Alessandra Carbone

58 papers B 1C 2Journal 51Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics.
IEEE Trans. Pattern Anal. Mach. Intell.
Alessandra Carbone, Aurélien Decelle, Lorenzo Rosset, Beatriz Seoane
2025 J jnl
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences.
Bioinform.
Gianluca Lombardi, Beatriz Seoane, Alessandra Carbone
2023 J jnl
Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation.
Bioinform.
Yasser Mohseni Behbahani, Elodie Laine, Alessandra Carbone
2023 J jnl
Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics.
CoRR
Alessandra Carbone, Aurélien Decelle, Lorenzo Rosset, Beatriz Seoane
2022 J jnl
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes.
Bioinform.
Yasser Mohseni Behbahani, Simon Crouzet, Elodie Laine, Alessandra Carbone
2022 J jnl
From complete cross-docking to partners identification and binding sites predictions.
PLoS Comput. Biol.
Chloé Dequeker, Yasser Mohseni Behbahani, Laurent David, Elodie Laine, Alessandra Carbone
2022 J jnl
Soft disorder modulates the assembly path of protein complexes.
PLoS Comput. Biol.
Beatriz Seoane, Alessandra Carbone
2022 J jnl
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families.
Nucleic Acids Res.
Francesco Oteri, Edoardo Sarti, Francesca Nadalin, Alessandra Carbone
2021 C ed.
21st International Workshop on Algorithms in Bioinformatics, WABI 2021, Virtual Conference, August 2-4, 2021
WABI
Alessandra Carbone, Mohammed El-Kebir
2021 J jnl
MyCLADE: a multi-source domain annotation server for sequence functional exploration.
Nucleic Acids Res.
Riccardo Vicedomini, Clémence Blachon, Francesco Oteri, Alessandra Carbone
2021 J jnl
The complexity of protein interactions unravelled from structural disorder.
PLoS Comput. Biol.
Beatriz Seoane, Alessandra Carbone
2020 J jnl
COVTree: Coevolution in OVerlapped sequences by Tree analysis server.
Nucleic Acids Res.
Elin Teppa, Diego J. Zea, Francesco Oteri, Alessandra Carbone
2020 J jnl
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.
PLoS Comput. Biol.
Flavia Corsi, Richard Lavery, Elodie Laine, Alessandra Carbone
2020 J jnl
Predicting substitutions to modulate disorder and stability in coiled-coils.
BMC Bioinform.
Yasaman Karami, Paul Saighi, Rémy Vanderhaegen, Denis Gerlier, Sonia Longhi, Elodie Laine, Alessandra Carbone
2020 J jnl
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.
Bioinform.
Laurent David, Riccardo Vicedomini, Hugues Richard, Alessandra Carbone
2018 J jnl
Meet-U: Educating through research immersion.
PLoS Comput. Biol.
Nika Abdollahi, Alexandre Albani, Éric 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
2018 J jnl
Protein-protein interaction specificity is captured by contact preferences and interface composition.
Bioinform.
Francesca Nadalin, Alessandra Carbone
2017 J jnl
BIS2Analyzer: a server for co-evolution analysis of conserved protein families.
Nucleic Acids Res.
Francesco Oteri, Francesca Nadalin, Raphaël Champeimont, Alessandra Carbone
2017 J jnl
INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool.
J. Chem. Inf. Model.
Chloé Dequeker, Elodie Laine, Alessandra Carbone
2017 J jnl
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.
Nucleic Acids Res.
Hugues Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
2016 J jnl
A multi-objective optimization approach accurately resolves protein domain architectures.
Bioinform.
Juliana S. Bernardes, Fabio R. J. Vieira, Gerson Zaverucha, Alessandra Carbone
2016 J jnl
Dissecting protein architecture with communication blocks and communicating segment pairs.
BMC Bioinform.
Yasaman Karami, Elodie Laine, Alessandra Carbone
2016 J jnl
Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.
PLoS Comput. Biol.
Juliana S. Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone
2015 J jnl
Computability in Europe 2010.
J. Log. Comput.
Alessandra Carbone, Fernando Ferreira, Benedikt Löwe, Elvira Mayordomo
2015 J jnl
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions.
PLoS Comput. Biol.
Elodie Laine, Alessandra Carbone
2014 — ch.
Extracting Coevolving Characters from a Tree of Species.
