding specific file paths. Start using shortlinks today ahead of the July 21, 2027 transition. ⬇️More ⬇️ www.wwpdb.org/news/news?ye... #PDB
wwpdb.org
Use Shortlinks to Transition to the PDB Beta Archive
wwPDB: Worldwide Protein Data Bank
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Carl T. Bergstrom @carlbergstrom.com · 13/08/2026
You live any universe and on a planet where 4 billion years of adaptive evolution lead up to this happening today.
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Peter Kenny @pwk2024.bsky.social · 13/08/2026
Opportunity for Chemistry Curator - Chemical Biology Services (ChEBI) at EMBL-EBI (Hinxton Cambridgeshire UK) ref: JR4291 | duration 3 years (extendable) | closing: 06-Sep-2026 #cheminformatics #chemsky 🧪 embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
embl.wd103.myworkdayjobs.com
Chemistry Curator - Chemical Biology Services
The Chemical Biology Services Team at the European Bioinformatics Institute (EMBL-EBI) is looking for a talented scientist with a flair for data curation to be responsible for the quality of chemical ...
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Ady Ragucci @aragucci.bsky.social · 12/08/2026
Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial diadenylate cyclase domains synthesize diverse nucleotide signals in anti-phage defense
Bacterial diadenylate cyclase (DAC) enzymes synthesize the nucleotide signal 3′3′ cyclic di-AMP (3′3′-c-di-AMP) to control osmoregulation, cell-wall homeostasis, and DNA-damage responses. Here we disc...
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Edvard I Moser @edvardmoser.bsky.social · 06/08/2026
Out now in @science.org : How does the brain rapidly scan space to guide navigation? We found that the brain’s internal map is continuously retuned from moment to moment, focusing neural activity on what matters most. 🧵1/8 👉 www.science.org/doi/10.1126/...
science.org
Adaptive modulation of theta sweeps in the brain’s navigation circuit
Efficient navigation requires prioritizing information from behaviorally relevant locations. In rats, such selective sampling may arise from theta-paced sweeps in grid and place cell populations, whic...
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pen(Taka) @iwatobipen.bsky.social · 26/07/2026
Try to use nesso-1 for binding affinity prediction #cheminformatics #rdkit #folding ai Now there are lots of AI tools for drug discovery. I think it's difficult to expect 8 years before when I moved to cheminformatics team from MedChem 🙂 And one of the hot area is Folding AI such as Boltz, Alpha…
iwatobipen.wordpress.com
Try to use nesso-1 for binding affinity prediction #cheminformatics #rdkit #folding ai
Now there are lots of AI tools for drug discovery. I think it's difficult to expect 8 years before when I moved to cheminformatics team from MedChem 🙂 And one of the hot area is Folding AI such as Boltz, Alpha fold and OpenFold etc. Boltz-2 has not only cofolding prediction module but also binding affinity prediction module. It will be useful if the module works well.
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openRxiv @openrxiv.bsky.social · 23/07/2026
The Curvenote Reader button is live on bioRxiv! 😎 Click it to explore papers in a new way—zoom figures, pull up references without leaving the page. Button appears 48 hours after papers drop. Feedback? DM us or hit the GitHub repo. openrxivlabs.org/articles/rea...
openrxivlabs.org
Why we’re expanding the openRxiv Labs Curvenote Reader experiment
Read on for early results and what we’ll be looking at in the next phase.
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Reposted by Fernán Agüero
Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 24/07/2026
🚨New PDBe webinar Bringing structural biology to AI: exploring the PDBe MCP servers The session will explore the capabilities offered by the PDBe MCP servers with practical examples. 🗓️ 9 September 2026 🕘 14:30-15:30 (BST) ⬇️ Register here ⬇️ www.ebi.ac.uk/training/eve... #PDB
ebi.ac.uk
Bringing structural biology to AI: exploring the PDBe MCP servers -
Bringing structural biology to AI: exploring the PDBe MCP servers -
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George Davey Smith @mendelrandom.bsky.social · 22/07/2026
Does the (live) shingles vaccine protect against dementia? Fergus Hamilton and colleagues provide important evidence in a new preprint using hospital data from the whole of England in a regression discontinuity design from which we *don't* show evidence of a meaningful protective effect /cont
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Simon Willison @simon.fedi.simonwillison.net.ap.brid.gy · 23/07/2026
I wrote about the completely wild incident where OpenAI were testing a new model and it broke out of its sandbox and broke INTO Hugging Face to steal the answers to the benchmark simonwillison.net/2026/Jul/22/opena…
simonwillison.net
OpenAI’s accidental cyberattack against Hugging Face is science fiction that happened
This story is wild. The short version: OpenAI were running a cybersecurity test against an unreleased model, with the model’s guardrail features turned off. Rather than solve the test, the …
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Stephan Hacker @stephanhacker2.bsky.social · 23/07/2026
Rules, for what can be a good drug, are extremely valuable in #DrugDiscovery. Nevertheless, it seems like once in a while all of these rules need to be thrown out of the window as exemplified by Nibrozetone that is investigated in Phase III for cancer treatment. drughunter.com/molecule/rrx...
drughunter.com
nibrozetone
Nibrozetone (RRx-001), identified via a phenotypic screen of compounds from the rocket fuel industry, has been advanced by EpicentRx into multiple clinical trials. The molecule additionally received a...
