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Johannes Wilbertz

@jowilbertz.bsky.social
126 followers 405 following 94 posts

Biologist in biotech (www.ksilink.com). Looking for drug targets in stem cell models with high-throughput imaging. Counting everything I can, but still appreciating the beauty of qualitative findings. johanneswilbertz.github.io

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Reposted by Johannes Wilbertz
Anne Carpenter @drannecarpenter.bsky.social · 04/11/2025
Required reading for cell biologists to get a sense of basic statistical principles! www.nature.com/articles/s41...
nature.com
Ten essential tips for robust statistics in cell biology - Nature Cell Biology
Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical metho...
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Reposted by Johannes Wilbertz
Anne Carpenter @drannecarpenter.bsky.social · 10/10/2025
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
mitochondria from bipolar patients are closer to the nucleus in these images; control patients' are spread out further
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
9/ Thanks to our collaborators at KSILINK (co-first author Amelie Weiss), LCSB (co-first author Vyron Gorgogietas) and Fraunhofer ITMP. #Parkinsons #Neurodegeneration #MorphologicalProfiling #iPSC #DrugDiscovery #Mitochondria
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
8/ This work highlights the power of morphological profiling in human disease-relevant models to uncover multi-phenotype rescue mechanisms. Data & code: github.com/Ksilink/Notebooks/tree/main/Neuro/PD_MorphProfileScreening
github.com
Notebooks/Neuro/PD_MorphProfileScreening at main · Ksilink/Notebooks
Ksilink Notebooks. Contribute to Ksilink/Notebooks development by creating an account on GitHub.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
7/ We propose that mild mitochondrial uncoupling may reduce αSyn burden and oxidative stress, offering a neuroprotective strategy. Tyrphostin A9 is a tool compound—not a therapeutic—but opens new avenues for drug discovery.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
6/ Structural analogues (AG879, AG1024) reproduced key effects, suggesting a class effect. Interestingly, αSyn lowering was not due to proteasomal degradation or transcriptional repression, but likely via autophagy induction.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
5/ We validated Tyrphostin A9’s effects across multiple assays: ✅ JC-1 dye (Δψm) ✅ ROS & GSH assays ✅ MEA (neuronal firing) ✅ Western blot (αSyn species) ✅ Seahorse (OCR) ✅ Autophagy markers (pAMPK, LC3B, p62)
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
4/ Top hits included Tyrphostin A9, a known mitochondrial uncoupler. It reduced ROS, normalized mitochondrial membrane potential, increased respiration, and lowered αSyn protein levels—without acute toxicity.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
3/ Our approach captured 127 cellular features per well, spanning αSyn distribution, TH expression, mitochondrial health, and more. Hits were ranked by similarity to isogenic control neurons (SNCA-corr) using Mahalanobis distance and cosine similarity.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
2/ PD is complex—multiple cellular stressors converge in midbrain dopaminergic neurons. We modeled PD using patient-derived SNCA triplication neurons (↑αSyn) and screened 1,020 compounds for phenotypic rescue using image-based profiling.
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Johannes Wilbertz @jowilbertz.bsky.social · 17/09/2025
🧵1/ 🚨 Our new paper is out! We used high-content morphological profiling in human iPSC-derived dopaminergic neurons to uncover a neuroprotective mechanism in Parkinson’s disease (PD): mild mitochondrial uncoupling. 🔗 doi.org/10.1038/s415...
doi.org
Morphological profiling reveals neuroprotection via mitochondrial uncoupling in human dopaminergic neurons - Scientific Reports
Scientific Reports - Morphological profiling reveals neuroprotection via mitochondrial uncoupling in human dopaminergic neurons
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Reposted by Johannes Wilbertz
Eric Topol @erictopol.bsky.social · 04/08/2025
One in 4 people carry one copy of the APOE4 allele, the strongest known genetic risk factor for Alzheimer's disease. We've just learned how that risk is mediated—the immune system erictopol.substack.com/p/our-braini...
