Alessandra Carbone

Ugarte A, Vicedomini R, Bernardes JS, Carbone A. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. Microbiome. (2018).

Douam F, Fusil F, Enguehard M, Dib L, Nadalin F, Schwaller L, Hrebikova G, Mancip J, Mailly L, Montserret R, Ding Q, Maisse C, Carlot E, Xu K, Verhoeyen E, Baumert T, Ploss A, Carbone A*, Cosset FL*, Lavillette D*. A protein coevolution method designed for conserved sequences uncovers critical features of the original HCV fusion mechanism and provides molecular basis for the design of effective antiviral strategies. PLoS Pathogens. (2018).

Oteri F, Nadalin F, Champeimont R, Carbone A. BIS2Analyzer: a server for coevolution analysis of conserved protein families. Nucleic Acids Research. (2017).

Carbone A Conservation, co-évolution et dynamique : de la séquence à la fonction. in Colloque de Cerisy “Sciences de la vie, sciences de l’information”. Edited by: Maurel M-C., Pomerol J-C., Gaudin T., Lacroix D., ISTE Éditions Ltd (2017)

Dequeker C, Laine E, Carbone A. INTerface Builder: a fast protein-protein interface reconstruction tool. J Chem Inf Model. (2017).

Amato A, Dell'Aquila G, Musacchia F, Annunziata R, Ugarte A, Maillet N, Carbone A, Riberà d'Alcalà M, Sanges R, Iudicone D, Ferrante MI. Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions. Scientific Reports. 7(1), (2017).

Bernardes JS, Vaquero C, Carbone A. Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. Malar J. 16(1), (2017).

Laine E, Carbone A. Protein social behaviour makes a stronger signal for partner identification than surface geometry. Proteins. 85(1), pp.137-154 (2017).

Nadalin F, Carbone A. Protein-protein interaction specificity is captured by contact preferences and interface composition. Bioinformatics. (2017).

Champeimont R, Laine E, Hu S-W, Penin F, Carbone A. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins. Scientific Reports. 6, (2016).

Fortunato AE, Jaubert M, Enomoto G, Bouly J-P, Raniello R, Thaler M, Malviya S, Bernardes JS, Rappaport F, Gentili B, Huysman MJJ, Carbone A, Bowler C, Riberà d'Alcalà M, Ikeuchi M, Falciatore A. Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean. The Plant Cell. 28(3), pp.616 - 628 (2016).

Karami Y, Laine E, Carbone A. Dissecting protein architecture with communication blocks and communicating segment pairs. BMC Bioinformatics. 17, pp.133–148 (2016).

Vamparys L, Laurent B, Carbone A, Sacquin-Mora S. Great interactions: How binding incorrect partners can teach us about protein recognition and function. Proteins. (2016).

Bernardes JS, Zaverucha G, Vaquero C, Carbone A. Improvement in protein domain identification is reached by breaking consensus, with the agreement of many profiles and domain co-occurrence. PLoS Computational Biology. 12(7), (2016).

Ripoche H, Laine E, Ceres N, Carbone A. JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures. Nucleic Acids Research. (2016).

Carbone A L'encodage des réseaux évolutifs dans les protéines: de la séquence à la fonction. in Leçon de mathématiques d'aujourd'hui. Cassini. (2016)

Vakirilis N, Sarilar V, Drillon G, Fleiss A, Agier N, Meyniel J-P, Blanpain L, Carbone A, Devillers H, Dubois K, Gillet-Markowska A, Graziani S, Huu-Vang N, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res. (2016).

Laine E, Carbone A. Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PLoS Comput Biol. 11(12), pp.e1004580 (2015).

Bernardes JS, Vieira FRJ, Zaverucha G, Carbone A. A multi-objective optimization approach accurately resolves protein domain architectures. Bioinformatics. (2015).

Rogato A, Richard H, Sarazin A, Voss B, Cheminant Navarro S, Champeimont R, Navarro L, Carbone A, Hess WR, Falciatore A. The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics. 15, pp.698 (2014).

Carbone A Extracting Coevolving Characters from a Tree of Species. in Discrete and Topological Models in Molecular Biology. Springer Berlin Heidelberg. pp. 45-65 (2014)

Mathelier A, Carbone A. Predicted human structural clusters of miRNAs target cancer genes. Atlas Genet Cytogenet Oncol Haematol. (2014).

Champeimont R, Carbone A. SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis. BMC Bioinformatics. 15, pp.391 (2014).

Drillon G, Carbone A, Fischer G. SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS One. 9(3), pp.e92621 (2014).

Drillon G, Carbone A, Fischer G. Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. Journal of Logic and Computation. 23, pp.815–838 (2013).