Books

A.Carbone and S.Semmes, A Graphic Apology for Symmetry and Implicitness, Mathematical Monographs, Oxford University Press, 2000. (500 pages) [ZentralblattMATH Review]

A.Carbone, Geometry and Combinatorics of Proof Structures, manuscript in preparation (270 pages).

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Edited Books

A. Carbone, M. El-Kebir (Eds), collection of selected articles from the conference WABI 2021, special edition of Algorithms in Molecular Biology, Springer, Chicago, 2022.

A. Carbone, M. El-Kebir (Eds), WABI 2021, proceedings, LIPIcs, Volume 201, 2021 (online at www.dagstuhl.de/dagpub/978-3-95977-200-6).

A.Carbone, F.Ferreira, B.Lowe, E.Majordomo (Eds), Computability in Europe 2010, special issue of the Journal of Logic and Computation, 2014, doi: 10.1093/logcom/exs075

G. Nuel, B. Prum, Analyse statistique des sequences biologiques: modélisation markovienne, alignements et motifs. A. Carbone (Ed), Collection of Bioinformatics by Hermes Sciences, 2007.

A.Carbone, N.Pierce, DNA Computing, LNCS 3892, Springer, 2006. Proceedings of The 11th International Workshop on DNA Computing, DNA11, London, Ontario, Canada, June 2005.

P.Bourgine, A.Carbone, M.Gromov, F.Képès, Macromolecular Networks, a collection of articles on the theme, in the journal ComPlexUs, Kluwer, April 2003. [content]

A.Carbone, M.Gromov and P.Pruzinkiewicz, Pattern Formation in Biology, Vision and Dynamics. World Scientific Publishing Company, 2000. Introduction by A. Carbone, M. Gromov, P. Pruzinkiewicz, I. Vardi. (7 pages) [preface] [Gazette des Mathématiciens Review][World Scientific Content - Abstract]

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Articles

E. Sarti, J. Henri, A. Carbone, “Multiple gene copies, diverse functions: exploring single- and multidomain architectures in the Calvin-Benson-Bassham Cycle”, submitted, 2025.

R. Vicedomini, N. Righetti, L. Polit, S. Condemi, L. Longo, A. Carbone, “Genetic dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation”, submitted, 2025.

G. Lombardi, A. Carbone, “MuLAN: Mutation-driven Light Attention Networks for investigating protein-protein interactions from sequences”, submitted, 2025. [bioRxiv]

A. Carbone, L. Longo, S. Condemi, ”Starch4Sapiens: dans le ventre de l'évolution humaine”, Histoire de la recherche contemporaine, revue du CNRS, submitted, 2025.

G. Lombardi, B. Seoane, A. Carbone, “LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences”, Bioinformatics, 2025.

M. Tekpinar, L. David, T. Henri, A. Carbone, “PRESCOTT: a population aware, epistatic and structural model accurately predicts missense effect”, Genome Biology, 2025. [MedRxiv]

S. Lemaire, G. Lombardi, A. Mancini, A. Carbone, J. Henri, “Functional recoding of Chlamydomonas reinhardtii thioredoxin type-h into photosynthetic type-f by switching selectivity determinants”, Frontiers in Plant Biology, 2025.

A. Carbone, E. Laine, G. Lombardi, “Unlocking protein evolution insights: efficient and interpretable mutational effect predictions with GEMME”, Protein Design and Evolution: Methods and Protocols, in the Springer book series Methods in Molecular Biology, (F. Pazos ed.), Springer, 2025. [bioRxiv]

A. Carbone, A. Decelle, L. Rosset, B. Seoane, “Fast and Functional Structured Data Generators Rooted in Out-of-Equilibrium Physics”, IEEE Transactions on Pattern Analysis and Machine Intelligence, 2024. [arXiv]

K. Volzhenin, L. Bittner, A. Carbone, “SENSE-PPI reconstructs interactomes within, across, and between species at the genome scale”, iScience, 2024.

S. Darvish Shafighi, A. Geras, B. Jurzysta, A. Sahaf Naeini, I. Filipiuk, L. Rczkowski, H. Toosi, L. Koperski, K. Thrane, C. Engblom, J. Mold, X. Chen, J. Hartman, D. Nowis, A. Carbone, J. Lagergren, E. Szczurek, "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope", Nature Communications, 2024. [bioRxiv]

Y. Mohseni Behbahani, P. Saighi, E. Laine, A. Carbone, "LEVELNET to visualise, explore and compare protein-protein interaction networks", Proteomics, 2023.

Y. Mohseni Behbahani, E. Laine, A. Carbone, "Deep Local Analysis estimates effects of mutations on protein-protein interactions", Bioinformatics, 2023.

G. Teano, L. Concia, L. Carron, L. Wolff, K. Adamusovà, M. Fojtovà, M. Bourge, A. Kramdi, V. Colot, U.Grossniklaus, C. Bowler, C. Baroux, A. Carbone, A. Probst, P. Prochàzkovà, Schrumpfovà, J. Fajkus, S Amiard, S. Grob, C. Bourbousse and F. Barneche, "Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis", Cell Reports 2023. [bioRxiv]

L. Carron, L. Concia, S. Grob, F. Barneche, A. Carbone, J. Mozziconacci, A layer cake model for plant and metazoan chromatin, manuscript, 2023. [bioRxiv]

Mohseni-Behbahani Y, Crouzet S, Laine E, Carbone A. Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. Bioinformatics, 2022.

