Lightnews — Scholar-powered news

Reposted by Mireya Plass

Mireya Plass @mireyaplass.bsky.social · 6d

🚨New preprint from the lab! This work led by @akshayjg.bsky.social & @smfernandezmoya.bsky.social shows how the RNA binding protein STAU2 regulates the timing of neurogenesis in iPSC-derived human cells
www.biorxiv.org/content/10.1...

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro

RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly u...

www.biorxiv.org

1 10 15

Mireya Plass @mireyaplass.bsky.social · 5d

This project would have been impossible without the work of our collaborators Agnieskza Rybak-Wolf, @monikapiwecka.bsky.social & Alessandra Gioregtti.

Mireya Plass @mireyaplass.bsky.social · 6d

🚨New preprint from the lab! This work led by @akshayjg.bsky.social & @smfernandezmoya.bsky.social shows how the RNA binding protein STAU2 regulates the timing of neurogenesis in iPSC-derived human cells
www.biorxiv.org/content/10.1...

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro

RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly u...

www.biorxiv.org

2

Mireya Plass @mireyaplass.bsky.social · 6d

If you wanna know all the details about the role of this interesting protein, please read the full pre-print on bioRxiv!
#RBP #neurogenesis #iPSCs #scRNA-seq #STAU2

1

Mireya Plass @mireyaplass.bsky.social · 6d

Which leads to an accelerated differentiation and depletion of the neural progenitor pool in both 2D cultures and organoids

1 1

Mireya Plass @mireyaplass.bsky.social · 6d

In neuroepithelial cells, STAU2 controls the activity of Gene regulatory networks important for the maintenance of Stem Cell Profile

1 1

Mireya Plass @mireyaplass.bsky.social · 6d

Using single-cell transcriptomics, we have found that STAU2 alters mainly the transcriptomic profile of neuroepithelial cells

1 1

Mireya Plass @mireyaplass.bsky.social · 6d

Upon deletion of STAU2, we observe metabolic changes and accelerated differentiation of iPSCs

1 1 2

Mireya Plass @mireyaplass.bsky.social · 6d

🚨New preprint from the lab! This work led by @akshayjg.bsky.social & @smfernandezmoya.bsky.social shows how the RNA binding protein STAU2 regulates the timing of neurogenesis in iPSC-derived human cells
www.biorxiv.org/content/10.1...

Staufen2 modulates the temporal dynamics of human neurogenesis in vitro

RNA-binding proteins (RBPs) play a central role in post-transcriptional regulation during brain development, yet their specific functions in coordinating human neural lineage decisions remain poorly u...

www.biorxiv.org

1 10 15

Mireya Plass @mireyaplass.bsky.social · Sep 3

#SENC2025 has just started. Looking forward to these 3 days showing the best neuroscience research in Spain.

2

Mireya Plass @mireyaplass.bsky.social · Aug 29

Nice! Congratulations to all the team!

1

Reposted by Mireya Plass

Manuel Irimia @mirimiam.bsky.social · Aug 7

Very happy to share the peer-reviewed version of our work on the cis-regulatory determinants of #microexon #splicing regulation by SRRM3/4, published in @natsmb.nature.com!

rdcu.be/ezGqT

Work led by @sobonnal.bsky.social, with Simon Bajew & @rmartinezcorral.bsky.social. @crg.eu @upf.edu

Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4

Nature Structural & Molecular Biology - Using massively parallel splicing assays and mathematical modeling, Bonnal et al. uncover that conserved splice site strength and exon length encode...

rdcu.be

1 11 30

Reposted by Mireya Plass

Manuel Irimia @mirimiam.bsky.social · Aug 6

🧬🧬🧬 New review from the lab:

Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks

authors.elsevier.com/sd/article/S...

By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.

Three major trends in comparative transcriptomics

1 14 37

Reposted by Mireya Plass

Human Technopole @humantechnopole.bsky.social · Jul 29

🎓 Just graduated and passionate about Computational #Biology, Structural Biology, #Genomics or #Neurogenomics? Apply by 8 Sept for 1 of 9 fully funded PhD scholarships via the SEMM Program at HT in Milan!

