Bussi Lab
Research group lead by @bussigio.bsky.social at SISSA | #RNA, #moleculardynamics, and more | web: http://bussilab.org
- New #openreview from our group at prereview.org/reviews/1847...! @bussigio.bsky.social and @sdimarco.bsky.social reviewed a #preprint by Pavel Banas and coworkers on the evaluation of enhanced sampling methods for force field benchmarking. Also available at doi.org/10.5281/zeno...
- Our review on Machine Learning for #RNA Secondary Structure Prediction is now published in @rnajournal.bsky.social ! dx.doi.org/10.1261/rna.... Summary in this previous thread bsky.app/profile/buss...
- New #preprint alert! 🧬 Machine Learning for #RNA Secondary Structure Prediction: a #review of current methods and challenges, by Giuseppe Sacco, @bussigio.bsky.social, and Guido Sanguinetti arxiv.org/abs/2511.02622
- New #preprint alert! 🧬 MERGE-RNA: a physics-based model to predict #RNA secondary structure ensembles with chemical probing, lead by Giuseppe Sacco, in collaboration with Guido Sanguinetti and Redmond Smyth's lab arxiv.org/abs/2512.20581
- Our work presented today at the XBW2025 workshop homepage.uni-graz.at/de/georg.pab...! Maurizio Gilioli presented our recent #MD simulations of nucleoproteins from influenza A virus
- Reposted by Bussi Lab[Not loaded yet]
- 🎉Our group has been awarded a prestigious #FIS grant! #RNAScale - Exploring RNA Dynamics across Scales: From Base Pairs to Viral Genomes 👉 www.bussilab.org/fis3 We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.
- This is a large, ERC-scale initiative aimed at developing new methodologies for RNA modelling by integrating chemical probing data with state-of-the-art simulations. The applied focus will be on understanding the genome architecture of Influenza A, in close connection with experiment.
- Reposted by Bussi Lab#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...
- The work describing the #CASP16 solvation challenge has been published in Proteins journal! doi.org/10.1002/prot...
- A recent manuscript describing our and others’ efforts to predict the solvation shell of a group I intron is now available on bioRxiv! 🔬 doi.org/10.1101/2025...
- Our work presented at the Ultra-Highfield NMR and 4D Structural Biology workshop www.bnmrz.org/4dstructbiol organized by @sattler-lab.bsky.social! @bussigio.bsky.social will show our works on #RNA dynamics integrating #MD, #SAXS, and #NMR and validating a #CASP16 target using #cryoEM data
- New #preprint alert! 🧬 Machine Learning for #RNA Secondary Structure Prediction: a #review of current methods and challenges, by Giuseppe Sacco, @bussigio.bsky.social, and Guido Sanguinetti arxiv.org/abs/2511.02622
- A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699
- PLUMED is widely used to analyze and enhance #moleculardynamics simulations. This tutorial shows how to benchmark and optimize its #performance, explaining tricks to speed up calculations involving large sets of distances, angles, or torsions. ⚙️
- A recent manuscript describing our and others’ efforts to predict the solvation shell of a group I intron is now available on bioRxiv! 🔬 doi.org/10.1101/2025...
- 📽️ The recording of @bussigio.bsky.social 's talk at CASP RNA Special Interest Group is now available at www.youtube.com/watch?v=NRCg...
- Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
- Our work presented today at the Biophysical Modeling of the Structure and Function of Viruses @cecamevents.bsky.social workshop at the @iescargese.bsky.social! @bussigio.bsky.social will report on the recent #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
- Congratulations to Elisa Posani for successfully defending her PhD thesis "Ensemble Refinement of Cryo-Electron Microscopy-Derived RNA Structures Using Molecular Dynamics Simulations"! Cosupervision with @magistratolab.bsky.social
- Congratulations to Ivan Gilardoni for successfully defending his PhD thesis "Development and application of methods to integrate molecular simulations with experimental measurements"!
