Cosmin Saveanu

From wig to #bigwig - a fast conversion can be done with the ENCODE program, aptly named #wigToBigWig. Going from 120Mb to 30Mb in a few seconds on an old Linux machine.

>wigToBigWig input.wig chromosomesizes.txt output.bw

https://www.encodeproject.org/software/wigtobigwig/

PS still learning […]

Example of a barplot created with the tidyplots package in R. Two conditions are illustrated, and for each condition, three fractions of RNA were analysed and the plot presents the data for 4 different RNAs.

For data visualization, #tidyplots is fantastic. On the solid bases of other R packages, many of the #tidyverse, it allows rapid creation of multidimensional #barplots, for example. I've updated my previous very short guide for doing this […]

[Original post on framapiaf.org]

Screenshot illustrating the use of patchwork to align two different ggplot plots. It shows a coverage plot in the upper part of it and, in the lower part, the structure of the transcripts for which the RNA seq data were obtained.

#cowplot is a great package to combine #ggplot2 plots for publications. #patchwork is an alternative that better manages alignment of the plot axes. For example, adding an independent annotation plot (#ggtranscript) to a genome coverage RNA seq plot […]

[Original post on framapiaf.org]

@vijayrathinam.bsky.social @vinnieviruses.bsky.social ‪@raflynn5.bsky.social‬ discovers why RNA undergoes glycosylation: N-glycans on glycoRNAs hide self-RNA from endosomal TLRs promoting ‘silent’ clearance of dead cells @nature.com
www.nature.com/articles/s41...

Systematic benchmarking of basecalling models for RNA modification detection with highly-multiplexed nanopore sequencing Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...

Fresh preprint from the
@novoalab.bsky.social !😀📌 Do you want to barcode up to 96 #RNA samples in your #nanopore flowcells? How well do RNA #modification-aware models perform? What if there is #noBasecallingModel for your modification-of-interest? Find it out here!😊 www.biorxiv.org/content/10.1...

📢 New paper: Targeted decontamination of sequencing data with CLEAN

We introduce CLEAN, a reproducible pipeline for removing spike-ins, host DNA, and rRNA from short & long sequences.

💡 Fast, reproducible, scalable.

Read the paper: doi.org/10.1093/narg...
Code & docs: github.com/rki-mf1/clean

How RNA sensors bind their ligands, how this binding is coupled to upregulation of type I interferon–stimulated genes, and the ways in which mutations in RNA sensors and genes that play important roles in RNA homeostasis have been linked to autoimmune and autoinflammatory diseases bit.ly/4bowQEb

Pseudouridine RNA avoids immune detection through impaired endolysosomal processing and TLR engagement Toll-like receptors (TLRs) 7 and 8 detect RNA degradation products to sense infection. However, modified nucleosides common in self-RNA—most notably pseudouridine—evade recognition. This study finds t...

#Pseudouridine #RNA avoids immune detection through impaired endolysosomal processing and TLR engagement: Cell www.cell.com/cell/fulltex...

Studying relative RNA localization from nucleus to the cytosol Abstract. The precise coordination of important biological processes, such as differentiation and development, relies heavily on the regulation of gene exp

📊 RNA localization matters for gene regulation. We present a method to estimate transcript distributions between nucleus & cytosol using nuclear, cytosolic and whole-cell RNAseq.

🔵🧬 doi.org/10.1093/narg...

@crg.eu @rodericguigo.bsky.social

La réponse de l’ANSM au sujet du manque de donnée sur le Spasfon / phloroglucinol Fin décembre, j’ai enfin reçu des réponses à mes courriers de la part de l’ANSM. J’ai d’abord reçu une réponse par courriel le 18 décembre au courrier que j’avais envoyé plu…

L'article reprend ce billet de blog que j'ai publié il y a quelques mois julietteferrydanini.com/2025/01/28/l...

Hey educators, tidyplots.org is great for teaching students data visualization because it is

🕊️ Free and open-source
🚀 Easy, intuitive and fast
💾 Loaded with demo datasets
🏆 Embracing best practices
🌈 Beautiful

#rstats #phd #dataviz #education

Screenshot of the online interface of Excalidraw, showing two rectangles and the available tools for drawing.

To add a little fun to any presentation or drawing, #Excalidraw is just perfect. Right click allows to export to clipboard a png copy of the drawing and the whole canvas can be exported as #svg, to be further modified, in #Inkscape, for example.

https://github.com/excalidraw/excalidraw

Introducing ReLiC! 🤩

The Subramaniam Lab (@rasilab.bsky.social) at @fredhutch.bsky.social and @uwgenome.bsky.social have published a scalable and high-throughput RNA-linked #CRISPR approach to measure the responses of RNA metabolic processes.

Abstract @natmethods.nature.com: go.nature.com/43IG6Rq

Impressive work on functional screening in human cells:
https://pubmed.ncbi.nlm.nih.gov/40442371/
With one of the most detailed data analysis and visualization code available:
https://github.com/rasilab/nugent_2024

PS The use of barcoded RNA reminded me our own past work in yeast ( […]

Mastering transcription termination: a new key mechanism to preserve the integrity of the genome Transcription termination by RNA polymerase II is essential to preserve genome integrity in eukaryotes. In their paper published in Nucleic Acids Research, the authors reveal that the SPT6 protein, in...

