Giulia Palermo

Check out our new review on Graph #NeuralNetworks in #MolecularDynamics!
We show how #AI is used for #ForceField development, free-energy, and analysis - including our attention-based GNN workflow - and how you can integrate your favorite AI into #compchem!
www.sciencedirect.com/science/arti...

Want to know everything about #ArtificialIntelligence, #DeepLearning, and #CompChem to study and engineer #GeneEditing systems — from #CRISPR-Cas proteins to base and prime editors, and #RNA Guided Transposons?
Check out our new piece in @NatureSMB !
www.nature.com/articles/s41...

Thrilled to share that I’ll be joining @uclacb.bsky.social as Professor in July 2026!
Grateful to my amazing students, postdocs, colleagues @UCR, collaborators, and mentors.
A new chapter begins, advancing #compchem, #AI to explore #RNA, #DNA, #CRISPR, and emerging directions in #Biophysics.

Developed by the multi-talented @pabloarantes.bsky.social & @SouvikSinha members of my lab:
ParametrizANI brings #MachineLearning - based #ForceField parametrization available to everyone
Available on Github: github.com/palermolab/P...

🚀 Many thanks to @SDSC_UCSD and @HPCwire for highlighting our work using @NSF supercomputers to uncover how “jumping genes” can transform #GeneEditing technologies!
www.sdsc.edu/news/2025/PR...
#Supercomputing #HPC #CRISPR #RNA #CompChem

✨Best way to end the week! Just learned from Kevin Freedman @ucriverside.bsky.social that, at the end of the exam, students in his Dynamics of Biological Systems class draw their favorite professor.
Guess who got picked...
♥️♥️♥️
#biophysics #TeachingJoy #STEM #LoveScience

This is work mainly done by Mohd Ahsan, an incredibly talented postdoc in the lab. Grateful for the experimental validation by David Taylor lab @utaustin.bsky.social and NMR by George P. Lisi lab @brownuresearch.bsky.social

🚀New from our lab @biorxivpreprint.bsky.social!
We reveal a cryptic metal binding pocket that dinamically forms in #CRISPR-Cas9 and regulates the metal-dependent activity of #Cas9.
#MarkovModels & #QuantumChemistry corroborated by biochem & #NMR experiments.
www.biorxiv.org/content/10.1...

@pabloarantes.bsky.social is continuing working on improving the tool

Developed by the incredbly creative @pabloarantes.bsky.social & @SouvikSinha in our lab!

GitHub - palermolab/ParametrizANI: ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI - palermolab/ParametrizANI

New from our lab!
🚀 ParametrizANI - a #NeuralNetworks tool for molecular parametrization.
Predicts potential energy surfaces with near-DFT/CC accuracy, at a fraction of the computational cost!
#AI #QuantumChemistry #CompChem #ML 🤖
chemrxiv.org/engage/chemr...
Try it:
github.com/palermolab/P...

So exciting to be @proteinsociety.bsky.social meeting with my lab!

🔬🧬 Excited to be at the @proteinsociety.bsky.social meeting in SF! Curious how #NeuralNetworks can decode biomolecular mechanisms? Don’t miss the poster by ChinmaiPindi and AmunPatel ! #Proteins #AI #CRISPR #DNA

This was developed by Chinmai Pindi, Mohd Ahsan and Souvik Sinha, Ph. D, three amazing lab members! More on #NeuralNetworks, #GNN & new #AI approaches is yet to come! Stay tuned !

By leveraging deep learning–based graph representations, our GAT model provides interpretable mechanistic insights from complex molecular simulations and is readily adaptable to a wide range of biological systems.

New study @biorxivpreprint
We revea, how TnsC filaments form and grow in #CRISPR-associated transposons using #FreeEnergy sims & introduce #DeepLearning-based Graph Attention Networks for decoding biomolecular systems!
www.biorxiv.org/content/10.1...
#GNN #MolecularDynamics #StructuralBiology

New paper from our lab just out @pnas.org! 🚀
Using free energy simulations, #AIphaFold and #cryoEM refinement, we uncovered a key conformational change in a paradigm-shifting #CRISPR-associated #transposon capable of precise gene knock-ins. 🔍🧬
www.pnas.org/doi/epub/10....

Thrilled to join #ACSSpring2025 and meet my friends! Don't miss my talk on how #AI & #EnhancedSampling can describe gene editing & refine #cryoEM maps. We’ll be presenting our latest research on #CRISPR-associated transposon systems + other exciting advancements! #compchem #RNA
#compchem #RNA

An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a - Nature Communications CRISPR-Cas12a is a powerful RNA-guided genome-editing system. Saha et al. show that an alpha-helical lid plays the central role in guiding the target DNA toward the single RuvC nuclease domain, result...

www.nature.com/articles/s41...
Here it is, sorry @martinvoegele.bsky.social for the delay

#BPS2025 waiting for the national lecture 🥳 @giuliapalermo.bsky.social @labvanni.bsky.social @sriraksha.bsky.social @sesamedusa.bsky.social

🚀 Exciting new poster from our lab at #BPS2025!

🧬 @Ahsan09966804 showcases how #MolecularDynamics & #AI can enhance #CryoEM map refinement.

📍 Catch it at Board 18 (1824-Pos) today, don’t miss out! #Biophysics #CompBio

Carolina Sarto @carosarto.bsky.social, a brilliant student from the University of Buenos Aires, will be presenting her work on #RNA synthesis in #DengueVirus🦠 at #BPS2025.

Don’t miss her poster today L3074-Pos (LB13). She’s looking for a postdoc, and I have no doubt she’ll thrive!

@carosarto.bsky.social

Excited to be at #BPS2025! 🚀 Our lab is contributing to the #cryoEM symposium, showcasing how computational methods and AI are revolutionizing cryo-EM analysis. See you there! 🔬💡 #Biophysics #AI
Read our papers to know more:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...

New paper from our lab @elife.bsky.social . We show how #DirectedEvolution reshaped #CRISPR for expanding DNA recongition.
This is work by Kazi Hossain, an incredibly talented student visiting my lab from the Czub lab, now in Orozco's lab & Lukasz Nierzwicki.
doi.org/10.7554/eLif...

New paper from our lab @naturecomms.bsky.social!
We reveal the dynamics and mechanism of target DNA traversal in #CRISPR Cas12a, a conundrum in the field!
nature.com/articles/s41...
#compchem
We thank the amazing #HPC resources of PSC #Anton2 and SDSC

Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e Abstract. CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were deve

Do you want to know why #ABE 8e is the most efficient adenine base editor? Read our paper with the amazing
Audrey Lapinaite!
@narjournal.bsky.social

The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency!
academic.oup.com/nar/article/...

Happy Bluesky! Nel blu dipinto di blu 🩵🩵🩵