iiinova — where your digital self keeps evolving

GenomiqueENS @genomiqueens.bsky.social · 19/03/2026

Have you ever wondered how the nanopores look like on the MinION Flow Cell from @nanoporetech.com ? We did it for you with the Spinning disk W1 Yokogawa Sora Nikon microscope thanks to the @ibensens.bsky.social Imaging plateform IMACHEMENS ! 🔬 Isn't that hypnotic?! 🎇 😵‍💫

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GenomiqueENS @genomiqueens.bsky.social · 27/01/2026

To limit the biais due to the fragmentary annotation in chick (particularly in the 3’UTR), we improved the annotation thanks to a companion bulk @nanoporetech.com RNA-seq and a specific bioinformatics analysis.

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GenomiqueENS @genomiqueens.bsky.social · 27/01/2026

We collaborated with the Morin team from @ibensens.bsky.social by constructing the libraries combining @10xgenomics.bsky.social and performing Illumina sequencing.

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GenomiqueENS @genomiqueens.bsky.social · 27/01/2026

Our expertise in single-cell transcriptomics in organisms with fragmentary annotation is illustrated by this new study in chick, revealing new roles for Cdkn1 in the neurogenic transition.

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GenomiqueENS @genomiqueens.bsky.social · 15/12/2025

😄We are thrilled to announce that our protocol “Gene re-annotations using ONT long-read RNAseq data” is available on dx.doi.org/10.17504/protocols.io.36wgqd5qyvk5/v1 It will enable you to improve the annotation of exotic/non-model species based on long-read RNA-seq data such as @nanoporetech.com.🧬💻

dx.doi.org

Gene re-annotations using ONT long read RNASeq data

This protocol offers detailed, step-by-step instructions for anyone looking to reannotate their genes using long reads from cDNA or direct RNA RNA-Seq datasets (ONT data). The g...

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GenomiqueENS @genomiqueens.bsky.social · 15/12/2025

Are you working with exotic/non-model species? 🐸🐠🐓🦋🐝 Your annotation needs improvement to ensure RNA-seq or single-cell RNA-seq counts are correctly handled (for exemple the 3’UTRs)?

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GenomiqueENS @genomiqueens.bsky.social · 10/12/2025

This protocol, combining SMART-Seq® mRNA kit (Takara Bio Europe) and EXP-PCA001 and SQK-PCB114 kits (@nanoporetech.com) allows full-length transcripts to be obtained.

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GenomiqueENS @genomiqueens.bsky.social · 10/12/2025

🎉 We are thrilled to announce that our protocol “Library construction for ONT long read cDNA”, developed at our GenomiqueENS core facility, is available on protocol.io. dx.doi.org/10.17504/protocols.io.4r3l21oepg1y/v1

protocol.io

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GenomiqueENS @genomiqueens.bsky.social · 10/12/2025

🧬Searching for a Nanopore RNA-seq protocol that generates longer reads than the manufacturer’s protocol, and applicable for low-input material ? 🤔

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GenomiqueENS @genomiqueens.bsky.social · 01/12/2025

✨ Our core facility can produce scRNA-seq+ @nanoporetech.com data, don’t hesitate to contact us.✨ We thank his jury members for the fruitful scientific exchanges : Marie Sémon, Vincent Lacroix, Kevin Lebrigand, Reini Luco, Chunclong Chen.

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GenomiqueENS @genomiqueens.bsky.social · 01/12/2025

Interested to know more about @nanoporetech.com sequencing coupled with @10xgenomics.bsky.social? Check our benchmark on Bioarxiv www.biorxiv.org/content/10.1...

biorxiv.org

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GenomiqueENS @genomiqueens.bsky.social · 01/12/2025

🎉 We are very proud of Ali Hamraoui who defend his PhD thesis on bioinformatics approaches to study isoforms with single-cell long-read technologies.

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GenomiqueENS @genomiqueens.bsky.social · 30/07/2025

🤝 Why it matters Understanding isoform diversity at the single-cell level is crucial for uncovering novel regulatory mechanisms. Our benchmark serves as a reference point for researchers selecting appropriate tools and workflows.

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GenomiqueENS @genomiqueens.bsky.social · 30/07/2025

✨ Key findings Accurate isoform quantification remains challenging, with variability across protocols and methods. Some pipelines handle UMIs and barcodes more efficiently, improving isoform detection. We provide best practice recommendations and a fully reproducible framework for future studies.

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GenomiqueENS @genomiqueens.bsky.social · 30/07/2025

dedicated to resolving alternative splicing at single-cell resolution. The evaluation spans 10 state-of-the-art methods, tested across simulated and real @10xgenomics.bsky.social datasets sequenced on multiple #illumina and @nanoporetech.com platforms.

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GenomiqueENS @genomiqueens.bsky.social · 30/07/2025

🚀 Our new preprint is now live on bioRxiv! “A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data” 🔗 Read here: www.biorxiv.org/content/10.1... 🔬 About the study We present the first comprehensive benchmark of bioinformatics tools 👇

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GenomiqueENS @genomiqueens.bsky.social · 12/06/2025

🎉 Our core facility has just renewed its certifications ISO 9001 and NFX-50-900 ! These certifications are particularly important with regards to our users, but also as we are member of @fr-genomics.bsky.social.

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GenomiqueENS @genomiqueens.bsky.social · 19/03/2025

#AsaruSim is a flexible and efficient tool to simulate single-cell and spatial long-read RNA sequencing data. #AsaruSim is part of our upcoming efforts to benchmark state-of-the-art single-cell and spatial Nanopore long-read sequencing methods. Stay tuned for the results in the upcoming weeks…

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