Bachellier S., Clement J.-M., Hofnung M., Gilson E. (1997) Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics. 145:551-562.
Bachellier, S., E. Gilson, M. Hofnung and C. W. Hill. (1996) Repeated sequences, pp. 2012-2040 in Escherichia coli and Salmonella: Cellular and Molecular Biology, edited by F. Neidhardt et al. ASM Press, Washington, DC.
Bachellier S., Perrin D., Hofnung M., Gilson E. (1993) Bacterial interspersed mosaic elements (BIMEs) are present in the genome of Klebsiella. Mol. Microbiol. 7:537-544.
Bachellier S., Saurin W., Perrin D., Hofnung M., Gilson E. (1994) Structural and functional diversity among bacterial interspersed mosaic elements (BIMEs). Mol. Microbiol. 12:61-70.
Blaisdell B.E., Rudd K.E., Matin A. and Karlin S. (1993) Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups. J. Mol. Biol. 229: 833-848.
Buckle M., Buc H., Travers A.A. (1992) DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen. EMBO J. 11:2619-2625.
Burge C. B. (1998) Modeling dependencies in pre-mRNA splicing signals. In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology. Elsevier Science, Amsterdam, pp. 127-163.
Burge C. B., Karlin S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8:346-354.
Burge C. B., Tuschl T. H., Sharp, P. A. (1998) Splicing of precursors to mRNAs by the spliceosomes. In Gesteland, R. F., Cech, T. and Atkins, J. F., eds. The RNA World II. Cold Spring Harbor Laboratory Press (in press).
Burge C. (1997) Identification of genes in human genomic DNA. PhD thesis. Stanford University, Stanford, California, USA. (The GenScan program is available at the web site of the Pasteur Institute).
Burge C., Karlin S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94.
Burge C. B., Padgett R. A., Sharp P. A. (1998) Evolutionary fates and origins of U12-type introns. Molecular Cell. in press.
Burset M., R. Guigó (1996) Evaluation of gene structure prediction programs. Genomics. 34:353-357.
Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J. L., Chatenay D., Caron F. DNA: an extensible molecule. Science. 271:792-794.
Colland F., Orsini G., Brody E.N., Buc H., Kolb A. (1998) The bacteriophage T4 AsiA protein: a molecular switch for sigma 70-dependent promoters. Mol Microbiol 27:819-829.
Coissac E., Maillier E., Netter P. (1997) A comparative study of duplications in bacteria and eukaryotes: The importance of telomeres. Mol. Biol. Evol. 14:1062-1074.
d'Aubenton Carafa Y., Brody E., Thermes C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol. 216:835-858.
Duret L., Bucher P. (1997) Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7:399-406.
Duret L., Dorkeld F., Gautier C. (1993) Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res. 21:2315-2322.
Duret L., Mouchiroud D., Gautier C. (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40:308-317.
Eichenberger P., Dethiollaz S., Buc H., Geiselmann J. (1997) Structural kinetics of transcription activation at the malT promoter of Escherichia coli by UV laser footprinting. Proc. Natl. Acad. Sci. USA 94:9022-9027.
Flatters D., Lavery R. (1998) Sequence-dependent dynamics of TATA-Box binding sites. Biophys. J. 75:372-381.
Flatters D., Young M., Beveridge D. L., Lavery R. (1997) Conformational properties of the TATA-box binding sequence of DNA. J. Biomol. Struct. Dyn. 14:757-765.
Gélis F., Schbath S. (1996) R'MES : Recherche de Mots Exceptionnels dans les Séquences d'ADN, Guide de l'utilisateur - Version 1. Rapport technique de l'INRA, Département de Biométrie et Intelligence Artificielle, Jouy-en-Josas. (to get it, visit the web page).
Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. (1991) Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 19:1375-1383.
Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. (1991) The BIME family of bacterial highly repetitive sequences. Res. Microbiol. 142:217-222.
Gilson E., Bachellier S., Perrin S., Perrin D., Grimont P. A., Grimont F., Hofnung M. (1991) The BIME family of bacterial highly repetitive sequences. Res. Microbiol. 141:1103-1116.
Guigó R., Fickett J. W. (1995) Distinctive sequence features in protein coding, genic non-coding, and intergenic human DNA. Journal of Molecular Biology. 253:51-60.
Guigó R. (1997) Computational gene identification. J. of Mol. Medicine. 75:389-393.
Guigó R. (1997) Computational gene identification: An open problem. Computers and Chemistry. 21:215-222.
Guigó R. (1998) DNA composition, codon usage and exon prediction. In M. Bishop, ed. Nucleic Acid and Protein Databases Academic Press, in press.
Guigó R. (1998) Assembling genes from predicted exons in linear time with dynamic programming. J. of Comput. Biol. accepted.
Hartmann B., Lavery R. (1996) DNA structural forms. Q. Rev. Biophys. 29:309-368.
