I firmly believe that well-documented datasets must be re-analysed! Too many projects needlessly generate more data just to chase arbitrary benchmarks — an extra 2% accuracy or a few more identified proteins. We can be so much smarter! 🧵

UofT-TCAIREM@uoft-tcairem.bsky.social · 2mo ago

Why #biology must prioritize #data reanalysis in the era of #artificialintelligence | @plosbiology.org journals.plos.org/plosbiology/... #AIhealth #AI #HealthAI #MedTech

Every time I read a paper that challenges our view of the central dogma, I'm amazed by the complexity of biology and almost overwhelmed by the challenge of unraveling this compelixity. Tsour et al., Nature (2026) - www.nature.com/articles/s41... (1/3)

Alternate RNA decoding results in stable and abundant proteins in mammals - Nature

Alternate RNA decoding, an understudied process, leads to peptide sequence modifications that can have substantial functional effects on protein stability, tissue-specific proteomes and dise...

nature.com

“Künstliche Intelligenz und reale Außenwelt” Planck, M; Naturwissenschaftern (1940)

Science Magazine@science.org · 2mo ago

Max Planck, a legendary pioneer of quantum mechanics and the 1918 Nobel laureate in physics, had two papers retracted decades after his death for reasons that remain mysterious. Learn more: https://scim.ag/4exoz3T

The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)

At one point, a stu­dent joked that if I kept “editing” so much, I might as well submit the article under my own name and save us both time.

Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.

Dreaming of a career in cancer research? Join the International PhD Program at DKFZ - Germany’s largest biomedical research center. Explore #cancerresearch including #cancerbiology, #bioinformatics, #epidemiology & #medicalphysics. The Summer Selection is open now 👉 apply here: t1p.de/hl56b

Downside of LLM culture that I have not seen mentioned anywhere before: The best way to understand something is to explain it to someone else, and people don't ask people to explain things anymore

Poorly performing antibodies have plagued biomedical sciences for decades. This article explores alternatives, hoping for specific protein binders: The antibodies don’t work! The race to rid labs of molecules that ruin experiments www.nature.com/articles/d41...

The antibodies don’t work! The race to rid labs of molecules that ruin experiments

Poorly performing antibodies have plagued biomedical sciences for decades. Several fresh initiatives hope to change this.

nature.com

Benchmarking Software for DDA-PASEF Immunopeptidomics www.sciencedirect.co... --- #proteomics #prot-paper

Holy fuck, am I reading this correctly? Are they going to do a single-blind RCT (i.e., some babies will get placebo instead of HepB vax and their parents won't know)??? This seems insanely unethical, like Tuskegee levels of unethical public-inspection.federalregister.gov/2025-23245.pdf

🚨 What if evolution is the ”law”… and networks are the machines that do the work? In this paper (just published) I try to formalize how living systems are non-equilibrium, information-processing, adaptive matter. With a great biological flavor! 🧪🌐🌍🧬🦠 👉 iopscience.iop.org/article/10.1... 🧵 1/

This week is World #AntimicrobialResistance Awareness week This article collection spans the breadth of #AMR across pathogens (bacteria, viruses, fungi, parasites), covers epidemiological monitoring, diagnostics, treatment, etc

Antimicrobial resistance: a silent pandemic

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Affinity has been my favorite design software for awhile now. Now that its free is even better!

David A Knowles@davidaknowles.bsky.social · 10mo ago

I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new... Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.

New paper from the @klingmuelab.bsky.social & Timmer labs out in @cp-cellsystems.bsky.social: #Diclofenac & #acetaminophen unexpectedly shape #IL-6 and #hepcidin signaling in #liver cells. 🔗 doi.org/10.1016/j.ce... 👇 Thread with key findings

msBayesImpute: A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data www.biorxiv.org/cont... --- #proteomics #prot-preprint

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

Mathematical modelling for biologists - Modelling concepts in biological research

Mathematical modelling for biologists - Modelling concepts in biological research

ebi.ac.uk

1/New paper on peroxisome assembly, reporting the detailed mechanism of PEX39, a new peroxin involved in PTS2 protein transport. Fantastic work by ‪@walterwchen.bsky.social‬ and a dream team of collaborators, as explained below. www.nature.com/articles/s41...

PEX39 facilitates the peroxisomal import of PTS2-containing proteins - Nature Cell Biology

Chen et al. show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the im...

nature.com

SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics pubs.acs.org/doi/10.... --- #proteomics #prot-paper

Our work on new paradigm in peroxisome biogenesis and PEX39 (1st human peroxisomal biogenesis protein (peroxin/PEX) found in > 20 yr) is out in @natcellbio.nature.com! Equal collab w/Tony Rodrigues (Jorge Azevedo lab), @dwendscheck.bsky.social (Bettina Warscheid lab) www.nature.com/articles/s41...

PEX39 facilitates the peroxisomal import of PTS2-containing proteins - Nature Cell Biology

Chen et al. show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the im...

nature.com

🥳🥳🥳 Congratulations to everyone involved and in particular to @dwendscheck.bsky.social! I am soooo happy to see that this story is online now and that I could contribute to it ❤️

Daniel Wendscheck@dwendscheck.bsky.social · last yr.

Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics

📈 Last week I had the chance to present my project on the influence of #interferon on antigen processing by the proteasome at the 2nd #Heidelberg Interferon Symposium! 🦠🧬🧫 1/3

PXD051501 🚨 Pex39 facilitates peroxisomal import of PTS2 proteins – ScPex18 AP-MS data 🚨 New dataset alert! 🚨

Great first day at the #IFNSymposiumHD, with BBQ dinner, drinks and especially: great people and discussions 😊 Now looking forward to the second day, which will be kicked off by @meganstanifer.bsky.social shortly!

Let's leave behind simplistic & naive notions. .

📣Attention please! 🦠🧫🧬Interferon researcher in and around Heidelberg are kindly welcome to register for the 2nd Interferon at DKFZ symposium in July! 📜Submit your abstract until tomorrow here: indico.dkfz.de/event/1320/

A unified pan-cancer proteome atlas www.cell.com/cancer-... --- #proteomics #prot-paper

@miquai.bsky.social and Robert Hazen explore a bold new law of nature: complexity steadily rises - not just in biology, but in everything from rocks to life. A fascinating weekend read. Thoughts welcome. #Science #Biology #Evolution #LawsOfNature #FunctionalInformation #ResearchSky #WeekendReads

A New Law of Nature Attempts to Explain the Complexity of the Universe

A novel suggestion that complexity increases over time, not just in living organisms but in the nonliving world, promises to rewrite notions of time and evolution.

wired.com

Start your day right with 1,184,046 error messages 😂

More evidence for the role of protein degradation in significantly shaping the proteome of brain tissue!

Nikolai Slavov@slavov-n.bsky.social · last yr.

Alzheimer's disease (AD) is associated with numerous proteome changes. We find large & consistent decrease in the abundance and stoichiometry of 20S proteasome subunits. ⬛️ It leads to abnormal accumulation of 20S substrate proteins. 🧵 biorxiv.org/content/10.1...