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Reposted by Johannes Wilbertz
Helena Klara Jambor @helenajambor.bsky.social · 13/06/2025
... and a few minutes ago our Chart-Checklist came out in @natcellbio.nature.com 🥳🎉 Gift link for #TCTeAC: rdcu.be/eqPpi www.nature.com/articles/s41...
nature.com
A checklist for designing and improving the visualization of scientific data - Nature Cell Biology
Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data visualization research in a checkl...
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Reposted by Johannes Wilbertz
Carl T. Bergstrom @carlbergstrom.com · 18/05/2025
Elon Musk wanted to buy Wikipedia so that he could determine our society’s collective view of truth. He couldn’t, so he created grok. Do not let these machines be arbiters of truth. It is abundantly clear that they are being used to push absurd far-right conspiracies.
theguardian.com
Musk’s AI bot Grok blames ‘programming error’ for its Holocaust denial
Grok doubted 6 million death toll, days after peddling conspiracy theory of ‘white genocide’ in South Africa
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Reposted by Johannes Wilbertz
Arjun Raj @arjunraj.bsky.social · 07/05/2025
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try! nimbusimage.com
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Johannes Wilbertz @jowilbertz.bsky.social · 05/05/2025
Congrats Jacky! It's all about the journey!
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Reposted by Johannes Wilbertz
Stephen Turner @stephenturner.us · 23/04/2025
tl;dr: Python or R or both www.nature.com/articles/d41...
nature.com
Which programming language should I use? A guide for early-career researchers
Computer scientists and bioinformaticians address four key questions to help rookie coders to make the right choice.
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
6/n Some more info here: github.com/johanneswilb...
github.com
GitHub - johanneswilbertz/ChatGPT_scientific_abstracts: Investigated the frequency of specific words before and after 2022 in PubMed abstracts
Investigated the frequency of specific words before and after 2022 in PubMed abstracts - johanneswilbertz/ChatGPT_scientific_abstracts
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
5/n --> Conclusion: LLMs can lead to the increase of some words in text ("delve"), but also to the decrease of others in an active voice context ("we show").
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
4/n --> Consistent Frequency For a general term like "in this study", the results for 2023-2024 were exactly on the trendline based on the 2014-2022 data. So probably, there is no reason to believe that publication numbers rose in general after 2022, but only certain word frequencies changed.
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
3/n --> Decreased Frequency Unexpectedly, there was a drop in abstracts using widespread words like "our results" or "we show" after 2022. This might indicate the use of LLMs by researchers, as LLM-generated text often uses passive rather than active language ("this shows" versus "we show").
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
2/n --> Increased Frequency Some words are clearly more frequently found in biomedical literature after 2022, such as "pertinent", "treasure trove" or "shedding light". This could be due to overall publication numbers increasing for LLM-unrelated reasons.
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Johannes Wilbertz @jowilbertz.bsky.social · 10/04/2025
I explored whether scientific literature provides evidence of AI use in research publications. I analyzed the use of certain words before & after 2022 using PubMed, focusing on terms commonly used by ChatGPT (e.g., "delve") & standard scientific phrases ("in this study", "our results"). 1/n
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Reposted by Johannes Wilbertz
Nature Biotechnology @natbiotech.nature.com · 09/04/2025
Proteome-wide measurements of dose–response curves for 144 drugs reveal drug mechanisms of action go.nature.com/4a9lMs8 rdcu.be/egMl1
go.nature.com
Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics - Nature Biotechnology
Proteome-wide measurements of dose–response curves for 144 drugs reveal drug mechanisms of action.
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Johannes Wilbertz @jowilbertz.bsky.social · 08/04/2025
Must-read to review for everyone who is puzzled by and maybe even tries to understand microglia plasticity.
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Reposted by Johannes Wilbertz
Renzo Mancuso @mancusorenzo.bsky.social · 07/04/2025
I am so excited to share our review on microglial heterogeneity @natureneuro.bsky.social! It was a fantastic effort by the lab, led by @c9laura72.bsky.social and Alma Mohebiany. We provide a critical view on the plethora of microglial cell states in health and disease. www.nature.com/articles/s41...
nature.com
Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration - Nature Neuroscience
Microglia have key roles in CNS development and neurodegeneration. Here, the authors provide an overview of microglia heterogeneity, cell-state annotation and model systems.
