Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026Improved 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) 000
Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026No 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) 100
Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026Four-base DMS analysis. The new rf-count and rf-norm now support four-base DMS experiments (developed by the Mustoe lab). (5/n) 100
Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026Consensus 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) 100
Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026Structure-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) 110
Danny IncaRNAto @incarnatolab.bsky.social · 09/10/2026Speed. Significant gains in runtimes across the board, between 3-25X, depending on the module. (2/n) 100
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.comRNAFramework/CHANGELOG.md at master · dincarnato/RNAFrameworkRNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework 143
Danny IncaRNAto @incarnatolab.bsky.social · 04/09/2026RFview 1.1.7 for #RNA secondary structure visualization is out! Check it out: github.com/dincarnato/R...github.comRelease RFview v1.1.7 · dincarnato/RFviewJSRFview v1.1.7 000
Danny IncaRNAto @incarnatolab.bsky.social · 04/08/2026Thanks Leo! Will I see you in Munich in September or in Heidelberg in October?? 111
Reposted by Danny IncaRNAtoTony Mustoe @amustoe.bsky.social · 04/08/2026It 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! 071
Danny IncaRNAto @incarnatolab.bsky.social · 03/08/2026Thrilled 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... 0187
Reposted by Danny IncaRNAtoElena Rivas @rivaselenarivas.bsky.social · 05/07/2026New! 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. 02814
Reposted by Danny IncaRNAtoZeshi Li (Jack) @lizeshi.bsky.social · 17/06/2026Excited 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.orgSOLiD-MaP: A Photoproximity Labeling Platform for Small Molecule Binding Site Mapping on RNARNA-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... 1104
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026And 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) 010
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026A 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) 110
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026Stockholm alignment visualization with covariation annotations; Direct alignment fetching from #Rfam; SVG export; Web, GUI and CLI interfaces (9/n) 120
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026Key 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) 110
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026An 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) 100
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026Next 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.comGitHub - dincarnato/RFviewJS: A Javascript library and stand-alone Electron app for RNA secondary structure interactive plottingA Javascript library and stand-alone Electron app for RNA secondary structure interactive plotting - dincarnato/RFviewJS 120
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) 110
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) 110
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) 110
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026If 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) 110
Danny IncaRNAto @incarnatolab.bsky.social · 13/06/2026Today 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) 1608
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.comGitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysisRNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework 053
Danny IncaRNAto @incarnatolab.bsky.social · 11/02/2026To 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! 010
Danny IncaRNAto @incarnatolab.bsky.social · 09/02/2026Beyond 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. 010
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! 140
Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025Second: 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/gBhpnisGshorturl.atdraco - DRACO 021
Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025The biggest improvement is the introduction of paired-end support in rf-count (for more information, check the documentation: shorturl.at/LZcou). (2/n) 110
Danny IncaRNAto @incarnatolab.bsky.social · 12/12/2025As 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) 121
Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025Until 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) 000
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) 100
Danny IncaRNAto @incarnatolab.bsky.social · 13/10/2025Highlights: 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) 100
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.comGitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysisRNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework 1101
Reposted by Danny IncaRNAtoMarcin Magnus @mmagnus42.bsky.social · 10/10/2025Please 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 072
Danny IncaRNAto @incarnatolab.bsky.social · 11/10/2025So 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.comNucleotide dependency analysis of genomic language models detects functional elements - Nature GeneticsMapping pairwise nucleotide dependencies by leveraging genomic language models highlights functional genomic elements and predicts deleterious genetic variants more effectively than alignment-based conservation metrics. 0256
Reposted by Danny IncaRNAtoJörg Vogel @jorg-vogel-lab.bsky.social · 08/10/2025Two 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. 16879
Danny IncaRNAto @incarnatolab.bsky.social · 06/10/2025Check out this new fantastic method from @rivaselenarivas.bsky.social to predict #RNA structure + 3D motifs and pseudoknots guided by covariation 020
Danny IncaRNAto @incarnatolab.bsky.social · 01/08/2025Happy #RNA day to all my fellow RNA lovers! 040
Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025And a huge thanks to @erc.europa.eu for funding that made all of this possible! (11/n) 030
Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025Shoutout to rockstar Ivana Borovská, who led this incredible work, and to our collaborators, particularly @mtwolfinger.bsky.social and Wim Velema! (10/n) 141
Danny IncaRNAto @incarnatolab.bsky.social · 27/07/2025While 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) 161