Marcel Schilling

Legnini Group - Human Technopole Laboratory for Molecular and Systems Biology of RNA   The Legnini Group at Human Technopole combines molecular and systems biology approaches to study gene regulation. We use synthetic biology and opt...

1/6 We're hiring! Fully funded postdoc position in my group
humantechnopole.it/en/research-...

🧠 How do brain organoids help researchers study the earliest stages of Alzheimer’s disease?

#mdcBerlin's Agnieszka Rybak-Wolf explains what drives her and how advanced brain organoid models help her team explore how the disease may be initiated.

🔗 Full article: www.mdc-berlin.de/news/news/ag...

Looks like it's back for now.

Does anyone have any information what's up with @biorxivpreprint.bsky.social and when we can expect biorxiv.org to be back online? Is that another @cloudflare.social issue? I wonder if they cause more outages than they protect from at this point. 🤔

🔬 pertpy: a unified, scalable framework for single-cell perturbation analysis, now out in Nature Methods

Designed for modern perturbation data - CRISPR, drug screens, patient treatments - scaling to millions of cells and 1000s of conditions.
👉 www.nature.com/articles/s41...

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes Nature Ecology & Evolution - Analysis of the 3D chromatin architecture and cis-regulatory elements in a sea urchin and a sea star reveals mechanisms of 3D chromatin organization in echinoderms...

Our work on the evolution of the regulatory genome of echinoderms is now out in @natecoevo.nature.com. Led by my former PhD Marta Magri, Danila Voronov & Saoirse Foley. Great collaboration of Arnone, Hinman & Maeso labs, started long time ago with our missed José Luis Gomez-Skarmeta: rdcu.be/eXX8l

“Remote and partial clocks expand the circadian neuronal network, driving widespread molecular rhythmicity in Drosophila” Circadian clocks orchestrate daily physiology and behavioral rhythms, yet the extent to which cells lacking canonical clock components exhibit robust temporal regulation remains unclear. Here we addre...

Our new paper is out on bioRxiv and we’re really excited about it!
www.biorxiv.org/content/10.6...

We show that circadian clocks in the fly brain are far more distributed than the classic view. Huge kudos to the authors, especially @inespatop.bsky.social and Anne, and to our collaborators!!

Decoding cnidarian cell type gene regulation - Nature Ecology & Evolution This study reconstructs the gene regulatory networks that define cell types in the sea anemone Nematostella vectensis, providing a valuable resource for comparative regulatory genomics and the evoluti...

Lovely Xmas gift 🎄—our paper is out today in @natecoevo.nature.com www.nature.com/articles/s41...! Huge thanks to everyone who made it possible, especially @aelek.bsky.social and @arnausebe.bsky.social

Still a couple of weeks to apply for a fully funded PhD position in #AI and #RNA biology!!!

Bulk RNA-seq to the rescue of differential expression analysis i... Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data is…

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...

🔊 We are excited to announce a new Associate Professor (Prof.Agregada) at @geneticsub.bsky.social @biologiaub.bsky.social!
👏 Congrats to Dr. Cristina González on her new position!
🧬 Her group aims to understand the metabolic modulation of early regeneration events using planarians as a model system.

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

Interested in measuring RNAPII elongation rates? We developed DRB/TTchem-seq2 to directly measure rates across 3,000+ genes 🧬
genome.cshlp.org/content/earl...
This fantastic work led by Haiyue Liu reveals gene and intra-genic variation, links to histone marks & elongation factors
Details below! 👇

You misspelled Fellowship Committee.😉

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...

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...

🚨We are looking for post-doctoral candidates to apply for a MSCA fellowship.

Projects on gene regulation in neural development or neurdegenerative diseases using single-cell omics.

Computational & wet-lab candidates are welcomed! #postdoc #MSCA #Barcelona #singlecell.

LSI PhD programme | Living Systems Institute | University of Exeter

🚨 We’re recruiting PhD students! 🚨

Join the Stem Cell Biology and Evolution lab at @lsiexeter.bsky.social to study planarians, stem cells & evolution.

2 projects available - 1 week left to apply!
Interested and no PhD yet? Apply now. Or help us spread the word! 🙌

www.exeter.ac.uk/research/ins...

Franz Arnold Ake from @idibell.bsky.social presented SCALPEL, a Nextflow-based pipeline to quantify and characterize isoforms at single-cell resolution. Fascinating work that will be applied to study alternative polyadenylation during neural differentiation and neurodegenerative diseases.🧠

Thank you for the interesting evening with beers, science, and nice company (and in my case: a free (scientific) Spanish practice session).

Thx @dhdegroot.bsky.social for troubleshooting my submission. ❤️

@shaunmahony.bsky.social & @erikvannimwegen.bsky.social: I submitted a sample from doi.org/10.15252/msb... to Bonsai and this is what I got.
You can explore the dataset here: bonsai.unibas.ch/bonsai-scout....
My code and comments can be found at codeberg.org/mschilli/bon....

A web search for 'bonsai nimwegen' returning pictures of bonsai trees and a link to a bonsai and landscaping business in the Dutch city Nijmegen.

PS: I also like the name but it's clearly not the best in terms of SEO. 😉

Doesn’t change the fact that I like the idea of Bonsai. In the case of cell cycle I might be more cautious then when analyzing a differentiation dataset, but if IIRC, Schwabe et al. found that UMAP doesn’t find the circle either.

We might not *know*, but we do have some good arguments that they actually might: doi.org/10.15252/msb...

Wow! One day, two celebrations. I hope you had an opportunity to celebrate. 🍻

SCALPEL, a Nextflow based pipeline for quantification of isoform at single-cell resolution | Franz Arnold Ake | Nextflow Summit 2025 Join us at the Nextflow Summit 2025 for the latest developments and innovations from the Nextflow world.

Enjoy the #NextflowSummit, @franzake.bsky.social!

Excited to see you are spreading the word!

summit.nextflow.io/2025/boston/...

…using Python 😉

Python? 😉😅

It’s so nice to see this work finally out! It developed so much since its early days. The idea of long lived RNA as experience decoys is huge. Still a lot of work to be done but this is a great first step forward. Happy to have been part of it!

Huge effort from @anaconesa.bsky.social at @scb.iec.cat comparing long-read RNA technologies @pacbio.bsky.social @nanoporetech.com and softwares #sqanti3, #bambu, #talon, #isoquant, for isoform discovery, still challenging to disentangle real biology from artefacts