Oteri F, Sarti E, Nadalin F, Carbone A. "iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families", Nucleic Acids Research, 2022. [link]

Le Moigne T, Sarti E, Nourisson A, Carbone A, Lemaire SD, Henri J. "Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii", Journal of Structural Biology, 2022. [link]

B. Seoane, A. Carbone, "Soft disorder modulates the assembly path of protein complexes", PLoS Computational Biology, 2022.

R.Vicedomini, J.P.Bouly, E.Laine, A.Falciatore, A.Carbone, "Multiple profile models extract features from protien sequence data and resolve functional diversity of very different protein families", Molecular Biology and Evolution, 2022. [link]

C. Dequeker, Y. Mohseni Behbahani, L. David, E. Laine, A. Carbone, "From complete cross-docking to partners identification and binding sites predictions", PLoS Computational Biology, 2022. [link]

J. Wu, D. Danko, E. Afshinnekoo, D. Bezdan, M. Bhattacharyya, E. Castro-Nallar, ... & MetaSUB Consortium. "Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association", Environmental Research, 207, 112183, 2022.

J. Perez-Vargas, E. Teppa, F. Amirache, C. Combet, A. Bockmann, F. Fusil, A. Carbone*, F.L. Cosset*, "A fusion peptide in preS1 and the protein-disulde isomerase ERp57 are involved in HBV membrane fusion process", eLife, 2021. [link]

R. Vicedomini, L. Polit, S. Condemi, L. Longo, A. Carbone, "Dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation", 2021. [bioRxiv]

Danko, David, et al. & MetaSUB Consortium. "A global metagenomic map of urban microbiomes and antimicrobial resistance." Cell, 2021.

Vicedomini R, Blachon C, Oteri F, Carbone A. MyCLADE: a multi-source domain annotation server for sequence functional exploration. Nucleic Acids Research, 2021.

B.Seoane, A.Carbone. The complexity of protein interactions unravelled from structural disorder, PLoS Computational Biology, 2021. [link]

Y.Karami, P.Saighi, R.Vanderhaegen, D.Gerlier, S.Longhi, E.Laine, A.Carbone. Predicting substitutions to modulate disorder and stability in coiled-coils, BMC Bioinformatics, 2020. [bioRxiv]

R.Laplaza, F.Peccati, R.A.Boto,  C. Quan, A. Carbone, J-P. Piquemal, Y. Maday, J. Contreras-García. NCIPLOT4: A New Step Towards a Fast Quantification of Noncovalent Interactions, WIREs Computational Molecular Science, 2020. [ChemRxiv]

R.Boto, F.Peccati, R.Laplaza, C.Quan, A.Carbone, J-P.Piquemal, Y.Maday, J.Contreras-Garcia. NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions. Journal of Chemical Theory and Computation, 2020.

G.Drillon, R.Champeimont, F.Oteri, G.Fischer, A.Carbone. Phylogenetic reconstruction based on synteny block and gene adjacencies, Molecular Biology and Evolution, 2020. [bioRxiv]

E.Teppa, D.Zea, F.Oteri, A.Carbone, COVTree: Coevolution in OVerlapped sequences by Tree analysis server. Nucleic Acids Research, 2020.

L.David, R.Vicedomini, H.Richard, A.Carbone, Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinformatics, 2020.

E. Teppa, F. Nadalin, C. Combet, D. Zea, L. David, A. Carbone, Coevolution analysis of amino-acids reveals diversified drug resistance solutions in viral sequences: a case study of hepatitis B virus. Virus Evolution, 2020.

F.Corsi, R.Lavery, E.Laine, A.Carbone, Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties, PLoS Computational Biology, 2020. [bioRxiv]

M.F.Lensink, G.Brysbaert, N.Nadzirin, S.Velankar, R.A.G.Chaleil, T.Gerguri, P.A.Bates, E.Laine, A.Carbone, S.Grudinin, and others, Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment, Proteins: Structure, Function, and Bioinformatics, 2019.

E.Laine, Y.Karami, A.Carbone, GEMME: a simple and fast global epistatic model predicting mutational effects, Molecular Biology and Evolution, 2019. [bioRxiv] See the MBE cover.

C.Dequeker, E.Laine, A.Carbone, Decrypting protein surfaces by combining evolution, geometry, and molecular docking, Proteins: Structure, Function, and Bioinformatics, 2019.

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

N.Lagarde, A.Carbone, S.Sacquin-Mora, Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. Proteins: Structure, Function, and Bioinformatics, 2018.

R.Raucci, E.Laine, A.Carbone, Local Interaction Signal Analysis: a new approach for the prediction of protein-protein binding affinity. Structure, 2018. Featured by "Faculty of 1000".

F.Douam, F.Fusil, M.Enguehard, L.Dib, F.Nadalin, L.Schwaller, G.Hrebikova, J.Mancip, L.Mailly, R.Montserret, Q.Ding, C.Maisse, E.Carlot, K.Xu, E.Verhoeyen, T.Baumert, A.Carbone*, FL.Cosset*, D.Lavillette*, 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. (* corresponding authors)

S.Briquet, A.Ourimi, C.Pionneau, J.Bernardes, A.Carbone, S.Chardonnet, C.Vaquero. Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation. PLoS One, 2018.

