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Danny IncaRNAto

@incarnatolab.bsky.social
994 followers 656 following 77 posts

Associate Professor in Molecular Genetics | University of Groningen | Chief R&D Officer @ Serna Bio | #RNA structural ensembles & dynamics | www.incaRNAtolab.com | Views are my own

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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
Improved motif discovery. The rf-motifdiscovery module has been rewritten to mimic the DREME algorithm, further implementing the generation of motif logos without relying on WebLogo3. And much more! (7/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
No more external dependency for structure plots. rf-fold now draws secondary structure plots natively, including an option to color bases on a continuous reactivity gradient. ViennaRNA RNAplot is no longer required. (6/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
Four-base DMS analysis. The new rf-count and rf-norm now support four-base DMS experiments (developed by the Mustoe lab). (5/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
Consensus folding across replicates. rf-fold now incorporates RNAalifold, restrained with the reactivity profiles of all replicates at once, yielding a single consensus structure rather than per-replicate models aggregated afterwards. (4/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
Structure-informed alignment building and covariation analysis. A new module, rf-covalign, builds and refines structure-informed alignments of homologous sequences, and performs covariation analysis, wrapping Infernal and R-scape. (3/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
Speed. Significant gains in runtimes across the board, between 3-25X, depending on the module. (2/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026
#RNA Framework 2.9.8 is out! Check the full CHANGELOG: github.com/dincarnato/R.... Get the latest version at: github.com/dincarnato/R... This release features a major renovation of the engine. A few highlights in a short thread (1/n).
github.com
RNAFramework/CHANGELOG.md at master · dincarnato/RNAFramework
RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework
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Danny IncaRNAto @incarnatolab.bsky.social · 04/09/2026
RFview 1.1.7 for #RNA secondary structure visualization is out! Check it out: github.com/dincarnato/R...
github.com
Release RFview v1.1.7 · dincarnato/RFviewJS
RFview v1.1.7
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Danny IncaRNAto @incarnatolab.bsky.social · 04/08/2026
Thanks Leo! Will I see you in Munich in September or in Heidelberg in October??
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Tony Mustoe @amustoe.bsky.social · 04/08/2026
It was such a pleasure writing this with @incarnatolab.bsky.social! There has been so much exciting progress in probing the complexity of RNA folding in cells. Although we couldn't cover it all, we did our best to highlight several major emerging areas. I’m excited to see where the field goes next!
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Danny IncaRNAto @incarnatolab.bsky.social · 03/08/2026
Thrilled to share the latest review I had the incredible pleasure to write together with @amustoe.bsky.social, out today in #COSB, about probing #RNA structural ensembles, non-equilibrium intermediates and isoforms. Check it out: www.sciencedirect.com/science/arti...
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Elena Rivas @rivaselenarivas.bsky.social · 05/07/2026
New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.
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Zeshi Li (Jack) @lizeshi.bsky.social · 17/06/2026
Excited to share the very first #preprint since I started my lab at @utrechtuniversity.bsky.social We explored the area of small molecule- #RNA interaction, and present SOLiD-MaP: a #photoproximity labeling platform for mapping small molecule binding site on RNA. www.biorxiv.org/content/10.6...
biorxiv.org
SOLiD-MaP: A Photoproximity Labeling Platform for Small Molecule Binding Site Mapping on RNA
RNA-targeting small molecules are emerging as promising therapeutic modalities, but their development requires methods that define binding sites and evaluate RNA target selectivity. Existing approache...
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
And of course, (3) #ClaudeAI was of great help in implementing the standalone #Electron app and in debugging. Please let me know your thoughts! Happy to implement new features upon request! (11/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
A couple of honorable mentions: (1) The Radiate algorithm was ported from the original #VARNA implementation by Yann Ponty; (2) The NAView algorithm was ported from Ivo Hofacker's adaptation of Bruccoleri & Heinrich algorithm, and adapted to enable helix rotation in a Radiate-like fashion (10/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
Stockholm alignment visualization with covariation annotations; Direct alignment fetching from #Rfam; SVG export; Web, GUI and CLI interfaces (9/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
Key features: Single JS file, no build step, no dependencies; NAView and Radiate layout algorithms, automatic layout choice, with interactive helix rotation; Reactivity coloring (using RNA Framework's XML reactivity files) with customizable color maps (8/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
An interactive web version is available at: rfview.incarnatolab.com Additionally, you can see a few examples of #RFviewJS in action: Secondary structure + reactivity (rfview.incarnatolab.com/examples/dem...) & Stockholm alignment + covariation (rfview.incarnatolab.com/examples/dem...). (7/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
Next to it, #RFview is the standalone desktop app built on the same engine via #Electron, and it runs an all operating systems. #RFviewJS is available from #GItHub (github.com/dincarnato/R...), and the complete API documentation is available from #ReadtheDocs (rfviewjs-docs.readthedocs.io). (6/n)
github.com
GitHub - dincarnato/RFviewJS: A Javascript library and stand-alone Electron app for RNA secondary structure interactive plotting
A Javascript library and stand-alone Electron app for RNA secondary structure interactive plotting - dincarnato/RFviewJS
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
#RFviewJS fills this gap. It's a zero-dependency JavaScript library that can be dropped into any webpage to get interactive, editable RNA structure visualization out of the box, with support for reactivity data, covariation annotations, Stockholm alignment visualization. (5/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
#Forna (rna.tbi.univie.ac.at/forna/) brought RNA secondary structure visualization to the browser, but with limited control. (4/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
#R2R (sourceforge.net/projects/wei...) produces beautiful publication-quality figures of Stockholm alignments, but once the plot is generated, adjusting it means editing config files and re-running (or some manual editing in Illustrator). (3/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
