Maïwen Caudron-Herger

Definitely a great meeting!
#RNAconfluence in Heidelberg

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 

We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/

Peer Bork on top of Zugspitze, ready to race down

Peer Bork, Jan Korbel, others at Sonnenkar ski lift at Zugspitze

Après-Ski scientific sessions from 16:00 till very late.

For many years, Peer Bork organised Bio-IT retreats to bring together the bioinformaticians across EMBL, in Garmisch-Partenkirchen and later Feldberg. Days out on the mountain followed by forward-looking and meta-science oriented sessions in the hut that fueled many projects and careers.

Franziska Faber and I are recruiting shared postdocs, PhD students to work on Fusobacterium & new BGCs. www.helmholtz-hiri.de/fileadmin/HI...

rbp2gov2.dkfz.de

The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts.

We have been mapping mRNA modifications for over a decade.

=> Characterizing their functions -- especially on translation -- is a research frontier.

When people celebrate the individual genius of folks in science, they should also
mourn the collective loss of genius of folks who were actively discouraged or disadvantaged from a career in science because of the same person(s)

Rethinking RNA-binding proteins: Riboregulation challenges prevailing views The advent of system-wide proteomic approaches has largely expanded the number of RNA-binding proteins (RBPs). This review discusses how recent discoveries are transforming our understanding of biolog...

Regulation by RNAs might be even more extensive than we thought. Many enzymes and other proteins not previously considered as RNA-binding proteins do seem to fall into this class & might have their activity regulated by RNA.
www.cell.com/cell/fulltex...

Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine ...

🎉 We’re excited to share our very first preprint!! 🎉
"Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells"
👉 doi.org/10.1101/2025...

#FirstPreprint #StemCells #Metabolism #Epigenetics #AcetylCoA #HBP #Pluripotency #NewScience

Mathematical modelling for biologists - Modelling concepts in biological research Mathematical modelling for biologists - Modelling concepts in biological research

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...

Including both molecular and epidemiological examples

My colleagues Baptise Rafanel et al. investigated how a newly invading transposon can be silenced. They found that not only antisense insertions in piRNA clusters such as flamenco, but also insertions in the 3‘UTR of genes can drive potent silencing.

Head of the Cell Biology and Biophysics Unit The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organisation, and one of the world’s leading research institutions. An intergovernmental organisation of 29 Member S...

EMBL Cell Biology and Biophysics department is searching for a new director. A major position to lead this field in Europe and beyond.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...

Contrasting photographs of the night-time skylines of Manhattan (left) and Nijmegen (right), with matching genome-wide association plots underneath each.

Not sure who came up with "Manhattan Plot", but in 2014 I coined the alternative term "Nijmegen Plot" (inspired by the Dutch town where I live) to describe underwhelming results from our earliest genome-wide association scans of language/reading traits.

How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions.
www.cell.com/molecular-ce...

Finally out!
I’m thrilled to share our new paper (Wolin et al., Cell 2025).

This paper describes SPIDR, a high-throughput method for mapping RBP binding sites.

By combining #SPIDR with #cryoEM, we identified the exact binding site of LARP1 within the #mRNA channel of the 40S ribosomal subunit.

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...

Opportunity alert!

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

tinyurl.com/ydn6e3ac

Structure of the microtubule anchoring factor NEDD1 bound to the γ-tubulin ring complex. new study from Hugo Muñoz-Hernández, Yixin Xu, Michal Wieczorek @mike-wieczorek.bsky.socia @ethz.ch and colleagues: rupress.org/jcb/article/...

#Cytoskeleton #StructuralBiology #CryoEM

Structure-informed design of an ultrabright RNA-activated fluorophore - Nature Chemistry Fluorogenic RNA aptamers such as Mango are powerful tools for RNA imaging. An ultrabright RNA-activated fluorophore with improved photophysical performance has now been developed using a structure-inf...

Out now in @natchem.nature.com! Lots to unpack here, but in short - we show that SMM enabled fragment based design is useful on RNAs to improve chemical properties like affinity and brightness of fluorophore ligands.

www.nature.com/articles/s41...

Have a look at this short Journal Club I had the great pleasure to write for @natrevmcb.nature.com
about a 2012 landmark study by Castello et al.

Read only link: rdcu.be/elEYW

Measurements of molecular size and shape on a chip Size and shape are critical discriminators between molecular species and states. We describe a microchip-based high-throughput imaging approach offering rapid and precise determination of molecular pr...

An amazing new enabling technology. Measurements of molecular size and shape on a chip. Couldn't be prouder of our friend Madhavi Krishnan of @ox.ac.uk this was and is one among the must fun collaborations I ever had. www.science.org/doi/10.1126/...

Barbara McClintock proposed – over 40 years ago – that transposable element activity could be a response to stress, and I think that we are still only beginning to understand how right she was.

#EMBOClimateResilience
“The way in which our universities have divided up the sciences does not reflect the ways in which nature has divided up its problems”
@embo.org
@monicabettencourt.bsky.social

We are organizing a conference for young researchers at the intersection between physics & biology: www.embl.org/about/info/c... @embl.org @events.embl.org @intcha.bsky.social
Please consider applying/registering -- the deadline is already in one week!

Today all 27 EU countries endorsed the Warsaw Declaration.

Thank you for your solid support in calling for the independence of the European Research Council to be preserved and for the role of the ERC to be expanded.
polish-presidency.consilium.europa.eu/media/r5fa13...
🇪🇺

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Our study on the #riboregulation of key mitotic factors is now published in Nature Communications
www.nature.com/articles/s41...

Additional findings include:
- RNA stimulates AURKA kinase activity
- RNA stabilises AURKA conformation

#RNA #RNAsky #mitosis #spindle

🧪 Open position: Scientific Grant Writer