Andrea Pasquadibisceglie
@andpdb.bsky.social
📤 184
📥 878
📝 12
Staff scientist
@tigem.bsky.social
| Computational structural biologist
reposted by
Andrea Pasquadibisceglie
BioExcel CoE
22 days ago
🎗️ reminder that our
#webinar
on "Mastering the Accelerated Weight Histogram method" will take place next week; 🗓️ 10 February 2026, 15:00 CET ✍️
bioexcel.eu/5t76
#moleculardynamics
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Andrea Pasquadibisceglie
Khmelinskaia Lab
23 days ago
🗓️ Save the Date! The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹 🗓️ October 28–30, 2026 Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.
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Andrea Pasquadibisceglie
AI x Bio Discovery
24 days ago
Ab initio prediction of RNA structure ensembles with RNAnneal
[new] ...leverages generative deep learning with statistical physics and MD to determine 3D structural ensembles from primary sequences, aiding design.
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Andrea Pasquadibisceglie
Jeffrey J. Gray
27 days ago
Final stretch to apply for undergraduate summer internships in the Rosetta Commons! Come design proteins, develop AI and physics-based methods to model biomolecules, and impact health, materials, and sustainability! Application deadline is Sunday Feb 1.
rosettacommons.org/education/reu/
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Undergraduates
Rosetta Commons Research Experience for Undergraduates (REU) AI for Biomolecular Structure Prediction and Design Interns in this geographically-distributed REU program participate in research using…
https://rosettacommons.org/education/reu/
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Andrea Pasquadibisceglie
Elisa Fadda
about 1 month ago
Excellent overview of the (mind-blowing) effects of the Shingles vaccine against dementia by
@erictopol.bsky.social
Ground Truth 🧪 "Two new studies add to a remarkable body of evidence for benefit" ⬇️
open.substack.com/pub/erictopo...
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Spotlight on the Shingles Vaccine—Again!
Two new studies add to a remarkable body of evidence for benefit
https://open.substack.com/pub/erictopol/p/spotlight-on-the-shingles-vaccineagain?utm_source=share&utm_medium=android&r=1wyvuy
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Andrea Pasquadibisceglie
Andrew Plested
about 2 months ago
"While the concept of condensates is successfully rewriting cell biology textbooks, there is some danger of overhype and backlash." This workshop summary is great - particularly the idea to shift from "Is it a condensate?" to "what problem does that solve?" but "successfully" stood out for me here
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Andrea Pasquadibisceglie
Yamuna Krishnan
2 months ago
Organelles do NOT have a single uniform pH. And if you think they must, because “protons diffuse fast,” this paper is for you. A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
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Andrea Pasquadibisceglie
Kresten Lindorff-Larsen
2 months ago
Experimental structures provide valuable hypotheses and accelerate but do not replace evolutionary and statistical analyses of protein sequences
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Andrea Pasquadibisceglie
Smut Clyde, X-Ray Haruspex
3 months ago
Rate your score on Factor Fexcectorn. Well done, Scientific Reports.
pubpeer.com/publications...
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Andrea Pasquadibisceglie
Python Software Foundation
4 months ago
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share.
pyfound.blogspot.com/2025/10/NSF-...
🧵
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The official home of the Python Programming Language
https://www.python.org/sponsors/application/
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Andrea Pasquadibisceglie
di Bernardo Lab
6 months ago
Join our lab
dibernardo.tigem.it
for the
#ERC-funded
project DIMERCIRCUITS at
@tigem.bsky.social
. We are building synthetic gene circuits to power next-generation gene and cell therapies. We are looking for candidates with a PhD in
#SyntheticBiology
or related. Apply by email:
[email protected]
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Andrea Pasquadibisceglie
Tigem
5 months ago
🚀 Launch your career in advanced gene and cell therapies! 🚀 RAREFIND
#MSCA-COFUND
#PhD
Programme opens its call for applications! 👉Know more and apply now: www.rarefind-cofund.eu
#RAREFINDPhD
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Andrea Pasquadibisceglie
Martin Pacesa
6 months ago
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian,
@sokrypton.org
, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
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reposted by
Andrea Pasquadibisceglie
di Bernardo Lab
7 months ago
We are hiring a Bioinformatician expert in NGS for our Bioinformatics Core
@tigem.bsky.social
please share with anyone that may be interested.
