Alessandra Carbone

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 20

Top Topics

Protein Interaction

Selectional Restrictions

Experimentally Determined

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Yasser Mohseni Behbahani, Elodie Laine, Alessandra Carbone
Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation. Bioinform. 39 (Supplement-1) (2023)
Alessandra Carbone, Aurélien Decelle, Lorenzo Rosset, Beatriz Seoane
Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics. CoRR (2023)
Yasser Mohseni Behbahani, Simon Crouzet, Elodie Laine, Alessandra Carbone
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. Bioinform. 38 (19) (2022)
Beatriz Seoane, Alessandra Carbone
Soft disorder modulates the assembly path of protein complexes. PLoS Comput. Biol. 18 (11) (2022)
Chloé Dequeker, Yasser Mohseni Behbahani, Laurent David, Elodie Laine, Alessandra Carbone
From complete cross-docking to partners identification and binding sites predictions. PLoS Comput. Biol. 18 (1) (2022)
Francesco Oteri, Edoardo Sarti, Francesca Nadalin, Alessandra Carbone
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. Nucleic Acids Res. 50 (W1) (2022)
Riccardo Vicedomini, Clémence Blachon, Francesco Oteri, Alessandra Carbone
MyCLADE: a multi-source domain annotation server for sequence functional exploration. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Beatriz Seoane, Alessandra Carbone
The complexity of protein interactions unravelled from structural disorder. PLoS Comput. Biol. 17 (1) (2021)
Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine, Alessandra Carbone
Predicting substitutions to modulate disorder and stability in coiled-coils. BMC Bioinform. (19) (2020)
Elin Teppa, Diego J. Zea, Francesco Oteri, Alessandra Carbone
COVTree: Coevolution in OVerlapped sequences by Tree analysis server. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Flavia Corsi, Richard Lavery, Elodie Laine, Alessandra Carbone
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. PLoS Comput. Biol. 16 (2) (2020)
Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinform. 36 (13) (2020)
Francesca Nadalin, Alessandra Carbone
Protein-protein interaction specificity is captured by contact preferences and interface composition. Bioinform. 34 (3) (2018)
Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphaël Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana S. Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes
Meet-U: Educating through research immersion. PLoS Comput. Biol. 14 (3) (2018)
Chloé Dequeker, Elodie Laine, Alessandra Carbone
INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool. J. Chem. Inf. Model. 57 (11) (2017)
Francesco Oteri, Francesca Nadalin, Raphaël Champeimont, Alessandra Carbone
BIS2Analyzer: a server for co-evolution analysis of conserved protein families. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Hugues Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures. Nucleic Acids Res. 45 (Database-Issue) (2017)
Yasaman Karami, Elodie Laine, Alessandra Carbone
Dissecting protein architecture with communication blocks and communicating segment pairs. BMC Bioinform. 17 (S-2) (2016)
Juliana S. Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. PLoS Comput. Biol. 12 (7) (2016)
Juliana S. Bernardes, Fabio R. j. Vieira, Gerson Zaverucha, Alessandra Carbone
A multi-objective optimization approach accurately resolves protein domain architectures. Bioinform. 32 (3) (2016)
Elodie Laine, Alessandra Carbone
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PLoS Comput. Biol. 11 (12) (2015)
Alessandra Carbone, Fernando Ferreira, Benedikt Löwe, Elvira Mayordomo
Computability in Europe 2010. J. Log. Comput. 25 (4) (2015)
Raphaël Champeimont, Alessandra Carbone
SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis. BMC Bioinform. 15 (2014)
Elodie Laine, Alessandra Carbone
Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking. ICIAP Workshops (2013)
Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone
Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. PLoS Comput. Biol. 9 (12) (2013)
Guénola Drillon, Alessandra Carbone, Gilles Fischer
Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. J. Log. Comput. 23 (4) (2013)
Linda Dib, Alessandra Carbone
CLAG: an unsupervised non hierarchical clustering algorithm handling biological data. BMC Bioinform. 13 (2012)
Juliana S. Bernardes, Alessandra Carbone, Gerson Zaverucha
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. BMC Bioinform. 12 (2011)
Alessandra Carbone, Linda Dib
Co-evolution and information signals in biological sequences. Theor. Comput. Sci. 412 (23) (2011)
Alessandra Carbone
A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs. Inf. Comput. 208 (5) (2010)
Anthony Mathelier, Alessandra Carbone
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinform. 26 (18) (2010)
Alessandra Carbone, Linda Dib
Co-evolution and Information Signals in Biological Sequences. TAMC (2009)
Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. PLoS Comput. Biol. 5 (1) (2009)
Alessandra Carbone
Logical structures and genus of proofs. Ann. Pure Appl. Log. 161 (2) (2009)
Julie Baussand, Alessandra Carbone
A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence. PLoS Comput. Biol. 5 (9) (2009)
Alessandra Carbone, Stefan Engelen
Information Content of Sets of Biological Sequences Revisited. Algorithmic Bioprocesses (2009)
Julie Baussand, Alessandra Carbone
Chronique : Métagénomique bactérienne et virale. Tech. Sci. Informatiques 26 (1-2) (2007)
Alessandra Carbone
Group Cancellation and Resolution. Stud Logica 82 (1) (2006)
Alessandra Carbone, Nadrian C. Seeman
Molecular Tiling and DNA Self-assembly. Aspects of Molecular Computing (2004)
Alessandra Carbone, Chengde Mao, Pamela E. Constantinou, Baoquan Ding, Jens Kopatsch, William B. Sherman, Nadrian C. Seeman
3D Fractal DNA Assembly from Coding, Geometry and Protection. Nat. Comput. 3 (3) (2004)
Alessandra Carbone, Andrei Yu. Zinovyev, François Képès
Codon adaptation index as a measure of dominating codon bias. Bioinform. 19 (16) (2003)
Alessandra Carbone, Misha Gromov
Functional labels and syntactic entropy on DNA strings and proteins. Theor. Comput. Sci. 303 (1) (2003)
Alessandra Carbone, Nadrian C. Seeman
Coding and geometrical shapes in nanostructures: A fractal DNA-assembly. Nat. Comput. 2 (2) (2003)
Alessandra Carbone
Streams and strings in formal proofs. Theor. Comput. Sci. 288 (1) (2002)
Alessandra Carbone
The Cost of A Cycle Is A Square. J. Symb. Log. 67 (1) (2002)
Alessandra Carbone
Quantified Propositional Logic and the Number of Lines of Tree-Like Proofs. Stud Logica 64 (3) (2000)
Alessandra Carbone, S. Semmes
Looking From The Inside And From The Outside. Synth. 125 (3) (2000)
Alessandra Carbone
Turning Cycles into Spirals. Ann. Pure Appl. Log. 96 (1-3) (1999)
Alessandra Carbone
Duplication of Directed Graphs and Exponential Blow Up of Proofs. Ann. Pure Appl. Log. 100 (1-3) (1999)
Alessandra Carbone
Interpolants, Cut Elimination and Flow Graphs for the Propositional Calculus. Ann. Pure Appl. Log. 83 (3) (1997)
Alessandra Carbone
. Notre Dame J. Formal Log. 32 (4) (1991)
Alessandra Carbone, Franco Montagna
Much shorter proofs: A bimodal investigation. Math. Log. Q. 36 (1) (1990)
Alessandra Carbone, Franco Montagna
Rosser Orderings in Bimodal Logics. Math. Log. Q. 35 (4) (1989)