Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. - Daniele Raimondi; Gabriele Orlando; Wim F. Vranken (Bioinform., 2015)

SVM-dependent pairwise HMM: an application to protein pairwise alignments. - Gabriele Orlando; Daniele Raimondi; Taushif Khan; Tom Lenaerts; Wim F. Vranken (Bioinform., 2017)

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. - Daniele Raimondi; Ibrahim Tanyalcin; Julien Ferté; Andrea M. Gazzo; Gabriele Orlando; Tom Lenaerts; Marianne Rooman; Wim F. Vranken (Nucleic Acids Res., 2017)

Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. - Daniele Raimondi; Gabriele Orlando; Yves Moreau; Wim F. Vranken (Bioinform., 2018)

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates. - Gabriele Orlando; Daniele Raimondi; Francesco Tabaro; Francesco Codicè; Yves Moreau; Wim F. Vranken (Bioinform., 2019)

Accurate prediction of protein beta-aggregation with generalized statistical potentials. - Gabriele Orlando; Alexandra Silva 004; Sandra Macedo-Ribeiro; Daniele Raimondi; Wim F. Vranken (Bioinform., 2020)

ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. - Gabriele Orlando; Daniele Raimondi; Luciano Porto Kagami; Wim F. Vranken (Nucleic Acids Res., 2020)

Insight into the protein solubility driving forces with neural attention. - Daniele Raimondi; Gabriele Orlando; Piero Fariselli; Yves Moreau (PLoS Comput. Biol., 2020)

In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention. - Daniele Raimondi; Gabriele Orlando; Emiel Michiels; Donya Pakravan; Anna Bratek-Skicki; Ludo Van Den Bosch; Yves Moreau; Frederic Rousseau 001; Joost Schymkowitz (Bioinform., 2021)

b2bTools: online predictions for protein biophysical features and their conservation. - Luciano Porto Kagami; Gabriele Orlando; Daniele Raimondi; François Ancien; Bhawna Dixit; Jose Gavaldá-García; Pathmanaban Ramasamy; Joel Roca-Martínez; Konstantina Tzavella; Wim F. Vranken (Nucleic Acids Res., 2021)

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. - Daniele Raimondi; Gabriele Orlando; Nora Verplaetse; Piero Fariselli; Yves Moreau (Frontiers Bioinform., 2022)