Discrete and Topological Models in Molecular Biology
Alessandra Carbone
2014 J jnl
SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis.
BMC Bioinform.
Raphaël Champeimont, Alessandra Carbone
2013 J jnl
Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs.
J. Log. Comput.
Guénola Drillon, Alessandra Carbone, Gilles Fischer
2013 — conf
Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking.
ICIAP Workshops
Elodie Laine, Alessandra Carbone
2013 J jnl
Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information.
PLoS Comput. Biol.
Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone
2012 J jnl
CLAG: an unsupervised non hierarchical clustering algorithm handling biological data.
BMC Bioinform.
Linda Dib, Alessandra Carbone
2011 J jnl
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models.
BMC Bioinform.
Juliana S. Bernardes, Alessandra Carbone, Gerson Zaverucha
2011 J jnl
Co-evolution and information signals in biological sequences.
Theor. Comput. Sci.
Alessandra Carbone, Linda Dib
2010 J jnl
A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs.
Inf. Comput.
Alessandra Carbone
2010 J jnl
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Bioinform.
Anthony Mathelier, Alessandra Carbone
2009 J jnl
A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence.
PLoS Comput. Biol.
Julie Baussand, Alessandra Carbone
2009 C conf
Co-evolution and Information Signals in Biological Sequences.
TAMC
Alessandra Carbone, Linda Dib
2009 — conf
Information Content of Sets of Biological Sequences Revisited.
Algorithmic Bioprocesses
Alessandra Carbone, Stefan Engelen
2009 J jnl
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling.
PLoS Comput. Biol.
Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone
2009 J jnl
Logical structures and genus of proofs.
Ann. Pure Appl. Log.
Alessandra Carbone
2007 J jnl
Chronique : Métagénomique bactérienne et virale.
Tech. Sci. Informatiques
Julie Baussand, Alessandra Carbone
2006 B ed.
DNA Computing, 11th International Workshop on DNA Computing, DNA 2005, London, ON, Canada, June 6-9, 2005. Revised Selected Papers.
DNA
Alessandra Carbone, Niles A. Pierce
2006 J jnl
Group Cancellation and Resolution.
Stud Logica
Alessandra Carbone
2004 J jnl
3D Fractal DNA Assembly from Coding, Geometry and Protection.
Nat. Comput.
Alessandra Carbone, Chengde Mao, Pamela E. Constantinou, Baoquan Ding, Jens Kopatsch, William B. Sherman, Nadrian C. Seeman
2004 — conf
Molecular Tiling and DNA Self-assembly.
Aspects of Molecular Computing
Alessandra Carbone, Nadrian C. Seeman
2003 J jnl
Coding and geometrical shapes in nanostructures: A fractal DNA-assembly.
Nat. Comput.
Alessandra Carbone, Nadrian C. Seeman
2003 J jnl
Codon adaptation index as a measure of dominating codon bias.
Bioinform.
Alessandra Carbone, Andrei Yu. Zinovyev, François Képès
2003 J jnl
Functional labels and syntactic entropy on DNA strings and proteins.
Theor. Comput. Sci.
Alessandra Carbone, Misha Gromov
2002 J jnl
Streams and strings in formal proofs.
Theor. Comput. Sci.
Alessandra Carbone
2002 J jnl
The Cost of A Cycle Is A Square.
J. Symb. Log.
Alessandra Carbone
2000 J jnl
Looking From The Inside And From The Outside.
Synth.
Alessandra Carbone, S. Semmes
2000 J jnl
Quantified Propositional Logic and the Number of Lines of Tree-Like Proofs.
Stud Logica
Alessandra Carbone
1999 J jnl
Duplication of Directed Graphs and Exponential Blow Up of Proofs.
Ann. Pure Appl. Log.
Alessandra Carbone
1999 J jnl
Turning Cycles into Spirals.
Ann. Pure Appl. Log.
Alessandra Carbone
1997 J jnl
Interpolants, Cut Elimination and Flow Graphs for the Propositional Calculus.
Ann. Pure Appl. Log.
Alessandra Carbone
1991 J jnl
Provable Fixed Points in I Δ
Notre Dame J. Formal Log.
Alessandra Carbone
1990 J jnl
Much shorter proofs: A bimodal investigation.
Math. Log. Q.
Alessandra Carbone, Franco Montagna
1989 J jnl
Rosser Orderings in Bimodal Logics.
Math. Log. Q.
Alessandra Carbone, Franco Montagna