iiinova — where your digital self keeps evolving

tmoeckli @tmoeckli.bsky.social · 26/07/2026

This also means smaller, less-funded labs get a real shot at groundbreaking discoveries! Not every insight requires expensive new experiments, sometimes the answer is already sitting in a public repository waiting to be asked the right question!

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tmoeckli @tmoeckli.bsky.social · 26/07/2026

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! 🧵

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tmoeckli @tmoeckli.bsky.social · 02/07/2026

How is the proteomics world going to approach this? Do we all need complementary RNAseq data for custom fastas? Is de-novo sequencing the way? (3/3)

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tmoeckli @tmoeckli.bsky.social · 02/07/2026

This study uncovers a "shadow" layer of the mammalian proteome: thousands of stable proteins produced through alternative RNA decoding that bypasses the conventional rules of translation. Remarkably, some of these non-canonical proteoforms are more abundant than their canonical counterparts. (2/3)

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tmoeckli @tmoeckli.bsky.social · 02/07/2026

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)

nature.com

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...

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tmoeckli @tmoeckli.bsky.social · 27/06/2026

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

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Reese Richardson @reeserichardson.bsky.social · 05/06/2026

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)

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Science News @scinews.bsky.social · 25/05/2026

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.

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Sholto David @sholtodavid.bsky.social · 17/05/2026

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.

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Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 27/03/2026

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

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julesh @julesh.mathstodon.xyz.ap.brid.gy · 21/02/2026

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

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tmoeckli @tmoeckli.bsky.social · 04/02/2026

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...

dx.plos.org

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.

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tmoeckli @tmoeckli.bsky.social · 04/02/2026

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

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Nikolai Slavov @slavov-n.bsky.social · 30/12/2025

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...

nature.com

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.

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PastelBio @pastelbio.bsky.social · 21/12/2025

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

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Niema Moshiri @niema.net · 17/12/2025

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

public-inspection.federalregister.gov

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Manlio De Domenico @manlius.bsky.social · 16/12/2025

🚨 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/

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Nature Communications @natcomms.nature.com · 22/11/2025

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

bit.ly

Antimicrobial resistance: a silent pandemic

SPONSOR FEATURES

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Will Fondrie @willfondrie.com · 19/11/2025

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

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tmoeckli @tmoeckli.bsky.social · 11/11/2025

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.

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tmoeckli @tmoeckli.bsky.social · 11/11/2025

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

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tmoeckli @tmoeckli.bsky.social · 11/11/2025

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

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tmoeckli @tmoeckli.bsky.social · 11/11/2025

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

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PastelBio @pastelbio.bsky.social · 07/10/2025

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

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John Lees @johnlees.bacpop.org · 15/08/2025

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

ebi.ac.uk

Mathematical modelling for biologists - Modelling concepts in biological research

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · 30/07/2025

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...

nature.com

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...

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PastelBio @pastelbio.bsky.social · 31/07/2025

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

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tmoeckli @tmoeckli.bsky.social · 30/07/2025

🥳🥳🥳 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 ❤️

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tmoeckli @tmoeckli.bsky.social · 13/07/2025

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

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tmoeckli @tmoeckli.bsky.social · 13/07/2025

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

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tmoeckli @tmoeckli.bsky.social · 13/07/2025

📈 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

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PRIDE Database @pride-ebi.bsky.social · 12/07/2025

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

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The Binder Lab (DKFZ Heidelberg) @thebinderlab.bsky.social · 11/07/2025

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!

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Nikolai Slavov @slavov-n.bsky.social · 30/06/2025

Let's leave behind simplistic & naive notions. .

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tmoeckli @tmoeckli.bsky.social · 25/06/2025

📣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/

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PastelBio @pastelbio.bsky.social · 18/06/2025

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

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tmoeckli @tmoeckli.bsky.social · 18/06/2025

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

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tmoeckli @tmoeckli.bsky.social · 06/06/2025

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

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Andrew Leduc @andrewleduc.bsky.social · 30/05/2025

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

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Peter Gleick @petergleick.bsky.social · 31/05/2025

There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd. It's not just budgets but research, institutions, expertise, and training the next generation.

Graphs showing 25 years of budgets for the National Institute of Health, NASA, and the NSF. In all cases, the proposed budget for next year is far, far below any year of the previous quarter century.

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Andrew Burgess @drandrewburgess.bsky.social · 27/05/2025

Love today’s #xkcd comic on #MassSpec 🤣

BEFORE THE BATHROOM SCALE WAS INVENTED, THE ONLY
WAY TO WEIGH PEOPLE WAS MASS SPECTROMETRY.

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PLOS Biology @plosbiology.org · 08/05/2025

The antiviral cytokine interferon is thought to act through the induction of hundreds of genes. In this #PLOSBiology Perspective, @jschoggins.bsky.social highlights recent findings that instead suggest distinct viruses are targeted by small subsets of the induced gene repertoire. 🧪 plos.io/4m7hOYi

plos.io

Old cytokine, new tricks: A refined model of interferon’s antiviral activity

Interferon is a central component of the vertebrate antiviral immune response, thought to act through induction of hundreds of interferon-stimulated genes, with some redundancy. This Perspective highl...

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The Binder Lab (DKFZ Heidelberg) @thebinderlab.bsky.social · 09/05/2025

Second Heidelberg Interferons Symposium coming up!! If you are based in HD or Mannheim (@dkfz.bsky.social, @uniheidelberg.bsky.social, @hlsalliance.bsky.social, @embl.org,...) and interested in any facet of these incredible #cytokines, join us on 🗓️ July 10/11 🏫 Marsilius Kolleg ✍🏻 bit.ly/IFN2025

Advertising flyer for the symposium, keynote lectures by Nadine Laguette from Montepellier (Crosstalk between DNA damage response and DNA sensing), Megan Stanifer from Florida (Lambda interferon in the gut epithelium) and Alessandra Mortellaro from Milano (type I interferons in hematopoiesis), plus local keynotes by Ana Martín-Villalba, Marieke Essers and Stefan Jordan.

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