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Joe Greener @jgreener64.bsky.social · 17/07/2026
Function of a protein: something the protein does. Function in maths: a mapping from X to Y. Function in code: re-use code to do a task. Function at a conference: have a drink and look at posters.
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Martin Donath @squidfunk.com · 17/07/2026
Material for MkDocs 9.7.7 is out. It fixes a DOM-based XSS issue in the optional search.suggest feature, which was responsibly disclosed to us. Please update. Material for MkDocs will continue receiving security updates through November 5, 2026. github.com/squidfunk/mk...
github.com
Release mkdocs-material-9.7.7 · squidfunk/mkdocs-material
Warning Material for MkDocs is approaching end of life Material for MkDocs is scheduled to reach end of life on November 5, 2026. Until then, maintenance is limited to critical bug fixes and securi...
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The Transmitter @thetransmitter.bsky.social · 17/07/2026
Nobel laureate Susumu Tonegawa, who pioneered cell-type-specific transgenic mice and the study of engrams, has passed away at the age of 86. By @claudia-lopez.bsky.social www.thetransmitter.org/memory/susum...
thetransmitter.org
In memoriam: Susumu Tonegawa, ‘intellectual giant’
He won the Nobel Prize for his work on immunology and then went on to define the field of learning and memory.
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Manas Mahale @manasmahale.bsky.social · 19/07/2026
This Week In Cheminformatics Issue #030 is out. This week we look into How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty
thisweekincheminformatics.substack.com
This Week In Cheminformatics: Issue #030
How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers...and maybe the last one of these from PT.
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The Scholarly Kitchen @scholarlykitchen.bsky.social · 20/07/2026
Guest Post — Why Research Expectations Have Outpaced the Systems That Enabled Them (Part 1) scholarlykitchen.sspnet.org/2026/07/20/g...
scholarlykitchen.sspnet.org
Guest Post — Why Research Expectations Have Outpaced the Systems That Enabled Them (Part 1) - The Scholarly Kitchen
Today's guest blogger questions the operating model around scholarly research and asks why these capabilities are so difficult to sustain at scale.
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Sternberg Lab @sternberglab.bsky.social · 09/07/2026
1/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...
biorxiv.org
Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase
Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a...
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 10/07/2026
PhyKIT v2.2.0 is out! PhyKIT has been rigorously profiled and optimized across the entire codebase, resulting in speedups ranging from ~1.0x to 16.6x, with a geometric mean of 2.0x Python 3.10 through 3.13 is also supported
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Martin Donath @squidfunk.com · 06/07/2026
Zensical Studio is out, and the bigger picture is coming together. We're building the next-generation Docs-as-Code stack, end to end, and we're right on track. More in tomorrow's newsletter. zensical.org/about/newsle...
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Gerry Hammond @gerryhammond.bsky.social · 06/07/2026
The unparalleled productivity boost of the dual monitor set up!
One screen is showing the World Cup
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Biology Open @biologyopen.bsky.social · 08/07/2026
Who benefits from Fast & Fair peer review? It benefits everybody. It benefits authors because they get a fast and high-quality review. It benefits editors because the editors handling the manuscripts don’t have to spend a lot of time finding reviewers.
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Tatta Bio @tattabio.bsky.social · 01/07/2026
Two weeks ago, our FlashPPI paper was published in @pnas.org. Today, we introduce our updated model, FlashPPI2. Fine-tuned on new AlphaFold structures, this new model achieves a 17% improvement over FlashPPI on the E. coli protein interaction benchmark. seqhub.org/blog/flashppi2
seqhub.org
FlashPPI2: Enhanced Model, Scaled Across 130,000+ Genomes - SeqHub
FlashPPI2 drives up PPI prediction performance (AUPRC) by 17% while maintaining inference speed at minutes per genome — now deployed across SeqHub's database of over 130,000 microbial genomes.