Y.Karami, T.Bitard Feildel, E.Laine, A.Carbone, "Infostery" analysis of protein dynamics identifies highly sensitive residues and predicts deleterious mutations. Scientific Reports, 2018.

C. Dequeker, E. Laine, A. Carbone, INTerface Builder: a Fast Protein-Protein Interface Reconstruction Tool. J of Chemical Information and Modelling, ACS, 2017.

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

J. Bernardes, C. Vaquero, A. Carbone, Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. Malaria Journal, 2017.

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

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

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

E.Laine, A.Carbone, Protein social behaviour makes a stronger signal for protein partner identification than protein surface geometry. Proteins: Structure, Function, and Bioinformatics, 2016.

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

L.Vamparys, B.Laurent, A.Carbone, S.Sacquin-Mora, Great interactions: how binding incorrect partners can teach us about correct protein interfaces, Proteins: Structure, Function, and Bioinformatics, 2016.

R.Champeimont, E.Laine, S-W.Hu, F.Penin, A.Carbone, Coevolution analysis of genotypes identifies the Hepatitis C virus protein functional dependency network, Scientific Reports, 2016.

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

A.E. Fortunato, M. Jaubert, G. Enomoto, J-P. Bouly, R. Raniello, M. Thaler, S. Malviya, J. Silva Bernardes, F. Rappaport, A. Carbone, C. Bowler, M. Ribera d'Alcalà, M. Ikeuchi, A. Falciatore, Diatom phytochromes reveal the existence of far-red light based sensing in the oceans. The Plant Cell, 2016.

E.Laine, A.Carbone, Local geometry and evolutionary conservation of protein surfaces reveal the
multiple recognition patches in protein-protein interactions. PLoS Computational Biology, 2015.

J.Bernardes, F.R.J.Vieira, G.Zaverucha, A.Carbone, A multi-objective optimisation approach accurately resolves protein domain architectures. Bioinformatics, 2015.

Y.Karami, E.Laine, A.Carbone. Dissecting protein architecture with communication blocks and communicating segment pairs. BMC Bioinformatics, 2015.

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

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

A. Mathelier, A. Carbone. Predicted human structural clusters of miRNAs target cancer genes. In "Deep Insight" of the Atlas of Genetics & Cytogenetics in Oncology and Haematology, May 2014. Free online version.

Drillon G, Carbone A, Fischer G. SynChro: a fast and easy tool to reconstruct and visualize Synteny blocks along eukaryotic Chromosomes. PLoS ONE, 2014.

A.Lopes, S.Sacquin-Mora, V.Dimitrova, E.Laine, Y.Ponty, A.Carbone, Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information, PLoS Computational Biology, 2013.

A.Carbone, Extracting co-evolving characters from a tree of species. In Discrete and Topological Models in Molecular Biology, N.Jonoska, M.Saito, G.Rozenberg (eds.), Springer, 2013.

A.Mathelier, A.Carbone, Large scale chromosomal mapping of human microRNA structural clusters, Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt112.

L.Dib, A.Carbone, Protein fragments: functional and structural roles of their coevolution networks, PLoS ONE, 7(11): e48124, 2012.

L.Dib, A.Carbone, CLAG: an unsupervised non hierarchical clustering algorithm handling biological data, BMC Bioinformatics, 13:194, 2012.

G.Drillon, A.Carbone, G.Fischer. Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. Journal of Logic and Computation, doi: 10.1093/logcom/exr047, 2011.

J.S. Bernardes, A. Carbone, G. Zaverucha, A discriminative method for protein remote homology detection that combines Inductive Logic Programming and propositional models. BMC Bioinformatics, 12:83, 2011.

A.Mathelier, A.Carbone. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics, 26(18):2226--34, 2010.

A.Carbone, L.Dib, Co-evolution and information signals in biological sequences. Theoretical Computer Science, 2010. doi:10.1016/j.tcs.2010.10.040.

A.Mathelier, A.Carbone. Chromosomal periodicity and positional networks of genes in Escherichia coli. Molecular Systems Biology, 6:366, 2010. [Pdf]

J.Baussand, A.Carbone. A combinatorial approach to detect co-evolved amino-acid networks in protein families with variable divergence, PLoS Computational Biology, 5(9):e1000488, 2009.

S. Engelen, L.Trojan, S. Sacquin-Mora, R. Lavery, A. Carbone. Joint Evolutionary Trees: detection and analysis of protein interfaces, PLoS Computational Biology, 5(1): e1000267, 1--17, 2009.

A.Carbone. A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs, Information & Computation, 2009. doi:10.1016/j.ic.2009.01.007

A.Carbone. Logical structures and genus of proofs, Annals of Pure and Applied Logic, 161(2), 139--149, 2009.

S.Sacquin-Mora, A.Carbone, R.Lavery. Identification of protein interaction partners and protein-protein interaction sites via cross-docking simulations, Journal of Molecular Biology, 382:1276-1289, 2008.

