Eva Maria Novoa

Congratulations on the very nice work!

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...

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...

🚨 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)

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

Thank you for submitting your Letter of Intent (LOI) to CZI. We appreciate your interest in our work. CZI has decided not to continue with the second round of its Science Diversity Leadership Awards. We are committed to supporting groundbreaking research that advances the frontiers of scientific knowledge in pursuit of our mission to cure, prevent, or manage all diseases by the end of the century. We will provide information on future funding opportunities. We look forward to staying in touch. Bil Clemons, Program Officer, CZI

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. 😢💔

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...

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-...

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.

Wooops, Thank you @laurakwhite.bsky.social for poking me :) Indeed we had forgot to make it public - now fixed and should be publicly available, sorry for that!

Btw - i’d strongly recommend to run NanoConsensus through the MasterOfPores Nextflow workflow - which was already public :)

We would also thank the community for their interest in our work, which encouraged us to put the time and effort in upgrading Nano3P-seq to R10 chemistry. If you use the pipeline and/or code, please let us know how it goes - feedback very welcome! :)

6) This was a great team effort of @oguzhanbegik.bsky.social and #LeszekPryszcz.

GitHub - novoalab/polyTailor: Poly-A tail length estimation from Nano3P-seq libraries Poly-A tail length estimation from Nano3P-seq libraries - novoalab/polyTailor

5) PolyTailor is a new tool that can predict tail length and content without relying on the annotation of polyA sites on Nano3P-seq data. It is a user-friendly and fast, code is already available to use! github.com/novoalab/pol...

4) Deprecation of the R9 chemistry also led to the deprecation of basecalled fast5 files, which were crucial for Nano3P-seq tail length prediction analysis. So we released a new in-house analysis tool called PolyTailor!

3) We replaced the deprecated ONT kits DCS109&NBD104 with NBD114.24 barcoding kit. This kit is compatible with the new R10 chemistry and allows barcoding up to 24 libraries.

2) Template-switching oligos used for Nano3P-seq had a sequence context that was decreasing the tail prediction efficiency (due to TTC sequence at the adapter sequence end). We now changed our oligo sequence to improve tail prediction efficiency.

So, what did we change? 1) TGIRT, a group II intron RT we used for template-switching reaction of Nano3P-seq library preparation had been depracated. Fortunately, @NEBiolabs had recently released Induro, a highly processive group II intron RT, so we adapted our method to use this enzyme

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...

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...

(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.