👉 humantechnopole.it/en/news/call... #PhDlife

Call for Applications: Fully Funded PhD Scholarships in Systems Medicine - Human Technopole

Are you passionate about science and ready to take the next step in your research journey? Human Technopole is offering up to 9 fully funded PhD scholarships through the highly regarded SEMM PhD Progr...

humantechnopole.it

2 2

Mireya Plass @mireyaplass.bsky.social · Jul 28

If you like our recent work and are interested in developing a postdoc project related to isoform diversity in individual cell types and their regulation, get in contact!
We are looking for applicants for Marie Curie and EMBO postdoctoral fellowships #postdocposition #singlecell #RNA_processing

Mireya Plass @mireyaplass.bsky.social · Jul 14

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

www.nature.com

3 5

Reposted by Mireya Plass

Manuel Irimia @mirimiam.bsky.social · Jul 23

🚨🚨🚨

Please RT!

We're looking for a postdoc to join an exciting joint project between our lab @upf.edu & @crg.eu (Barcelona) and the Sander lab @mdc-berlin.bsky.social (Berlin) investigating how alternative splicing and microexons influences the maturation of pancreatic islets.

Deadline: 30/09/25👇

www.upf.edu

1 65 48

Reposted by Mireya Plass

Eduardo Eyras @edueyras.bsky.social · Jul 18

Quantification of transcript isoforms at the single-cell level using SCALPEL nature.com/articles/s41... by @miriplass.bsky.social and her team

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

nature.com

2 4

Reposted by Mireya Plass

Dominic Grün @dominicgrun.bsky.social · Jul 21

Join our "Advances in Single-Cell Technologies" meeting in December in Freiburg, co-organised with Marco Prinz and @katrinkierdorf.bsky.social. Excellent line-up of speakers covering spatial technologies, lineage tracing, computational methods, and more.
www.uniklinik-freiburg.de/single-cell-...

13 17

Reposted by Mireya Plass

Facultat de Medicina i Ciències de la Salut @medicinacs-ub.bsky.social · Jul 18

L’estudi de #recercaUB sobre l'eina #SCALPEL que ha liderat @mireyaplass.bsky.social s’ha publicat el juliol en #openaccess a la revista @natcomms.nature.com.

Universitat de Barcelona @ub.edu · Jul 17

#RecercaUB | 🔬 Un equip liderat de la #UniBarcelona i @idibell.bsky.social desenvolupa una eina per quantificar i caracteritzar l’ARNm amb una sensibilitat i especificitat molt superiors als mètodes actuals.

🎓 Lidera l’estudi Mireya Plass, de @medicinacs-ub.bsky.social.

SCALPEL: analitzar l’expressió gènica en alta resolució

web.ub.edu

2 3

Reposted by Mireya Plass

Nextflow @nextflow.io · Jul 17

🚨The #NextflowSummit Call for Speakers and Posters is Now Open! 🚨

🎤 Present your talk or poster at the Virtual #NextflowSummit by @seqera.io (Oct 23–24).
📍Or showcase your poster in-person in Barcelona at the Nextflow Training and @nf-co.re Hackathon (Oct 28–29)

hubs.la/Q03xGPp_0

5 5

Reposted by Mireya Plass

Alfonso Martinez Arias @amartinezarias.bsky.social · Jul 15

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...

1 16 43

Reposted by Mireya Plass

Qian Cheng @qchengx1e3.bsky.social · Jul 13

A computational tool #SCALPEL for #isoform quantification at the single-cell level using 3’ scRNA-seq data @franzake.bsky.social @mireyaplass.bsky.social #BiotechNatureComms

doi.org/10.1038/s414...

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

doi.org

1 2

Reposted by Mireya Plass

Mireya Plass @mireyaplass.bsky.social · Jul 14

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications

Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

www.nature.com

1 16 34

Mireya Plass @mireyaplass.bsky.social · Jul 14

#SCALPEL is the result of the work of @franzake.bsky.social with the support of @mschilli.com, Sandra M. Fernández-Moya, @akshayjg.bsky.social, Ana Gutiérrez-Franco & Lei Li.
You can find #SCALPEL on Github here 👉 github.com/plasslab/SCA...

GitHub - plasslab/SCALPEL: Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.

Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline. - plasslab/SCALPEL

github.com

3

Mireya Plass @mireyaplass.bsky.social · Jul 14

Additionally, #SCALPEL can be used in combination with long-read single-cell sequencing to provide accurate isoform quantification and identify additional 3'end isoforms

1 3

Mireya Plass @mireyaplass.bsky.social · Jul 14

And can be experimentally validated!

1 2