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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, F. Ferreira, B. Lowe, E. Majordomo (Eds), special issue CiE2010 of the Journal of Logic and Computation, 2011, in press.
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
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. In print.
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, 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. [Pdf]
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
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 croisé 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
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
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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