Fede Fuchs W

Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction Length matters—secondary structures of long, diverse RNAs in RNAndria and deep learning model eFold improve prediction accuracy.

Exciting new work from the Rouskin Lab out at @science.org
If you are interested in RNA structure and machine learning, you should probably read it..

Nuevo paper del Rouskin lab!
Si te interesa la estructura de ARN y machine learning, no te lo pierdas..

www.science.org/doi/10.1126/...

Interesante

Investigadores del Laboratorio de Anatomía Comparada y Evolución de los Vertebrados del Conicet (Lacev-Conicet) descubrieron un huevo de dinosaurio carnívoro en perfecto estado de conservación y lo anunciaron en un nuevo streaming de paleontología www.lanacion.com.ar/sociedad/inv...

A must read from Luisa, Emi, and team.

PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility - Nature Communications Gene regulation in oocytes relies heavily on poly(A) tail-length changes. Here, the authors develop PAL-AI, a neural network model that predicts tail-length changes, identifies regulatory motifs, and ...

Check out the latest study from our lab, led by Coffee Xiang (@coffeebond007.bsky.social) www.nature.com/articles/s41... (1/2)

This work is the result of a collaboration between many wonderful people: @grantyang.bsky.social, Yve, Casper, Matty, Scott, myself, and Silvi from @harvardmed.bsky.social; Dan H from @stanfordpress.bsky.social; and, for the first time as a PI, the great Lauren Hagler from @tamu.bsky.social !!

4/4

Aside from the app itself, we found that DMS-MaPseq + SEISMICgraph can be used to in vitro validate multiple riboswitches at once using a library, and that many of those riboswitches stop functioning if pseudoU is used instead of regular U (an important finding for those working in RNA tx).

3/4

The platform offers a plethora of graphs (see pic), and supports data coming from ShapeMapper, RNA framework, and SEISMIC; it should make the life of anybody analyzing DMS/SHAPE-MaP a lot easier :)

2/4

SEISMICgraph: a web-based tool for RNA structure data visualization Abstract. In recent years, RNA has been increasingly recognized for its essential roles in biology, functioning not only as a carrier of genetic informatio

Our latest publication (doi.org/10.1093/nar/...) from the Rouskin (www.rouskinlab.com) & Hagler Labs (www.haglerlab.org) is out on @narjournal.bsky.social ! We developed a web interface for easy visualization of RNA structure chemical probing data (from DMS/SHAPE-MaP).

1/4

Lance 22.1 Mar Del Plata Canyon | SOI Divestream 817 YouTube video by Schmidt Ocean

A wonderful collab between CONICET (Argentina) and the Schmidt Ocean Institute led to the exploration of the Submarine Canyon in Argentina’s deep shores. It is hypnotic to see:

www.youtube.com/live/xg9NLXK...

A cool one

Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503 Precise control of microRNA (miRNA) expression is critical during development. An important mechanism of miRNA regulation is target-directed microRNA degradation (TDMD), a pathway in which the binding...

I am pleased to present our latest pre-print describing our identification of the long-sought triggers for target-directed microRNA degradation (TDMD) of miR-322 and miR-503, work led by Collette LaVigne and Jaeil Han. For more info, read on! 👇
www.biorxiv.org/content/10.1...

This stunning post-apocalyptic drama is the one you should be watching There are hundreds of TV apocalypses to choose from, but The Eternaut, a fresh and compelling adaptation of a classic Argentinian comic book series, is the one to pick, says Bethan Ackerley

There are hundreds of TV apocalypses to choose from, but The Eternaut, a fresh and compelling adaptation of a classic Argentinian comic book series, is the one to pick, says Bethan Ackerley

Super super cool!

That looks cool, how did you do it ?!?!

U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation Kim et al. uncover a role for U1 snRNP in regulating internal promoter activity. Beyond its canonical role in splicing, U1 snRNP suppresses premature polyadenylation, enabling upstream transcription t...

Very excited to share our new paper out now in
@MolecularCell. We show how U1 snRNP -a well-known splicing factor- regulates the activity of alternative promoters in human cells www.cell.com/molecular-ce...

And on other news. My first contribution to science as a postdoc with @stirlingchurchman.bsky.social is out! We discuss the knowns and unknowns of post-transcriptional splicing. It was really fun to write with the great @karinechoquet

Everybody should

Tomorrow at the Systems Virology Journal Club, #AyanoKohlgruber will present her work with #SteveElledge on high-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits. pubmed.ncbi.nlm.nih.gov/38956325/

In vivo folding of nascent RNA! Awesome work from Leo (‪@leoschaerfen.bsky.social‬) and team, check it out:

Functional microRNA targeting without seed pairing MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to serve as guides, directing binding to partially complementary sites in mRNAs, ultimately causing post-transcriptional repression. Compleme...

Pleased to share my recent work from the Bartel Lab! Some miRNAs recognize novel target sites called 3'-only sites, which pair to the miRNA 3' region but not to the seed. These sites direct mRNA repression in cells and are engaged by different mechanisms to seed sites
www.biorxiv.org/content/10.1...

I would have to say circRNAs, never ending possibilities (since they have no ends)

MicroRNAs are just so much fun

RNA xkcd.com/3056

RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry Mammalian cells present RNA-binding proteins on the cell surface that form clustered domains containing glycoRNAs.

Excited to share the work of Jonathan Perr where he uncovered a surprisingly common feature of cell surfaces - the presentation and clustering of RNA binding proteins with #glycoRNA.

Critically support by #NIH @cp-cell.bsky.social www.cell.com/cell/abstrac...

Our very own Scott Grote got into Harvard’s PHD program in Virology! #ProudLab #RouskinLab

gROUNDbreaking approaches for advancing circRNA research: detection, function, therapeutics Circular RNAs (CircRNAs) are a rediscovered class of RNA species that originate from back-splicing events, which have been reported across all domains of life. Many circRNAs are stable, abundant and …

EMBO practical workshop dedicated to circular RNAs to be held from May 31 to June 6, 2025 at the University of Trento, Italy.

INFO & REGISTRATION: meetings.embo.org/event/25-cir...
DEADLINE: February 1, 2025

Has Bluesky replaced X for scientists? Take Nature’s poll The research community has flocked to the social-media platform Bluesky. Tell us about your experience.

We have a feeling you'll be interested in this one.

Nature is keen to find out how scientists are using Bluesky and whether it has become their go-to social-media platform. Take the survey! 🧪

The structural basis for RNA slicing by human Argonaute2 Mohamed et al. report the cryoelectron microscopy structure of human AGO2 with fully paired guide RNA. Their analysis reveals the structural basis for the slicing activity that drives RNAi, showing that the slicing-competent conformation is achieved by domain movements and RNA-protein contacts distinct from those of conformational intermediates and prokaryotic homologs.

Our collaborative AGO2 work with @bartellab.bsky.social is published! Abdallah and Peter used cryo-EM and biochemistry to determine the structure of AGO2 in a slicing competent conformation with a fully paired RNA. Read more about it here: tinyurl.com/AGO2-slicing

Felicitaciones Rodri y equipo!