Mathematique Informatique et Genome

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[1] Chiapello, H. (1999). Analyse comparée de l'usage des codons dans les génomes de plantes. PhD thesis, Université Paris 6.
[2] Gibrat, J.-F. (1999). Méthodes de reconnaissance de repliements : de la séquence en acides aminés à la structure tridimensionnelle des protéines. In Les Ecoles Physique et Chimie du Vivant, number 1. CNRS.
[3] Reinert, G. and Schbath, S. (1999). Compound Poisson approximations for occurrences of multiple words. In Statistics in Genetics and Molecular Biology, (F. Seillier, ed.). IMS Lecture Notes-Monograph Series. Vol. 33.
[4] Chiapello, H., Ollivier, E., Landès-Devauchelle, C., Nitschké, P. and Risler, J.-L. (1999). Codon usage as a tool to predict the cellular location of ribosomal proteins and aminoacyl-trna synthetases. Nucl. Acids Res. 27 (14) 2848-2851.
[5] El Karoui, M., Biaudet, V., Schbath, S. and Gruss, A. (1999). Characteristics of Chi distribution on several bacterial genomes. Research in Microbiology. 150 579-587.
[6] Francesco, V. D., Munson, P. and Garnier., J. (1999). Foresst: fold recognition from secondary structure predictions of protein. Bioinformatics. 15 131-140.
[7] Geetha, V., Francesco, V. D., Garnier, J. and Munson, P. (1999). Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologues. Protein Engineering. 12 ?-?
[8] Zurutuza, L., Muller, F., Gibrat, J.-F., Taillandier, A., Simon, B., Serre, J. and Mornet, E. (1999). Correlations of genotype and phenotype in hypophosphatasia. Hum. Mol. Genet. 8 1039-46.
[9] Schbath, S. and Bouvier, A. (1998). Finding words with unexpected frequencies in DNA sequences. In Explorapedia of Statistical and Mathematical Techniques for use in Research and Technology. http://www.bioss.sari.ac.uk/smart/unix/intro/slides/home.htm. [ http ]
[10] Chiapello, H., Lisacek, F., Caboche, M. and Hénaut, A. (1998). Codon usage and gene function are related in sequences of A. thaliana. Gene. 209 1-38.
[11] Diaz-Lazcoz, Y., Aude, J.-C., Nitschké, P., Chiapello, H., Landès-Devauchelle, C. and Risler, J.-L. (1998). Evolution of genes and evolution of species: the case of aminoacyl-tRNA synthetases. Mol. Biol. Evol. 15 (11) 1548-1561.
[12] Nitschké, P., Guerdoux-Jamet, P., Chiapello, H., Faroux, G., Hénaut, C., Hénaut, A. and Danchin, A. (1998). Indigo: a World-Wide-Web review of genomes and genes functions. FEMS Microbiology Reviews. 22 207-227.
[13] Reinert, G. and Schbath, S. (1998). Compound Poisson and Poisson process approximations for occurrences of multiple words in markov chains. J. Comp. Biol. 5 223-254.
[14] Zimmermann, K. and Gibrat, J.-F. (1998). In unison: regularization of protein secondary structure predictions that makes use of multiple sequence alignments. Protein Eng. 11 861-5.
[15] Francesco, V. D., McQueen, P., Garnier, J. and Munson, P. (1997b). Incorporating global information into secondary structure prediction with hidden markov models of protein folds. In Proc. 4th Int. Conf. Intel. Sys. Mol. Biol Halkidiki, Grece, 100-103.
[16] Francesco, V. D., Geetha, V., Garnier, J. and Munson, P. (1997a). Fold recognition using predicted secondary structure sequences and hidden markov models of protein folds. Proteins:Struct. Funct. Genet. 1 123-128.
[17] Francesco, V. D., Garnier, J. and Munson, P. (1997c). Protein topology recognition from secondary structure sequences-application of the hidden markov models to the alpha class proteins. J. Mol. Biol. 267 446-463.
[18] Gibrat, J.-F. (1997). Fast calculation of the first and second derivatives of the conformational energy of oligomeric proteins with respect to a set of variables mixing dihedral angles and rigid-body variables. J. Chim. Phys. 94 1234-1256.
[19] Schbath, S. (1997a). Coverage processes in physical mapping by anchoring random clones. J. Comp. Biol. 4 61-82.
[20] Schbath, S. (1997b). An efficient statistic to detect over- and under-represented words in DNA sequences. J. Comp. Biol. 4 189-192.