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Johannes Wilbertz @jowilbertz.bsky.social · 03/04/2025
Next time you are out of breath during a run, try switching of this annoying STOP codon in your KEAP1 gene. Or alternatively, accept that you will never run as long and fast as a horse.
science.org
Running a genetic stop sign accelerates oxygen metabolism and energy production in horses
Horses are among nature’s greatest athletes, yet the ancestral molecular adaptations fueling their energy demands are poorly understood. Within a clinically important pathway regulating redox and meta...
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Johannes Wilbertz @jowilbertz.bsky.social · 24/03/2025
By contrast, the absence of marathon running (or sports in general) leads probably to irreversible changes in the brain. * hypothesises a marathon runner
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Johannes Wilbertz @jowilbertz.bsky.social · 24/03/2025
Not AI, but CRISPR A&I is what it takes to understand gene regulation.
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Johannes Wilbertz @jowilbertz.bsky.social · 23/03/2025
Nice example of how to be friendly, positive, and very determined at the same time.
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Reposted by Johannes Wilbertz
Mark Cuban @mcuban.bsky.social · 22/03/2025
From 2010 to 2016 (latest data I have ), NIH research contributed to EVERY drug approved by the FDA
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Johannes Wilbertz @jowilbertz.bsky.social · 11/03/2025
Something I learned today: Although human mitochondria contain more than 1100 proteins, only 13 of them are encoded by mtDNA.
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Johannes Wilbertz @jowilbertz.bsky.social · 07/03/2025
Full of interesting stuff if you're into translation. www.science.org/doi/10.1126/...
science.org
A subcellular map of translational machinery composition and regulation at the single-molecule level
Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion micros...
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Johannes Wilbertz @jowilbertz.bsky.social · 05/03/2025
"This isn’t about politics — it’s about the systematic dismantling of the very infrastructure that made American innovation possible."
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Johannes Wilbertz @jowilbertz.bsky.social · 04/03/2025
Form follows function? Not so sure about that. But morphology and calcium fluxes do not seem to follow the transcriptome. www.nature.com/articles/s41...
nature.com
Transcriptomic neuron types vary topographically in function and morphology - Nature
Transcriptomic profiling of neurons from the zebrafish optic tectum identified more than 60 cell types; functional imaging revealed that response tuning, morphology and connectivity of specific cell t...
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Johannes Wilbertz @jowilbertz.bsky.social · 01/03/2025
Pubmed #Science
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Reposted by Johannes Wilbertz
James Briscoe @jamesbriscoe.bsky.social · 21/02/2025
"Genes are... the easy part" @philipcball.bsky.social argues biologists need to embrace complexity from the start, rather than beginning with oversimplified "one gene, one trait" models +1 www.cell.com/cell-systems...
cell.com
Should biology put complexity first?
The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing damage to its complex nature? The answer might be foun...
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Johannes Wilbertz @jowilbertz.bsky.social · 21/02/2025
Interesting paper about how the integrated stress response induces cell death independent from a specific stress stimulus. Also featuring some nice applications of ISRIB, a stress response inhibitor. @altoslabs.bsky.social www.nature.com/articles/s41...
nature.com
The integrated stress response engages a cell-autonomous, ligand-independent, DR5-driven apoptosis switch - Cell Death & Disease
Cell Death & Disease - The integrated stress response engages a cell-autonomous, ligand-independent, DR5-driven apoptosis switch
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Johannes Wilbertz @jowilbertz.bsky.social · 17/02/2025
Evidence that C9orf72 microglia have a cell-autonomous pro-inflammatory phenotype (NLRP3) that contributes to non-cell autonomous mechanisms of motor neuron degeneration in ALS doi.org/10.1101/2025...
doi.org
Transcriptomic analysis of C9orf72-mutated iPSC-derived microglia implicates cell-autonomous upregulation of selected NLRP3 inflammasome genes in motor neuron degeneration
Hexanucleotide repeat expansion (HRE) in the non-coding region of the gene C9orf72 is the most prevalent mutation in Amyotrophic Lateral Sclerosis (ALS) and frontotemporal dementia. The C9orf72 HRE co...
