Gènomique Analytique

Pdfs and abstracts

Equipe de Génomique Analytique
Université Pierre et Marie Curie, INSERM U511
Responsable : Alessandra Carbone, Alessandra DOT Carbone AT lip6 DOT fr

Articles

A.Carbone, M.Gromov, Mathematical slices of molecular biology, La Gazette des Mathematiciens, Numéro spécial 88:11-80, Société Mathématique de France, 2001.

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

A.Carbone, N.C.Seeman, A Root to Fractal DNA Assembly, Natural Computing, 1:469-480, 2002.

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.

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

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

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.

A.Carbone, N.C.Seeman, Coding and Geometrical Shapes in Nanostructures: fractal DNA assemblies, Natural Computing, 2:133-151, 2003.

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.

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.

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.

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.

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.

A.Carbone, Computational prediction of genomic functional cores specific to different microbes. Journal of Molecular Evolution, 63(6):733-746, 2006.

M. Carpentier, J. Pothier, Protein Pairwise Structural Comparison Methods : a Review. 2007. In press.

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

J.Baussand, A.Carbone, Metagénomique bactérienne et virale - nouvelles définitions d'espace microbiale et nouveaux défis algorithmiques. Special issue "Modeling and simulations for Post-genomics", Techniques et Sciences Informatiques, Hérmes, 245-255, 2007.

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.

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.

A.Carbone, Codon bias is a major factor explaining phage evolution in translationally biased hosts, Journal of Molecular Evolution, 2008.

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 press.

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, 1-6, 2008. In press.

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, 2008. In press.

S.Engelen, L.A.Trojan, S.Sacquin-Mora, R.Lavery, A.Carbone, JET: detection and analysis of protein interfaces based on evolution, PLoS Computational Biology, 5(1): e1000267, 1--17, 2009. doi:10.1371/journal.pcbi.1000267

J.Baussand, A.Carbone, A combinatorial approach to detect co-evolved amino-acid networks in protein families with variable divergence, submitted, 2008.

Books

Pattern Formation in Biology, Vision and Dynamics. A.Carbone, M.Gromov, P.Pruzinkiewicz editors. World Scientific Publishing Company, 2000.

Macromolecular Networks. P.Bourgine, A.Carbone, M.Gromov, F.Képès editors. Collection of articles appeared as a journal issue of ComPlexUs, Kluwer, April 2003.

DNA Computing. A.Carbone, N.Pierce editors. LNCS 3892, Springer, 2006. Proceedings of the 11th International Workshop on DNA Computing - DNA11, June 6-9 2005, London Ontario, Canada.



	People \| Projects \| Data&Software \| Stages \| Seminars \| publications
Pdfs and abstracts	Equipe de Génomique Analytique Université Pierre et Marie Curie, INSERM U511 Responsable : Alessandra Carbone, Alessandra DOT Carbone AT lip6 DOT fr

	Articles

	A.Carbone, M.Gromov, Mathematical slices of molecular biology, La Gazette des Mathematiciens, Numéro spécial 88:11-80, Société Mathématique de France, 2001.

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

	A.Carbone, N.C.Seeman, A Root to Fractal DNA Assembly, Natural Computing, 1:469-480, 2002.

	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.

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

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

	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.

	A.Carbone, N.C.Seeman, Coding and Geometrical Shapes in Nanostructures: fractal DNA assemblies, Natural Computing, 2:133-151, 2003.

	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.

	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.

	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.

	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.

	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.

	A.Carbone, Computational prediction of genomic functional cores specific to different microbes. Journal of Molecular Evolution, 63(6):733-746, 2006.

	M. Carpentier, J. Pothier, Protein Pairwise Structural Comparison Methods : a Review. 2007. In press.

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

	J.Baussand, A.Carbone, Metagénomique bactérienne et virale - nouvelles définitions d'espace microbiale et nouveaux défis algorithmiques. Special issue "Modeling and simulations for Post-genomics", Techniques et Sciences Informatiques, Hérmes, 245-255, 2007.

	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.

	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.

	A.Carbone, Codon bias is a major factor explaining phage evolution in translationally biased hosts, Journal of Molecular Evolution, 2008.

	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 press.

	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, 1-6, 2008. In press.

	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, 2008. In press.

	S.Engelen, L.A.Trojan, S.Sacquin-Mora, R.Lavery, A.Carbone, JET: detection and analysis of protein interfaces based on evolution, PLoS Computational Biology, 5(1): e1000267, 1--17, 2009. doi:10.1371/journal.pcbi.1000267

	J.Baussand, A.Carbone, A combinatorial approach to detect co-evolved amino-acid networks in protein families with variable divergence, submitted, 2008.

	Books

	Pattern Formation in Biology, Vision and Dynamics. A.Carbone, M.Gromov, P.Pruzinkiewicz editors. World Scientific Publishing Company, 2000.

	Macromolecular Networks. P.Bourgine, A.Carbone, M.Gromov, F.Képès editors. Collection of articles appeared as a journal issue of ComPlexUs, Kluwer, April 2003.

	DNA Computing. A.Carbone, N.Pierce editors. LNCS 3892, Springer, 2006. Proceedings of the 11th International Workshop on DNA Computing - DNA11, June 6-9 2005, London Ontario, Canada.