[21] Cooke, R., Raynal, M., Grellet, F., Delseny, M., Hofte, H., Desprez, T., Amselem, J., Chiapello, H., Caboche, M., Moisan, A., Jourjon, M., Charpenteau, J., Guérier, D., Giraudat, J., Quigley, F., Thomas, F., Yu, D., Mache, R., Parmentier, Y., Marcillac, G., Gigot, C., Fleck, J., Philips, G., Axelos, M., Barbet, C., D., T. and B., L. (1996). Further progress towards a catalogue of all Arabidopsis genes : analysis of a set of 5000 non-redundant ESTs. The Plant Journal. 9 (1) 101-124.
[22] Francesco, V. D., Garnier, J. and Munson, P. (1996). Improving protein secondary structure prediction with aligned homologous sequences. Protein Science. 5 106-113.
[23] Garnier, J., Gibrat, J.-F. and Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266 540-53.
[24] Gibrat, J.-F., Madej, T. and Bryant, S. (1996). Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6 377-85.
[25] Schbath, S. (1995b). Étude asymptotique du nombre d'occurrences d'un mot dans une chaîne de Markov et application à la recherche de mots de fréquence exceptionnelle dans les séquences d'ADN. PhD thesis, Université René Descartes, Paris V.
[26] Declerck, N., Joyet, P., Trosset, J.-Y., Garnier, J. and Gaillardin., C. (1995). Hyperthermostable mutants of b. licheniformis α-amylase: multiple amino acid replacements and molecular modeling. Protein Engineering. 8 1029-1037.
[27] Madej, T., Gibrat, J.-F. and Bryant, S. (1995). Threading a database of protein cores. Proteins. 23 356-69.
[28] Prum, B., Rodolphe, F. and Turckheim, É. (1995). Finding words with unexpected frequencies in DNA sequences. J. R. Statist. Soc. B. 57 205-220.
[29] Schbath, S., Prum, B. and Turckheim, E. d. (1995). Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2 417-437.
[30] Schbath, S. (1995a). Compound Poisson approximation of word counts in DNA sequences. ESAIM: Probability and Statistics. 1 1-16. (http://www.emath.fr/ps/).
[31] Bouzida, D., Garnier, J., Brower, R., Cornette, J. and Delisi., C. (1994). Monte carlo study of the effect of β2-microglobulin on the binding cleft of the hla-a2 complex. Protein Science. 3 911-919.
[32] Gibrat, J.-F., Garnier, J. and Go, N. (1994). Normal mode analysis of oligomeric proteins: reduction of the memory requirement by consideration of rigid geometry and molecular symmetry. J. Comp. Chem. 15 820-837.
[33] Levin, J., Pascarella, S., Argos, P. and Garnier, J. (1993a). Quantification of secondary structure prediction improvement using distantly related proteins. In Protein structure by distance analysis, (H.Bohr and S.Brunak, ed.), 302-314. IOS Press, Amsterdam.
[34] Collura, V., Higo, J. and Garnier, J. (1993). Modeling of protein loops by simulated annealing. Protein Science. 2 1502-1510.
[35] Hofte, H., Desprez, T., Amselem, J., Chiapello, H., Caboche, M., Moisan, A., Jourjon, M., Charpenteau, J., Berthomieu, P., Guérier, D., Giraudat, J., Quigley, F., Thomas, F., Yu, D., Mache, R., Raynal, M., Cooke, R., Grellet, F., Delseny, M., Parmentier, Y., Marcillac, G., Gigot, C., Fleck, J., Philips, G., Axelos, M., Barbet, C., Tremousaygue, D. and Lescure, B. (1993). An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from A. thaliana. The Plant Journal. 4 (6) 1051-1061.
[36] Levin, J., Pascarella, S., Argos, P. and Garnier, J. (1993b). Quantification of secondary structure prediction improvement using multiple alignments. Protein Engineering. 6 849-854.
[37] Robson, B. and Garnier, J. (1993). Protein structure prediction. Nature. 361 505-506.
[38] Gibrat, J.-F., Higo, J., Collura, V. and Garnier, J. (1992). A simulated annealing method for modeling the antigen combining site of antibodies. Immunomethods. 1 107-125.
[39] Higo, J., Collura, V. and Garnier, J. (1992). Development of an extended simulated annealing method : application to the modeling of complementary determining regions of immunoglobulins. Biopolymers. 32 33-43.
[40] Gibrat, J.-F. and Go, N. (1991). Normal mode analysis of human lysozyme: study of the relative moyion of the two domains and characterization of the harmonic motion. J. Chim. Phys. 88 2581-2585.
[41] Garnier, J. and Levin, J. (1991). The protein structure code. what is its present status ? CABIOS. 7 133-142.
