Articles up to 2008 | SSB - Statistics for Systems Biology

Articles from 1995 to 2008

2008

Villers, F., Schaeffer, B., Bertin, C. and Huet, S. (2008). Assessing the validity domains of graphical gaussian models in order to infer relationships among components of complex biological systems. Statistical Applications in Genetics and Molecular Biology, 7(2): paper 14.
Martin-Magniette, M.-L., Mary-Huard, T., Bérard, C. and Robin, S. (2008). ChIPmix: mixture model of regressions for two-color ChIP-chip analysis. Bioinformatics. 24 i181-186. [DOI]
Robin, S. and Stevanov, V. (2008). Simultaneous occurrences of runs in independent Markov chains. Methodology and Computing in Applied Probability. 11 267-275 [DOI]
Lebre, S. and Bourguignon, P.-Y. (2008). An EM algorithm for estimation in the Mixture Transition Distribution Model. Journal of Statistical Computation and Simulation. 78 713-729. [url]
Martin, J., Regad, L., Etchebest, C. and Camproux, A. (2008b). Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes. Proteins. 73 672-689.
Mercier, R., Petit, M.-A., Schbath, S., Robin, S., El Karoui, M., Boccard, F. and Espeli, O. (2008). The MatP/matS site specific system organizes the Terminus region of the E. coli chromosome into a Macrodomain. Cell. 1-11. [ DOI ]
Butucea, C., Matias, C. and Pouet, C. (2008). Adaptivity in convolution models with partially known noise distribution. Electronic Journal of Statistics. 2 897-915.
Nicolas, P., Mondot, S., Achaz, G., Bouchenot, C., Bernardet, J.-F. and Duchaud, E. (2008). Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74 3702-3709. [ DOI ]
Giraud, C. (2008). Estimation of Gaussian graphs by model selection. Electronic Journal of Statistics. 2 542-563.
Vergne, N. and Abadi, M. (2008). Poisson approximation for search of rare words in DNA sequences. ALEA. 4 223-244. [ .pdf ]
Vergne, N. (2008). Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences. Statistical Applications in Genetics Molecular Biology. 7 1. [ http ]
Mary-Huard, T., Aubert, J., Mansouri-Attia, N., Sandra, O. and Daudin, J.-J. (2008). Statistical methodology for the analysis of dye-switch microarray experiments. BMC Bioinformatics. 9 98.
Martin, J., Regad, L., Lecornet, H. and Camproux, A.-C. (2008a). Structural deformation upon protein-protein interaction: a structural alphabet approach. BMC Structural Biology. 8 12.
Miele, V., Vaillant, C., D'Aubenton, Y., Thermes, C. and Grange, T. (2008). Dna physical properties determine nucleosome occupancy from yeast to fly. Nucleic Acids Research. 36 3746-3756.
Zanghi, H., Ambroise, C. and Miele, V. (2008). Fast online graph clustering via erdös-rényi mixture. Pattern Recognition. 3592-3599.
Nuel, G. (2008b). Pattern markov chains: optimal Markov chain embedding through deterministic finite automata. J. App. Proba. 226-243.
Nuel, G. (2008a). Cumulative distribution function of a geometric poisson distribution. J. Stat. Comp. and Sim. 385-394.
Rodolphe, F., Martin, J. and Della-Chiesa, E. (2008). Theoretical description of chromosome architecture after multiple back-crossing. Theoretical Population Biology. 289-299.
Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M.-H., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A. and Giraud, T. (2008). Assessing the performance of single-copy genes for recovering robust phylogenies. Systematic Biology. 613-627. [ DOI ]
Daudin, J. and Mary-Huard, T. (2008). Estimation of the conditional risk in classification : The swapping method. Comp. Stat. Data Anal. 3220-3232. [ DOI ]
Celisse, A. and Robin, S. (2008). Nonparametric density estimation by explicit leave-p-out cross-validation. Comput. Statist. Data Analysis. 2350-68.
Picard, F., Daudin, J.-J. and Robin, S. (2008b). A mixture model for random graphs. Stat. Comput. 173-183.
Touzain, F., Schbath, S., Debled-Rennesson, I., Aigle, B., Leblond, P. and Kucherov, G. (2008). SIGffRid: a tool to search for σ factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. BMC Bioinformatics. 9:73 1-23. [ http ]
Picard, F., Daudin, J.-J., Koskas, M., Schbath, S. and Robin, S. (2008a). Assessing the exceptionality of network motifs. J. Comp. Biol. 15:1 1-20. [ http ]
Touyar, N., Schbath, S., Cellier, D. and Dauchel, H. (2008). Poisson approximation for the number of repeats in a Markov chain model. J. Appl. Prob. 45 440-455.
Guedj, M., Nuel, G. and Prum, B. (2008). A note on allelic tests in case-control association studies. Annals of Human Genetics. 407-409.
Elis, S., Batellier, F., Couty, I., Balzergue, S., Martin-Magniette, M.-L., and Monget, P. Blesbois, E. and Govoroun, M. (2008). Search for the genes involved in oocyte maturation and early embryo development in the hen. BMC Genomics. 9 1471-2164. [DOI]
Martin-Magniette, M.-L., Aubert, J., Bar-Hen, A., Elftieh, S., Magniette, F., Renou, J.-P. and Daudin, J.-J. (2008). Normalization for triple-target microarray experiments. BMC Bioinformatics. 9 1471-2105. [DOI]
Navajas, M., Migeon, A., Alaux, C., Martin-Magniette, ML., Robinson, GE., Evans, JD., Cros-Arteil, S., Crauser, D and Le Conte, Y. (2008). Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection. BMC Genomics. 9 1471-2164. [DOI]
Cossegal, M., Chambrier, P., Mbelo, S. Balzergue, Martin-Magniette, M.-L., Moing, A., Deborde, C., Guyon, V., Perez, P. and Rogowsky, P. (2008). Transcriptional and Metabolic Adjustments in ADP-Glucose Pyrophosphorylase-Deficient bt2 Maize Kernels. Plant Physiol. 146 1553-1570. [DOI]
Ruffel, S., Freixes, S., Balzergue, S., Tillard, P., Jeudy, C., Martin-Magniette, M.-L. et al. (2008). Systemic Signaling of the Plant Nitrogen Status Triggers Specific Transcriptome Responses Depending on the Nitrogen Source in Medicago truncatula. Plant Physiol. 146 2020-2035. [DOI]
Gagnot, S., Tamby, J.-P., Martin-Magniette, M.-L., Bitton, F., Taconnat, L., Balzergue, S., Aubourg, S., Renou, J.-P., Lecharny A. and Brunaud V. (2008). CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Research. 36 D986-D990.
Benhamed, M. , Martin-Magniette, M.-L., Taconnat, L., Bitton, F., Servet, C., De Clercq, R., De Meyer, B., Buysschaert, C., Rombauts, S., Villarroel-Mandiola, R., Aubourg, S. et al. (2008). Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant Journal. 56 493--504.