J.Baussand, A.Carbone. Inconsistent distances in substitution matrices can be avoided by properly handling hydrophobic residues, Evolutionary Bioinformatics, 4:255--261, 2008. [Pdf]

A.Carbone, S.Engelen. Information content of sets of biological sequences revisited, in Algorithmic Bioprocesses, edited by A.Condon, D.Harel, J.N.Kok, A.Salomaa, E.Winfree, Natural Computing Series, Springer, 2008. In print. [Pdf]

A. Carbone. Codon bias is a major factor explaining phage evolution in translationally biased hosts, Journal of Molecular Evolution, 66(3):210--23, 2008. [Pdf]

J. Baussand, C. Deremble, A. Carbone. Periodic distribution of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins, Proteins: Structure, Function and Bioinformatics, 67(3):695-708, 2007. [Pdf]

J.Breton, E.Bart-Delabesse, S.Biligui, A.Carbone, X.Sellier, M.Okome-Nkoumou, C.Nzamba, M.Kombila, I.Accoceberry, M.Thellier. Genotypic analysis of Enterocytozoon bieneusi isolates from Gabon and Cameroon: reporting a new highly divergent sequence and a wide distribution of genotypes, Journal of Clinical Microbiology, 45(8):2580-2589, 2007. [Pdf]

A. Carbone. Group cancellation and resolution, Studia Logica, 82:75-95, 2006. [Pdf]

A. Carbone. Computational prediction of genomic functional cores specific to different microbes, Journal of Molecular Evolution, 63(6):733-746, 2006. [Pdf]
Featured by "Faculty of 1000", by "NewsRx - Life Science Weekly" and by "BioPortfolio News - Genomics & Genetics Weekly"

A. Carbone, R. Madden. Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis, Journal of Molecular Evolution, 61:456-469, 2005. [Pdf]

A. Carbone, C. Mao, P.E. Constantinou, B. Ding, J. Kopatsch, W.B. Sherman, N.C. Seeman. 3D Fractal DNA Assembly from Coding, Geometry and Protection, Natural Computing, 3:235-252, 2004. [Pdf]

A. Carbone, F. Képès, A. Zinovyev. Codon bias signatures, organisation of microorganisms in codon space and lifestyle, Molecular Biology and Evolution, 22(3):547-561, 2004. [Pdf]

A. Carbone, M. Gromov. Functional labels and syntactic entropy on DNA strings and proteins, Theoretical Computer Science, 303:35-51, 2003. [Pdf]

A. Carbone, N.C. Seeman. Coding and geometrical shapes in nanostructures: a fractal DNA-assembly, Natural Computing, 2:133-151, 2003. [Pdf]

A. Carbone, A. Zinovyev, F. Képès. Codon Adaptation Index as a measure of dominating codon bias, Bioinformatics, 19:2005-2015, 2003. [Pdf]

A. Carbone, N.C. Seeman. "Molecular Tiling and DNA self-assembly", in Aspects of Molecular Computing, N. Jonoska, G. Paun, G. Rozenberg (Eds), Lecture Notes in Computer Science 2950, Springer, 2003. [Pdf]

B. Mishra, R. Daruwala, Y. Zhou, N. Ugel, A. Policriti, M. Antoniotti, S. Paxia, M. Rejali, A. Rudra, V. Cherepinsky, N. Silver, W. Casey, C. Piazza, M. Simeoni, P. Barbano, M. Spivak, J-W. Feng, O. Gill, M. Venkatesh, F. Cheng, B. Sun, I. Ioniata, T.S. Anantharaman, E.J.A. Hubbard, A. Pnueli, D. Harel, V. Chandru, R. Hariharan, M. Wigler, F. Park, S.-C. Lin, Y. Lazebnik, F. Winkler, C. Cantor, A. Carbone, and M. Gromov. A Sense of Life: computational and experimental investigations with models of biochemical and evolutionary processes, OMICS - A Journal of Integrative Biology, Special Issue on BioCOMP, S. Kumar Ed., 7(3):253-268, 2003. [Pdf]

A. Carbone. The cost of a cycle is a square, Journal of Symbolic Logic, 67:35-60, 2002. [Pdf]

A. Carbone. Streams and strings in formal proofs, Theoretical Computer Science, 288(1):45-83, 2002. [Pdf]

A. Carbone, N.C. Seeman. Circuits and Programmable Self-Assembling DNA Structures, Proceedings of the National Academy of Sciences USA, 99:12577-12582, 2002. [Pdf]

A. Carbone, N.C. Seeman. A Route to Fractal DNA-Assembly, Natural Computing, 1:469-480, 2002. [Pdf]

A. Carbone, M. Gromov. Mathematical slices of molecular biology, La Gazette des Mathématiciens, Société Mathématique de France, special edition, 11-80 april 2001. Russian translation appeared in the book series Modern Mathematics, Scientific and Publishing House, Izhevsk, 2003. [ps]

A. Carbone. Cycles of relatively prime length and the Road Coloring Problem, Israel Journal of Mathematics, 123:303-316, 2001. [ps]

A. Carbone. Asymptotic cyclic expansion and bridge groups of formal proofs, Journal of Algebra, 242:109-145, 2001. [Pdf]

A. Carbone. Cycling in Proofs and Feasibility, Transactions of the American Mathematical Society, 352:2049-2075, 2000. [Pdf]

A. Carbone. Quantified propositional logic speeds-up propositional logic on the number of lines of tree-like proofs, Studia Logica, 64:333-339, 2000. [ps]

A. Carbone, S. Semmes. Looking from the inside and from the outside, Synthèse, 125:385-412, 2000. [ps]

A. Carbone. Duplication of directed graphs and exponential blow up of proofs, Annals of Pure and Applied Logic, 100:1-76, 1999. [Pdf]

