main.bib

@PHDTHESIS{sadovskiy,
  author       = {Садовский М.Г.},
  title        = {Информационно-статистический анализ нуклеотидных последовательностей. Диссертация на соискание ученой степени доктора физико-математических наук.},
  school       = {СО РАН},
  year         = {2004},
  address      = {Красноярск},  
  language     = {russian},
  pages        = {394},  
}

@BOOK{bio_school,
    author       = {Беляев Д.К., Бородкин П.М., Воронцов Н.Н. и др.},
      title        = {Общая биология: Учеб. для 10-11 кл. общеобразоват. учереждений.},
        publisher    = {Просвещение},
          address      = {Москва},
            year         = {2003},
              language     = {russian},
                pages        = {303},    
}

@BOOK{gatlin_info_theory,
    author       = {Gatlin L.L.},
      title        = {Information Theory and the Living System},
        publisher    = {Columbia UniversityPress},
          address      = {New York},
            year         = {1972},
              language     = {english},
                pages        = {303},    
}

@ARTICLE{gatlin_info_content_dna,
    author       = {Gatlin L.L.},
      title        = {The information content of DNA},
        journal      = {J.Theor.Biol.},
          year         = {1966},
            volume       = {10},  
              pages        = {281--300},
                language     = {english},
}

@BOOK{alexandrov,
    author       = {Александров А.А., Александров В.В., Бородовский Ю.М. и др.},
      title        = {Компьютерный анализ генетических текстов},
        publisher    = {Наука},
          address      = {Москва},
            year         = {1990},
              language     = {russian},
                pages        = {264},    
}

@BOOK{ray_paton_computing_bio_metaphors,
    author       = {},
      title        = {Computing with biological metaphors Edited by Ray Paton},
        publisher    = {New York:Chapman \& Hall},
          address      = {London},
            year         = {1994},
              language     = {english},
                pages        = {452},    
}

@ARTICLE{comp_dna_sequence_analysis,
    author       = {Karlin S., Cardon L.R.},
      title        = {Computational DNA Sequence Analysis},
        journal    = {Ann.Rev. of Microbiology},
          year         = {1994},
            volume       = {48},  
              pages        = {619--654},  
                language     = {english},
}

@ARTICLE{knopka_seq_and_codes,
    author       = {Konopka A.K.},
      title        = {Sequences and Codes: Foundamentals of Biomolecular Cryprology},
        journal    = {In:Biocomputings: Informatics and Genome Projects (D.Smith, Ed.)},
          address      = {San Diego},
            publisher    = {Acad.Press},   
              pages        = {119--174},  
                language     = {english},
}

@ARTICLE{knopka_theor_molbio,
    author       = {Konopka A.K.},
      title        = {Theoretical Molecular Biology},
        journal    = {In: Molecular Biology and Biotechnology, (R.A.Meyers, Ed.)},
          address      = {Weinheim},
            publisher    = {VCH Publishers},   
              pages        = {888--896},  
                language     = {english},
}

@ARTICLE{bionics_revisited,
    author       = {Rosen R.},
      title        = {Bionics Revisited},
        journal    = {In: The Machine as Metaphor and Tool (Eds. H.Haken,A.Karlquist, U.Svedin)},
          address      = {Berlin},
            publisher    = {Springer-Verlag},
              year         = {1993},    
                pages        = {87--100},  
                  language     = {english},
}

@ARTICLE{schenon,
    author       = {Shannon C.E., Weaver W.},
      title        = {The Mathematical Theory of Communication},
        journal    = {University of Illinois Press},
          address      = {Urbana,Illinois},
            year         = {1949},    
              pages        = {429},  
                language     = {english},
}

@ARTICLE{analysis_on_sec_comprison,
    author       = {Michaljevic M.J.},
      title        = {Analysis of the decoding approach based on the sequence comparison},
        journal    = {9th Conf. Appl. Math.},
          address      = {Budva},
            publisher    = {Novi Sad},  
              year         = {1994},  
                pages        = {313--319},  
                  language     = {english},
}

@ARTICLE{theory_transmission_processing_inf,
    author       = {Vitushkin A.G.},
      title        = {Theory of transmission and processing of information},
        journal    = {9th Conf. Appl. Math.},
          address      = {N.Y.},
            publisher    = {Pargamon Press},  
              year         = {1962},  
                pages        = {467},  
                  language     = {english},
}

