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Gregor Rot 🌈

@grexor.bsky.social
72 followers 125 following 124 posts

Bioinformatics + Software Engineering + Full Stack WebDev 🏡 grexor.github.io 📚 pubscan.org/0009-0001-7888-6687 ▶️ youtube.com/@grexorai

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Gregor Rot 🌈 @grexor.bsky.social · 20h
It would have been great to present #expressRNA and #spatialAPA at @scverse.bsky.social in Copenhagen, but somehow just realised too late. Next year! expressrna.org #expressRNA #scverse2026 #spatialAPA
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Gregor Rot 🌈 @grexor.bsky.social · 07/10/2026
Ali Žerdin "Smo tovarišija, ki ima pred sabo en cilj: ta cilj je, da prepreči, da ta prostor postane avtoritaren." www.youtube.com/watch?v=FHhZ...
youtube.com
Večer resničnih zgodb: Ne v mojem imenu
YouTube video by Inštitut 8. marec
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Gregor Rot 🌈 @grexor.bsky.social · 04/10/2026
“Fame is the thirst of youth, - but I am not So young as to regard man’s frown or smile As loss or guerdon of a glorious lot; I stood and stand alone, - remembered or forgot.”
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Maria Hondele @mariahondele.bsky.social · 29/09/2026
Nuclear speckles are “hot”, but how do they actually sequester mRNPs? We find that stalled mRNPs are retained in nuclear speckles by a combinatorial RNA-binding protein network. www.biorxiv.org/content/10.6...
biorxiv.org
A combinatorial pre-mRNP retention factor network couples nuclear speckle architecture to splicing quality control
Cells must prevent incompletely spliced transcripts from entering the cytoplasm, yet how splicing status is recognized and converted into selective nuclear retention remains unclear. Here, we identify...
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Lars Juhl Jensen @larsjuhljensen.bsky.social · 01/10/2026
Everyone has relied on 1) people develop expert scientific judgement through learning-by-doing, and 2) experience is consequently a good proxy for that. Unfortunately learning-by-asking-ChatGPT does not work. AI can thus cause a future shortage scientific talent. medium.com/zs-associate...
medium.com
The economics of expertise: what AI means for the future of scientific talent
AI is reshaping scientific expertise in R&D. Leaders must preserve the experiences that build judgment as routine work becomes automated
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Gregor Rot 🌈 @grexor.bsky.social · 29/09/2026
Why is Israel so afraid of the film NAZA? We spoke to its directors – Stateside with Kai and Carter www.theguardian.com/us-news/vide...
theguardian.com
Why is Israel so afraid of the film NAZA? We spoke to its directors – Stateside with Kai and Carter
Composed of interviews with 24 anonymous Israeli intelligence officers and soldiers, the documentary NAZA is a haunting exposé of the tools that the Israeli military uses to carry out the remote killi...
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The Francis Crick Institute @crick.ac.uk · 29/09/2026
Our AI for Biological Discovery online seminar series continues with “Communities of AI agents for scientific discoveries” by James Zou, Stanford University, on 7 October at 15:00 BST. Register now for the webinar: www.eventbrite.co.uk/e/ai-in-biol...
eventbrite.co.uk
AI in Biology Seminar | Professor James Zou
A new AI for Biological Discovery Seminar Series, presented by the Francis Crick Institute.
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Gregor Rot 🌈 @grexor.bsky.social · 26/09/2026
🧬 New in expressRNA: MCP, so you can "talk" with expressRNA, find out analyses, results, discover how bioinformatics is done on the platform and more. Open you expressRNA profile where you can find MCP URL and token to connect it to Claude, ChatGPT or another LLM. #expressRNA #MCP #AI #LLM
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Gregor Rot 🌈 @grexor.bsky.social · 25/09/2026
I knew it 😀🤣😳 #books
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CTGCT (Centre for the Technologies of Gene and Cell Therapy) @ctgct.bsky.social · 23/09/2026
📢 Abstract submission closes in 7 days! Researchers, students, and professionals: this is your chance to present your work at #CTGCTDay2026. 📅 Deadline: 30 September 2026 🔗 Submit your abstract: forms.cloud.microsoft/e/NdYJDATNwN @kemijski.bsky.social @ucltro.bsky.social @umcutrecht.bsky.social
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Gregor Rot 🌈 @grexor.bsky.social · 21/09/2026
The smaller the model, the better it will work 😀
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Gregor Rot 🌈 @grexor.bsky.social · 20/09/2026
New in expressRNA: native iCLIP analysis. Upload FASTQ — nf-core/clipseq + iCount run as a real Nextflow pipeline: crosslink/peak calling, motif discovery, live genome browser. expressrna.org #iCLIP #bioinformatics #clip #expressRNA
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Gregor Rot 🌈 @grexor.bsky.social · 17/09/2026
#pybio, open-source Python toolkit for genomics (Ensembl genome downloads, custom genome import, STAR/STARsolo mapping), just got a proper docs site replacing the old PDF. grexor.github.io/pybio/ #pybio #bioinformatics #genomics #opensource
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Gregor Rot 🌈 @grexor.bsky.social · 16/09/2026
🧬 New in expressRNA: scanRBP — predict which RNA-binding proteins bind your sequence. Paste it in, get an interactive clustered heatmap across 1000+ RBP motifs (mCross + CISBP-RNA). Free, no install. Try it: www.expressrna.org/index.html?a... #bioinformatics #expressRNA
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Gregor Rot 🌈 @grexor.bsky.social · 15/09/2026
La vita e orribile e meravigliosa, Čechov e un genio 😀 #books
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Gregor Rot 🌈 @grexor.bsky.social · 12/09/2026
Nisem razumu kej dosti ma morje in Devin pej so fajn 😀
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Gregor Rot 🌈 @grexor.bsky.social · 11/09/2026
🧬 New in expressRNA: RNAmotifs2 cluster motif analysis. Auto-runs on every APA analysis, or upload your own splicing/polyA event table. Enriched motif clusters + RNA-maps, FDR & permutation stats. Live example: www.expressrna.org/index.html?a... Built on RNAmotifs2: github.com/grexor/rnamo...