2007

Ibrahim, M., Nicolas, P., Bessières, P., Bolotin, A., Monnet, V. and Gardan, R. (2007). A genome-wide survey of short coding sequences in streptococci. Microbiology. 153 3631-3644. [ DOI ]
Fayyaz, A., Mercier, S., Ferre, L. and Hassenforder, C. (2007b). New approximate p-value of gapped local sequence alignments. C. R. Acad. Sci. Paris. 346 87-92.
Same, A., Ambroise, C. and Govaert, G. (2007). An online classification em algorithm based on the mixture model. Statistics and Computing. 209-218.
Hassenforder, C. and Mercier, S. (2007). Exact distribution of the local score for markovian sequences. Annals of the Institue of Statistical Mathematics. 741-755.
Fayyaz, A., Mercier, S. and Ferre, L. (2007a). h-tuple approach to evaluate statistical significance of biological sequence comparison with gaps. Statistical Applications in Genetics and Molecular Biology. 22. [ http ]
Nuel, G. and Prum, B. (2007a). Analyse statistique des séquences biologiques: modélisation markovienne, alignements et motifs. Hermes.
Forner, K., Lamarine, M., Guedj, M., Dauvillier, J. and Wojcik, J. (2007). Universal false discovery rate estimation methodology for genome-wide association studies. Human Heredity. 65 183-194. [ http ]
Aschard, H., Guedj, M. and Demenais, F. (2007). A multiple-marker two-step approach for genome-wide association studies. BMC Proceedings. 1 S134. [ http ]
Martin, J., de Brevern, A. G. and Camproux, A.-C. (2007). In silico local structure approach: a case study on outer membrane proteins. Proteins. 92-109.
Yockteng, R., Marthey, S., Chiapello, H., Hood, M., Rodolphe, F., Gendrault-Jacquemard, B., A.and Devier, Wincker, P., Dossat, C. and Giraud, T. (2007). Expressed sequences tags of the anther smut fungus, microbotryum violaceum, identify mating and pathogenicity genes. BMC Genomics. 272. [ DOI ]
Nicolas, P., Bessieres, P., Ehrlich, S., Maguin, E. and van de Guchte, M. (2007a). Extensive horizontal transfer of core genome genes between two lactobacillus species found in the gastrointestinal tract. BMC Evol Biol. 7 141. [ DOI ]
Lebarbier, E. and Mary-Huard, T. (2007). Une introduction au critère bic : fondements théoriques et interprétation. Journal de la SFDS. 39-57.
Duchaud, E., Boussaha, M., Loux, V., Bernardet, J.-F., Michel, C., Kerouault, B., Mondot, S., Nicolas, P., Bossy, R., Caron, C., Bessières, P., Gibrat, J.-F., Claverol, S., Dumetz, F., Hénaff, M. L. and Benmansour, A. (2007). Complete genome sequence of the fish pathogen flavobacterium psychrophilum. Nat Biotechnol. 25 763-769. [ DOI ]
Chich, J.-F., David, O., Villers, F., Schaeffer, B., Lutomski, D. and Huet, S. (2007). Statistics for proteomics: Experimental design and 2-DE differential analysis. Journal of Chromatography B. 849 (1-2) 261-272.
Robin, S., Bar-Hen, A., Daudin, J.-J. and Pierre, L. (2007a). A semi-parametric approach for mixture models : Application to local false discovery rate estimation. Comput. Statist. Data Analysis. 51 5483-5493.
Mary-Huard, T., Robin, S. and Daudin, J. (2007b). A penalized criterion for variable selection in classification. Bioinformatics. 98(4) 695-705.
Halpern, D., Chiapello, H., Schbath, S., Robin, S., Hennequet-Antier, C., Gruss, A. and El Karoui, M. (2007). Identification of dna motifs implicated in maintenance of bacterial core genomes by predictive modelling. PLoS Genetics. 3(9) e153. [ DOI ]
Picard, F., Robin, S., Lebarbier, E. and Daudin, J.-J. (2007). A segmentation/clustering model for the analysis of array cgh data. Biometrics. 63 758-766.
Mary-Huard, T., J.-J., D., Baccini, M., Biggeri, A. and Bar-Hen, A. (2007a). Biases induced by pooling samples in microarray experiments. Bioinformatics. 23 313-318.
Nuel, G. and Prum, B. (2007b). Analyse statistique des séquences biologiques: modélisation markovienne, alignements et motifs. Hermes.
Nicolas, P., Kim, K.-M., Shibata, D. and Tavaré, S. (2007b). The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comput Biol. 3 (3) e28. [ DOI ]
Avalos, M., Grandvalet, Y. and Ambroise, C. (2007). Parsimonious additive models. Computational Statistics and Data Analysis. 51 2851-2870.
Robin, S., Schbath, S. and Vandewalle, V. (2007b). Statistical tests to compare motif count exceptionalities. BMC Bioinformatics. 8:84 1-20. [ http ]
Roquain, E. and Schbath, S. (2007). Improved compound Poisson approximation for the number of occurrences of multiple words in a stationary Markov chain. Adv. Appl. Prob. 39 1-13. [ .ps ]
Stefanov, V., Robin, S. and Schbath, S. (2007). Waiting times for clumps of patterns and for structured motifs in random sequences. Discrete Applied Mathematics. 155 868-880. [ .pdf ]
Guedj, M., Della-Chiesa, E., Picard, F. and Nuel, G. (2007). Computing power in case-control association studies through use of quadratic approximations: application to meta-statistics. Annals of Human Genetics. 262-270.

