@dgautheret.bsky.social
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Trying to make sense of
#RNA
information.
reposted by
Pierre Peterlongo
2 days ago
1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs.
github.com/pierrepeterlongo/logan_blaster
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GitHub - pierrepeterlongo/logan_blaster: Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Lo...
Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Logan-Search results) run a local blast ...
https://github.com/pierrepeterlongo/logan_blaster
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reposted by
Zamin Iqbal
6 days ago
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated,"
www.npr.org/2026/05/21/n...
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Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
https://www.npr.org/2026/05/21/nx-s1-5828768/science-funding-cuts-nih-trump-administration
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reposted by
bioRxiv Bioinfo
16 days ago
Testing the mutation accumulation hypothesis in aging with AlphaGenome
https://www.biorxiv.org/content/10.64898/2026.05.10.724136v1
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The Metappuccino paper is out in Bioinformatics!
academic.oup.com/bioinformati...
Given an input list of SRA sample IDs, Metappuccino infers and normalizes metadata over 15 categories, specially aimed at human transcriptomics studies 1/3
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Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research
AbstractMotivation. High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accum
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag166/8665235
26 days ago
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Impressive. That opens a new path to ncRNA functional classification.
add a skeleton here at some point
about 2 months ago
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reposted by
Yann Duroc
2 months ago
La tribune du Monde était donc une opération de Pollinis (Tousse) « Parce que bien cuisiner commence par bien choisir » … il n’existe aucune preuve de différence intrinsèque gustatives entre variétés conventionnelles ou ogm mais on écrit ça tranquille
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reposted by
Elena Rivas
2 months ago
www.nature.com/articles/s42...
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What does it take to learn the rules of RNA base pairing? A lot less than you may think - Communications Biology
Deep-learning models typically require large parameter spaces and extensive training data. Here the authors demonstrate that learning the fundamental biological rules of RNA base pairing can be achiev...
https://www.nature.com/articles/s42003-026-09921-3
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reposted by
Ombeline Rossier
2 months ago
Happy to present the latest Corynephage discovered and characterized by Bachelor students at University Paris-Saclay
@univparissaclay.bsky.social
add a skeleton here at some point
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reposted by
Yann Duroc
2 months ago
cet article est un exemple chimiquement pur du bingo anti biotechnologies pathétique
add a skeleton here at some point
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reposted by
Yann Duroc
2 months ago
comme attendu cette émission n'aura pas permis une juste information du public sur le sujet des NGT ! un fil de débunk (avec toutes les ressources à la fin) 🧵⬇️ 1/35
add a skeleton here at some point
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reposted by
Páll Melsted
3 months ago
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv
www.biorxiv.org/content/10.6...
and github
github.com/pachterlab/k...
Figure 1 shows they key result
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reposted by
Bastien Degardins
3 months ago
I had the occasion of presenting nice results about the detection of biological events in De Bruijn Graph at
#DSB2026
, in the context of my PhD work on
#Vizitig
! Thanks to the organizers and colleagues for this amazing and super-inspiring event (and
@camillemrcht.bsky.social
for the picture).
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👇 😨
add a skeleton here at some point
4 months ago
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reposted by
Florian Ingels
4 months ago
PREPRINT ALERT I heard you craving for more combinatorics, here are some more for y'all !
add a skeleton here at some point
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reposted by
Ragnar {Groot Koerkamp}
4 months ago
More minimizer papers! 😆
add a skeleton here at some point
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www.biorxiv.org/cgi/content/...
What’s behind Metapuccino? ☕️, by PhD student Fiona Hak,
@camillemrcht.bsky.social
and Melina Gallopin. A thread 👇
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Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research
Motivation: High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read ...
https://www.biorxiv.org/cgi/content/short/2025.10.31.685769v1
7 months ago
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reposted by
Rob Patro
7 months ago
My algorithmic friends (
@camillemrcht.bsky.social
) doing LLM stuff :
www.biorxiv.org/content/10.1...
! And also, screaming last names in the author list ;P. Given my level of trust in Camille, though, perhaps it's time for me to engage more seriously with these models in research...
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Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research
Motivation: High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read ...
https://www.biorxiv.org/content/10.1101/2025.10.31.685769v1
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reposted by
Thomas Blein
7 months ago
Interested in
#lncRNA
and
#ArtificiaIntelligence
? In the frame of our recently founded French-Korean bilateral project DHARP, we are recruiting a post-doc in bioinformatics and artificial intelligence in our team at
@ips2parissaclay.bsky.social
Application limit: 01/12/2025
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reposted by
Stephen Turner
7 months ago
PubMed is running on autopilot during shutdown, but key independent committee has been abolished
www.bmj.com/content/391/...