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Gregor Rot 🌈 @grexor.bsky.social · 10/09/2026
Wanted my treadmill runs in Strava. Turns out the Woodway console speaks FTMS — a standard Bluetooth LE profile for fitness machines (speed, incline, distance, time). Use an app (kinni for example), read the stream over Bluetooth. Small, fun learning project 🏃‍♂️ grexor.github.io/running_wood... #run
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Gregor Rot 🌈 @grexor.bsky.social · 10/09/2026
www.theguardian.com/world/2026/s...
theguardian.com
Secret systems used by Israel in mass killings of Gaza civilians revealed in new film
Testimony from Israeli military insiders involved in surveillance and remote killings features in documentary produced by the Guardian
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Gregor Rot 🌈 @grexor.bsky.social · 09/09/2026
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Gregor Rot 🌈 @grexor.bsky.social · 09/09/2026
Interesting for the purpose to understand Nietzsche 😀 #books
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Gregor Rot 🌈 @grexor.bsky.social · 08/09/2026
What is it?
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Manuel Irimia @mirimiam.bsky.social · 03/09/2026
🚨🚨🚨 As part of the MSCA-DN DECODES, we're looking for a PhD student to study splicing programs in beta cells and diabetes at @melisupf.bsky.social @crg.eu Join 14 other PhD students across Europe to decipher the splicing code in human disease. More info below 👇 www.findaphd.com/phds/project...
findaphd.com
DECODES at University of Santiago de Compostela on FindAPhD.com
PhD Project - DECODES at University of Santiago de Compostela, listed on FindAPhD.com
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Gregor Rot 🌈 @grexor.bsky.social · 31/08/2026
Goodbye Couchsurfing, welcome Couchers! grexor.github.io/couchers.html
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Gregor Rot 🌈 @grexor.bsky.social · 29/08/2026
"Non scriverò più libri. Ho trascurato il mondo della vita" www.youtube.com/watch?v=Jpiu...
youtube.com
Umberto Galimberti (esclusivo): "Non scriverò più libri. Ho trascurato il mondo della vita"
YouTube video by Clinica Rizzola
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Gregor Rot 🌈 @grexor.bsky.social · 28/08/2026
Also: alternative splicing analysis via splicekit (github.com/bedapub/spli...) has been live since July. Try it: expressrna.org — get in touch if you'd like your data analyzed on the platform :-) #transcriptomics #bioinformatics #spatialAPA #expressRNA
expressrna.org
expressRNA: post-transcriptional research platform
Upload 3′-end sequencing experiments, quantify polyA sites and run differential APA analyses with CLIP-seq RNA-Map integration. Open, collaborative, and free.
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Gregor Rot 🌈 @grexor.bsky.social · 28/08/2026
August was good to #expressRNA: two new analysis types. 🗺️ Spatial Patterns — compare polyA usage & expression across multiple Visium sections between conditions (v1 + v2) 📈 Gene expression time courses from RNA-seq — plot expression across your own ordered sample sequence
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SIRD - Swiss Initiative for RNA & Disease @swissinitiativerna.bsky.social · 28/08/2026
🔬🧪 Scientifica 2026 starts tomorrow! Visit the SIRD booth and discover how RNA helps us understand and treat diseases. 🗓 29. & 30. August 2026 | 🕒 11-17 Uhr | 📍 ETH Zürich | Polyterrasse 🔗 More Infos: buff.ly/gglg1y9 @ethzurich @uzh @stadtzh
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Mark Robinson @markrobinsonca.bsky.social · 24/08/2026
That's exciting. From a hackathon in December 2023 (spatialhackathon.github.io/past.html) to a preprint in June 2025 (www.biorxiv.org/content/10.1...) to this publication out today (doi.org/10.1038/s415...).
spatialhackathon.github.io
Past Events
Github Pages for SpatialHackathon
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Gregor Rot 🌈 @grexor.bsky.social · 27/08/2026
buy buy buy buy buy consume consume consume consume consume #books
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Jan Kirsch, M.D., M.P.H. @drjanicekirsch.bsky.social · 21/08/2026
An advance against melanoma A personalized mRNA vaccine was found to reduce risk of spread and to increase disease-free and overall survival in high-risk or advanced melanoma. It teaches immune cells to target the patients' particular tumor. www.cnbc.com/2026/08/19/m...
