Rosser Orderings in Bimodal Logics. - Alessandra Carbone; Franco Montagna (Math. Log. Q., 1989)

Much shorter proofs: A bimodal investigation. - Alessandra Carbone; Franco Montagna (Math. Log. Q., 1990)

Provable Fixed Points in I Δ0 + Ω1. - Alessandra Carbone (Notre Dame J. Formal Log., 1991)

Interpolants, Cut Elimination and Flow Graphs for the Propositional Calculus. - Alessandra Carbone (Ann. Pure Appl. Log., 1997)

Duplication of Directed Graphs and Exponential Blow Up of Proofs. - Alessandra Carbone (Ann. Pure Appl. Log., 1999)

Turning Cycles into Spirals. - Alessandra Carbone (Ann. Pure Appl. Log., 1999)

Quantified Propositional Logic and the Number of Lines of Tree-Like Proofs. - Alessandra Carbone (Stud Logica, 2000)

Looking From The Inside And From The Outside. - Alessandra Carbone; S. Semmes (Synth., 2000)

The Cost of A Cycle Is A Square. - Alessandra Carbone (J. Symb. Log., 2002)

Streams and strings in formal proofs. - Alessandra Carbone (Theor. Comput. Sci., 2002)

Codon adaptation index as a measure of dominating codon bias. - Alessandra Carbone; Andrei Yu. Zinovyev; François Képès (Bioinform., 2003)

Coding and geometrical shapes in nanostructures: A fractal DNA-assembly. - Alessandra Carbone; Nadrian C. Seeman (Nat. Comput., 2003)

Functional labels and syntactic entropy on DNA strings and proteins. - Alessandra Carbone; Misha Gromov (Theor. Comput. Sci., 2003)

Molecular Tiling and DNA Self-assembly. - Alessandra Carbone; Nadrian C. Seeman (Aspects of Molecular Computing, 2004)

3D Fractal DNA Assembly from Coding, Geometry and Protection. - Alessandra Carbone; Chengde Mao; Pamela E. Constantinou; Baoquan Ding; Jens Kopatsch; William B. Sherman; Nadrian C. Seeman (Nat. Comput., 2004)

Group Cancellation and Resolution. - Alessandra Carbone (Stud Logica, 2006)

Chronique : Métagénomique bactérienne et virale. - Julie Baussand; Alessandra Carbone (Tech. Sci. Informatiques, 2007)

Information Content of Sets of Biological Sequences Revisited. - Alessandra Carbone; Stefan Engelen (Algorithmic Bioprocesses, 2009)

Logical structures and genus of proofs. - Alessandra Carbone (Ann. Pure Appl. Log., 2009)

A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence. - Julie Baussand; Alessandra Carbone (PLoS Comput. Biol., 2009)

Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. - Stefan Engelen; Ladislas A. Trojan; Sophie Sacquin-Mora; Richard Lavery; Alessandra Carbone (PLoS Comput. Biol., 2009)

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. - Anthony Mathelier; Alessandra Carbone (Bioinform., 2010)

A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs. - Alessandra Carbone (Inf. Comput., 2010)

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. - Juliana S. Bernardes; Alessandra Carbone; Gerson Zaverucha (BMC Bioinform., 2011)

Co-evolution and information signals in biological sequences. - Alessandra Carbone; Linda Dib (Theor. Comput. Sci., 2011)

CLAG: an unsupervised non hierarchical clustering algorithm handling biological data. - Linda Dib; Alessandra Carbone (BMC Bioinform., 2012)

Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking. - Elodie Laine; Alessandra Carbone (ICIAP Workshops, 2013)

Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. - Guénola Drillon; Alessandra Carbone; Gilles Fischer (J. Log. Comput., 2013)

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. - Anne Lopes; Sophie Sacquin-Mora; Viktoriya Dimitrova; Elodie Laine; Yann Ponty; Alessandra Carbone (PLoS Comput. Biol., 2013)

SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis. - Raphaël Champeimont; Alessandra Carbone (BMC Bioinform., 2014)