@ARTICLE{kholmagorov_logic_probability,
    author       = {Колмогоров А.Н.},
      title        = {К логическим основаниям теории информации и теории вероятностей},
        journal    = {Проблемы передачи информации},
          volume       = {5},
            year         = {1969},  
              pages        = {3--7},  
                language     = {russian},
}

@ARTICLE{kholmagorov_combinary_informatic,
    author       = {Колмогоров А.Н.},
      title        = {Комбинаторные основания теории информации и исчисления вероятностей},
        journal    = {УМН},
          volume       = {38, вып.4},
            year         = {1983},  
              pages        = {27--36},  
                language     = {russian},
}

@ARTICLE{structute_context_complexity,
  author       = {Eriksson K.-E., Lindgren K., Mansson B.A.},
  title        = {Structure, context, complexity, organization:physical aspects of information and value},
  address      = {Singapore},  
  journal    = {N.J.: World Scientific},
  year         = {1987},  
  pages        = {325},  
  language     = {english},
}

@ARTICLE{analytics_uncertainty_info,
  author       = {Hirshleifer C, Riley J.G.},
  title        = {The analytics of uncertainty and information},
  address      = {Cambridge},  
  journal    = {NewYork: Cambridge University Press},
  year         = {1992},  
  pages        = {502},  
  language     = {english},
}


@BOOK{aho,
  author       = {Ахо А., Хопкрофт Дж., Ульман Дж.},
  title        = {Построение и анализ вычислительных алгоритмов},
  address      = {Москва},  
  publisher    = {Мир},
  year         = {1979},  
  pages        = {462},  
  language     = {russian},
}

@ARTICLE{kholmagorov_three_ways_to_count_info,
  author       = {Колмогоров А.Н.},
  title        = {Три подхода к определению понятия "количество информации"},
  journal    = {Проблемы передачи информации},
  volume       = {1},
  year         = {1965},  
  pages        = {3--11},  
  language     = {russian},
}

@ARTICLE{nemitikova_cluster_in_dna,
  author       = {Немытикова Л.А.},
  title        = {Использование серийных характеристик для исследования эффекта кластеризации элементов в ДНК-молекулах},
  journal    = {Методы анализа данных (Вычислит, системы, вып. 150)},
  address      = {Новосибирск},  
  publisher    = {ИМ СО РАН},  
  year         = {1994},
  pages        = {147--163},  
  language     = {russian},
}

@ARTICLE{levin_zvonkiy_complexity,
  author       = {Левин Л.А., Звонкий А.К.},
  title        = {Сложность задания конечных объектов и развитие идейинформации и случайности на основе теории алгоритмов},
  journal    = {УМН},
  volume       = {256},
  year         = {1970},  
  pages        = {83--124},  
  language     = {russian},
}

@ARTICLE{lempel_ziv_complexity,
  author       = {Lempel A., Ziv J.},
  title        = {On the Complexity of Finite Sequences},
  journal    = {IEEE Trans.of Inf. Theory},
  volume       = {IT-22, issue 1},
  year         = {1976},  
  pages        = {75--81},
  language     = {english},
}

@ARTICLE{gusev_complexity_profiles,
  author       = {Гусев В.Д.},
  title        = {Сложностные профили символьных последовательностей},
  journal    = {Методы обработки символьных последовательностей и сигналов (Выч. системы, вып.  132)},
  address      = {Новосибирск},  
  publisher    = {ИМ СО АН СССР},    
  year         = {1989},  
  pages        = {35--63},  
  language     = {russian},
}

@ARTICLE{gusev_characters_char_sequance,
  author       = {Гусев В.Д.},
  title        = {Характеристики символьных последовательностей},
  journal    = {Проблемы обработки информации (Выч. системы, вып. 88)},
  address      = {Новосибирск},  
  publisher    = {ИМ СО АН СССР},    
  year         = {1981},  
  pages        = {11--34},
  language     = {russian},
}

@PHDTHESIS{chupachina_1993,
  author       = {Чупахина О.М.},
  title        = {Сложностный анализ генетических текстов},
  school       = {Сложностный анализ генетических текстов},
  year         = {1993},
  pages        = {18},
  language     = {russian},
}

@ARTICLE{zurek_1990,
  author       = {Zurek W.H.},
  title        = {Algorithmic Information Content, Church-Turing Thesis, Physical Entropy,and Maxwell's Demon, in Complexity, Entropy and the Physics of Information},
  journal    = {Addison-Wesley},
  address      = {Redwood City, California},  
  year         = {1990},  
  pages        = {73--89},  
  language     = {english},
}

