ViennaRNA Package v2.7.1 is out! 🧬🎉 Solid update: smoother probing-informed folding (SHAPE/DMS), improved constraints handling, and nicer Python multistrand base-pair probs.
Get: tbi.univie.ac.at/RNA/
Source: github.com/ViennaRNA/Vi...
#ViennaRNA #RNA #ComputationalBiology #SHAPE #DMS #OpenSource
Calling #RNA & #Virology researchers! 🧬🦠
Submissions are open for the open-access Special Issue '𝗙𝘂𝗻𝗰𝘁𝗶𝗼𝗻𝗮𝗹 𝗥𝗡𝗔𝘀 𝗶𝗻 𝗩𝗶𝗿𝗼𝗹𝗼𝗴𝘆' in MDPI Viruses, which I'm guest editing.
📝 Original research & reviews welcome!
🗓️ Deadline: Feb 28, 2026
michaelwolfinger.com/blog/2025/bl...
#FunctionalRNA #RNAstructure
Calling all #RNA & #AI researchers! 🧬🤖 Submissions are open for the new open‑access collection “Exploring RNA Biology with Deep Learning Algorithms” in RNA Biology that I am guest editing with @yiliangding.bsky.social & Cliff Zhang. michaelwolfinger.com/blog/2025/bl... #DeepLearning #bioinformatics
Exploring RNA biology with Deep Learning Algorithms 🚀
Thrilled to guest-edit this OA collection in RNA Biology! 🧬🤖 Seeking cutting-edge work on:
• AI-powered transcriptomics
• RNA structure prediction
• RNA–protein interaction models
Submit by Nov 30 2025👇
think.taylorandfrancis.com/article_coll...
Some exciting news! 🥳👍 finally dropped our open-source AI model to predict translation rates from mRNA sequences online for free academic use! Hope it's widely used among RNA scientists! Code:
github.com/Sanofi-Publi...; Model: zenodo.org/records/1537...; Preprint: www.biorxiv.org/content/10.1...
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Fellow #RNA lovers, please repost 🙏: 2 ERC-funded Post-doc positions are available in our lab to investigate #RNA structural ensemble and their dynamics in living cells. Application link: t.co/pYJ3H3j705
Got interested? Read the full story here: academic.oup.com/bioinformati...
#RNA #Biotechnology #ViennaRNA #ComputationalBiology
8/n
Incorporating modified bases into #RNA structure predictions can reveal striking changes in RNA functionality.
For instance, using more than 600 #tRNA sequences from tRNAdb, we've shown how modified bases significantly impact predicted structures.
#Bioinformatics #SyntheticBiology
7/n
If a loop lacks specific parameters, we substitute the unmodified counterpart as a fallback—making predictions more flexible and accurate. 🖥️
#NucleotideModifications #RNAComputing
6/n
What makes the #ViennaRNA Package unique? 🤔
We don't rely on a pre-compiled, complete set of energy parameters for modified bases. Instead, we use a mix of hard- and soft-constraints to adjust predictions where we have parameters.
#RNAScience #RNABioinformatics
5/n
Did you know? The #ViennaRNA Package can handle a wide range of RNA modifications, including:
#Inosine (I)
#Pseudouridine (P)
#N6-methyladenosine (m6A)
#7-deaza-adenosine (7DA)
#Nebularine (purine)
#Dihydrouridine (D)
#Bioinformatics #ComputationalBiology #RNAStructure #SyntheticBiology
4/n
They play vital roles in regulating gene expression by influencing processes like splicing, stability, and translation. To truly understand cellular processes and disease mechanisms, we must explore how these modifications shape RNA structure and function.
#ViennaRNA
3/n
#RNA molecules are incredibly versatile, and one way they showcase this is through post-transcriptional modifications. These modifications expand the classic four-letter RNA alphabet (A, C, G, U) to include over 300 unique bases! 🌟
#RNAResearch #RNAEditing #LifeSciences
2/n
As my first post on Bluesky, I’d like to share something I recently posted on #LinkedIn about the incredible versatility of #RNA molecules and how #modifications expand their functionality. I’ll break it down into smaller posts here—let me know what you think! 🚀
1/n