Found 47 results
Author Title Type [ Year(Desc)]
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.
E. Cilia, Pancsa, R., Tompa, P., Lenaerts, T., and Vranken, W. F., The DynaMine webserver: predicting protein dynamics from sequence, Nucleic Acids Research, 2014.
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.
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.
W. F. Vranken, NMR structure validation in relation to dynamics and structure determination, Progress in nuclear magnetic resonance spectroscopy, vol. 82, pp. 27–38, 2014.
E. Cilia, Teso, S., Ammendola, S., Lenaerts, T., and Passerini, A., Predicting virus mutations through statistical relational learning., BMC bioinformatics, vol. 15, p. 309, 2014.
C. Olsen, Bontempi, G., Emmert-Streib, F., Quackenbush, J., and Haibe-Kains, B., Relevance of different prior knowledge sources for inferring gene interaction networks, Frontiers in Genetics, vol. 5, 2014.
M. Lopes, Kutlu, B., Miani, M., Bang-Berthelsen, C. H., Størling, J., Pociot, F., Goodman, N., Hood, L., Welsh, N., Bontempi, G., and , Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference, Genomics, 2014.
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.
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.
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. 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.
G. Bontempi and Flauder, M., From Dependency to Causality: A Machine Learning Approach, Journal of Machine Learning Research, vol. 16, pp. 2437-2457, 2015.
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.
P. Bellot, Olsen, C., Salembier, P., Oliveras-Verges, A., and Meyer, P., NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference, BMC Bioinformatics, vol. 16, p. 312, 2015.
A. Gutmanas, Adams, P. D., Bardiaux, B., Berman, H. M., Case, D. A., Fogh, R. H., Güntert, P., Hendrickx, P. M. S., Herrmann, T., Kleywegt, G. J., Kobayashi, N., Lange, O. F., Markley, J. L., Montelione, G. T., Nilges, M., Ragan, T. J., Schwieters, C. D., Tejero, R., Ulrich, E. L., Velankar, S., Vranken, W. F., Wedell, J. R., Westbrook, J., Wishart, D. S., and Vuister, G. W., NMR Exchange Format: a unified and open standard for representation of NMR restraint data., Nature Structural & Molecular Biology, vol. 22, pp. 433–434, 2015.
P. Smirnov, Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D. M. A., Grossmann, P., Beck, A. H., Aerts, H. J. W. L., Lupien, M., Goldenberg, A., and Haibe-Kains, B., PharmacoGx: an R package for analysis of large pharmacogenomic datasets, Bioinformatics, 2015.
A. Rosato, Vranken, W., Fogh, R. H., Ragan, T. J., Tejero, R., Pederson, K., Lee, H. - W., Prestegard, J. H., Yee, A., Wu, B., Lemak, A., Houliston, S., Arrowsmith, C. H., Kennedy, M., Acton, T. B., Xiao, R., Liu, G., Montelione, G. T., and Vuister, G. W., The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013, Journal of Biomolecular NMR, vol. 62, pp. 413–424, 2015.
R. Huculeci, Garcia-Pino, A., Buts, L., Lenaerts, T., and van Nuland, N., Structural insights into the intertwined dimer of Fyn SH2, Protein Science, p. n/a–n/a, 2015.
A. Colaprico, Silva, T. C., Olsen, C., Garofano, L., Cava, C., Garolini, D., Sabedot, T. S., Malta, T. M., Pagnotta, S. M., Castiglioni, I., Ceccarelli, M., Bontempi, G., and Noushmehr, H., TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data, Nucleic Acids Research, 2015.