@ARTICLE{zurek_1989,
  author       = {Zurek W.H.},
  title        = {Algorithmic Randomness and Physical Entropy},
  journal    = {Physical Review A},
  volume     = {40},
  year         = {1989},  
  pages        = {4731--4751},
  language     = {english},
}

@ARTICLE{enthropy_complexity_offinite,
  author       = {Jimenez-Montano M.A., Ebeling W., Pohl Th.},
  title        = {Entropy and complexity offinite sequences as fluctuating quantities},
  journal    = {BioSystems},
  volume     = {64},
  year         = {2002},  
  pages        = {23--32},
  language     = {english},
}

@ARTICLE{zeigarnik_graph_theoretic,
  author       = {Zeigarnik A.V., Temkin O.N.},
  title        = {A graph-theoretic model of complex reaction mechanisms:a new complexity index for reaction mechanisms},
  journal    = {Kinetics and Catalysis},
  volume     = {37},
  year         = {1996},  
  pages        = {372--385},
  language     = {english},
}

@ARTICLE{margalef_information_uncertainty,
    author       = {Margalef RS.},
      title        = {Information and uncertainty in living systems, a view from ecology},
        journal    = {Bio--Systems},
          volume     = {38},
            year         = {1996},  
              pages        = {141--146},  
                language     = {english},
}

@BOOK{enthropy_new_perspectives,
    author       = {B.H.Weber, D.J.Depew, J.D.Smith.},
      title        = {Entropy, information, and evolution: new perspectives on physical and biological evolution},
        address      = {Cambridge},  
          publisher    = {Mass.: MIT Press},
            year         = {1988},  
              pages        = {487},  
                language     = {english},
}

@ARTICLE{gelfand_computional_analysis_dna,
    author       = {Гельфанд М.С.},
      title        = {Компьютерный анализ последовательностей ДНК},
        journal    = {Мол.биология},
          volume     = {32, № 1},
            year         = {1998},  
              pages        = {103--120},  
                language     = {russian},
}

@ARTICLE{uchmanov_phylogenetic_trees,
  author       = {Юшманов С.В.},
  title        = {Восстановление биологической эволюции. Построение филогенетических деревьев},
  journal    = {Мат.вопросы кибернетики. Вып.З},
  address      = {Москва},  
  publisher    = {Наука},  
  year         = {1991},  
  pages        = {51--76},  
  language     = {russian},
}

@BOOK{trifonov_brendel_gnomic_dictionary,
  author       = {Trifonov E.N., Brendel V.},
  title        = {Gnomic, A Dictionary of Genetic Codes location},
  address      = {Philadelphia},  
  publisher    = {BalabanPublishers},  
  year         = {1986},  
  pages        = {421},  
  language     = {english},
}

@ARTICLE{gorban_correlation,
    author       = {Горбань А.Н., Попова Т.Г., Садовский М.Г.},
      title        = {Корреляционный подход к сравнениюнуклеотидных последовательностей},
        journal      = {ЖОБ},
          volume     = {55, № 4/5},
            year         = {1994},  
              pages        = {420--430},  
                language     = {russian},
}

@ARTICLE{sadovsky_investigation_statustic,
  author       = {Popova T.G., Sadovsky M.G.},
  title        = {Investigating statistical properties of genetic texts: newmethod to compare two genes},
  journal      = {Modelling, Measurement \& Control, ser. C},
  volume     = {45, № 4},
  publisher    = {AMSEPress},  
  year         = {1994},  
  pages        = {27--36},  
  language     = {english},
}

@ARTICLE{levenchtain_metric,
  author       = {Левенштейн В.И.},
  title        = {О совершенных кодах в метрике выпадений и вставок},
  journal      = {Дис-кретн.математика},
  volume     = {3, №1},
  year         = {1991},  
  pages        = {3--20},  
  language     = {russian},
}

@ARTICLE{sankoff_edit_distance_genome,
    author       = {Sankoff D.},
      title        = {Edit distance for genome comparison based on non-local operations: Combin.Pattern Match},
        journal      = {Lect. Notes Comput.Sci.},
          volume     = {644},
            year         = {1992},  
              pages        = {121--135},  
                language     = {english},
}

@ARTICLE{roytberg_similarity_search,
  author       = {Roytberg M.A.},
  title        = {Similarity search in two biological sequences},
  journal      = {Proc.of the Conf."Modeling and computer methods in molecular biology and genetics"},
  address      = {Novosibirsk},
  year         = {1990},  
  pages        = {7--8},  
  language     = {english},
}