A. Carbone. Turning cycles into spirals, Annals of Pure and Applied Logic, 96:57-73, 1999. [Pdf]

A. Carbone, S. Semmes. Propositional Proofs via Combinatorial Geometry and the Search for Symmetry, Colloquium Logicum - Annals of the Kurt Gödel Society, Czech Academy of Science Press, 3:85-98, 1999. [ps]

A. Carbone, S. Semmes. Making proofs without Modus Ponens: an introduction to the combinatorics and complexity of cut elimination, Bullettin of the American Mathematical Society, 34:131-159, 1997. [Pdf]

A. Carbone. Interpolants, Cut Elimination and Flow Graphs for the Propositional Calculus, Annals of Pure and Applied Logic, 83:249-299, 1997. [Pdf]

A. Carbone. The Craig Interpolation Theorem for Schematic Systems, Colloquium Logicum - Annals of the Kurt Gödel Society, Springer-Verlag, 2:87-100, 1996. [ps]

A. Carbone. Provable Fixed Points in IDelta0 + Omega1, Notre Dame Journal of Formal Logic. 32:562-572, 1991.

A. Carbone, F. Montagna. Much Shorter Proofs: a Bimodal Investigation, Zeitschrift fur Mathematische Logik und Grundlagen der Mathematik. 36, 1990.

A. Carbone, F. Montagna. Rosser Orderings in Bimodal Logics, Zeitschrift fur Mathematische Logik und Grundlagen der Mathematik. 35:343-358, 1989.

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Collections - invited papers

A. Carbone, Conservation, co-évolution et dynamique : de la séquence à la fonction, collection from the 2016 Colloque de Cerisy Sciences de la vie, sciences de l’information, M-C. Maurel, J-C. Pomerol, T. Gaudin, D. Lacroix (eds.), ISTE, 2017.

A.Carbone, L'encodage des réseaux évolutifs dans les protéines: de la séquence à la fonction. In Leçon de mathématiques d'aujourd'hui, G.Senizergues (eds.), Cassini, 2017.

E. Laine, A. Carbone, Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking, 2nd International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics, PR PS BB 2013, satellite at 17th International Conference on Image Analysis and Processing (ICIAP).

A.Carbone, L.Dib, Co-evolution and information signals in biological sequences, in LNCS 5532, Jianer Chen and Barry Cooper (eds), Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation, ChangSha, China, May 2009. Pages 6-17.

A.Carbone and A.Mathelier. Environmental and physiological insights from microbial genome sequences. Elements of Computational Systems Biology, Huma Lodhi and Stephen Muggleton (eds.), Wiley Book Series in Bioinformatics, 325-339, 2009. [Pdf]

A.Carbone. Adaptation studied with the Self-Consistent Codon Index: genomic spaces, metabolic network comparison, minimal gene sets and viral classification. Proceedings of the Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, Genopole, Evry, May 2007. [Pdf]

J.Baussand, A.Carbone. Metagénomique bactérienne et virale - nouvelles définitions d'espace microbien et nouveaux défis algorithmiques. Technique et Sciences Informatiques, special issue on "Modeling and simulations in postgenomics", Hérmes, 245-255, 2007. [Pdf]

A. Carbone. Pathways of deduction, Geometries of nature, living systems and human cognition - New Interactions of Mathematics with Natural Sciences and Humanities, L. Boi editor, World Scientific, Hackensack, NJ, 383-400, 2005. [Pdf]

A. Carbone. Spazio dei geni, spazio dei genomi e determinazione di un genoma minimale, Annals of the Centro di Ricerca Matematica Ennio de Giorgi, Scuola Normale di Pisa. 2005. [Pdf]

A. Carbone. Revisiting the codon adaptation index from a whole-genome perspective: gene expression, codon bias, and metabolic networks in the context of genomes comparison, Proceedings of the Belgian Royal Academy of Sciences, Mathematics and Genomics, 18 October 2003. 29-35, 2005. [Pdf]

A. Carbone. Cooperativity and symmetry at biological scales, in GROUP-24: Physical and Mathematical Aspects of Symmetries (Proceedings of the 24th International Colloquium on Group Theoretical Methods in Physics, Paris, 15-20 Juillet 2002), Institute of Physics, Conference Series Number 173, J-P. Gazeau, R. Kerner, J-P. Antoine, S. Métens and J-Y. Thibon Eds., Institute of Physics Publishing, Bristol and Philadelphia, 51-60, 2003. [ps]

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PROCEEDINGS WITH REFEREE PROCESS

G. Lombardi, A. Carbone, “MuLAN: Mutation-driven Light Attention Networks for investigating protein-protein interactions from sequences”, 22nd International Conference on Computational Methods in Systems Biology (CMSB) 2024, Pise, Italy, 2024.

L. Rosset, A. Carbone, A. Decelle, and B. Seoane, ”Fast and Functional structured data generator”. ICML 2023, Workshop on Structured Probabilistic Inference & Generative Modeling (SPIGM), Honolulu, Hawaii, United States, 2023.

Y. Mohseni Behbahani, E. Laine, and A. Carbone, "Deep Local Analysis estimates effects of mutations on protein-protein interactions". Machine Learning for Structural Biology (MLSB), workshop at NeurIPS 2022.

Y. Mohseni Behbahani, E. Laine, A. Carbone. DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes. Machine Learning for Structural Biology (MLSB), Workshop at NeurIPS 2021.

Y. Mohseni Behbahani, E.Laine, A. Carbone. DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes. Methodes Algorithmiques pour les Structures et Interactions Macromoleculaires (MASIM), Lyon 2021.