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Gregor Rot 🌈 @grexor.bsky.social · 21/08/2026
I love you Čehov, thank you 😀❤️
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Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 20/08/2026
Now online! Happy to have been part of this remarkable study on TDP-43 from the Butcher Lab @uwbiochem.bsky.social www.nature.com/articles/s41...
nature.com
TDP-43 controls RNA structure through high affinity lattice interactions - Nature Communications
TDP-43 is an essential RNA-binding protein. Here, the authors show how it binds single-stranded poly(UG) RNA through high affinity 1D lattice interactions. The N-terminal domain functions to accelerat...
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Gregor Rot 🌈 @grexor.bsky.social · 15/08/2026
💡 Importing a full sample set from ArrayExpress (with annotation) into expressRNA just needs a project ID (PRJNA or similar). #transcriptomics #bioinformatics #expressRNA
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Gregor Rot 🌈 @grexor.bsky.social · 15/08/2026
🦠 Showcase: Dictyostelium discoideum RNA-seq timeseries data, from "Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum." www.expressrna.org/index.html?a...
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Gregor Rot 🌈 @grexor.bsky.social · 15/08/2026
GO enrichment, live: for whatever gene set you're exploring, see which Gene Ontology terms are enriched — rendered as a browsable tree, not just a flat table of p-values.
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Gregor Rot 🌈 @grexor.bsky.social · 15/08/2026
Draw a profile: sketch a hypothetical expression pattern with your mouse, and get back the genes whose real expression matches it best (Pearson correlation) — no need to already know which gene you're looking for.
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Gregor Rot 🌈 @grexor.bsky.social · 15/08/2026
New in expressRNA: Gene Expression Time Course 😀 Arrange samples into your own ordered sequence — dev stages, a time series, treatment steps — then plot how one or more genes' expression unfolds across it (CPM/log2CPM). 🧵👇
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Charlie Hebdo @charliehebdo.fr · 12/08/2026
Le dessin du jour, par Félix charliehebdo.fr/dess...
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Quaid Morris @quaidmorris.bsky.social · 07/08/2026
Excited to share the results of the Codebook Project, an international effort to identify accurate DNA-binding motifs and genomic binding loci for >300 uncharacterized human transcription factors (TFs) www.nature.com/articles/s41...
nature.com
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
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Charlie Hebdo @charliehebdo.fr · 03/08/2026
Le dessin du jour, par Juin charliehebdo.fr/dess...
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Lars Juhl Jensen @larsjuhljensen.bsky.social · 27/07/2026
Great opportunity if you're in or near Copenhagen: a one-day symposium on biological applications of deep learning. I hope to see you there! youtube.com/shorts/qyHDT...
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Gregor Rot 🌈 @grexor.bsky.social · 25/07/2026
Please someone tell Strava to center monthly x-axis labels 🤣
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Steven Robbins @stevenjrobbins.bsky.social · 22/07/2026
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...
nature.com
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
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Gregor Rot 🌈 @grexor.bsky.social · 22/07/2026
Haha reminds me also of ML papers with “AUC is 0.865 which is 0.02 better than state of the art” 😀
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Gregor Rot 🌈 @grexor.bsky.social · 17/07/2026
“the old world is dying, and the new world struggles to be born: now is the time of monsters” - Antonio Gramsci
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Alejandro Montenegro @aemonten.bsky.social · 15/07/2026
Interesting. Full deletion of all introns in yeast was actually my project in the Staley lab, *20 years ago*. I actually found a bunch of phenotypes. We did this in collaboration with the Guthrie lab. www.cell.com/cell/abstrac...
cell.com
A spliceosome-independent eukaryote generated by complete intron removal
Elimination of all spliceosomal introns reveals a spliceosome-independent eukaryote.
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Andreas Gschwind @argschwind.bsky.social · 15/07/2026
Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/
nature.com
An encyclopedia of human enhancer–gene regulatory interactions - Nature
An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...
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Gregor Rot 🌈 @grexor.bsky.social · 07/07/2026
working on expressRNA 😀
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Oxford Nanopore @nanoporetech.com · 29/06/2026
Many RNAs originally annotated as non-coding may encode proteins, with signals found across UTRs and overlapping known ORFs. Mike Clark shares how Oxford Nanopore enables this kind of transcript-level insight. Learn more: bit.ly/3SgUa19
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