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dgautheret.bsky.social @dgautheret.bsky.social · 7d

The MSc. Bioinformatics students of U. Paris-Saclay are organizing the Junior Conference on Computational Biology (JC2B) 2025: AI and predictive models in bioinformatics
November 13, 2025 - I2BC, CNRS, Gif-sur-Yvette, France
Register for free : bioi2.i2bc.paris-saclay.fr/jc2b/#regist...

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Aude Bernheim @audeber.bsky.social · Jul 24

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...

www.science.org

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Institut Pasteur | 130 years of biomedical research @pasteur.fr · Jul 24

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏

‪@rayan.chiki.bsky.social

#Bioinformatics

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dgautheret.bsky.social @dgautheret.bsky.social · Jul 23

Ca a l'air bien, non?
www.nature.com/articles/d41...

How to speed up peer review: make applicants mark one another

‘Distributed peer review’ of grants makes process more than twice as fast — and includes some cheat-prevention measures.

www.nature.com

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Antoine Limasset @npmalfoy.bsky.social · Jul 5

Paper Alert!

Our preprint on the K2R index, being able to efficiently associate kmers to the reads containing them is finally out there!

A thread!
academic.oup.com/bioinformati...

K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets

AbstractSummary. Biological sequence analysis often relies on reference genomes, but producing accurate assemblies remains a challenge. As a result, de nov

academic.oup.com

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UCSC Genome Browser @genomebrowser.bsky.social · Jul 16

New ENCODE4 long-read RNA-seq transcripts track for hg38 and mm10. Triplets (e.g. [1,1,3]) indicate start site, exon combination, and stop site for each transcript. Enrichment scores show how these change across tissue and cell line samples.

Read more: genome.ucsc.edu/gold...

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Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 10

#JOBIM2025 Mathilde Girard ends the session with a simple but effective idea: re oder the reads before using an off the shelf compressor to improve compression gain

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Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 10

#JOBIM2025 @bdegardins.bsky.social presents his PhD work on Vizitig, a multi sample graph exploration tool, with a focus on RNA - this afternoon we'll do a demo on pangenomes with the same tool

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Antoine Limasset @npmalfoy.bsky.social · Jul 3

Paper alert!
We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ...
TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor!
academic.oup.com/bioinformati...
A thread!

OReO: optimizing read order for practical compression

AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana

academic.oup.com

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 2

Preprint alert from the group 🚨 super fast grep-like sequence selection

Antoine Limasset @npmalfoy.bsky.social · Jul 2

A common approach is to use k-mer indexes to identify datasets that share a significant number of k-mers with a query sequence.
This problem has been studied extensively, and I recommend the survey of @camillemrcht.bsky.social, a great introduction to the subject
genome.cshlp.org/content/31/1...

Data structures based on k-mers for querying large collections of sequencing data sets

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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dgautheret.bsky.social @dgautheret.bsky.social · Jun 20

What a thread!

Antoine Limasset @npmalfoy.bsky.social · Jun 19

Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.

Short thread!

www.biorxiv.org/content/10.1...

github.com/Yohan-Hernan...

www.biorxiv.org

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dgautheret.bsky.social @dgautheret.bsky.social · Jun 17

Now indexing 10k RNA-seq samples with accurate counts!

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 17

REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1

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Camille Marchet ⚡ @camillemrcht.bsky.social · Jun 11

Hey yeast lovers. Do you like pangenomes?
O'Donnel et al. 2023 produced T2T assemblies of different strains, including phased haplotypes for yeast.

Here I selected 10 phased haplotypes and the S288C reference,
and looked for the MST28 / YAR033W gene reported to contain SVs such as indels.

👇🏻👇🏻

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Camille Marchet ⚡ @camillemrcht.bsky.social · May 14

A great and non technical, yet super relevant piece on implications of this scam

Vincent J Lynch 🐘🦣🦥 🦇🐋🐢🐍 @devoevomed.bsky.social · May 13

I've written a Substack about the #ColossalBioSci #DeExtinction #DisInformation campaign; it's focused on polluting the information landscape, rather than the underlying science (except for species concepts, I talk about them)

open.substack.com/pub/devoevom...

The Extinction of Truth

Or, a Colossal Pile of Bullshit

open.substack.com

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Noam Teyssier @noamteyssier.bsky.social · May 9

Just merged in an awesome new feature for xsra to support named pipes with @robp.bsky.social.

This lets you skip an intermediary write step and go straight from SRA to downstream tools.

It works with accessions that are both on- or off-disk.

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Stephen Turner @stephenturner.us · Apr 28

gtexr: R interface to the GTEx Portal API docs.ropensci.org/gtexr/ #rstats

Query the GTEx Portal API

A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. The GTEx project is a comprehensive public resource for studying tissue-specific gene expression and regulation in human…

docs.ropensci.org

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geraldine woessner @gewoessner.bsky.social · Apr 24

J'ai rarement vu une désinformation d'une telle ampleur, de la part d'un journal soi-disant sérieux, faisant dire à une expertise de l'Anses à peu près l'inverse de ce qu'elle dit vraiment...
C'est fou.
Même si c'est désormais récurrent.
On reprend tout ? 🧵

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Tuuli Lappalainen @tuuliel.bsky.social · Mar 17

This is so destructive and idiotic. mRNA vaccines are one of the most exciting opportunities to tackle diseases - from infectious disease to cancer and beyond - and these morons want to shut it down.

Alex Wayne @aawayne.bsky.social · Mar 16

Exclusive: NIH officials have advised scientists to remove reference to mRNA vaccines from their grant applications, in expectation the Trump administration intends to abandon most research in the field.

By @arthurallen202.bsky.social

kffhealthnews.org/news/article...

Scientists Say NIH Officials Told Them To Scrub mRNA References on Grants - KFF Health News

Two senior scientists say National Institutes of Health officials advised them to remove references to mRNA vaccines in grant applications, and they fear the Trump administration will abandon a promis...

kffhealthnews.org

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Elena Rivas @rivaselenarivas.bsky.social · Mar 16

correct RNAhub webserver address
rnahub.org

We don't use cookies to track you - a session cookie is used exclusively for form protection (CSRF Token) only when submitting a search

rnahub.org

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dgautheret.bsky.social @dgautheret.bsky.social · Mar 5

Bioinfo PhDs from abroad and french PhDs willing to return: There is still time to apply and be part of this super innovative project on cancer transcriptomics.

dgautheret.bsky.social @dgautheret.bsky.social · Jan 10

Dear young investigator in cancer bioinformatics: check our postdoc position on reference-free, organ agnostic transcriptome signatures of cancer at I2BC, Gif sur Yvette.
emploi.cnrs.fr/Offres/CDD/U...

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Surfin' NuRD @surfinnurd.bsky.social · Mar 2

Remember, EuropePMC is actually better than #PubMed because it includes ALL preprints in search results, not just those including NIH-funded research.

europepmc.org

Europe PMCHome - Europe PMC

Europe PMC is an archive of life sciences journal literature.

europepmc.org