E. Laine, H. Ripoche, A. Carbone. Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, USA, published in Biophys J. 110:S347A-348A, 2016.

Y. Karami, S. Amselem, E. Laine, A. Carbone, Disease-related mutations in proteins: A study of dynamically correlated networks and coevolved residue clusters, Congress of the European Society for Evolutionary Biology, Lausanne, Switzerland, August 10-14, 2015

E. Laine, A. Carbone, Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking. In A. Petrosino, L. Maddalena, P. Pala (Eds.), IEEE International Conference on Image Analysis and Processing (ICIAP) 2013 Workshops, LNCS 8158, pp. 318–325. Springer, Heidelberg, 2013.

J.Baussand, A.Carbone. A co-evolution model to identify evolutionarily conserved networks of amino-acids interactions in protein families, Proceedings of the 11th Evolutionary Biology Meeting, Marseille, September 18-21, 2007 (1 page).

S. Sacquin-Mora, R. Lavery, L. Trojan, A. Carbone, Une opération de docking croié à grande échelle pour la détection de partenaires protéiques potentiels. Proceedings of the workshop Mathématiques et Interactions, Institut Henri Poincaré, October 2006 (5 pages). [pdf]

A.Carbone, N.Seeman. Circuits and programmable self-assembling DNA structures, Proceedings of DNA 8. Hokkaido University, Sapporo, Japan, 2002. (1 page)

A. Carbone. Strutture di Simulazione per un Calcolo Classico, Proceedings of the Third Conference on Logic Programming GULP, Rome (Italie), May 11-13, 65-77, 1988.

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Posters

A. Kobayashi, J. Park, A. Brion, G. Lombardi, A. Carbone, J-P. Concordet, J. Miné-Hattab, ”Single molecule tracking of phase separating FUS during early stages of DNA repair”, 19th Dresden Polymer Discussion, focused on Biomolecular Condensates and Polymer Phase Transitions, Meissen, Germany, 2025.

L. Longo, C. Cagnato, E. Badetti, S. Condemi, A. Carbone, ”AnthropoCENE”: Expanding the foodscape was key for Homo sapiens in the past. Considerations on present day drawback of an evolutionary success. Climpast 2024, University of Bern, Switzerland, 2024.

L. Rosset, A. Carbone, A. Decelle, B. Seoane. ”Fast and Functional structured data generator”. 1st Structured Probabilistic Inference & Generative Modeling (SPIGM) workshop at the International Conference on Machine Learning - ICML 2023, Hawaii, 2023.

G. Lombardi, A. Carbone, "Predicting Binding Affinity Changes in Protein Complexes with Protein Language Models". MLCSB COSI: Machine Learning in Computational and Systems Biology, ISMB/ECCB, Lyon, 2023.

F. Oteri, E. Sarti, F. Nadalin, A. Carbone. iBIS2Analyzer a web server for a phylogeny-driven coevolution analysis of protein families, ISMB 2022 (virtual), Michigan, US, 2022.

E. Sarti, J. Henri, T. Le Moigne, A. Carbone. Paralog function annotation with ProfileView, ISMB 2022 (virtual), Michigan, US, 2022.

Y. Mohseni Behbahani, E. Laine, A. Carbone, "Deep Local Analysis evaluates protein docking conformations with locally oriented cubes". 30th conference on Intelligent Systems for Molecular Biology (ISMB). July 10-14, 2022.

Y. Mohseni Behbahani, S. Grudinin, E. Laine, A. Carbone, "Deep Local Analysis Ranker Server for estimating inter-subunit interfaces accuracy in multimeric complexes". 15th edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP). Dec 10-13, 2022.

Y. Mohseni Behbahani, E. Laine, A. Carbone. Prediction of the effects of mutations on protein-protein interactions with geometric deep learning. ACM-BCB 2021 and WABI 2021, Chicago, 2021.

Y. Mohseni Behbahani, E. Laine, A. Carbone. Prediction of the effects of mutations on protein-protein interactions with geometric deep learning. VarI COSI, ISMB/ECCB 2021, virtual, 2021.

Y. Mohseni Behbahani, E. Laine, A. Carbone. DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes. BioML thematic School Graph as models in life sciences: Machine learning and integrative approaches, Orsay, 2021.

S. Darvish Shafighi, A. Geras, A.S. Naeini, B. Jurzysta, H. Toosi, I. Filipiuk, L. Rczkowski, L. Koperski, A. Carbone, J. Lagergren and E. Szczurek. TUMOROSCOPE: Inferring a map of tumor subclones from Spatial Transcriptomics and bulk DNA sequencing data, RECOMB 2021, 2021.

B. Seoane, A. Carbone, Disorder modulates the order of assembly of protein complexes, BioML thematic School Graph as models in life sciences: Machine learning and integrative approaches, Orsay, 2021.

Y. Mohseni Behbahani, E. Laine, A. Carbone. Prediction of the effects of mutations on protein-protein interactions with geometric deep learning. BioML thematic School Graph as models in life sciences: Machine learning and integrative approaches, Orsay, 2021.

F. Corsi, C. Dequeker, E. Laine and A.Carbone. Decrypting protein surfaces using evolutionary information, geometry and docking. CAPRI 2019, Hinxton, UK, April 3-5, 2019.

L. David, R. Vicedomini, H. Richard and A. Carbone. S3A: A Scalable and Accurate Annotated Assembly Tool for Gene Assembly. JOBIM2019, Nantes, Juin 2019.