[42] Gibrat, J.-F., Robson, B. and Garnier, J. (1991). Influence of the local amino acid sequence upon the zones of the torsional angles phi and psi adopted by residues in proteins. Biochemistry. 30 1578-86.
[43] Bomford, R., Garnier, J. and Robson, B. (1990). Computer aided peptide and protein-engineering sofware development. Biotechnology R & D in the EC (BAP) 1985-1989. A Vassarotti and E. Magnien. Elsevier, Paris. 1 105.
[44] Gibrat, J.-F. and Go, N. (1990). Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins. 8 258-79.
[45] Garnier, J., Levin, J., Gibrat, J.-F. and Biou, V. (1990). Secondary structure prediction and protein design. Biochem. Soc. Symp. 57 11-24.
[46] Garnier, J. (1990). Protein structure prediction. Biochimie. 72 513-524.
[47] Robson., J. G. B. (1989). The gor method for predicting secondary structures in proteins. In Prediction of Protein Structure and the Principles of Protein Conformation, (G. Fasman, ed.), 417-465. Plenum. Press New York.
[48] Binart, N., Chambrand, B., Dumas, B., Rowlands, D., Bigogne, C., Levin, J., Garnier, J., Baulieu, E. and Catelli., M. (1989a). The cDNA-derived amino acid sequence of chick heat shock protein Mr 90,000 (HSP 90) reveals a 'DNA like' structrure potential site of interaction with steroid receptors. Bioch. Bioph. Res. Com. 159 140-147.
[49] Binart, N., Chambraud, B., Levin, J., Garnier, J. and Baulieu, E. (1989b). A highly charged sequence of chick hsp90 : a good candidate for interaction with steroid receptors. J. Steroid Biochem. 34 369-374.
[50] Cherfils, J., Gibrat, J.-F., Levin, J., Batut, J. and Kahn, D. (1989). Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition. J. Mol. Recognit. 2 114-21.
[51] Garnier, J. (1989). Modélisation des peptides et des protéines - intéractions chimie - biologie - mécanismes de reconnaissance moléculaire. M. Deléage ed. Editions INSERM. Tec. Doc. Lavoisier. 12 293-333.
[52] Garnier, J. (1988). Protein structure prediction and protein design. In 8th Int. Biotechnology Symposium, 324-336.
[53] Biou, V., Gibrat, J.-F., Levin, J., Robson, B. and Garnier, J. (1988). Secondary structure prediction: combination of three different methods. Protein Eng. 2 185-91.
[54] Levin, J. and Garnier, J. (1988). Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim. Biophys. Acta. 955 283-295.
[55] Garnier, J. and Robson., B. (1987). Conformational calculations on oncogene products in Computer simulation of carcinogenic processes. (B. Silverman, ed.), 67-90. C.R.C. Press, Boca Raton, Florida.
[56] Fishleigh, R., Robson, B., Garnier, J. and Finn, P. (1987). Studies on rationales for an expert system approach to the interpretation of protein sequence data. preliminary analysis of the human epidermal growth factor receptor. FEBS Letters. 214 219-225.
[57] Gibrat, J.-F., Garnier, J. and Robson, B. (1987). Further developments of protein secondary structure prediction using information theory. new parameters and consideration of residue pairs. J. Mol. Biol. 198 425-43.
[58] Robson, B. and Garnier, J. (1986). Introduction to Proteins and Protein Engineering. Elsevier.
[59] Levin, J., Robson, B. and Garnier, J. (1986). An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Letters. 205 303-308.
[60] Garnier, J. (1985). Simulation de la conformation des peptides et des protéines : développement de nouveaux polypeptides biologiquement actifs. J. de Chimie Physique. 82 592-598.
[61] Robson, B., Platt, E., Finn, P., Millard, P., Gibrat, J.-F. and Garnier, J. (1985). Prediction of the conformation and antigenic determinants of the V-sis viral oncogene product homologous with human platelet-derived growth factor. Int. J. Pept. Protein Res. 25 1-8.
[62] Robson, B., Douglas, G. and Garnier, J. (1983). A simple method and basic program for secondary structure prediction on a microcomputer. In Computing in Biological Science, (Graisow and Barrett, ed.), 132-142. Elsevier Biomedical Press.
[63] Garnier, J., Gaye, P., Mercier, J. and Robson, B. (1980). Structural properties of signal peptides and their membrane insertion. Biochimie. 62 231-239.
[64] Garnier, J., Osguthorpe, D. and Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120 97-120.
[65] Garnier, J., Salesse, R., Rerat, B., Rerat, C. and Blake, C. (1976). Comparison of x-ray data to estimated secondary structures from amino acid sequence and circular dichroism of human prealbumin. J. Chim. Phys. 73 1018-1023.

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