EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning
Published in Journal of Molecular Biology, 2023 PDF
Publications
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Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies
Published in Current Opinion in Structural Biology, 2023 PDF
Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions
Published in PLOS Computational Biology, 2023 PDF
Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity
Published in eLife, 2023 PDF
ScanNet: A Web Server for Structure-based Prediction of Protein Binding Sites with Geometric Deep Learning
Published in Journal of Molecular Biology, 2022 PDF
Reduced B-cell antigenicity of Omicron lowers host serologic response
Published in Cell Reports, 2022 PDF
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction
Published in Nature Methods, 2022 PDF
RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles
Published in Cell Systems, 2021 PDF
Blind deconvolution for spike inference from fluorescence recordings
Published in Journal of Neuroscience Methods, 2020 PDF
‘Place-cell’ emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space
Published in Journal of Physics A: Mathematical and Theoretical, 2020 PDF