E. Teppa, A. Carbone. A web server for identication and analysis of coevolution in overlapping proteins. JOBIM2019, Nantes, Juin 2019.

E. Teppa, A. Carbone. CovTree: a web server for identication and analysis of coevolution in overlapping proteins. ISMB/ECCB 2019, Bâle, Juillet 2019.

E. Laine, Y. Karami, A. Carbone. GEMME: a simple and fast global epistatic model predicting mutational eects. ISMB/ECCB 2019, Bâle, Juillet 2019.

F. Corsi, E. Laine and A.Carbone. JET2DNA: a tool for accurate prediction of protein-DNA interfaces based on evolutionary information, physico-chemical and geometrical properties. ISMB/ECCB 2019, B^ale, Juillet 2019.

F.Corsi, E.Laine, A.Carbone. JET2DNA: accurate prediction of protein-DNA interfaces based on evolutionary information, physico-chemical and geometrical properties. ISMB 2018, Chicago, Illinois, USA. July 6-19 2018.

F.Corsi, E.Laine, A.Carbone. JET2DNA: a tool for accurate prediction of protein-DNA interfaces based on evolutionary information, physico-chemical and geometrical. ECCB 2018, Athens, Greece, September 8-12 2018.

F.Corsi, E.Laine, A.Carbone. JET2DNA: a tool for accurate prediction of protein-DNA interfaces based on evolutionary information, physico-chemical and geometrical. ESCS 2018 (European Student Council Symposium, pre-meeting at ECCB 2018), Athens, Greece, September 8-12 2018 (poster with flash talk).

E.Teppa, F.Nadalin, C.Combet, J.Pérez-Vargas, F-L.Cosset, A.Carbone. Coevolution analysis finds amino-acids involved in immune evasion in Hepatitis B Virus. JOBIM 2018, Marseille, France. July 3-6 2018.

C.Dequeker, E.Laine, A.Carbone, Large scale analysis of protein interactions. JOBIM 2018, Marseille, France. July 3-6 2018.

L.David, H.Richard, R.Vicedomini, A.Carbone. S3A: A Scalable and Accurate Annotated Assembly Tool for Targeted Gene Assembly, RECOMB 2018, Paris, April 23-25, 2018.

J.Pérez-Vargas, F.Nadalin, C.Combet, C.Sureau, A.Carbone and F-L.Cosset. Characterization of cell entry determinants mediated by HBV surface glycoproteins. 17e réunion du réseau national hépatities virales de l'ANRS, Centre de Congrès UIC, Paris, 2017.

F.Nadalin, A.Carbone. Residue propensity and local geometry of the interface contacts define the specificity of protein-protein interactions. 15th European Conference on Computational Biology (ECCB 2016), 2016. The Hague, The Netherlands.

A.Ait-hamlat, C.Durand, P.Charbord, T.Jaffredo A.Carbone. Hub centered network deconvolution improves Gene Regulatory Networks Reconstruction. 15th European Conference on Computational Biology (ECCB 2016), 2016. The Hague, The Netherlands.

C.Dequeker, R.Raucci, E.Laine, A.Carbone. Large scale analysis of protein interactions. 15th European Conference on Computational Biology (ECCB 2016), 2016, The Hague, The Netherlands.

F.Corsi, A.Carbone, E.Laine. Towards an accurate prediction of protein-DNA interfaces based on evolutionary information, physico-chemical properties of residues and local geometry of the protein structure. 15th European Conference on Computational Biology (ECCB 2016), 2016, The Hague, The Netherlands.

E.Laine, A.Carbone. Local geometry and evolutionary conservation of protein surfaces reveal the multiple recognition patches in protein-protein interactions. 6th CAPRI Evaluation Meeting, University of Tel Aviv, 2016, Tel Aviv, Israel.

L. Vamparys, A. Carbone, S. Sacquin-Mora. What binding incorrect partners can teach us about protein interfaces : lessons from a high-throughput cross-docking study. 29th Annual Symposium of the Protein Society, 2015, Barcelone, Espagne.

Fortunato AE, Annunziata R, Cheminant S, Huysman MJJ, Bernardes J, Carbone A, Petroutsos D, Finazzi G, Falciatore A. Towards a molecular characterization of Circadian Clock components in marine diatoms. DYNAMO Labex Symposium: Evolution, biogenesis and dynamics of energy transducing membranes, 2014, Paris, France.

A.Ugarte, J.Bernardes, A.Carbone, META-CASH : a tool to identify domains and functional annotation of metatranscriptomic sequences, ISMB/ECCB 2014, September 2014, Strasbourg, France.

Y.Karami, S.Amselem E.Laine, A.Carbone, Disease-related mutations in proteins: a study of dynamically correlated networks and coevolved residue clusters, ISMB/ECCB 2014, September 2014, Strasbourg, France.

G.Drillon, A.Carbone and G. Fischer, PhyChro: Phylogenetic reconstruction based on chromosomal rearrangements. In Comparative genomics of eukaryotic microorganisms: Complexity patterns in eukaryotic genomes, EMBO conference, San Feliu, Spain, 2013.

J.Bernardes, G.Zaverucha, C.Vaquero, A.Carbone, Large scale analysis of the Plasmodium falciparum proteome through a multitude of diversified profiles, 2013 Annual Molecular Parasitology Meeting, September 2013, Woods Hole, MA, USA.

