| |
1
|
Archer G. and Titterington D. (1995). Parameter estimation for hidden Markov chains. Technical report, University of Glasgow, Department of Statistics.
|
| |
2
|
Baum L.E. and Petrie T. (1966). Statistical inference for probabilistic functions of finite fiate Markov chains. The Annals of Mathematical Statistics, 37, 1554- 1563.
|
| |
3
|
Baum L.E., Petrie T., Soules O. and Weiss N. (1970). A maximization technique occuring in the statistical analysis of probabilistic functions of Markov chains. The Annals of Mathematical Statistics, 41, 164-171.
|
| |
4
|
Biaudet V., Samson F. and Bessi~res P. (1997). Micado ~ a network-oriented database for microbial genomes. Comput. Applic. Biosci., 13, 431-438.
|
| |
5
|
Celeux G. and Diebolt J. (1985). The SEM algorithm: a probabilistic teacher algorithm derived from the EM algorithm for the mixture problem. Computational Statistics Quaterly, 2, 73-82.
|
| |
6
|
Cervantes C., Ji G., Ramirez J.L. and Silver S. (1994). Resistance to arsenic compounds in microorganisms. FEMS Microbiol. Re,'., 15, 355-367.
|
| |
7
|
Churchill, G.A. (1989). Stochastic models for heterogeneous DNA sequences. Bulletin of Mathematical Biology, 51, 79-94.
|
| |
8
|
Davies J. (1994). Inactivation of antibiotics and the dissemination of resistance genes. Science, 264, 375- 382.
|
| |
9
|
Dempster A.P., Laird N.M. and Rubin D.B. (1977). Maximum likelihood from incomplete data via the EM algorithm. 7. Royal Statist. Soc. Set. B, 39, 1-38.
|
| |
10
|
Doolittle W.F. (1998). You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet., 14, 307- 311.
|
| |
11
|
Geman S. and Geman D. (1984). Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images, /EEE Trans. Pattn. Anal. Mach. Intel., 6, 721-741.
|
| |
12
|
Gouy M. and Gautier C. (1982). Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res., 10, 7055-7074.
|
| |
13
|
Groisman E.A. and Ochman H. (1997). How Salmonella became a pathogen. Trends Microbiol., 5, 343-349.
|
| |
14
|
Hacker J., Blum-Oehler G., Muhldorfer I. and Tschape H. (1997). Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23, 1089-1097.
|
| |
15
|
Kolsto A.B. (1997). Dynamic bacterial genome organization. 3/lol. Microbiol., 24, 241-248.
|
| |
16
|
Kunst F. et al. (1997). The complete genome of the gram-positive bacterium Bacillus subtilis. Nature, 390, 249-256.
|
| |
17
|
Lazarevic V., Mauel C., Soldo P., Freymond P.P., Margot P. and Karamata D. (1995). Sequence analysis of the 308 to 311 segment of the Bacillus subtilis 168 chromosome, a region devoted to cell wall metabolism, containing non-coding grey holes which reveal chromosomal rearrangements. Microbiology, 141, 329- 335.
|
| |
18
|
Lazarevic V., Soldo B., Dusterhoft A., Hilbert H., Mauel C. and Karamata D. (1998). Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage $P/~. Proc. Nafi. Acad. Sci. USA, 95, 1692-1697.
|
| |
19
|
Makrides S.C. (1996). Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol. Rev., 60, 512-538.
|
| |
20
|
Muri E (1997). Comparaison d'algorithmes d'identification de chMnes de Markov cach~es et application ~1 la detection de regions homog~nes duns les sequences d'ADN. PhD thesis, Universit6 Ren~ Descartes, Paris V.
|
| |
21
|
Muri E (1998). Modelling bacterial genomes using hidden Markov models. Compstat'98 Proceedings in Computational Statistics, R. Payne and P. Green (Ed. Physica-Verlag.), 89-100.
|
| |
22
|
Osbom A.M., Bruce K.D., Strike P. and Ritchie D.A. (1997). Distribution, diversity and evolution of the bacterial mercury resistance (mer) operon. FEMS Microbiol. Rev., 19, 239-262.
|
| |
23
|
Pem~re G., Bessi/~res P. and Labedan B. (1999). The Enhanced Microbial Genomes Library. Nucleic Acids Res., 27, 63-65.
|
| |
24
|
Polard P. and Chandler M. (1995). Bacterial transposases and retroviral integrases. }Viol. Microbiol., 15, 13-23.
|
| |
25
|
Qian W. and Titterington D.M. (1990). Parameter estimation for hidden Gibbs chains. Statist. Probab. Lett., 10, 49-58.
|
| |
26
|
Rabiner L.R.A. (1989). Tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEE, 77, 257-286.
|
| |
27
|
Recchia G.D and Hall R.M. (1995). Gene cassettes: a new class of mobile element. Microbiology, 141, 3015-3027.
|
| |
28
|
Redner R.A. and Walker H.E (1984). Mixture densities, maximum likelihood and the EM algorithm. SIAM Review, 26, 195-239.
|
| |
29
|
Robert C.P., Celeux G. and Diebolt J. (1993). Bayesian estimation of hidden Markov chains: a stochastic implementation. Statist. Probab. Lett., 16, 77-83.
|
| |
30
|
Robert C.P. (1996). MEthodes de Monte Carlo par Chafnes de Markov. Economica.
|
| |
31
|
Samson F., Biaudet V. and Bessi~res P. (1998). A graphical interface for microbial genome maps. J. Comp. Biol., (submitted).
|
| |
32
|
Silver S. and Phung L.T. (1996). Bacterial heavy metal resistance: new surprises. Annu. Rev. Microbiol., 50, 753-789.
|
| |
33
|
Syvanen M. (1994). Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet., 28, 237-261.
|
| |
34
|
Takemaru K., Mizuno M., Sato T., Takeuchi M. and Kobayashi Y. (1995). Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology, 141,323-327.
|
| |
35
|
Wood H.E., Dawson M.T., Devine K.M. and McConnell D.J. (1990). Characterization of PBSX, a defective prophage of Bacillus subtilis. J. bacteriol., 172, 2667- 2674.
|
| |
36
|
Zahler S.A., Korman R.Z., Rosenthal R., Hemphill H.E. (1977). Bacillus subtilis bacteriophage SP/5: localization of the prophage attachment site, and specialized transduction. J. Bacteriol., 129, 556-558.
|