{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T05:08:55Z","timestamp":1775020135673,"version":"3.50.1"},"reference-count":22,"publisher":"Pleiades Publishing Ltd","issue":"4","license":[{"start":{"date-parts":[[2008,12,1]],"date-time":"2008-12-01T00:00:00Z","timestamp":1228089600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2008,12,1]],"date-time":"2008-12-01T00:00:00Z","timestamp":1228089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Probl Inf Transm"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1134\/s0032946008040066","type":"journal-article","created":{"date-parts":[[2009,1,23]],"date-time":"2009-01-23T09:11:32Z","timestamp":1232701892000},"page":"333-351","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Gibbs field approach for evolutionary analysis of regulatory signal of gene expression"],"prefix":"10.1134","volume":"44","author":[{"given":"V. A.","family":"Lyubetsky","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E. A.","family":"Zhizhina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L. I.","family":"Rubanov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"137","published-online":{"date-parts":[[2009,1,24]]},"reference":[{"key":"4006_CR1","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3247-4","volume-title":"Statistical Methods in Bioinformatics: An Introduction","author":"W. Ewens","year":"2001","unstructured":"Ewens, W. and Grant, G., Statistical Methods in Bioinformatics: An Introduction, New York: Springer, 2001."},{"key":"4006_CR2","volume-title":"Mathematics of Evolution and Phylogeny","year":"2005","unstructured":"Mathematics of Evolution and Phylogeny, Gascuel, O., Ed., New York: Oxford Univ. Press, 2005."},{"key":"4006_CR3","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/0-387-29455-4_20","volume-title":"Bioinformatics of Genome Regulation and Structure II","author":"V. Lyubetsky","year":"2006","unstructured":"Lyubetsky, V., Gorbunov, K., Rusin, L., and V\u2019yugin, V., Algorithms to Reconstruct Evolutionary Events at Molecular Level and Infer Species Phylogeny, Bioinformatics of Genome Regulation and Structure II, Kolchanov, N., Hofest\u00e4dt, R., and Milanesi, L., Eds., New York: Springer, 2006, pp. 189\u2013204."},{"key":"4006_CR4","volume-title":"Genes & Genomes: A Changing Perspective","author":"M. Singer","year":"1991","unstructured":"Singer, M., and Berg, P., Genes & Genomes: A Changing Perspective, Mill Valley: Univ. Science Book, 1991. Translated under the title Geny i genomy, Moscow: Mir, 1998."},{"issue":"1","key":"4006_CR5","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1142\/S0219720007002576","volume":"5","author":"V.A. Lyubetsky","year":"2007","unstructured":"Lyubetsky, V.A., Pirogov, S.A., Rubanov, L.I., and Seliverstov, A.V., Modeling Classic Attenuation Regulation of Gene Expression in Bacteria, J. Bioinform. Comput. Biol., 2007, vol. 5, no. 1, pp. 155\u2013180.","journal-title":"J. Bioinform. Comput. Biol."},{"issue":"10","key":"4006_CR6","doi-asserted-by":"publisher","first-page":"4365","DOI":"10.1073\/pnas.74.10.4365","volume":"74","author":"F. Lee","year":"1977","unstructured":"Lee, F. and Yanofsky, C., Transcription Termination at the trp Operon Attenuators of Escherichia coli and Salmonella typhimurium: RNA Secondary Structure and Regulation of Termination, Proc. Natl. Acad. Sci. USA, 1977, vol. 74, no. 10, pp. 4365\u20134369.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"5","key":"4006_CR7","first-page":"1350","volume":"19","author":"A.A. Mironov","year":"1985","unstructured":"Mironov, A.A. and Kister, A.E., Theoretical Analysis of RNA Secondary Structure Formation Kinetics during Transcription and Translation. Accounting for Imperfect Helices, Mol. Biol. (Moscow), 1985, vol. 19, no. 5, pp. 1350\u20131357.","journal-title":"Mol. Biol. (Moscow)"},{"issue":"s.1\u20132","key":"4006_CR8","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1007\/BF02179399","volume":"79","author":"P.M. Bleher","year":"1995","unstructured":"Bleher, P.M., Ruiz, J., and Zagrebnov, V.A., On the Purity of Limiting Gibbs State for the Ising Model on the Bethe Lattice, J. Stat. Phys., 1995, vol. 79, nos. 1\u20132, pp. 473\u2013482.","journal-title":"J. Stat. Phys."},{"issue":"2","key":"4006_CR9","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1214\/aoap\/1019487349","volume":"10","author":"W. Evans","year":"2000","unstructured":"Evans, W., Kenyon, C., Peres, Y., and Schulman, L.J., Broadcasting on Trees and the Ising Model, Ann. Appl. Probab., 2000, vol. 10, no. 2, pp. 410\u2013433.","journal-title":"Ann. Appl. Probab."},{"issue":"2","key":"4006_CR10","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1007\/s00220-004-1147-y","volume":"250","author":"F. Martinelli","year":"2004","unstructured":"Martinelli, F., Sinclair, A., and Weitz, D., Glauber Dynamics on Trees. Boundary Conditions and Mixing Time, Comm. Math. Phys., 2004, vol. 250, no. 2, pp. 301\u2013334.","journal-title":"Comm. Math. Phys."},{"key":"4006_CR11","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"R. Durbin","year":"1998","unstructured":"Durbin, R., Eddy, S., Krogh, A., and Mitchison, G., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge: Cambridge Univ. Press, 1998. Translated under the title Analiz biologicheskikh posledovatel\u2019nostei, Moscow-Izhevsk: Regulyarnaya i haoticheskaya dinamika, 2006."