Cosmin Saveanu
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cosminribo.bsky.social
Cosmin Saveanu
@cosminribo.bsky.social
56 followers 120 following 3 posts
Scientist. My primary fediverse account is on mastodon: @cosminribo@framapiaf.org
Bsky users can see my posts there by following the, arguably long, @cosminribo.framapiaf.org.ap.brid.gy
Posts Replies Media Videos
Reposted by Cosmin Saveanu
narjournal.bsky.social
⭐NAR Breakthrough! ⭐
🧬 A synthetic RNA forms a #G-quadruplex without a G-rich sequence, using a complex 3D fold and GTP as a ligand. This suggests G-quadruplexes may be far more widespread in biologically important RNAs. Read more: doi.org/10.1093/nar/...

#NARBreaktrhough #RNA #StructuralBiology
December 22, 2025 at 3:48 PM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
Thank you #biorxiv staff for processing the pre-prints so quickly and nicely. Our latest manuscript addresses a rather specialized, albeit important, question in mRNA degradation in yeast. To what extent the Lsm1-7/Pat1 complex is involved in the degradation of mRNA by decapping activation ? By […]
Original post on framapiaf.org
framapiaf.org
December 19, 2025 at 3:08 PM
Reposted by Cosmin Saveanu
monicamedhist.bsky.social
This report in Nature on the costs of competing for & administering scientific grants is shocking: "In other words, European taxpayers will have spent more on the funding process than on the funding itself, and the scientific ecosystem has been drained." www.nature.com/articles/d41... 🧪
Point of no returns: researchers are crossing a threshold in the fight for funding
With so little money to go round, the costs of competing for grants can exceed what the grants are worth. When that happens, nobody wins.
www.nature.com
December 19, 2025 at 6:46 PM
Reposted by Cosmin Saveanu
dijiang319.bsky.social
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
Chromatin buffers torsional stress during transcription
During eukaryotic transcription, Pol II must overcome nucleosome obstacles and, because of DNA’s helical structure, must also rotate relative to DNA, generating torsional stress. However, there is lim...
www.science.org
December 19, 2025 at 10:31 PM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
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 […]
Original post on framapiaf.org
framapiaf.org
September 4, 2025 at 7:35 AM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
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]
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.
September 20, 2025 at 1:01 PM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
#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]
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.
September 8, 2025 at 3:15 PM
Reposted by Cosmin Saveanu
labwaggoner.bsky.social
@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...
August 6, 2025 at 6:27 PM
Reposted by Cosmin Saveanu
evamarianovoa.bsky.social
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...
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...
www.biorxiv.org
August 3, 2025 at 2:23 PM
Reposted by Cosmin Saveanu
martinhoelzer.bsky.social
📢 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
August 4, 2025 at 7:02 AM
Reposted by Cosmin Saveanu
rnajournal.bsky.social
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
July 1, 2025 at 6:03 PM
Reposted by Cosmin Saveanu
milofasken.bsky.social
#Pseudouridine #RNA avoids immune detection through impaired endolysosomal processing and TLR engagement: Cell www.cell.com/cell/fulltex...
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...
www.cell.com
July 1, 2025 at 8:09 PM
Reposted by Cosmin Saveanu
guigolab.bsky.social
📊 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
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
doi.org
July 2, 2025 at 6:42 AM
Reposted by Cosmin Saveanu
ferrydanini.bsky.social
L'article reprend ce billet de blog que j'ai publié il y a quelques mois julietteferrydanini.com/2025/01/28/l...
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…
julietteferrydanini.com
July 2, 2025 at 8:01 AM
Reposted by Cosmin Saveanu
jbengler.de
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
December 6, 2024 at 8:36 PM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
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
Screenshot of the online interface of Excalidraw, showing two rectangles and the available tools for drawing.
June 17, 2025 at 2:52 PM
Reposted by Cosmin Saveanu
scienceinseattle.com
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
June 11, 2025 at 9:07 PM
Reposted by Cosmin Saveanu
cosminribo.framapiaf.org.ap.brid.gy
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 ( […]
Original post on framapiaf.org
framapiaf.org
June 12, 2025 at 7:11 AM
Reposted by Cosmin Saveanu
institutcochin.bsky.social
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...
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...
institutcochin.fr
May 21, 2025 at 10:55 AM
Reposted by Cosmin Saveanu
wellcometrust.bsky.social
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...
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.
wellcome.org
April 24, 2025 at 1:10 PM
Reposted by Cosmin Saveanu
plosbiology.org
#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
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.
February 19, 2025 at 5:41 PM
Reposted by Cosmin Saveanu
onamy.bsky.social
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...
Classements d’admissibilité au concours CNRS 2025
Comme en 2021, en 2022, en 2023 et en 2024 la C3N s’engage à rendre publiques les listes des candidates et des candidats admissibles classés par ordre de mérite.
c3n-cn.fr
April 11, 2025 at 7:17 PM
Reposted by Cosmin Saveanu
alfmicrobe.bsky.social
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/...
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-...
www.science.org
April 10, 2025 at 7:43 PM
Reposted by Cosmin Saveanu
tom-mathers.bsky.social
Nematodes wearing bacterial coats.

Nikolaus Leisch at #EESWildModels
April 9, 2025 at 11:42 AM
Reposted by Cosmin Saveanu
exploration.esa.int
⏱️ 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/
April 10, 2025 at 8:45 AM