If you work with #RNA secondary structures, you know the pain. #VARNA (varna.lisn.upsaclay.fr), arguably the best tool for structure visualization, is a Java desktop application, therefore it can't be embedded in web pages. (2/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026
Today I am so incredibly excited to share with you a new tool from the lab, #RFviewJS (and its stand-alone version #RFview). Two tools I built to fill a gap that has frustrated me for years. #RNA secondary structure visualization (1/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 04/06/2026
#RNA Framework 2.9.7 is out! Several additions, important fixes and improvements. Please update! Check it out: github.com/dincarnato/R... & see the CHANGELOG (buff.ly/4gtJ67u) for the details!
github.com
GitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework
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Danny IncaRNAto @incarnatolab.bsky.social · 11/02/2026
To all the #RNAFramework users who updated to v2.9.6: please issue a "git pull" to ensure the latest Core::Utils module gets updated as this escaped the last commit. Apologies for the inconvenience!
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Danny IncaRNAto @incarnatolab.bsky.social · 09/02/2026
Beyond significant speed-ups, this version features a complete rewrite of the rf-correlate module for calculating pairwise correlations between samples. The new version has no sample number limit, and it generates clustered correlation heatmaps.
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Danny IncaRNAto @incarnatolab.bsky.social · 09/02/2026
#RNA Framework 2.9.6 is out! Several additions, important fixes and improvements. Please update! Check it out: buff.ly/4guLWsP & see the CHANGELOG (buff.ly/4gtJ67u) for the details!
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Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025
Second: DRACO v1.3 is out! Greatly improved algorithm for increased sensitivity and accuracy in the reconstruction of #RNA conformation reactivity profiles. The biggest improvement: replicate support (for more information, check the documentation: shorturl.at/zY3nu). Check it out: lnkd.in/gBhpnisG
shorturl.at
draco - DRACO
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Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025
The biggest improvement is the introduction of paired-end support in rf-count (for more information, check the documentation: shorturl.at/LZcou). (2/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025
As it's almost Christmas, here're 2 presents from the lab! 🎄 First: #RNA Framework 2.9.5 is out! Several additions, fixes and improvements. Check it out: lnkd.in/gi3QDNeq & see the CHANGELOG (shorturl.at/Lcobs) for the details! (1/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025
Until a fix will be released, we advice users to install ViennaRNA v2.7.0 in a separate folder and to provide the path to RNAplot v2.7.0 via the -vrp parameter of rf-fold. (4/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025
!!! Important note: A bug was introduced in ViennaRNA v2.7.0, which breaks the pseudoknot detection functionality of rf-fold. However, RNAplot v2.7.0 is required to take advantage of the new secondary structure plotting functionality. (3/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025
Highlights: new normalization method in rf-norm (Mitchell method, pubmed.ncbi.nlm.nih.gov/37334863/), statistics plots in rf-count & rf-count-genome, and secondary structure plots in rf-fold (powered by ViennaRNA v2.7.0) (2/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025
#RNA Framework 2.9.4 is out! Several additions, fixes, improvements. Check it out: github.com/dincarnato/R... & see the CHANGELOG (buff.ly/4gtJ67u) for the details! (1/n)
github.com
GitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework
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Reposted by Danny IncaRNAto
Marcin Magnus @mmagnus42.bsky.social · 10/10/2025
Please join us for our next seminar, featuring Danny IncaRNAto, PhD: “Discovery of RNA regulatory structural switches via ensemble mapping” @incarnatolab.bsky.social #rna #casprnasig #rnastructure
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Danny IncaRNAto @incarnatolab.bsky.social · 11/10/2025
So excited to see this out in @natgenet.nature.com! An amazing collaboration with @gagneurlab.bsky.social, I am happy I was (a small) part of. Nucleotide dependencies can capture regulatory elements, including #RNA structures! Congrats to the whole team! Check it out: www.nature.com/articles/s41...
nature.com
Nucleotide dependency analysis of genomic language models detects functional elements - Nature Genetics
Mapping pairwise nucleotide dependencies by leveraging genomic language models highlights functional genomic elements and predicts deleterious genetic variants more effectively than alignment-based conservation metrics.
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Danny IncaRNAto @incarnatolab.bsky.social · 10/10/2025
Looking forward!
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Reposted by Danny IncaRNAto
Jörg Vogel @jorg-vogel-lab.bsky.social · 08/10/2025
Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.
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Danny IncaRNAto @incarnatolab.bsky.social · 06/10/2025
Check out this new fantastic method from @rivaselenarivas.bsky.social to predict #RNA structure + 3D motifs and pseudoknots guided by covariation
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Danny IncaRNAto @incarnatolab.bsky.social · 01/08/2025
Happy #RNA day to all my fellow RNA lovers!
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Danny IncaRNAto @incarnatolab.bsky.social · 30/07/2025
Thanks Lars! It definitely was :-)
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Danny IncaRNAto @incarnatolab.bsky.social · 29/07/2025
Thanks Dirk-Jan!
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Danny IncaRNAto @incarnatolab.bsky.social · 29/07/2025
Thanks Rita!
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Danny IncaRNAto @incarnatolab.bsky.social · 28/07/2025
Thanks Fede!
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Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025
Thanks Sebastian!
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Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025
Thanks Ivano!
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Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025
And a huge thanks to @erc.europa.eu for funding that made all of this possible! (11/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025
Shoutout to rockstar Ivana Borovská, who led this incredible work, and to our collaborators, particularly @mtwolfinger.bsky.social and Wim Velema! (10/n)
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Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025
While our study still presents many limitations, we sincerely hope this will represent a stepping stone in better understanding and characterizing the structural dynamics of cellular RNAs, and their roles in regulating gene expression. (9/n)
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