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Reposted by Johannes Wilbertz
Gaël Varoquaux @gaelvaroquaux.bsky.social · 14/02/2025
🖊️AI for health: the impossible necessity of unbiased data Is unbiased data important to build health AI? Yes! Can there be unbiased data? No! Building health on biased data discriminates The notion of bias depends on the intended use: gael-varoquaux.info/science/ai-f...
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Johannes Wilbertz @jowilbertz.bsky.social · 13/02/2025
Interesting article. Many links to lysosomal biology and insights on how loss of function mutations in neurodegenerative disease are tackled by various companies.
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Reposted by Johannes Wilbertz
FMI science @fmiscience.bsky.social · 12/02/2025
🚨Job alert: We're hiring a Data Scientist (Image Analysis) to join our Facility for Advanced Imaging & Microscopy. The facility provides cutting-edge light and electron microscopy, high-content screening, image analysis and spatial-transcriptomics services. Apply at: www.fmi.ch/education-ca...
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Reposted by Johannes Wilbertz
Milo B. Fasken, Ph.D. @milofasken.bsky.social · 06/02/2025
Nice! #RNAdecay #mRNAdecay #QualityControl #Cytoplasm #RNAsky #RNA www.nature.com/articles/s41...
nature.com
Cytoplasmic mRNA decay and quality control machineries in eukaryotes - Nature Reviews Genetics
In this Review, Dowdle and Lykke-Andersen discuss advances in our understanding of the machinery and mechanisms involved in the control of cytoplasmic mRNA decay and comment on implications for the de...
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Johannes Wilbertz @jowilbertz.bsky.social · 05/02/2025
We published an updated version of our pre-print describing morphological profiling and compound screening in human dopaminergic neurons on @biorxiv-neursci.bsky.social doi.org/10.1101/2024...
doi.org
Morphological profiling reveals neuroprotection via mitochondrial uncoupling in human dopaminergic neurons
Parkinson's disease (PD) involves multiple pathological processes in midbrain dopaminergic (mDA) neurons, including protein degradation defects, vesicular trafficking disruption, endolysosomal dysfunc...
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Johannes Wilbertz @jowilbertz.bsky.social · 02/02/2025
This quote in the article got me thinking a lot. What if each reductionist finding itself is "correct" but that putting it all back together won't work because each reductionist finding came with specific assumptions which will sum up to a lot of noise in the final model.
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Johannes Wilbertz @jowilbertz.bsky.social · 02/02/2025
This is really a fantastic blog post by @brooksleitner.bsky.social about the potential of AI for neuropsychiatric drug development on multiple levels. Brooks also warns that everything needs to be applicable to the human brain. Massive compute based on in vitro reductionist data might not fix it.
open.substack.com
Is Techbio Ready for Neuroscience?
Techbio companies are using AI in numerous ways to develop new drugs; what approaches will work for neurologic and neuropsychiatric diseases?
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cureshank.bsky.social @cureshank.bsky.social · 28/01/2025
Here is a "starter pack" to quickly find/follow other accounts interested in #SHANK3 #Phelan-McDermid syndrome. Contact Ana Mingorance @cnsdrughunter.bsky.social if you would like to be included in the starter pack! go.bsky.app/5LKoxop
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Johannes Wilbertz @jowilbertz.bsky.social · 25/01/2025
Another link between viral infection and neurodegenerative disease. Interesting mechanism related to the nuclear pore complex. biorxiv.org/content/earl...
biorxiv.org
Enterovirus D68 2A protease causes nuclear pore complex dysfunction and motor neuron toxicity
The picornavirus Enterovirus D68 (EV-D68) is an important pathogen associated with acute flaccid myelitis (AFM). The pathogenesis of AFM involves infection of spinal motor neurons and motor neuron dea...
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Reposted by Johannes Wilbertz
Mark Davison @bigexperiment.bsky.social · 24/01/2025
Great organoids paper. If you want to freeze and recover viable organoids, without them exploding on thaw, there is a way. DM me. 🧪
nature.com
Rapid and scalable personalized ASO screening in patient-derived organoids - Nature
A scalable platform for generating patient-specific organoids for testing personalized oligonucleotide therapeutics is described.
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