@ARTICLE{vernoslov_samson,
    author       = {Вернослов С.Е., Кондратов А.С., Ройтберг М.А.},
      title        = {Программный комплекс "Самсон" для анализа первичной структурыбиополимеров},
        journal      = {Молекулярная биология},
          volume     = {24, № 2},
            year         = {1989},  
              pages        = {524--529},  
                language     = {russian},
}

@ARTICLE{roytberg_computation_biopolymers,
    author       = {Finkelstein A.V., Roytberg M.A.},
      title        = {Computation of biopolymers: a general approach todifferent problems},
        journal      = {BioSystems},
          volume       = {30},
            year         = {1993},  
              pages        = {33--46},  
                language     = {english},
}

@ARTICLE{deken_limit_largest_subsequences,
    author       = {Deken T.G.},
      title        = {Some limit results for largest common subsequences},
        journal      = {Discrete Mathematics},
          volume       = {26, № 1},
            year         = {1979},  
              pages        = {17--31},  
                language     = {english},
}

@ARTICLE{chvatal_longes_common_subsequence,
  author       = {Chvatal V., Sankoff D.},
  title        = {Longest common subsequences of two random sequences},
  journal      = {J.Appl.Probability},
  volume       = {12},
  year         = {1975},  
  pages        = {306--315},  
  language     = {english},
}

@ARTICLE{gorban_auto_classification_nucleotide,
  author       = {Gorban A.N., Popova T.G., Sadovsky M.G.},
  title        = {Automatic classification of nucleotidesequences and its relation to natural taxonomy and protein function},
  journal      = {Proc. of 1st Int.Conf. on Bioinformatics of Genome Regulation and Structure},
  address      = {Novosibirsk},  
  volume       = {2},
  year         = {1998},  
  pages        = {314--317},  
  language     = {english},
}

@ARTICLE{gorban_classification,
    author       = {Gorban A.N., Popova T.G., Sadovsky M.G.},
      title        = {Classification of symbol sequences over theirfrequency dictionaries: towards the connection between structure and natural taxonomy},
        journal      = {Open Systems \& Information Dynamics},
          volume       = {v.7, № 1},
            year         = {2000},  
              pages        = {1--17},  
                language     = {english},
}

@ARTICLE{gorban_frequency_dictionaries,
    author       = {Gorban A.N., Popova T.G., Sadovsky M.G.},
      title        = {Information content of the frequency dictionaries, reconstruction, transformation and classification of dictionariesand genetic texts},
        journal      = {Intelligent Engineering Systems through Artificial Neural Networks:v.l 1 --- Smart Engineering System Design},
          address      = {N.-Y.},
            publisher    = {ASME Press},
              year         = {2001},  
                pages        = {657--663},  
                  language     = {english},
}

@ARTICLE{sadovsky_comparisio_symbol_sequences,
    author       = {Sadovsky M.G.},
      title        = {Comparison of Symbol Sequences: No Editing, No Alignment},
        journal      = {OpenSystems \& Information Dynamics},
          volume       = {9, № 1},
            year         = {2002},  
              pages        = {19--36},  
                language     = {english},
}

@ARTICLE{sadovsky_method_compare_seq_on_entropy,
    author       = {Sadovsky M.G.},
      title        = {The method of comparison of nucleotide sequences based on theminimum entropy principle},
        journal      = {Bulletine of Mathematical Biology},
          volume       = {65},
            year         = {2003},  
              pages        = {309--332},  
                language     = {english},
}

@ARTICLE{blaisdcll_markov_chain_analysis_for_dna_parts,
    author       = {Blaisdcll B.E.},
      title        = {Markov chain analysis finds a significant influence of neighboring bases onthe occurrence of a base in eukaryotic nuclear DNA sequence protein-coding and non-coding},
        journal      = {Mol.Evolution},
          volume       = {21},
            year         = {1985},  
              pages        = {278--288},  
                language     = {english},
}

@ARTICLE{levy_walk_model,
    author       = {Buldyrev S.V., Goldberger A.L., Havlin S.},
      title        = {Generalized Levy-walk model for DNA nucleotide sequences location},
        journal      = {Phys.Review E},
          volume       = {47},
            year         = {1993},  
              pages        = {4514--4523},  
                language     = {english},
}