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reposted by
Andrea Pasquadibisceglie
Adrien Schahl
8 months ago
Very nice presentation of
@eriklindahl.bsky.social
about his work to integrate AI, MD and experiments. 🤩
#EBSA2025
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Excited to be at
#EBSA2025
! Today I'll present my postdoc project carried out under the supervision of
@delemottelab.bsky.social
and with the collaboration of Sara Liin and her amazing team!
8 months ago
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reposted by
Andrea Pasquadibisceglie
Tigem
10 months ago
🌍 Attending
#ASGCT2025
in
#NewOrleans
? Don’t miss this Scientific Symposium hosted by the Coalition of International Gene Therapy Societies: 📌 Clinical Trials Around the Globe 🗓️ [Today, May 16th] 🕗 8:00 AM – 9:45 AM 📍 Room 293–296
#GeneTherapy
#ASGCT
#AAV
#Retina
#LiverGeneTherapy
#RareDisease
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reposted by
Andrea Pasquadibisceglie
Simon Waddington
11 months ago
A new paper hitting the press: Gene therapy for AIPL-1 retinal dystrophy. Almost all kids with this can only perceive light, at best. Getting early will help with vision also neurodevelopment and psychosocial aspects. 🧬 ⭐ 👁
www.thelancet.com/journals/lan...
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Gene therapy in children with AIPL1-associated severe retinal dystrophy: an open-label, first-in-human interventional study
Our findings indicate that young children with AIPL1-related retinal dystrophy benefited substantially from subretinal administration of rAAV8.hRKp.AIPL1, with improved visual acuity and functional vi...
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(24)02812-5/fulltext
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Andrea Pasquadibisceglie
Sammy Chan
11 months ago
Preprint! All-atom structures of 2 folding intermediates on the ribosome, along parallel pathways & conserved across Ig domains, by 19F NMR & MD Co-led by
@julianstreit.bsky.social
, & thanks
twlodarski.bsky.social
, Alki, Lisa & John Christodoulou!
#nmrchat
#compbio
www.biorxiv.org/content/10.1...
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Structures of protein folding intermediates on the ribosome
The ribosome biases the conformations sampled by nascent polypeptide chains along folding pathways towards biologically active states. A hallmark of the co-translational folding (coTF) of many protein...
https://www.biorxiv.org/content/10.1101/2025.04.07.647236v1
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Andrea Pasquadibisceglie
Alexis Verger 🧬🧫🧪
11 months ago
BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by
@yehlincho.bsky.social
@martinpacesa.bsky.social
@sokrypton.org
🧶🧬
www.biorxiv.org/content/10.1...
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Andrea Pasquadibisceglie
Diego del Alamo
11 months ago
Yet another PLM, this one with 100B params, that fails to outperform AF2 (93M params) when MSAs are provided
www.nature.com/articles/s41...
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Andrea Pasquadibisceglie
Simon Olsson
11 months ago
We are recruiting a colleague to our division at Chalmers in Data-Driven Life Science (broadly defined), a competitive starting package is offered and you get to be part of a support, yet young and ambitious research environment. Apply here:
www.chalmers.se/en/about-cha...
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Vacancies
https://www.chalmers.se/en/about-chalmers/work-with-us/vacancies/?rmpage=job&rmjob=13685&rmlang=UK
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Honored to be part of
@tigem.bsky.social
and Fondazione Telethon
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11 months ago
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Andrea Pasquadibisceglie
Jorge Bravo Abad
11 months ago
Leung et al. used deep autoencoders with outlier detection to guide weighted ensemble simulations of NTL9 folding, achieving up to threefold better efficiency than standard methods.
pubs.acs.org/doi/full/10....