Extracting Coevolving Characters from a Tree of Species. - Alessandra Carbone (Discrete and Topological Models in Molecular Biology, 2014)

Computability in Europe 2010. - Alessandra Carbone; Fernando Ferreira 001; Benedikt Löwe; Elvira Mayordomo (J. Log. Comput., 2015)

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. - Elodie Laine; Alessandra Carbone (PLoS Comput. Biol., 2015)

A multi-objective optimization approach accurately resolves protein domain architectures. - Juliana S. Bernardes; Fabio R. J. Vieira; Gerson Zaverucha; Alessandra Carbone (Bioinform., 2016)

Dissecting protein architecture with communication blocks and communicating segment pairs. - Yasaman Karami; Elodie Laine; Alessandra Carbone (BMC Bioinform., 2016)

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence. - Juliana S. Bernardes; Gerson Zaverucha; Catherine Vaquero; Alessandra Carbone (PLoS Comput. Biol., 2016)

BIS2Analyzer: a server for co-evolution analysis of conserved protein families. - Francesco Oteri; Francesca Nadalin; Raphaël Champeimont; Alessandra Carbone (Nucleic Acids Res., 2017)

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures. - Hugues Ripoche; Elodie Laine; Nicoletta Ceres; Alessandra Carbone (Nucleic Acids Res., 2017)

INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool. - Chloé Dequeker; Elodie Laine; Alessandra Carbone (J. Chem. Inf. Model., 2017)

Protein-protein interaction specificity is captured by contact preferences and interface composition. - Francesca Nadalin; Alessandra Carbone (Bioinform., 2018)

Meet-U: Educating through research immersion. - Nika Abdollahi; Alexandre Albani; Éric Anthony; Agnes Baud; Mélissa Cardon; Robert Clerc; Dariusz Czernecki; Romain Conte; Laurent David; Agathe Delaune; Samia Djerroud; Pauline Fourgoux; et al. (PLoS Comput. Biol., 2018)

Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. - Laurent David; Riccardo Vicedomini; Hugues Richard; Alessandra Carbone (Bioinform., 2020)

Predicting substitutions to modulate disorder and stability in coiled-coils. - Yasaman Karami; Paul Saighi; Rémy Vanderhaegen; Denis Gerlier; Sonia Longhi; Elodie Laine; Alessandra Carbone (BMC Bioinform., 2020)

COVTree: Coevolution in OVerlapped sequences by Tree analysis server. - Elin Teppa; Diego J. Zea; Francesco Oteri; Alessandra Carbone (Nucleic Acids Res., 2020)

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. - Flavia Corsi; Richard Lavery; Elodie Laine; Alessandra Carbone (PLoS Comput. Biol., 2020)

MyCLADE: a multi-source domain annotation server for sequence functional exploration. - Riccardo Vicedomini; Clémence Blachon; Francesco Oteri; Alessandra Carbone (Nucleic Acids Res., 2021)

The complexity of protein interactions unravelled from structural disorder. - Beatriz Seoane; Alessandra Carbone (PLoS Comput. Biol., 2021)

Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. - Yasser Mohseni Behbahani; Simon Crouzet; Elodie Laine; Alessandra Carbone (Bioinform., 2022)

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. - Francesco Oteri; Edoardo Sarti; Francesca Nadalin; Alessandra Carbone (Nucleic Acids Res., 2022)

From complete cross-docking to partners identification and binding sites predictions. - Chloé Dequeker; Yasser Mohseni Behbahani; Laurent David; Elodie Laine; Alessandra Carbone (PLoS Comput. Biol., 2022)

Soft disorder modulates the assembly path of protein complexes. - Beatriz Seoane; Alessandra Carbone (PLoS Comput. Biol., 2022)

Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation. - Yasser Mohseni Behbahani; Elodie Laine; Alessandra Carbone (Bioinform., 2023)

Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics. - Alessandra Carbone; Aurélien Decelle; Lorenzo Rosset; Beatriz Seoane (IEEE Trans. Pattern Anal. Mach. Intell., 2025)