@ARTICLE{churchill_hidden_markov,
    author       = {Churchill G.A.},
      title        = {Hidden Markov chains and the analysis of genome structure},
        journal      = {Comput.Chemistry},
          volume       = {16},
            year         = {1992},  
              pages        = {107--115},  
                language     = {english},
}

@ARTICLE{duret_expression_pattern,
    author       = {Duret L., Mouchiroud D.},
      title        = {Expression pattern and, surprisingly, gene length shape codonusage in Caenorhabditis, Drosophila, and Arabidopsis II},
        journal      = {Proc.Natl.Acad.Sci. USA},
          volume       = {96, №8},
            year         = {1999},  
              pages        = {4482--4487},  
                language     = {english},
}

@ARTICLE{kxogh_hidden_markov,
    author       = {Kxogh A., Mian I.S., Haussler D.},
      title        = {A hidden Markov model that finds genes in E. coliDNA},
        journal      = {Nucleic Acids Res.},
          volume       = {22},
            year         = {1994},  
              pages        = {4768--4778},  
                language     = {english},
}

@ARTICLE{pevzner_sequences_versus_markov,
    author       = {Pevzner P.A.},
      title        = {Nucleotide sequences versus Markov models location},
        journal      = {Abstr. of Workshopon Open Problems of Computational Molecular Biology},
          address      = {Telluride, Colorado},
            year         = {1991},  
              pages        = {50--54},  
                language     = {english},
}


@BOOK{yoterman_math_dna_analysis,
    author       = {Уотермен М.С.},
      title        = {Математические методы для анализа последовательностей ДНК.},
        address      = {Москва},  
          publisher    = {Мир},  
            year         = {1999},  
              pages        = {349},  
                language     = {russian},
}

@ARTICLE{sence_codons_are_found_in_specific_context,
    author       = {Yarus M., Folley L.S.},
      title        = {Sense codons are found in specific context},
        journal      = {J.Mol. Biology},
          volume       = {182},
            year         = {1985},  
              pages        = {529--540},  
                language     = {english},
}

@ARTICLE{correlation_approache_to_identify,
    author       = {Ossadnik S.M., Buldyrev S.V., Goldberger A.L.},
      title        = {Correlation approach to identify coding regions in DNAsequences},
        journal      = {Biophys.J.},
          volume       = {67},
            year         = {1994},  
              pages        = {64--70}, 
                language     = {english},
}

@ARTICLE{long_range_correlations_in_dna,
    author       = {Arneodo A., Bacry E., Muzy J.F.},
      title        = {Characterizing long-range correlations in DNA sequences from wavelet analysis},
        journal      = {Phys.Rev.Lett.},
          volume       = {74},
            year         = {1995},  
              pages        = {3293--3296},  
                language     = {english},
}

@ARTICLE{kozlov_2000,
    author       = {Козлов К.Н., Мясникова Е.М., Самсонова М.Г.},
      title        = {Метод пространственной регистрации картин экспрессии генов сегментации у мушки дрозофилы с использованием вейвлетного разложения},
        journal      = {Вычислит.технологии},
          volume     = {5, № 2}, 
            year         = {2000},  
              pages        = {112--127},  
                language     = {russian},
}

@ARTICLE{lixoshvai_2000,
    author       = {Лихошвай В.А., Матушкин Ю.Г.},
      title        = {Компьютерная модель для анализа эволюционного дрейфа синонимичных кодонов вдоль мРНК},
        journal      = {Вычислит.технологии},
          volume     = {5, № 2},
            year         = {2000},  
              pages        = {57--63},  
                language     = {russian},
}


@ARTICLE{universality_in_dna_statistical_structure,
  author       = {Azbel M.Y.},
  title        = {Universality in a DNA statistical structure},
  journal      = {Phys.Rev.Lett.},
  volume       = {75},
  year         = {1995},  
  pages        = {168--171},  
  language     = {english},
}

@ARTICLE{distribution_triplets_in_genetic_seq,
    author       = {Yu Shi, Ido Kantcr, David Kessler},
      title        = {Distributions of triplets in genetic sequences},
        journal      = {Physica A},
          volume       = {252},
            year         = {1998},  
              pages        = {48--60},  
                language     = {english},
}

@ARTICLE{minint_subtillis_hidden_markov,
    author       = {Nicolas P., Bize L., Muri F.},
      title        = {Mining Bacillus subtillis genome heterogeneity using hidden Markov models},
        journal      = {NucleicAcids Res.},
          volume       = {30, № 6},
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