2006

Same, A., Ambroise, C. and Govaert, G. (2006). A classification em algorithm for binned data. Computational Statistics and Data Analysis. 51 (2) 466-480.
Schibler, L., Roig, A., Mahe, M.-F., Laurent, P., Hayes, H., Rodolphe, F. and Cribiu, E.-P. (2006). High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution. BMC Genomics. 7 194.
Nuel, G. (2006c). Pattern statistics on Markov chains and sensitivity to parameter estimation. Algo. Mol. Biol. 1 Article 17.
Nuel, G. (2006a). Effective p-value computations using Finite Markov Chain Imbedding (FMCI): application to local score and to pattern statistics. Algo. Mol. Biol. 1 Article 5.
Martin, J., Gibrat, J.-F. and Rodolphe, F. (2006). Analysis of an optimal hidden markov model for secondary structure prediction. BMC Structural Biology. 6 25.
Regad, L., Martin, J. and Camproux, A.-C. (2006). Identification of non random motifs in loops using a structural alphabet. In Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 1-9, Toronto, Ontario.
vande Guchte, M., Penaud, S., Grimaldi, C., Barbe, V., Bryson, K., Nicolas, P., Robert, C., Oztas, S., Mangenot, S., Couloux, A., Loux, V., Dervyn, R., Bossy, R., Bolotin, A., Batto, J., Walunas, T., Gibrat, J., Bessieres, P., Weissenbach, J., Ehrlich, S. and Maguin, E. (2006). The complete genome sequence of lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci U S A. 103 9274-9279.
Nicolas, P., Sun, F. and Li, L. M. (2006b). A model-based approach to selection of tag snps. BMC Bioinformatics. 7 303. [ DOI ]
Bryson, K., Loux, V., Bossy, R., Nicolas, P., Chaillou, S., van de Guchte, M., Penaud, S., Maguin, E., Hoebeke, M., Bessieres, P. and Gibrat, J.-F. (2006). Agmial: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 34 3533-3545.
Zhu, X., Ambroise, C. and McLachlan, G. (2006). Selection bias in working with the top genes in supervised classification of tissue samples. Statistical Methodology. 3 29-41.
Cord, A., Ambroise, C. and Cocquerez, J.-P. (2006). Feature selection in robust clustering based on laplace mixture. Pattern Recognition Letters. 27 (6) 627-635.
Arribas-Gil, A., Gassiat, E. and Matias, C. (2006). Parameter estimation in pair hidden Markov models. Scand. J. Statist. 33 (4) 651-671. [ http ]
Chich, J.-F., David, O., Villers, F., Schaeffer, B., Lutomski, D. and Huet, S. (2006). Statistics for proteomics: Experimental design and 2-de differential analysis. Journal of Chromatography B.
Guedj, M., Wojcik, J., Della-Chiesa, E., Nuel, G. and Forner, K. (2006b). A fast, unbiased and exact allelic test for case-control association studies. Human Heredity. 61 210-221.
Guedj, M., Robelin, D., Hoebeke, M., Lamarine, M., Wojcik, J. and Nuel, G. (2006a). Detecting local high-scoring segments: a first-stage approach for genome-wide association studies. SAGMB. 5.
Nuel, G. (2006b). Numerical Solutions for Patterns Statistics on Markov Chains. Stat. App. Gen. Mol. Biol. 5 (1) Article 26.
Nicolas, P., Tocquet, A.-S., Miele, V. and Muri, F. (2006a). A reversible jump Monte-Carlo Markov chain algorithm for bacterial promoter discovery. J. Comp. Biol. 13 651-667.
Lepage, E., Brinster, S., Caron, C., Ducroix-Crepy, C., Rigottier-Gois, L., Dunny, G., Hennequet-Antier, C. and Serror, P. (2006). Comparative genomic hybridization analysis of enterococcus faecalis: Identification of genes absent from food strains. Journal of Bacteriology. 188 6858-6868.
Matias, C., Schbath, S., Birmelé, E., Daudin, J.-J. and Robin, S. (2006). Network motifs: mean and variance for the count. REVSTAT. 4 31-51.

