Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization” Machine Learning J. 21, 51-83.

Berg,O. G. and von Hippel,P. H. (1987). Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193, 723-750.

Besag,J., Green,P., Higdon,D. and Mengersen,K. (1996) Bayesian computation and stochastic systems. Statistical Science, 10 (1), 3-66.

Bulyk, M. (2003) Computational prediction of transcription-factor binding site locations. Genome Biology, 5:201.

Chiang,D.Y., Moses,A.M., Kellis,M., Lander,E.S. and Eisen,M.B. (2003) Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol, 4(R43).

Favorov,A.V., Gelfand,M.S., Mironov,A.A., and Makeev,V.J. (2002) Yet another digging for DNA motifs Gibbs sampler. Proceedings of BGRS 2002, Novisibisk, 1, 31-33.

Frith,M.C., Li,M.C. and Weng,Z. (2003) Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31(13), 3666-8.

Gelfand,M.S., Novichkov,P.S., Novichkova,E.S. and Mironov,A.A. (2000) Comparative analysis of regulatory patterns in bacterial genomes. Briefings in Bioinformatics, 1, 357–371.

Geman,S. and Geman,D. (1984). Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images, IEEE Transactions on Pattern Analysis and Machine Intelligence. 6, 621-641.

Gerasimova,A.V., Gelfand,M.S., Makeev,V.J., Mironov,A.A. and Favorov,A.V. (2004) Primary describtion of ArcA regulon in gamma-proteobacteria genomes on the base of the regulatory protein binding site computational recognition. Biophysics [rus.], in press.

Harbison,C.T., Gordon,D.B., Lee,T.I., Rinaldi,N.J., Macisaac,K.D., Danford,T.W., Hannett,N.M., Tagne,J.B., Reynolds,D.B., Yoo,J., Jennings,E.G., Zeitlinger,J., Pokholok,D.K., Kellis,M., Rolfe,P.A., Takusagawa,K.T., Lander,E.S., Gifford,D.K., Fraenkel,E. and Young,R.A. (2004) Transcription regulatory code of a eukaryotic genome. Nature, 431, 99-104.

Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioiformatics, 15 (7/8), 563-577

Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol, 296, 1205-1214.

Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F., and Wootton,J.C. (1993). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.

Li,H., Rhodius,V., Gross,C. and Siggia,E. (2002) Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl. Acad. Sci. 99, 11772–11777.

Liu,J.S. (2001) Monte Carlo strategies in scientific computing. Springer-Verlag, NY, Berlin, Heidelberg.

Makeev,V.J., Lifanov,A.P., Nazina,A.G. and Papatsenko,D.A. (2003) Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res.  31(20), 6016-26.

Mironov,A.A., Koonin,E.V., Roytberg,M.A., Gelfand,M.S. (1999) Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res. 27(14). 2981-2989.

Mwangi,M.M., and Siggia,E.D. (2003) Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics. 4(18).

Pilpel,Y., Sudarsanam,P. and Church, G. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29, 153-159.

Qiu,P., Ding,W., Jiang,Y., Greene,J.R. and Wang, L. (2002) Computational analysis of composite regulatory elements. Mamm Genome, 13(6), 327-32.

Robert,C.P. (1998) Discretization and MCMC convergence assessment. Springer-Verlag, NY, Berlin, Heidelberg.

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(6), 761-773

Roth,F.P., Hughes,J.D., Estep,P.W. and Church,G. M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotech., 16, 939-945.

Sivia,D.S. (1996) Data Analysis. A Bayesian tutorial. Clarendon Press, Oxford.

Stormo,G.D. and Hartzell,G.W.,3rd (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA, 86(4), 1183-11877.

Thijs,G., Marchall,K., Lescot,M., Rombauts,S., De Moor,B., Rouze,P. and Moreau, Y. (2002) A Gibbs sampling method to detect over-represented motifs in the upstream regions of coexpressed genes. J. Comp. Biol., 9 (2), 447-464.

Thompson,W., Rouchka,E.C., Lawrence,C.E. (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res., 31(13), 3580-3585.

Tompa,M., Li,N., Bailey,T.L., Church,G.M., de Moor,B., Eskin,E., Favorov,A.V., Frith,M.C., Fu,Y., Kent,W.J., Makeev,V.J., Mironov,A.A., Noble,W.S., Pavesi,G., Pesole,G., Régnier,M., Simonis,N., Sinha,S., Thijs,G., van Helden,J. Vandenbogaert,M., Weng,Z., Workman,C., Ye,C. and Zhu,Z. (2004) An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites, Nature Biotech., in press.

van Helden,J., Rios,A. and Collado-Vides,J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res, 28, 1808-1818.