Lmst

🎓 EuroBioC2025 Bioconductor Carpentry Workshops – registration now open!

📍 Barcelona | 📅 15–16 Sept 2025

Bulk & single-cell RNA-seq analysis with expert instructors.

🔗 https://eventum.upf.edu/go/eurobioc2025CarpentryWorkshops

#EuroBioC2025 #RNAseq #Bioinformatics #RStats

Postdoc job opportunity! We're looking for early career researcher in evolutionary genomics to study the relation between intra-specific gene expression variability, polymorphism, and macro-evolutionary rates. We have all of the data in 3 fishes and amphioxus, just waiting for your expertise and enthusiasm!
https://tinyurl.com/3aewk286
#EvoDevo #MolecularEvolution #bioinformatics #PopulationGenomics #RNAseq #PostDoc

Nice RNAseq atlas of small but important crustacean Daphnia pulex, and study of "selection operating on genes expressed in different tissues" https://www.biorxiv.org/content/10.1101/2025.05.01.651673v1 #EvoDevo #MolecularEvolution #RNAseq #Daphnia #Crustacean

Next @deNBI #training course by @galaxyfreiburg: From Data to Discovery: #Metagenomics, #RNAseq - #NGS #Bioinformatics with @galaxyproject (Freiburg, June 30 – July 4, 2025). Registration deadline: May 11. Read more: https://www.denbi.de/training-courses-2025/1883-from-data-to-discovery-metagenomics-rna-seq-ngs-bioinformatics-with-galaxy

Expression quantitative trait locus (eQTL) mapping studies are limited by the need to study a large number of individuals. This study develops a method to scale up #eQTL studies by performing single-nucleus #RNAseq of #Arabidopsis pollen @PLOSBiology https://plos.io/4jPZOzD

Top: Diagram of snRNA-seq analysis pipeline. Heterozygous Arabidopsis F1 plants were generated by crossing Col-0 to five different accessions. Pollen was collected from these five F1 plants and pooled, before nuclei isolation, barcoding, and cDNA synthesis using the 10x snRNA-seq protocol. After sequencing, nuclei from the five genotypes were demultiplexed, and meiotic recombination events were predicted. Gene expression and recombination patterns were then compared to identify eQTLs. Figure created using BioRender. Bottom: Fluorescent microscopy image of Arabidopsis thaliana pollen.

Heng Li's bliog: Short RNA-seq read alignment with minimap2 https://lh3.github.io/2025/04/18/short-rna-seq-read-alignment-with-minimap2

"TL;DR: the new preset splice:sr in minimap2 can align short RNA-seq reads. It is similar to STAR in resource usage, approaches STAR in junction accuracy, and is overall better at SNP calling."

#bioinformatics #rnaseq #alignment #ngs #mapping

Pipeline release! nf-core/rnavar v1.1.0 - nf-core/rnavar 1.1.0 - Mighty Milano!

Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.1.0

#gatk4 #rna #rnaseq #variantcalling #worflow #nfcore #openscience #nextflow #bioinformatics

asking for a friend: do you know any database/framework to visualize RNAseq data ? (just like https://github.com/broadinstitute/gnomad-browser for WGS)

#database #rnaseq #bioinformatics

Plaisir du samedi de perm à la BU: lecture de #PGD "L. Gress, S. Maman-Haddad, N. Marty-Gasset, N. Vialaneix, A. Bonnet. Plan de gestion des données CO-LOcATION V. Finale. INRAE-UMR GenPhySE 2025 https://hal.inrae.fr/hal-05009536v1
#passionPGD #DMPporn #researchdata #openscience #DMP #RNAseq #biology #data

Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!

Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.0.0

#10xgenomics #10xgenomics #alevin #bustools #cellranger #kallisto #rnaseq #singlecell #starsolo #nfcore #openscience #nextflow #bioinformatics

📢 Don’t miss Dr. Alexander Lachmann’s talk on ARCHS4 updates! Learn how this resource can enhance your RNA-seq research

📅 Feb 27, 2025 | 🕑 2–3 PM ET

🔗 Register: https://maayanlab.cloud/turl/a60f13d9

#glycotime #CFDE #archs4 #RNAseq

Pipeline release! nf-core/denovotranscript v1.2.0 - nf-core/denovotranscript v1.2.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

🌍 Bioconductor Course, Kenya 2025 🎓

We’re thrilled to announce our first in-person Bioconductor course in Kenya, happening March 24–28, 2025, at the ILRI Campus in Nairobi!

This free, week-long course is for bioinformatics beginners, covering R, Bioconductor, and RNA-seq workflows, and aims to grow the Bioconductor community in Africa.

🔗 Apply now: https://buff.ly/40CJL02
🔗 Learn more: https://training.bioconductor.org/workshops/2025-03-Nairobi/index.html

#Bioinformatics #Carpentries #RStats #RNAseq

We obtained #RNAseq from tooth germs over the embryonic and postnatal period where the major events of morphogenesis occur, from bud, to cap, to bell stage until differentiation and enamel/dentin secretion, and obtained clusters of coexpressed genes per stage.

Global expression profiles and clusters of co-expressed genes with an expression peak at a specific stage of dental development.
(A) PCA based on 11,342 1:1 orthologs across mouse and hamster. Samples are colored per morphological stage, shapes correspond to upper and lower molar samples. (B) Coexpression clusters deﬁned by soft clustering of expression values of each species and tooth type. Each cluster corresponds to a set of genes with an expression peak at a specific stage of dental development. The average proﬁles of each cluster are represented, with expression levels centered at the value of the first stage and error bars showing standard deviations. Clusters are ordered according to their temporal proﬁles. Distribution of cluster sizes is given. Genes not associated with a cluster are not represented. (C) Summary of the GO enrichment analysis for the mouse lower molar coexpression clusters; enriched GO terms were categorized as shown in Fig S2, a maximum of 5 representative terms are shown with their fold enrichments.

These tracks are listed in a new “RNA-seq long reads (Gonzalez et al., 2023)” sub-section of the “Transcript Level Features” section in JBrowse.
#RNAseq #JBrowse

New long read RNA-Seq tracks displayed in JBrowse. These new tracks can be found under Transcript Level Features.
Shown here are RNA-Seq long reads encoding novel CDS for the gene Irk2.

Pipeline release! nf-core/rnaseq v3.18.0 - nf-core/rnaseq v3.18.0 - Lithium Lynx!

Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.18.0

#rna #rnaseq #nfcore #openscience #nextflow #bioinformatics

Is it possible to transform RSEM to TPMs? #rnaseq #bioinformatics

I've been seeing a few #transcriptome wide association studies (TWAS) papers lately. This is another example, from #sorghum, combining GWAS and TWAS to study flowering time. Bonus - I imagine that there's a lot more value that can be gained from the 822 #RNAseq samples made publicly available

https://www.biorxiv.org/content/10.1101/2024.12.12.628249v1.full.pdf

#PlantScience #PlantDevelopment #Sorghum