tmoeckli

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

Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm A systematic review of research articles reveals widespread poor practice in the presentation of continuous data. The authors recommend training for investigators and supply templates for easy use.

Haha, no piecharts work imo even fewer times. Of course, there are applications for bar graphs. Otherwise, they would not exist, but I believe you should think everytime you make on, if there would be a better alternative. I also like this paper: dx.plos.org/10.1371/jour...

Usually there is a better format for a figure then barplots anyway! Biologists are obsessed bars and it is most of the time a bad choice

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.

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...

Benchmarking Software for DDA-PASEF Immunopeptidomics www.sciencedirect.co...

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#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/

Antimicrobial resistance: a silent pandemic SPONSOR FEATURES

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

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

3️⃣ These drug effects vary between patients and may raise hepcidin, contributing to anemia risk in cancer or CKD.
Co-inhibiting BMP signaling could help balance this response.

2️⃣ Yet in liver cancer cells, diclofenac & acetaminophen amplify hepcidin via BMP-receptor stabilization — the opposite of what’s seen in primary hepatocytes.

1️⃣ Both drugs dampen IL-6–driven acute-phase proteins by boosting the feedback inhibitor SOCS3 and lowering STAT3 activation.

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...

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#proteomics #prot-preprint

Mathematical modelling for biologists - Modelling concepts in biological research Mathematical modelling for biologists - Modelling concepts in biological research

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

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...

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...

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

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#proteomics #prot-paper

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...

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...

🥳🥳🥳 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 ❤️

One aspect to highlight: Despite #signaling through the same #receptor, different #IFN subtypes induce distinct and in part contrary effects. Regulatory mechanisms seem to be deeply conserved.
Many thanks to the organizers @thebinderlab.bsky.social and Marieke Essers 3/3

It was great to see how ubiquitously interferons are involved in biology. From #stem #cell homeostasis, over cellular morphology and #antiviral defense mechanisms to anti-tumoral effects!
Big shoutout to all people presenting their in many parts unpublished work ❤️ 2/3

📈 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.

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📣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-...

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#proteomics #prot-paper

I am sad I miss it this year! Enjoy EuPA ❤️

Salami Tactics?

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.

@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