2005

Martin, J., Gibrat, J.-F. and Rodolphe, F. (2005a). How to choose the optimal hidden markov model for protein secondary structure prediction. IEEE Intelligent Systems. 60 (6) 19-25.
Martin, J., Letellier, G., Marin, A., Taly, J.-F., de Brevern, A. and Gibrat, J.-F. (2005b). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol. 5 17.
Miele, V., Bourguignon, P., Robelin, D., Nuel, G. and Richard, H. (2005). seq++: a package for biological sequences analysis with a range of markov-related models. BioInformatics. 21 (11) 2783-2784.
Nuel, G. (2005). S-SPatt: simple statistics for patterns on Markov chains. Bioinformatics. 21 (13) 3051-3052.
Robin, S., Rodolphe, F. and Schbath, S. (2005). DNA, Words and Models. Cambridge University Press, English version of ADN, mots et modèles, BELIN 2003.
Lebarbier, E. (2005). Detecting multiple change-points in the mean of gaussian process by model selection. Signal Processing. 85 117-736.
Hennequet-Antier, C., Chiapello, H., Piot, K., Degrelle, S., Hue, I., Renard, J., Rodolphe, F. and Robin, S. (2005). Anovarray: a set of sas macros for the analysis of variance of gene expression data. BMC Bioinformatics. 6 150.
Reinert, G., Schbath, S. and Waterman, M. (2005). Applied Combinatorics on Words. volume 105 of Encyclopedia of Mathematics and its Applications, chapter Statistics on Words with Applications to Biological Sequences. Cambridge University Press.
Gusto, G. and Schbath, S. (2005). FADO: a statistical method to detect favored or avoided distances between motif occurrences using the hawkes' model. Statistical Applications in Genetics and Molecular Biology. 4 0. Article 24.

2004

Marin, A., Malliavin, T., Nicolas, P. and Delsuc, M.-A. (2004). Prediction of the amino-acid type from the chemical shift values: investigation of the information carried by nmr experiments. J Biomol NMR. 30 (1) 47-60.
Mary-Huard, T., Daudin, J.-J., Robin, S., Bitton, F., Cabannes, E. and Hilson, P. (2004). Spotting effect in microarray experiments. BMC Bioinformatics. [ .pdf ]
Nuel, G. (2004). LD-SPatt: Large Deviations Statistics for Patterns on Markov Chains. J. Comput. Biol. 11 (6) 1023-1033.
Aubert, J., Bar-Hen, A., Daudin, J.-J. and Robin, S. (2004). Determination of the differentially expressed genes in microarray experiments using local FDR. BMC Bioinformatics. 5 125. [ http ]
Delmar, P., Robin, S., Le Roux, D. and Daudin, J.-J. (2004). Mixture model on the variance for the differential analysis of gene expression. J. R. Statist. Soc. B.
Schbath, S. (2004). A la recherche de mots de fréquence exceptionnelle dans les génomes. In Images des Mathématiques, volume 3, 100-106. CNRS. [ .ps ]

2003

Bar-Hen, A. and Robin, S. (2003). An iterative procedure for differential analmysis of gene expression. CRAS. 343-346.
Richard, H. and Nuel, G. (2003). SPA: Simple web tool to assess statistical significance of DNA patterns. Nucleic Acids Research. 31 (13) 3679-3681.
Hassenforder, C. and Mercier, S. (2003). Distribution exacte du score local, cas Markovien. C.R.A.S. 336 863-868. [ .html ]
Bourgait, I., Chiapello, H., Hennequet-Antier, C., Robin, S., Schbath, S., Gruss, A. and El Karoui, M. (2003). Genomic distribution of short motifs involved in dna repair in pathogenic and non pathogenic E. coli. In Second European Conference on Computational Biology (ECCB). Paris, France. September, 27-30 (selected short paper, 7-9).
Robelin, D. and Prum, B. (2003). Detecting short inverted segments in a biological sequenc. In Second European Conference on Computational Biology (ECCB). Paris, France. September, 27-30 (selected short paper, 41-43).
Robelin, D., Richard, H. and Prum, B. (2003). SIC: a tool to detect short inverted segments in a biological sequence. Nucl. Acids. Res. 31 (13) 3669-3671. [ abstract | http ]
Daudin, J.-J., Etienne, M.-P. and Vallois, P. (2003). Asymptotic behavior of the local score of independent and identically distributed random sequences. Stochastic Processes and their Applications. 107 1-28. [ http ]
Robin, S. (2003). Between Data Science And Applied Data Analysis. (S. Martin, W. Gaul, and M. Vichi, ed.), chapter Some Statistical Issues in Microarray Data Analysis, 337-347. Springer.
Hoebeke, M., Nicolas, P. and Bessières, P. (2003). MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics. 19 859-864.
Mercier, S., Cellier, D. and Charlot, F. (2003). An improved approximation for assessing the statistical significance of molecular sequence features. J. Appl. Prob. 40 ? [ abstract ]
Robin, S., Rodolphe, F. and Schbath, S. (2003). ADN, mots et modèles. BELIN.
Schbath, S. (2003). Statistical methods in physical mapping. In Encyclopedia of the Human Genome, number 434 in Mathematical genetics. Nature Publishing Group. [ .ps ]