},{"key":"4006_CR12","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1093\/genetics\/139.3.1429","volume":"139","author":"S.V. Muse","year":"1995","unstructured":"Muse, S.V., Evolutionary Analyses of DNA Sequences subject to Constraints on Secondary Structure, Genetics, 1995, vol. 139, pp. 1429\u20131439.","journal-title":"Genetics"},{"issue":"1","key":"4006_CR13","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1093\/genetics\/157.1.399","volume":"157","author":"N.J. Savill","year":"2001","unstructured":"Savill, N.J., Hoyle, D.C., and Higgs, P.G., RNA Sequence Evolution with Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods, Genetics, 2001, vol. 157, no. 1, pp. 399\u2013411.","journal-title":"Genetics"},{"issue":"4","key":"4006_CR14","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1093\/molbev\/msi099","volume":"22","author":"M.J. Telford","year":"2005","unstructured":"Telford, M.J., Wise, M.J., and Gowri-Shankar, V., Consideration of RNA Secondary Structure Significantly Improves Likelihood-based Estimates of Phylogeny: Examples from the Bilateria, Mol. Biol. Evol., 2005, vol. 22, no. 4, pp. 1129\u20131136.","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"4006_CR15","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1093\/molbev\/msl144","volume":"24","author":"S.L. Kosakovsky Pond","year":"2007","unstructured":"Kosakovsky Pond, S.L., Mannino, F.V., Gravenor, M.B., Muse, S.V., and Frost, S.D., Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA, Mol. Biol. Evol., 2007, vol. 24, no. 1, pp. 159\u2013170.","journal-title":"Mol. Biol. Evol."},{"key":"4006_CR16","volume-title":"Mathematical Methods for DNA Sequences","year":"1989","unstructured":"Mathematical Methods for DNA Sequences, Waterman, M.S., Ed., Boca Raton: CRC Press, 1989. Translated under the title Matematicheskie metody dlya analiza posledovatel\u2019nostei DNK, Moscow: Mir, 1999."},{"key":"4006_CR17","first-page":"605","volume-title":"Proc. 13th All-Russia Conf. on Mathematical Methods of Pattern Recognition, Zelenogorsk, Russia, 2007","author":"V.A. Lyubetsky","year":"2007","unstructured":"Lyubetsky, V.A., Zhizhina, E.A., Gorbunov, K.Yu., and Seliverstov, A.V., Model of Evolution of Nucleotide Sequence, in Proc. 13th All-Russia Conf. on Mathematical Methods of Pattern Recognition, Zelenogorsk, Russia, 2007, Moscow: MAKS Press, 2007, pp. 605\u2013609."},{"key":"4006_CR18","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1109\/TPAMI.1984.4767596","volume":"6","author":"S. Geman","year":"1984","unstructured":"Geman, S. and Geman, D., Stochastic Relaxation, Gibbs Distribution, and the Bayesian Restoration of Images, IEEE Trans. Pattern Anal. Machine Intelligence, 1984, vol. 6, pp. 721\u2013741.","journal-title":"IEEE Trans. Pattern Anal. Machine Intelligence"},{"issue":"4598","key":"4006_CR19","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1126\/science.220.4598.671","volume":"220","author":"S. Kirkpatrick","year":"1983","unstructured":"Kirkpatrick, S., Gelatt, C.D., and Vecchi, M.P., Optimization by Simulated Annealing, Science, 1983, vol. 220, no. 4598, pp. 671\u2013680.","journal-title":"Science"},{"issue":"2","key":"4006_CR20","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1111\/j.1574-6968.2004.tb09555.x","volume":"234","author":"A.G. Vitreschak","year":"2004","unstructured":"Vitreschak, A.G., Lyubetskaya, E.V., Shirshin, M.A., Gelfand, M.S., and Lyubetsky, V.A., Attenuation Regulation of Amino Acid Biosynthetic Operons in Proteobacteria: Comparative Genomics Analysis, FEMS Microbiol. Lett., 2004, vol. 234, no. 2, pp. 357\u2013370.","journal-title":"FEMS Microbiol. Lett."},{"key":"4006_CR21","first-page":"68","volume-title":"Proc. Int. Sci. Conf. on Computational Phylogenomics and Genosystematics, Moscow, 2007","author":"K.Yu. Gorbunov","year":"2007","unstructured":"Gorbunov, K.Yu. and Lyubetsky, V.A., Model of Evolution of Nucleotide Sequence Considering Its Secondary Structure, in Proc. Int. Sci. Conf. on Computational Phylogenomics and Genosystematics, Moscow, 2007, Moscow: Mosk. Gos. Univ., 2007, pp. 68\u201371."},{"issue":"5","key":"4006_CR22","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1134\/S0026893307050172","volume":"41","author":"K. Gorbunov","year":"2007","unstructured":"Gorbunov, K. and Lyubetsky, V., Reconstruction of Ancestral Regulatory Signals along a Transcription Factor Tree, Mol. Biol. (Moscow), 2007, vol. 41, no. 5, pp. 836\u2013842.","journal-title":"Mol. Biol. (Moscow)"}],"container-title":["Problems of Information Transmission"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1134\/S0032946008040066.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1134\/S0032946008040066","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1134\/S0032946008040066","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1134\/S0032946008040066.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T03:11:39Z","timestamp":1775013099000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1134\/S0032946008040066"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,12]]},"references-count":22,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["4006"],"URL":"https:\/\/doi.org\/10.1134\/s0032946008040066","relation":{},"ISSN":["0032-9460","1608-3253"],"issn-type":[{"value":"0032-9460","type":"print"},{"value":"1608-3253","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,12]]},"assertion":[{"value":"12 February 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 April 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}