Hebsgaard S., Korning P.G., Tolstrup N., Engelbrecht J., Rouzé P.,and Brunak S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24:3439-3452.
Hulton C.S.J., Higgins C.F. and Sharp P.M. (1991) ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5: 825-834.
Knudsen S., Guigó R., Smith T. F. (1993) GeneID - a computer server for prediction of genes in DNA sequences. In Lim H. A., Fickett J. W., Cantor C. R., Robins R. J., eds. Proceedings on the Second International Conference on Bioinformatics, Supercomputing, and Complex Genome Analysis. pages 545-553. World Scientific.
Kolb A., Busby S., Buc H., Garges S., Adhya S. (1993) Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62:749-795 .
Kunisawa T., and Nakamura M. (1991) Identification of regulatory building blocks in Escherichia coli genome. Protein Seq. Data Anal. 4:43-47.
Lavery R., Hartmann B. (1994) Modelling DNA conformational mechanics. Biophys. Chem. 50:33-45.
Lavigne M., Kolb A., Buc H. (1992) Transcription activation by cAMP receptor protein (CRP) at the Escherichia coli gal P1 promoter. Crucial role for the spacing between the CRP binding site and the -10 region. Biochemistry 31:9647-9656.
Lavigne M., Kolb A., Yeramian E., Buc H. (1994) CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13:4983-4990.Lavigne M., Herbert M., Kolb A., Buc H. (1992) Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J. Mol. Biol. 224:293-306.
Lebrun A., Lavery R. (1997) Unusual DNA conformations. Curr. Opin. Struct. Biol. 7:348-354.
Lebrun A., Shakked Z., Lavery R. (1997) Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc. Natl. Acad. Sci. USA 94:2993-2998.
Lebrun A., Lavery R. (1996) Modelling extreme stretching of DNA. Nucleic Acids Res. 24:2260-2267.
Lebrun A., Lavery R. (1996) Modeling a strand exchange tetraplex conformation. J. Biomol. Struct. Dyn. 13:459-464.
Leung M.-Y., Blaisdell B.E., Burge C. and Karlin S. (1991) An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J. Mol. Biol. 221:1367-1378.
Peresetsky A., Mathé C., Déhais P., Van Montagu M. (1998) Classification of Arabidopsis thaliana gene sequences: coding sequences cluster into two groups according to codon usage. Genetics. submitted.
Prevost C., Boudvillain M., Beudaert P., Leng M., Lavery R., Vovelle F. (1997) Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: an internal coordinate molecular modeling study. J. Biomol. Struct. Dyn. 14:703-714.
Reinert G., Schbath S. (1998) Compound Poisson and Poisson process approximations for occurrences of multiple words, and application to stem-loop motifs in DNA sequences. to appear in J. Comp. Biol.
Rocha E. P. C., Viari A., Danchin A. (1998) Oligonucletide bias in Bacillus subtilis: General trends and taxonomic comparisons. Nucleic Acids Res. 26:2971-2980.
Sanghani S. R., Zakrzewska K., Harvey S. C., Lavery R. (1996) Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature. Nucleic Acids Res. 24:1632-1637.
Schbath S., Prum B., de Turckheim É (1995) Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comp. Biol. 2:417-437.
Schbath S. (1995) Compound Poisson approximation of word counts in DNA sequences. ESAIM: Prob. Stat. 1:1-16.
Schbath S. (1997) An efficient statistic to detect over- and under- represented words in DNA sequences. J. Comp. Biol. 4:189-192.
Sharp P. A., Burge C. B. (1997) Classification of introns: U2-type or U12-type. Cell. 91:875-879
Sharples G.J. and Lloyd R.G. (1990) A novel repeated DNA sequence located in the intergenic regions of bacterial chromosome. Nucleic Acids Res. 18: 6503-6508.
Terryn N., Neyt P., De Clerq R., De Keyser A., Van Den Daele H., Ardiles W., Déhais P., Rouzé P., Gielen J., Villarroel R., Van Montagu M. (1997) Sequence analysis of a 24-kb continuous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1. FEBS Lett. 416:156-160.
Tolstrup N., Rouzé P., and Brunak S. (1997) A branch-point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res. 25:3159-3163.
Wang Y.P., Kolb A., Buck M., Wen J., O'Gara F., Buc H. (1998) CRP interacts with promoter-bound sigma54 RNA polymerase and blocks transcriptional activation of the dctA promoter. EMBO J . 17:786-796.
Wu H.-J., Gaubier-Comella P., Delseny M., Grellet F., Van Montagu M., Rouzé P. (1996) Non-canonical introns are at least 109 years old. Nature Genet. 14:383-384.
Zhang A., Rimsky S., Reaban M.E., Buc H., Belfort M. (1996) Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics. EMBO J. 15:1340-1349.
Zuber F., Kotlarz D., Rimsky S., Buc H. (1994) Modulated expression of promoters containing upstream curved DNA sequences by the Escherichia coli nucleoid protein H-NS. Mol. Microbiol. 12:231-240.