2002

Nicolas, P., Bize, L., Muri, F., Hoebeke, M., Rodolphe, F., Ehrlich, S., Prum, B. and Bessières, P. (2002). Mining bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucl. Acids Res. 30 1418-1426.
Bacro, J.-N., Daudin, J.-J., Mercier, S. and Robin, S. (2002). Back to the local score in the logarithmic case: a direct and simple proof. Ann. Inst. Statist. Math. 54 748-757. [ abstract | .ps ]
Robin, S., Daudin, J.-J., Richard, H., Sagot, M.-F. and Schbath, S. (2002). Occurrence probability of structured motifs in random sequences. J. Comp. Biol. 9 761-773. [ abstract | .ps ]
Robin, S. (2002). A compound Poisson model for words occurrences in DNA sequences. J. Royal Statist. Soc., C series. 51 437-451. [ abstract | .ps ]
Daudin, J., Ghachem, S., Descender, M., Robin, S., Hénault, A., Sekowska, A. and Danchin, A. (2002). Comparison of statistical methods for differential analysis of macroarray data. preprint. 0.
Nicodème, P., Salvy, B. and Flajolet, P. (2002). Motif statistics. Theoretical Computer Science. ? Extended version of an article published in the proceedings of 7th Annual European Symposium on Algorithms ESA'99, Prague, July 1999. [ abstract ]
Prum, B. (2002). Mathématiques et biologie. Bulletin de l'APMEP.

2001

Lavielle, M. and Lebarbier, E. (2001). An application of mcmc methods for the multiple change-points problem. Signal Processing. 81 39-53.
Mercier, S. and Daudin, J. (2001). Exact distribution for the local score of one i.i.d. random sequence. J. Comp. Biol. 8 373-380. [ abstract ]
Mercier, S., Cellier, D., Charlot, F. and Daudin, J. (2001). Exact and asymptotic distribution of the local score of one i.i.d. random sequence,. Lecture Notes in Comp. Science, volume for JOBIM 2000. 74-85.
Daudin, J. and Mercier, S. (2001). Distribution exacte du score local d'une suite de variables indépendantes et identiquement distribuées. C. R. Acad. Sci. Paris,. 329 (I) 815-820. [ abstract ]
Sekowska, A., Robin, S., Daudin, J.-J., Hénaut, A. and Danchin, A. (2001). Extracting biological information from dna arrays: an unexpected link between arginine and methionine metabolism in bacillus subtilis. Genome Biology. 2 (6) [ http ].
Robin, S. and Daudin, J.-J. (2001). Exact distribution of the distances between any occurrences of a set of words. Ann. Inst. Statist. Math. 36 (4) 895-905. [ abstract | .ps ]
Robin, S. and Schbath, S. (2001). Numerical comparison of several approximations of the word count distribution in random sequences. J. Comp. Biol. 8 349-359. [ .ps ]
Prum, B., Turckheim, É. and Vingron, M. (2001). Identifying repeat-containing protein sequences. ESAIM: Probability and Statistics.
Muri-Majoube, F. and Prum, B. (2001). Une approche statistique de l'analyse des génomes. La Gazette des Mathématiciens. 89 63-98.
Prum, B. (2001a). La recherche automatique des gènes. La Recherche. 1108 86-88.
Prum, B. (2001b). Probabilités, statistique et génomes. Matapli. 64.

