Need to #multiplex your #nanopore direct RNA runs? We are happy to announce an upgraded version of #SeqTagger #version2 with demuxing models for #mRNA (compatible with polyadenylated #rRNA) and #tRNA. Code and models publicly available in GitHub! github.com/novoalab/Seq...

GitHub - novoalab/SeqTagger: Super-fast and accurate demultiplexing of direct RNA-seq runs (Pryszcz*, Diensthuber*, et al., Genome Res 2025)

Super-fast and accurate demultiplexing of direct RNA-seq runs (Pryszcz*, Diensthuber*, et al., Genome Res 2025) - novoalab/SeqTagger

github.com

Please check out our latest #preprint to study #ACTIVELY TRANSLATING #tRNA populations and their dynamics upon #stress :) This was an wonderful collaborative effort between @novoalab.bsky.social @immagina.bsky.social and #Soares teams - thank you for making this possible!

Mie Monti@miemonti.bsky.social · 6mo ago

New preprint from @novoalab.bsky.social ! Which tRNAs are used by ribosomes during translation? We introduce tRIBO-seq, a nanopore method to sequence ribosome-associated tRNAs and track how the active tRNA pool changes across stress conditions. www.biorxiv.org/content/10.6... Thread 👇

It was our pleasure to host @james-bryson.bsky.social (BRIC, Copenhagen) at @crg.eu through the EU-LIFE Postdoctoral Exchange Program! Big thanks to James for presenting his work on advanced CRISPR tools for epitranscriptomic research, and to @eu-life.bsky.social for this opportunity!🧬✈️ #EULIFE #CRG

🧬 New review on nanopore basecalling models is out! ✨ Congrats to @soniacruciani.bsky.social (former Novoa Lab PhD, now postdoc at the Deplancke Lab, EPFL) and @evamarianovoa.bsky.social👏 📖 www.nature.com/articles/s41...

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...

biorxiv.org

🚨 New preprint alert 🚨 We systematically benchmarked @nanoporetech.com 's modification-aware basecalling models released for RNA on sets of in vitro and in vivo sequences and made some curious observations 🧬🔍. bit.ly/4lXqNul Follow along for a little recap (1/12)

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...

bit.ly

Happy to be the next (and 1st female) @crg.eu director. The CRG always stood out to me, for its excellence in understanding life's principles, with implications for health and biodiversity, & its collaborative, open and innovative way of doing science. Thrilled to join its amazing community in 2026!

New manuscript from the Novoa lab was published this week in Genome Biology! You can give it a read here: rdcu.be/ebiIs

Pretty sad. Just got the email that CZI is canceling the second round of Diversity Leadership Awards. Private industry will definitely not fill the hole that NIH and NSF are leaving. 😢💔

Working with germ-free mice with the Kambayashi Lab we saw a 'swollen' epididymal phenotype occurring, so we took a closer look doi.org/10.1530/REP-...

A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice

The microbiome encompasses the array of microorganisms inhabiting various niches in the body and is necessary for numerous physiological processes, including normal metabolism and a functioning immune...

doi.org

Are #rRNA #modifications equal a across cell types, conditions and #disease? Are they tuned upon #antibiotics exposure? In our recent works, we find that yes and yes! Exciting times ahead!! Please see authors.elsevier.com/c/1kF253vVUP... and www.nature.com/articles/s41... Feedback very welcome!! :)

New pre-print 📢:Cell-free translation from diverse human cell types: Fast, reproducible and scalable t.co/IAld0ocjDf @nickkouvelas.bsky.social @unibern.bsky.social #biorxiv #mRNA #Ribosome

How has native RNA sequencing contributed to epitranscriptomic research? This is one of the main questions we addressed in our recent review with @gdiensthuber.bsky.social Now live! authors.elsevier.com/a/1kS2f3vVUP...

This is a good recommendation. In addition, for bar plots or other plots where you're coloring large areas, add some transparency. The viridis colors are too dark and saturated for large areas. They were designed for points and lines(*). Compare left versus right.

Andrew Heiss@andrew.heiss.phd · 2y ago

The viridis palettes are great perceptually uniform color maps for #dataviz, but sometimes at the extremes they're too pale/dark. With ggplot and #rstats, though, you can truncate the palette to avoid the paler colors. I wrote a little guide for how datavizf24.classes.andrewheiss.com/news/2024-12...

Very happy to share our updated #Nano3P-seq protocol, adapted to #nanopore R10 chemistry. After a lot of troubleshooting both in the wet lab protocol but also the computational analysis pipeline, we finally made it! :-) www.biorxiv.org/content/10.1...

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution

RNA polyadenylation is crucial for RNA maturation, stability and function, with polyA tail lengths significantly influencing mRNA translation, efficiency and decay. Here, we provide a step-by-step pro...

biorxiv.org

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

I must admit that this annotated Nature abstract remains a useful recipe for constructing a summary paragraph. I show it to my students every time we get started.