- Congratulations to Davide Di Vora for successfully defending his master thesis on the "On-the-fly integration of experimental data and molecular simulations" at University of Trieste! 🥳
- Our work presented today at the ICTP Conference on Frontiers in Atomistic Simulations: from Physics to Chemistry and Biology! @ollyfutur.bsky.social and Ivan Gilardoni will share posters with our results on enhancing #RNA - Mg binding and on integrating #MD simulations and experiments
- New #openreview from our group at prereview.org/reviews/1672...! @sdimarco.bsky.social and @bussigio.bsky.social reviewed a #preprint by @potoyan.bsky.social on the Molecular Drivers of #RNA Phase Separation. Also available at doi.org/10.5281/zeno...
- A review reporting on the discussions held at the recent @cecamevents.bsky.social workshop on enzymatic plastic degradation that we co-organized in Trieste is now available on #arxiv
- Our research presented at the Cambridge Ellis Unit Summer School on Probabilistic Machine Learning! Giuseppe Sacco will present a poster reporting our machine-learned model for DMS-guided ensemble prediction of RNA systems www.ellis.eng.cam.ac.uk/summer-schoo...
- 📢 New #preprint alert! Our review "RNA Dynamics and Interactions Revealed through Atomistic Simulations" is now available on arxiv.org/abs/2507.08474 ! Written by @bussigio.bsky.social and @ollyfutur.bsky.social
- Our research presented at #StatPhys29! Ivan Gilardoni will present a poster reporting on our methodological work in integrating molecular simulations and experimental data statphys29.org
- 📢 Paper with @sattler-lab.bsky.social now published in @narjournal.bsky.social ! doi.org/10.1093/nar/... We combine #NMR, #SAXS, and #MD to construct conformational ensembles, showing that A-to-I hyper-editing leads to significant structural dynamics. MD simulations by @piompons.bsky.social
- A paper from our group (doi.org/10.1093/narg...) has been tested and reviewed in ReproHack www.reprohack.org/review/151! We got interesting feedback on how to improve documentation of our notebooks. Very useful initiative!
- New #openreview from our group at prereview.org/reviews/1573...! @bussigio.bsky.social and @ollyfutur.bsky.social reviewed a #preprint by Simon Olsson showing their Minimum-Excess-Work Guidance method. Also available at doi.org/10.5281/zeno...
- Our research presented at the proteinelectrostatics.org Protein Electrostatics 2025, Lisbon! @tf-silva.bsky.social shared our constant pH simulations on #RNA systems, from oligomers to introns!
- Our research presented at the meeting of the Division of Chemistry of Biological Systems of the @socchimita.bsky.social! Elisa Posani will show our integrative modelling of #RNA using #cryoEM data and @sdimarco.bsky.social will share our simulations of #RNA membrane interactions
- Our research presented at the GRC on computational #NMR organized by @katjapetzold.bsky.social in Les Diablerets! @bussigio.bsky.social will share our integrative approach to reconstruct the impact of A-to-I modifications on dynamics and our protocol to predict Mg2+ binding sites in #RNA molecules
- 📢 Paper on the RBP Footprint Grand Challenge—launched at RNA2021 — is out in @rnajournal.bsky.social doi.org/10.1261/rna....! A community-driven benchmark of methods for predicting RBP binding sites, with contributions from @tfroehlking.bsky.social, Mattia Bernetti, and @bussigio.bsky.social
- Congratulations to @tf-silva.bsky.social for winning the best poster prize at the #RNA modelling across scales @cecamevents.bsky.social workshop, describing our constant pH simulations of RNA systems 👏
- Our research was featured at the @cecamevents.bsky.social meeting #RNA modelling across scales at SISSA, Trieste! @ollyfutur.bsky.social gave a talk on our enhanced sampling strategy for exploring RNA-Mg2+ binding, and all other group members presented posters on their research
- Our research was featured at the @cecamevents.bsky.social meeting #RNA modelling across scales at SISSA, Trieste! @ollyfutur.bsky.social gave a talk on our enhanced sampling strategy for exploring RNA-Mg2+ binding, and all other group members presented posters on their research
- Our integrative approach using #MD and #cryoEM data to construct structural ensembles of #RNA just published on @natcomms.bsky.social doi.org/10.1038/s414... Lead by Elisa Posani, with @magistratolab.bsky.social @bonomimax.bsky.social @pjanos.bsky.social @navtejtoor.bsky.social and Daniel Haack 🎉