2000

Bacro, J. and Comet, J. (2000). Sequence alignment: an approximation law for the z-value with applications to databank scanning. Computers and Chemistry. 401-410. [ abstract ]
Goldstein, D., Muri-Majoube, F., Saragueta, P. and Prum, B. (2000). Inverse complementary homologues of cysteine signatures. C. R. Acad. Sci. 323 167-172.
Prum, B. (2000b). Une approche statistique de l'analyse des séquences gén etiques. La Revue du Palais de la Découverte. 276 56-65.
Prum, B. (2000a). Les chaînes de Markov dans l'analyse des génomes. Matapli. 62 17-24.
Reinert, G., Schbath, S. and Waterman, M. (2000). Probabilistic and statistical properties of words: an overview. J. Comp. Biol. 7 1-46. [ abstract | .ps ]
Schbath, S., Bossard, N. and Tavaré, S. (2000). The effect of non-homogeneous clone length distribution on the progress of an STS mapping project. J. Comp. Biol. 7 47-58. [ abstract | .ps ]
Schbath, S. (2000). An overview on the distribution of word counts in Markov chains. J. Comp. Biol. 7 193-201. [ abstract | .ps ]
Mathé, C. and Rodolphe, F. (2000). Translation conditional models for protein coding sequences. J. Comp. Biol. 7 249-260.

1999

Krause, A., Nicodème, P., Bornberg-Bauer, E., Rehmsmeier, M. and Vingron, M. (1999). WWW-access to the SYSTERS protein sequence cluster set. Bioinformatics. 15 262-263. Application Note accepted for the GCB Special Issue of Bioinformatics. [ abstract ]
Robin, S. and Daudin, J.-J. (1999). Exact distribution of word occurrences in a random sequence of letters. J. Appl. Prob. 36 179-193. [ abstract ]
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. [ abstract ]
Bouvier, A., Gélis, F. and Schbath, S. (1999), R'MES : Recherche de Mots Exceptionnels dans les Séquences d'ADN - version 2. Technical report, Guide de l'utilisateur. INRA, Biométrie, F78352 Jouy-en-Josas. [ .ps ]
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. 33 257-275. [ abstract | .ps ]

1998

Krause, A., Nicodème, P., Rehmsmeier, M. and Vingron, M. (1998). Automatic clustering of large sequence databases. In Proceedings of the German Conference on Bioinformatics GCB98, Köln.
Nicodème, P. (1998). SSMAL: similarity searching with alignment graphs. Bioinformatics. 14 (6) 508-515. [ abstract ]
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 ]
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. [ abstract | .ps ]

1997

Nicodème, P. and Steyaert, J. (1997). Selecting optimal oligonucleotide primers for multiplex PCR. In Fifth International Conference on Intelligent Systems for Molecular Biology, 210-213. AAAI Press. [ abstract ]
Schbath, S. (1997b). An efficient statistic to detect over- and under-represented words in DNA sequences. J. Comp. Biol. 4 189-192. [ abstract | .ps ]
Schbath, S. (1997a). Coverage processes in physical mapping by anchoring random clones. J. Comp. Biol. 4 61-82. [ abstract | .ps ]

1996

Schbath, S. (1996), Using non-homogeneous processes in physical mapping by anchoring random clones: Mathematical analysis and application to hotspots. Technical Report #96-6, Center for Applied Mathematical Sciences, University of Southern California, Los Angeles.
Gélis, F. and Schbath, S. (1996), RMES : Recherche de Mots Exceptionnels dans les Séquences d'ADN - version 1. Technical report, Notice d'utilisation. INRA, Biométrie, F78352 Jouy-en-Josas.

1995

Schbath, S. (1995a). Compound Poisson approximation of word counts in DNA sequences. ESAIM: Probability and Statistics. 1 1-16. (http://www.emath.fr/ps/). [ abstract | .ps ]
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. [ .ps ]
Schbath, S., Prum, B. and de Turckheim, E. (1995). Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2 417-437. [ abstract | .ps ]
Prum, B., Rodolphe, F. and Turckheim, É. (1995). Finding words with unexpected frequencies in DNA sequences. J. R. Statist. Soc. B. 57 205-220. [ abstract ]