Discovery of a new key mechanism to preserve the integrity of the #genome!
Fabienne Bejjani et al. reveal that the SPT6 protein plays a central role in properly stopping transcription and avoiding the accumulation of abnormal transcripts.

CNRS/ Inserm/ UPC

institutcochin.fr/en/mastering...

Will climate change lead to more fungal infections? | News | Wellcome Fungi can keep us healthy or cause disease. As climate change drives fungi to adapt, learn how we can harness the benefits and tackle the threats.

Fungi can protect the environment, grow food and even develop new medicines. 🍄

But they can also cause disease.

As climate change spreads pathogenic fungi to new places, more people worldwide will be at risk.

Learn more in our explainer ⤵️
wellcome.org/news/will-cl...

Left: A Drosophila neuromuscular junction with a reduced expression of the retrotransposon Copia, resulting in an expansion of synaptic material (Green = motor neuron, Red = anti-Copia, and Blue = postsynaptic marker). Right: The Copia capsid structure as determined by Cryo-EM. Image credits: laboratories of Travis Thomson and Brian Kelch.

#Transposons are parasitic genetic elements that act as raw material for evolution of new functions. @briankelch.bsky.social &co show that the capsid of the #virus-derived retrotransposon Copia mediates synaptic plasticity at the #Drosophila neuromuscular junction 🧪 @plosbiology.org plos.io/3X71IDa

Congratulations to all the candidates who qualified for the #CNRS #CRCN competition in #Section21. Such brilliant science and incredible enthusiasm! Keep it up!

c3n-cn.fr/2025/01/31/c...

Most bacterial gene families are biased toward specific chromosomal positions The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...

I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...

Nematodes wearing bacterial coats.

Nikolaus Leisch at #EESWildModels

⏱️ One second in 300 million years - that's how accurate ACES will be 💪
@esa.int's Atomic Clock Ensemble in Space will use its two ultra-precise atomic clocks to revolutionise timekeeping from orbit 💫. Learn more in our blog 👉 blogs.esa.int/exploration/the-clocks-of-aces/

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.

Proteome-wide measurements of dose–response curves for 144 drugs reveal drug mechanisms of action go.nature.com/4a9lMs8
rdcu.be/egMl1

A move you can afford Where a person will look next can be predicted based on how much it costs the brain to move the eyes in that direction.

We show that eye-movements are selected based on effort minimization - finally final in @elife.bsky.social
eLife's digest:
elifesciences.org/digests/9776...
& the 'convincing & important' paper:
elifesciences.org/articles/97760

I consider this my coolest ever project!

#VisionScience #Neuroscience

Excerpt from the paper: "By the evolutionary conservation of these switches and their statespecific interactions with protein, ligand, and water molecules, the TFs undergo a shift in their conformational ensembles that forbids prolonged operator DNA binding simultaneously with inducer binding. This is the invisible family secret that enables transcriptional regulation."

Also loving the term "family secret" to describe acquired properties that are specific to only a subset of proteins with a particular fold

RQC2 is a major player in peptide release from stalled ribosomes - PubMed Eukaryotic cells prevent the accumulation of potentially toxic aberrant polypeptides and maintain ribosome availability through surveillance and clearance mechanisms, including the evolutionarily cons...

A new publication from my lab a great work done with fantastic colleagues from #IGDR (Reynald Gillet’s team for all the cryoem work. pubmed.ncbi.nlm.nih.gov/40187343/

The Best Programmers I Know | Matthias Endler I have met a lot of developers in my life. Late…

Love this

endler.dev/2025/best-pr...

Almost all the points raised in that blog post apply to other domains. One of the best molecular biologist I met, had a profound knowledge of the tools he was using.

Many kits with 'proprietary components' are like some APIs. If something goes wrong, you can't 'debug' the process...

I've already had two federal grants terminated and face a 33% pay cut due to future terminations. It's painful, but not as painful as the conversations I'm having every day with brilliant trainees in graduate school and postdoctoral positions who see little future for themselves in US science.

GitHub - jokergoo/ComplexHeatmap: Make Complex Heatmaps Make Complex Heatmaps . Contribute to jokergoo/ComplexHeatmap development by creating an account on GitHub.

Many thanks to Zuguang Gu for the wonderful #Bioconductor package #ComplexHeatmaps. Fantastically documented and useful.

https://github.com/jokergoo/ComplexHeatmap

#rstats #heatmap #dataviz

🔬 Retour en images sur notre Cours Pasteur - Principes et Applications de la Microscopie de Fluorescence qui a réuni étudiant.e.s en Master et doctorant.e.s pour une immersion dans les principes et applications de l’imagerie scientifique

Découvrez les Cours Pasteur ➡️https://bit.ly/CoursPasteur