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Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding
A major challenge for many rare-event sampling strategies is the identification of progress coordinates that capture the slowest relevant motions. Machine-learning methods that can identify progress coordinates in an unsupervised manner have therefore been of great interest to the simulation community. Here, we developed a general method for identifying progress coordinates “on-the-fly” during weighted ensemble (WE) rare-event sampling via deep learning (DL) of outliers among sampled conformations. Our method identifies outliers in a latent space model of the system’s sampled conformations that is periodically trained using a convolutional variational autoencoder. As a proof of principle, we applied our DL-enhanced WE method to simulate the NTL9 protein folding process. To enable rapid tests, our simulations propagated discrete-state synthetic molecular dynamics trajectories using a generative, fine-grained Markov state model. Results revealed that our on-the-fly DL of outliers enhanced the efficiency of WE by >3-fold in estimating the folding rate constant. Our efforts are a significant step forward in the unsupervised learning of slow coordinates during rare event sampling.
https://pubs.acs.org/doi/full/10.1021/acs.jctc.4c01136
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reposted by
Andrea Pasquadibisceglie
Jorge Bravo Abad
11 months ago
Chronowska et al. introduce the Protein Design Archive, a curated database of over 1,500 de novo designs, revealing rapid growth from rational to deep learning–based methods. Their website offers key metrics and filtering tools for guiding future designs.
www.nature.com/articles/s41...
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The Protein Design Archive (PDA): insights from 40 years of protein design - Nature Biotechnology
Nature Biotechnology - The Protein Design Archive (PDA): insights from 40 years of protein design
https://www.nature.com/articles/s41587-025-02607-x
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Andrea Pasquadibisceglie
Nature Biotechnology
11 months ago
In Brief: A potential first-in-class treatment using
@boehringerglobal.bsky.social
's lentivirus-based CFTR gene addition therapy for cystic fibrosis begins clinical trials
www.nature.com/articles/s41...
rdcu.be/eecLO
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First inhaled lentiviral gene therapy enters cystic fibrosis trial - Nature Biotechnology
Nature Biotechnology - First inhaled lentiviral gene therapy enters cystic fibrosis trial
https://www.nature.com/articles/s41587-025-02616-w
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Andrea Pasquadibisceglie
Tigem
12 months ago
🚨 The latest study from
#NatureCommunications
, led by Pasquale Piccolo, systematically evaluated AAV-mediated liver transduction across different fibrosis models.
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reposted by
Andrea Pasquadibisceglie
12 months ago
🚀 PhD Opportunity – NC-mTORC1 & Genetic Diseases! Join
@tigem.bsky.social
& Univ. of Naples to explore Non-Canonical mTORC1 signaling in mTORopathies like BHD & TSC!
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reposted by
Andrea Pasquadibisceglie
Tigem
12 months ago
🚀 Our mission 🧬 Our mission is to push scientific boundaries through cutting-edge research, innovative therapies, and training the next generation of biomedical experts. Learn more:
www.tigem.it
✨
#Genetics
#RareDiseases
#MedicalResearch
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reposted by
Andrea Pasquadibisceglie
Diego del Alamo
about 1 year ago
Collective variables from MD simulations can be linked to the learned latent dimensions of an autoencoder for generative modeling of conformational interconversion trajectories
www.biorxiv.org/content/10.1...
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Andrea Pasquadibisceglie
Frank Noe
about 1 year ago
The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues.
github.com/microsoft/bi...
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reposted by
Andrea Pasquadibisceglie
BioExcel CoE
about 1 year ago
This year's version of GROMACS is out! If you want to hear about the new features and performance improvements join our
#webinar
on 18 February 2025 Registration ➡️
bit.ly/40Ebbme
#moleculardynamics
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Andrea Pasquadibisceglie
Kresten Lindorff-Larsen
about 1 year ago
Predicting absolute protein folding stability using generative models
@mcagiada.bsky.social
@sokrypton.org
& I used ESM-IF to predict ∆G for folding & conformational change Paper, code and colab 📜
dx.doi.org/10.1002/pro....