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Marc Somssich @somssich.bsky.social · 02/07/2026
"Why paying peer reviewers works" Very cool initiative by @biologyopen.bsky.social and EiC Daniel Goerlick. Paying vetted(!) peer reviewers increased turnaround time & quality of #PeerReview! I continue to be a big fan of the Company of @biologists.bsky.social & their work. 👍 #SciPub
nature.com
Why paying peer reviewers works, according to a journal’s editor-in-chief
A biology journal that paid peer reviewers found that the approach cut the time to a first editorial decision by 85% and maintained high-quality reviews.
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Toni Gabaldón @tonigabaldon.bsky.social · 10/06/2026
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
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kinetoplastids papers @kinetoplastpapers.bsky.social · 01/07/2026
Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites pubmed.ncbi.nlm.nih.gov/42376815/
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Towards Data Science @towardsdatascience.com · 03/07/2026
Turning to Pandas chunking, Dask, and Polars, Jiayan Yin proposes several approaches for navigating memory bottlenecks in your data engineering pipelines.
towardsdatascience.com
What Can We Do When Memory Becomes the New Bottleneck in Data Engineering? | Towards Data Science
How Pandas chunking, Dask, and Polars help process millions of records when adding more compute isn't an option.
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Jessica Hullman @jessicahullman.bsky.social · 29/06/2026
Lol, a paper that describes my life. My natural reaction to feeling like I'm finally getting the hang of something has always been to drop it and try something else. And somehow I still often feel like I'm not getting out fast enough.
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Drugs for Neglected Diseases initiative (DNDi) @dndi.org · 22/06/2026
How do we close the diagnostic gap for #Chagas disease? With only about 10% of people diagnosed and 1% receiving care, experts have defined priorities for better rapid & molecular diagnostics and improved access to care. doi.org/10.1186/s128... @bmc.springernature.com
doi.org
Advancing diagnostics for Chagas disease: key product characteristics and harmonized evaluation strategies - an expert meeting report - BMC Infectious Diseases
Chagas disease is a global public health issue, life-threatening parasitic disease, affecting mostly underserved communities in Latin America. Yet, 10% of infected individuals are diagnosed, and 1% receive etiological treatment. Priority actions for disease elimination by 2030 are streamlining diagnostic methods and evaluating and developing point-of-care diagnostics. We convened 44 researchers, test developers, and health authorities, to provide scientific advice and reach consensus on (i) a harmonized protocol for evaluation of rapid diagnostic tests; (ii) preferred molecular diagnostics characteristics (scope, performance, operational features, pricing, and evaluation standards); and (iii) economic impact evidence needed to have a transformational impact in primary healthcare. We considered global and national perspectives with discordant evidence from multiple disciplines. Our outcomes provide a reference on practical applications and recommendations to promote test development and evaluation. Finally, we debate about the appropriate approach moving forward to meet the diagnostic gap, and propose how investments could be stimulated.
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Dan Garisto @dangaristo.bsky.social · 29/05/2026
Unreliable and underperforming antibodies are a longstanding problem, so while the reveal of apparently manipulated antibody data in Thermo Fisher's catalog was a shock, the frustration it sparked among many researchers is perhaps no surprise. My reporting:
nature.com
Science sleuths uncover more than 100 suspicious images in Thermo Fisher antibody catalogue
Scientists have long worried about the reliability of commercial antibodies, and the latest findings have sparked fresh concerns.
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Biohub @biohub.org · 27/05/2026
Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein
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Scott McGrath @smcgrath.phd · 13/05/2026
Daraxonrasib is the first drug to substantially extend survival in pancreatic cancer trials. Median survival reached 13+ months compared to <7 months for chemo. It finally shuts down the "undruggable" KRAS protein, once called a greasy ball, using a novel molecular glue. #MedSky
nytimes.com
How an ‘Impossible’ Idea Led to a Pancreatic Cancer Breakthrough
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bioRxivpreprint @biorxivpreprint.bsky.social · 08/05/2026
Mannosylated nanoparticle immunogens enhance the circumsporozoite protein-specific B cell response and improve protection against sporozoite challenge www.biorxiv.org/content/10.64898/20…
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rOpenSci @handle.invalid · 05/05/2026
May is #MaintainerMonth! Meet the humans behind your favorite #RStats packages All month, we will spotlight the maintainers behind rOpenSci's software ecosystem. Stay tuned to meet them!
Hexstickers with the letter R inside.
rOpenSci Maintainers Month 2026.
rOpenSci.org
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Oded Rechavi @odedrechavi.bsky.social · 05/05/2026
We built an AI that will tell you what will get your grant rejected. It’s a tough critique, but it’s better to know when you can still do something about it 👇 @qedscience.bsky.social
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bioRxivpreprint @biorxivpreprint.bsky.social · 05/05/2026
PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search www.biorxiv.org/content/10.64898/20…
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