Daniele Raimondi

Publication Activity (10 Years)

Years Active: 2014-2023
Publications (10 Years): 16

Top Topics

Protein Interaction

Gene Regulatory

Physicochemical Properties

Dynamic Time Warping

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Antoine Passemiers, Pietro Folco, Daniele Raimondi, Giovanni Birolo, Yves Moreau, Piero Fariselli
How good Neural Networks interpretation methods really are? A quantitative benchmark. CoRR (2023)
Daniele Raimondi, Gabriele Orlando, Nora Verplaetse, Piero Fariselli, Yves Moreau
Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. Frontiers Bioinform. 2 (2022)
Antoine Passemiers, Yves Moreau, Daniele Raimondi
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation. Bioinform. 38 (10) (2022)
Daniele Raimondi, Gabriele Orlando, Emiel Michiels, Donya Pakravan, Anna Bratek-Skicki, Ludo Van Den Bosch, Yves Moreau, Frederic Rousseau, Joost Schymkowitz
In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention. Bioinform. 37 (20) (2021)
Daniele Raimondi, Jaak Simm, Adam Arany, Yves Moreau
A novel method for data fusion over entity-relation graphs and its application to protein-protein interaction prediction. Bioinform. 37 (16) (2021)
Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, François Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim F. Vranken
b2bTools: online predictions for protein biophysical features and their conservation. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim F. Vranken
Accurate prediction of protein beta-aggregation with generalized statistical potentials. Bioinform. 36 (7) (2020)
Daniele Raimondi, Gabriele Orlando, Piero Fariselli, Yves Moreau
Insight into the protein solubility driving forces with neural attention. PLoS Comput. Biol. 16 (4) (2020)
Giovanni Buroni, Yann-Aël Le Borgne, Gianluca Bontempi, Daniele Raimondi, Karl Determe
On-Board Unit Big Data: Short-term Traffic Forecasting in Urban Transportation Networks. DSAA (2020)
Gabriele Orlando, Daniele Raimondi, Luciano Porto Kagami, Wim F. Vranken
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Gabriele Orlando, Daniele Raimondi, Francesco Tabaro, Francesco Codicè, Yves Moreau, Wim F. Vranken
Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates. Bioinform. 35 (22) (2019)
Daniele Raimondi, Gabriele Orlando, Yves Moreau, Wim F. Vranken
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. Bioinform. 34 (18) (2018)
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim F. Vranken
SVM-dependent pairwise HMM: an application to protein pairwise alignments. Bioinform. 33 (24) (2017)
Daniele Raimondi, Ibrahim Tanyalcin, Julien Ferté, Andrea M. Gazzo, Gabriele Orlando, Tom Lenaerts, Marianne Rooman, Wim F. Vranken
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Daniele Raimondi, Andrea M. Gazzo, Marianne Rooman, Tom Lenaerts, Wim F. Vranken
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects. Bioinform. 32 (12) (2016)
Daniele Raimondi, Gabriele Orlando, Wim F. Vranken
Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. Bioinform. 31 (8) (2015)
Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns. PLoS Comput. Biol. 10 (11) (2014)