💾
github.com/KULL-Centre/...
👩💻
colab.research.google.com/github/KULL-...
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At TIGEM, we are looking for a motivated student/young researcher to start a new project on hyperactive enzyme design using deep-learning and physics-based methods! If you are interested, please get in touch with us
tigem.it/newsroom/car...
! Thank you for sharing it!
#compchem
#compbio
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Welcome to TIGEM
Telethon Institute of Genetics and Medicine
https://tigem.it/newsroom/career-opportunities/jounior-position-available
about 1 year ago
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I’m thrilled to announce that, in February next year, I’ll be starting a new role as a Staff Scientist at TIGEM in Italy! I’m truly grateful to my fantastic supervisor
@delemottelab.bsky.social
and the MBS group for an incredible two years in Stockholm! Tack så mycket!
about 1 year ago
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Andrea Pasquadibisceglie
Roland Dunbrack 🏳️🌈
about 1 year ago
David Baker visits all the Rosetta folks after his Nobel lecture. And photo of all three Chemistry laureates - David Baker, Demis Hassabis, and John Jumper. An honor to be here in Stockholm to see this.
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David Baker, Demis Hassabis and John Jumper
#Nobel
laureates in Chemistry. What a great time to be a postdoc in Stockholm!
about 1 year ago
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Hopfield & Hinton
#Nobel
Prize 2024 in Physics
about 1 year ago
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#NobelLectures
about 1 year ago
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Andrea Pasquadibisceglie
Amy Lu
about 1 year ago
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
🧵
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Andrea Pasquadibisceglie
Torsten Schwede
about 1 year ago
The results of
#CASP16
are online, pdf files of the presentations will be made available next Wednesday through the CASP website. The release of talk recordings will follow soon afterwards. Big thanks to all participants for an inspiring conference! 🧪 🧬
predictioncenter.org/casp16/
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Andrea Pasquadibisceglie
Max Bonomi
about 1 year ago
Do you want to work at the interface of molecular simulations, structural biology experiments and
#AI
? Come to Paris for a PhD at
@pasteur.fr
1 PhD position is available in our lab funded by ERC_Research. Please repost!!
#compchem
#compbio
Info 👇
research.pasteur.fr/b/15Hr
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One PhD thesis in integrative structural biology | Research - Institut Pasteur
https://research.pasteur.fr/b/15Hr
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reposted by
Andrea Pasquadibisceglie
Martin Vögele
about 1 year ago
Another deep-learning approach to sample conformational ensembles of proteins: BioEmu, out of Microsoft Research.
www.biorxiv.org/content/10.1...
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Scalable emulation of protein equilibrium ensembles with generative deep learning
Following the sequence and structure revolutions, predicting the dynamical mechanisms of proteins that implement biological function remains an outstanding scientific challenge. Several experimental t...
https://www.biorxiv.org/content/10.1101/2024.12.05.626885v1
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Andrea Pasquadibisceglie
Olexandr Isayev 🇺🇦 🇺🇸
about 1 year ago
While dockers are keep docking (now with diffusion and AI😀), Pat Walters and Ajay Jain show sobering assessment of ‘perceived’ accuracy of such methods! Diffdock shots fired 🔥 The conclusion is totally worth reading in full!
#chemsky
#compchemsky
arxiv.org/abs/2412.02889
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Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows
The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi...
https://arxiv.org/abs/2412.02889
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#CASP16
Does anyone know if the results for the ensemble category will be available at some point?
about 1 year ago
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Andrea Pasquadibisceglie
Torsten Schwede
about 1 year ago
Assessors’ conclusions of the 3D category (individual protein chains) of
#CASP16
🧪
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Andrea Pasquadibisceglie
Torsten Schwede
about 1 year ago
#CASP16
results are online at the prediction center website - conference starting tomorrow evening. Have a safe trip - see you soon!
predictioncenter.org/casp16/
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Home - CASP16
https://predictioncenter.org/casp16/
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