A. Lopes, S. Sacquin-Mora, V. Dimitrova, E. Laine, Y. Ponty, A. Carbone, Protein-protein interactions in a crowded environment: analysis via cross-docking and evolutionary information, ISMB/ECCB 2013, July 2013, Berlin, Germany.

E.Laine, A.Carbone, Accurate Prediction of Protein-Protein Contacts: from Patches to Sites, ISMB/ECCB 2013, July 2013, Berlin, Germany.

R.Champeimont, A.Carbone, Chromosomal organization of the yeast recombinosome is explained by convergent and divergent genes, ISMB/ECCB 2013, July 2013, Berlin, Germany.

J.Bernardes, A.Fortunato, A.Falciatore, A.Carbone, Phaeodactylum tricornutum genome re-annotation through multiple evolutionary models, The Molecular Life of Diatoms, EMBO workshop, Collège de France, June 2013, Paris, France.

Fortunato AE, Cheminant S, Huysman MJJ, Bernardes J, Carbone A, Petroutsos D, Finazzi G, Brembu T, Bones AM, Falciatore A. Looking for the Circadian Clock components in marine diatoms. EMBO Workshop: The Molecular Life of Diatoms, Collège de France, June 2013, Paris, France.

Fortunato AE, Cheminant S, Huysman MJJ, Bernardes J, Carbone A, Petroutsos D, Finazzi G, Brembu T, Bones AM, Falciatore A. Looking for the Circadian Clock components in marine diatoms. International Symposium on Plant Photobiology (ISPP), 2013, Edinburgh, UK.

F.Douam, L.Dib, V.Loan Dao Thi, G.Maurin, L.Schwaller, J.Fresquet, D.Mompelat, FL.Cosset, A.Carbone and D.Lavillette, Identification of functional networks in E1E2 glycoproteins unveils Hepatitis C Virus fusion mechanisms and new therapeutic opportunities, European Virology Congress, Lyon, 2013.

R.Champeimont, A.Carbone, Genome periodicity analysis using Fourier transforms in E. coli and yeasts, The Biology and Physics of Bacterial Genome Organization, workshop organized at the Lorentz Center, June 2012, Leiden, the Netherlands.

G.Drillon, A.Carbone, G.Fischer, Reconstruction of rearrangement history and ancestral genomes in yeast based on synteny packs, RECOMB 2010, April 2010, Lisbon, Portugal.

L.Dib, A.Carbone, Co-evolution of blocks of residues and sectors in protein structures, Protein Dynamics, Allostery and Function, Keystone Symposia, Ivet Bahar and Lila M. Gierasch (organizers), June 5 - 10, 2009, Keystone Resort, Keystone, Colorado.

L.Dib, A.Carbone, Co-evolution of blocks of residues and sectors in protein structures, ISMB/ECCB 2009, Stockholm, Sweden, Juin 2009.

A.Mathelier, A.Carbone, A novel ab initio method finding microRNA clusters in genomes, ISMB/ECCB 2009, Stockholm, Sweden, Juin 2009.

A.Mathelier, A.Carbone, Finding miRNAs homologs in genomes with no learning, JOBIM 2009, Nantes, France, 2009.

L.Dib, A.Carbone, Co-evolution of blocks of residues and sectors in protein structures, JOBIM 2009, Nantes, France, 2009.

C. Parizot, J. Baussand, M. Carpentier, K. Dorgham, Z. Amoura, A. Carbone, G. Gorochov, Longitudinal analysis of the human Treg repertoire, World Immune Regulation Meeting III special focus on ”Regulatory & Effector Mechanisms”, 22-25 Mars 2009, Davos, Suisse.

S.Sacquin-Mora, A.Carbone, R.Lavery. Identification of protein interaction partners and protein-protein interaction sites, Grand Challenges in Computational biology, Barcelona, Spain, 2-4 Juin 2008.

J.Baussand, A.Carbone. A combinatorial model of amino acids co-evolution: identification of conserved networks of interactions in protein families, BioSapiens Workshop, Bruxelles, Belgique, Avril 2008.

S. Sacquin-Mora, A. Carbone, R. Lavery. Coupling of cross-docking simulations and Evolutionary Trace methods for the detection of protein-protein interactions. Multi-Protein Complexes Involved in Cell Regulation, Keystone Symposia Conference, Cambridge, Angleterre, August 2006.

J.Baussand, A.Carbone. Periodic distribution of hydrophobic amino-acids used for distantly related proteins alignment and homology search, European Conference of Computational Biology, Elat, Israel, 2006.

J. Baussand, C. Deremble, A. Carbone. Intégration des Clusters Hydrophobes dans les alignements de séquences : un outils pour la détection et l'alignement des protéines de faible homologie, JOBIM 2005, Lyon, 2005.

S. Sacquin-Mora, A. Carbone, R. Lavery. Large scale investigation of protein-protein interactions via cross docking simulations and Evolutionary Trace methods. M2Cell, Workshop on Modeling from Macromolecules to Cells, Abbaye de Fontevraud, 2005.

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Expository papers

N.Abdollahi et al. Meet-U: educating through research immersion, PLoS Computational Biology, 2018.

F. Képès, A. Carbone. "Modelling Macromolecular Networks: two meetings in Paris, July, 2002", BioEssays, special issue dedicated to "Modelling complex biological systems", 24:1188-1190, 2002. [Pdf]

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