Publications

Found 45 results
Author Title [ Type(Desc)] Year
Conference Paper
P. Moulos, Kanaris, I., and Bontempi, G., Stability of feature selection algorithms for classification in high-throughput genomics datasets, in Bioinformatics and Bioengineering (BIBE), 2013 IEEE 13th International Conference on, 2013.
Journal Article
T. J. Ragan, Fogh, R. H., Tejero, R., Vranken, W., Montelione, G. T., Rosato, A., and Vuister, G. W., Analysis of the structural quality of the CASD-NMR 2013 entries, Journal of Biomolecular NMR, vol. 62, pp. 527–540, 2015.
D. Raimondi, Orlando, G., and Vranken, W. F., Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements, Bioinformatics, 2014.
M. Varadi, Vranken, W., Guharoy, M., and Tompa, P., Computational approaches for inferring the functions of intrinsically disordered proteins, Frontiers in Molecular Biosciences, vol. 2, p. 45, 2015.
K. Faust, Lima-Mendez, G., Lerat, J. - S., Sathirapongsasuti, J. Fah, Knight, R., Huttenhower, C., Lenaerts, T., and Raes, J., Cross-biome comparison of microbial association networks, Frontiers in Microbiology, vol. 6, 2015.
D. Raimondi, Tanyalcin, I., Ferté, J., Gazzo, A., Orlando, G., Lenaerts, T., Rooman, M., and Vranken, W., DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins, Nucleic Acids Research, vol. 45, pp. W201-W206, 2017.
G. Lima-Mendez, Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., J. Ignacio-Espinosa, C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M. - J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., coordinators, T. Oceans, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J., Determinants of community structure in the global plankton interactome, Science, vol. 348, 2015.
A. M. Gazzo, Daneels, D., Cilia, E., Bonduelle, M., Abramowicz, M., Van Dooren, S., Smits, G., and Lenaerts, T., DIDA: A curated and annotated digenic diseases database, Nucleic Acids Research, 2015.
D. Piovesan, Tabaro, F., cetić, I. Mi\v, Necci, M., Quaglia, F., Oldfield, C. J., Aspromonte, M. Cristina, Davey, N. E., Davidović, R., Dosztányi, Z., Elofsson, A., Gasparini, A., Hatos, A., Kajava, A. V., Kalmar, L., Leonardi, E., Lazar, T., Macedo-Ribeiro, S., Macossay-Castillo, M., Meszaros, A., Minervini, G., Murvai, N., Pujols, J., Roche, D. B., Salladini, E., Schad, E., Schramm, A., Szabo, B., Tantos, A., Tonello, F., Tsirigos, K. D., Veljković, N., Ventura, S., Vranken, W. F., Warholm, P., Uversky, V. N., A Dunker, K., Longhi, S., Tompa, P., and Tosatto, S. C. E., DisProt 7.0: a major update of the database of disordered proteins., Nucleic acids research, vol. 45, pp. D219–D227, 2017.
J. Jeschke, Bizet, M., Desmedt, C., Calonne, E., Dedeurwaerder, S., Garaud, S., Koch, A., Larsimont, D., Salgado, R., Van den Eynden, G., Gallo, K. Willard, Bontempi, G., Defrance, M., Sotiriou, C., and Fuks, F., DNA methylation–based immune response signature improves patient diagnosis in multiple cancers, The Journal of Clinical Investigation, vol. 127, 2017.
R. Huculeci, Cilia, E., Lyczek, A., Buts, L., Houben, K., Seeliger, M. A., van Nuland, N., and Lenaerts, T., Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity, Structure, 2016.
E. Cilia, Pancsa, R., Tompa, P., Lenaerts, T., and Vranken, W. F., The DynaMine webserver: predicting protein dynamics from sequence, Nucleic Acids Research, 2014.
R. Pancsa, Raimondi, D., Cilia, E., and Vranken, W. F., Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity, Biophysical Journal, vol. 110, pp. 572 - 583, 2016.
D. Raimondi, Orlando, G., and Vranken, W. F., An Evolutionary View on Disulfide Bond Connectivities Prediction Using Phylogenetic Trees and a Simple Cysteine Mutation Model, Plos One, vol. 10, p. e0131792, 2015.
M. Lopes and Bontempi, G., Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data, Frontiers in Genetics, vol. 4, 2013.
A. Zafra Ruano, Cilia, E., Couceiro, J. R., Sanz, J. Ruiz, Schymkowitz, J., Rousseau, F., Luque, I., and Lenaerts, T., From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors, PLoS Comput Biol, vol. 12, pp. 1-26, 2016.
G. Bontempi and Flauder, M., From Dependency to Causality: A Machine Learning Approach, Journal of Machine Learning Research, vol. 16, pp. 2437-2457, 2015.
E. Cilia, Pancsa, R., Tompa, P., Lenaerts, T., and Vranken, W. F., From protein sequence to dynamics and disorder with DynaMine, Nat Commun, vol. 4, 2013.
F. Pucci, Bourgeas, R., and Rooman, M., High-quality thermodynamic data on the stability changes of proteins upon single-site mutations, bioRxiv, 2016.
M. J. Skwark, Raimondi, D., Michel, M., and Elofsson, A., Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns., PLoS computational biology, vol. 10, p. e1003889, 2014.
F. Pucci and Rooman, M., Improved insights into protein thermal stability: from the molecular to the structurome scale, bioRxiv, 2016.
C. Olsen, Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., Haibe-Kains, B., and Quackenbush, J., Inference and validation of predictive gene networks from biomedical literature and gene expression data, Genomics, p. -, 2014.
A. Colaprico, Cava, C., Bertoli, G., Bontempi, G., and Castiglioni, I., Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer, vol. 2015, 2015.
D. Raimondi, Orlando, G., Messens, J., and Vranken, W. F., Investigating The Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State, Human Mutation, p. n/a–n/a, 2016.
D. Raimondi, Gazzo, A. M., Rooman, M., Lenaerts, T., and Vranken, W. F., Multi-level biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects, Bioinformatics, 2016.

Pages