@dgautheret.bsky.social
📤 122
📥 127
📝 24
Trying to make sense of
#RNA
information.
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
2 months ago
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5
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reposted by
Rob Patro
2 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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5
2
reposted by
Thomas Blein
3 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
3 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
3 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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22
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...
3 months ago
0
2
2
reposted by
Aude Bernheim
6 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
6 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
6 months ago
0
1
1
reposted by
Antoine Limasset
6 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
6 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 ⚡
6 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 ⚡
6 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
1
10
5
reposted by
Antoine Limasset
6 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
6 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
7 months ago
0
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Now indexing 10k RNA-seq samples with accurate counts!
add a skeleton here at some point
7 months ago
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reposted by
Camille Marchet ⚡
7 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 ⚡
8 months 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
8 months 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
9 months 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
9 months 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
10 months 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
10 months 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
10 months ago
0
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reposted by
Surfin' NuRD
11 months 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
11 months ago
Turning realms of "data" into a rectangular table is a most noble activity.
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reposted by
Randall Munroe
11 months ago
RNA
xkcd.com/3056
155
17881
2736
reposted by
Stephen Turner
12 months 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
about 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...
about 1 year ago
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@yannponty.bsky.social
Good move!
about 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
about 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)
about 1 year ago
1
1
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reposted by
Victor Javier
about 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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