🧪
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reposted by
Ben Langmead
8 months ago
New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here:
benlangmead.github.io/bwt-svg/
. (H/t to
@robert.bio
for pointing me to pyodide!) Full repo:
github.com/benlangmead/...
.
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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...
8 months ago
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reposted by
Aude Bernheim
10 months ago
🦠🧍♀️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/...
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https://www.science.org/doi/10.1126/science.adr8536
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reposted by
Institut Pasteur | 130 years of biomedical research
10 months ago
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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Ca a l'air bien, non?
www.nature.com/articles/d41...
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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.
https://www.nature.com/articles/d41586-025-02090-z
10 months ago
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reposted by
Antoine Limasset
11 months ago
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...
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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
https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf111/8131451
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reposted by
UCSC Genome Browser
11 months ago
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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reposted by
Camille Marchet ⚡
11 months ago
#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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reposted by
Camille Marchet ⚡
11 months ago
#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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reposted by
Antoine Limasset
11 months ago
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!
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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
https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf128/8155840
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reposted by
Bonsai Sequence Bioinformatics
11 months ago
Preprint alert from the group 🚨 super fast grep-like sequence selection
add a skeleton here at some point
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What a thread!
add a skeleton here at some point
12 months ago
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Now indexing 10k RNA-seq samples with accurate counts!
add a skeleton here at some point
12 months ago
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reposted by
Camille Marchet ⚡
12 months ago
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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reposted by
Camille Marchet ⚡
about 1 year ago
A great and non technical, yet super relevant piece on implications of this scam
add a skeleton here at some point
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reposted by
Noam Teyssier
about 1 year ago
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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reposted by
Stephen Turner
about 1 year ago
gtexr: R interface to the GTEx Portal API
docs.ropensci.org/gtexr/
#rstats
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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…
https://docs.ropensci.org/gtexr/
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reposted by
geraldine woessner
about 1 year ago
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 ? 🧵
add a skeleton here at some point
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reposted by
Tuuli Lappalainen
about 1 year ago
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.
add a skeleton here at some point
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reposted by
Elena Rivas
about 1 year ago
correct RNAhub webserver address
rnahub.org
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We don't use cookies to track you - a session cookie is used exclusively for form protection (CSRF Token) only when submitting a search
https://rnahub.org
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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.
add a skeleton here at some point
about 1 year ago
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reposted by
Surfin' NuRD
about 1 year ago
Remember, EuropePMC is actually better than
#PubMed
because it includes ALL preprints in search results, not just those including NIH-funded research.
europepmc.org
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Europe PMCHome - Europe PMC
Europe PMC is an archive of life sciences journal literature.
https://europepmc.org/
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reposted by
Wolfgang Huber
over 1 year ago
Turning realms of "data" into a rectangular table is a most noble activity.
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reposted by
Randall Munroe
over 1 year ago
RNA
xkcd.com/3056
154
17797
2723
reposted by
Stephen Turner
over 1 year ago
One of the cooler things I saw at the Nextflow summit a few months ago. Can't wait to try this.
add a skeleton here at some point
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reposted by
Richard Sever
over 1 year ago
This comes up frequently. bioRxiv has a no reviews/hypotheses/commentary policy. The rationale is signal:noise and a focus on being a venue for new research not discussion of existing work (for which there are excellent other venues e.g. PubPeer). 1/n
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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...
over 1 year ago
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@yannponty.bsky.social
Good move!
over 1 year ago
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This is just a fantastic ressource. It finds _any_ sequence in the whole SRA. That's 5 orders or magnitudes larger than NR/Genbank.
add a skeleton here at some point
over 1 year ago
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There are many papers about "predicting" lncRNAs from RNA-seq data. But I'm wondering: who ever needs to predict lncRNA? (1/3)
over 1 year ago
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reposted by
Victor Javier
over 1 year ago
I am happy to see that both papers have been published. Pymportx is Python port of Tximport
#bioinformatics
academic.oup.com/nargab/artic...
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Pymportx: facilitating next-generation transcriptomics analysis in Python
Abstract. The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this n
https://academic.oup.com/nargab/article/6/4/lqae160/7901285
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