Publications

“A global ocean atlas of eukaryotic genes”, 2018.

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.

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.

D. Raimondi, Orlando, G., Pancsa, R., Khan, T., and Vranken, W. F., “Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins.”, Scientific reports, vol. 7, p. 8826, 2017.

C. Reggiani, Coppens, S., Sekhara, T., Dimov, I., Pichon, B., Lufin, N., Addor, M. - C., Belligni, E. Fabia, Digilio, M. Cristina, Faletra, F., Ferrero, G. Battista, Gerard, M., Isidor, B., Joss, S., Niel-Bütschi, F., Perrone, M. Dolores, Petit, F., Renieri, A., Romana, S., Topa, A., Vermeesch, J. Robert, Lenaerts, T., Casimir, G., Abramowicz, M., Bontempi, G., Vilain, C., Deconinck, N., and Smits, G., “Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability”, Genome Medicine, vol. 9, p. 67, 2017.

F. Pucci and Rooman, M., “Physical and molecular bases of protein thermal stability and cold adaptation”, Current Opinion in Structural Biology, vol. 42, pp. 117 - 128, 2017.

Q. Hou, De Geest, P., Vranken, W. F., Heringa, J., and K Feenstra, A., “Seeing the Trees through the Forest: Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest.”, Bioinformatics (Oxford, England), p. btx005, 2017.

C. Cava, Colaprico, A., Bertoli, G., Graudenzi, A., Silva, T. C., Olsen, C., Noushmehr, H., Bontempi, G., Mauri, G., and Castiglioni, I., “SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data”, International Journal of Molecular Sciences, vol. 18, 2017.

G. Orlando, Raimondi, D., Khan, T., Lenaerts, T., and Vranken, W. F., “SVM-dependent pairwise HMM: an application to Protein pairwise alignments.”, Bioinformatics (Oxford, England), 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.

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.

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.

F. Pucci, Bourgeas, R., and Rooman, M., “High-quality thermodynamic data on the stability changes of proteins upon single-site mutations”, bioRxiv, 2016.

F. Pucci and Rooman, M., “Improved insights into protein thermal stability: from the molecular to the structurome scale”, bioRxiv, 2016.

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.

G. Orlando, Raimondi, D., and Vranken, W. F., “Observation selection bias in contact prediction and its implications for structural bioinformatics”, Scientific Reports, vol. 6, p. 36679 - , 2016.

O. Van Grembergen, Bizet, M., de Bony, E. J., Calonne, E., Putmans, P., Brohée, S., Olsen, C., Guo, M., Bontempi, G., Sotiriou, C., Defrance, M., and Fuks, F., “Portraying breast cancers with long noncoding RNAs”, Science Advances, vol. 2, 2016.

F. Pucci, Bourgeas, R., and Rooman, M., “Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC”, Scientific Reports, vol. 6, p. 23257 - , 2016.

R. Pancsa, Varadi, M., Tompa, P., and Vranken, W. F., “Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability”, Nucleic Acids Research, vol. 44, pp. D429-D434, 2016.

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.