@string{AAP="Ann. Appl. Prob."} @string{AIHP="Ann. Inst. Henri Poincaré"} @string{AP="Ann. Prob."} @string{AS="Ann. Statist."} @string{AdAP="Adv. Appl. Prob."} @string{ApS="Appl. Statist."} @string{AnAP="Ann. Appl. Prob."} @string{AFN="Application of Fibonacci Numbers"} @string{CABIOS="Comp. Applic. Biosci."} @string{BMB="Bull. Math. Biol"} @string{ESAIM="ESAIM: Probability and Statistics"} @string{JAM="J. Analyse Math."} @string{JAP="J. Appl. Prob."} @string{JASA="J. Amer. Statist. Soc."} @string{JBSD="J. Biomol. Struct. Dynamics"} @string{JCB="J. Comp. Biol."} @string{JCTA="J. Combinatorial Theory A"} @string{JMB="J. Mol. Biol."} @string{JME="J. Mol. Evol"} @string{JTB="J. Theor. Biol."} @string{JRSSB="J. R. Statist. Soc. B"} @string{MBE="Mol. Biol. Evol."} @string{MPCPS="Math. Proc. Camb. Phil. Soc."} @string{NAR="Nucl. Acids Res."} @string{PNAS="Proc. Natl. Acad. Sci. USA"} @string{PSI="Prob. Statist. Inference"} @string{PTRF="Prob. Theory Rel. Fields"} @string{P="Preprint"} @string{RTB="INRA, Biom\'etrie"} @string{SPA="Stoch. Proc. Appl."} @string{SPL="Statist. Prob. Letters"} @string{SS="Statistical Science"} @string{SSI="Statistica Sinica"} @string{TPA="Theory Prob. Appl."} @string{ZW="Z. Wahrscheinlichkeitsth"} @ARTICLE (AGG89, TITLE = "Two moments suffice for {P}oisson approximations : the {C}hen-{S}tein method", AUTHOR = "Arratia, R. and Goldstein, L. and Gordon, L.", JOURNAL = AP, VOLUME = 17, YEAR = 1989, PAGES = "9--25", KEYWORDS = "Poisson approximation, Chen-Stein method") @ARTICLE (AlE85, TITLE = "Significance of nucleotide sequence alignments~: {A} method for random sequence permutation that preserves dinucleotide and codon usage", AUTHOR = "Altschul, S. F. and Erickson, B. W.", JOURNAL = MBE, VOLUME = 2, YEAR = 1985, PAGES = "526--538", KEYWORDS = "alignment") @ARTICLE (AGG90, TITLE = "Poisson approximation and the {C}hen-{S}tein method", AUTHOR = "Arratia, R. and Goldstein, L. and Gordon, L.", JOURNAL = SS, VOLUME = 5, YEAR = 1990, PAGES = "403--434", KEYWORDS = "Poisson approximation, Chen-Stein method") @ARTICLE (AGW90, TITLE = "The {E}rd{\"o}s-{R}ényi law in distribution, for coin tossing and sequence matching", AUTHOR = "Arratia, R. and Gordon, L. and Waterman, M. S.", JOURNAL = AS, VOLUME = 18, YEAR = 1990, PAGES = "539--570", KEYWORDS = "alignment") @ARTICLE (ArW89, TITLE = "The {E}rd{\"o}s-{R}ényi strong law for pattern matching with a given porportion of mismatches", AUTHOR = "Arratia, R. and Waterman, M. S.", JOURNAL = AP, VOLUME = 17, YEAR = 1989, PAGES = "1152--1169", KEYWORDS = "alignment") @ARTICLE (ArM90a, TITLE = "Periodicities in coding and noncoding regions of the genes", AUTHOR = "Arqu\`es, D. G. and Michel, C. J.", JOURNAL = JTB, VOLUME = 143, YEAR = 1990, PAGES = "307--318", KEYWORDS = "DNA structure and biology") @ARTICLE (ArM90b, TITLE = "A model of {DNA} sequence evolution", AUTHOR = "Arqu\`es, D. G. and Michel, C. J.", JOURNAL = BMB, VOLUME = 52, YEAR = 1990, PAGES = "741--772", KEYWORDS = "autre") @ARTICLE (Ave87, TITLE = "The analysis of intron data and their use in the detection of short signals", AUTHOR = "Avery, P. J.", JOURNAL = JME, VOLUME = 26, YEAR = 1987, PAGES = "335--340", KEYWORDS = "DNA structure and biology") @ARTICLE (BCL92, TITLE = "Compound {P}oisson approximation for nonnegative random variables via {S}tein's method", AUTHOR = "Barbour, A. D. and Chen, L. H. Y. and Loh, W.-L.", JOURNAL = AP, VOLUME = 20, YEAR = 1992, PAGES = "1843--1866", KEYWORDS = "compound Poisson approximation, Stein method") @ARTICLE (BaE83, TITLE = "Poisson approximation for some statistics based on exchangeable trials", AUTHOR = "Barbour, A. D. and Eagleson, G. K.", JOURNAL = AAP, VOLUME = 15, YEAR = 1983, PAGES = "585--600", KEYWORDS = "Poisson approximation") @ARTICLE (BaE84, TITLE = "Poisson convergence for dissociated statistics", AUTHOR = "Barbour, A. D. and Eagleson, G. K.", JOURNAL = JRSSB, VOLUME = 46, YEAR = 1984, PAGES = "397--402", KEYWORDS = "Poisson approximation") @ARTICLE (BaH84, TITLE = "On the rate of Poisson convergence", AUTHOR = "Barbour, A. D. and Hall, P.", JOURNAL = MPCPS, VOLUME = 95, YEAR = 1984, PAGES = "473--480", KEYWORDS = "Poisson approximation") @ARTICLE (BHu99, TITLE = "An {A}nalytical {S}tudy of the {P}hase {T}ransition {L}ine in {L}ocal {S}equence {A}lignment with {G}aps", AUTHOR = "R. Bundschuh and T. Hwa", JOURNAL = "Recomb 99, Proc. of the third Ann. Internatnl. Conf. on Comp. Mol. Biol.", YEAR = 1999, PAGES = "70--76", KEYWORDS = "alignment") @ARTICLE (Bla85, TITLE = "Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucariotic nuclear {DNA} sequences both protein-coding and noncoding", AUTHOR = "Blaisdell, B. E.", JOURNAL = JME, VOLUME = 21, YEAR = 1985, PAGES = "278--288", KEYWORDS = "Markov chain models") @ARTICLE (BBT86a, TITLE = "Linguistics of nucleotide sequences : {M}orphology and comparison of vocabularies", AUTHOR = " Brendel, V. and Beckmann, J. S. and Trifonov, E. N.", JOURNAL = JBSD, VOLUME = 4, YEAR = 1986, PAGES = "11--21", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (BBT86b, TITLE = "Intervening sequences exhibit distinct vocabulary", AUTHOR = "Beckmann, J. S. and Brendel, V. and Trifonov, E. N.", JOURNAL = JBSD, VOLUME = 4, YEAR = 1986, PAGES = "391--400", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (BCK92, TITLE = "Over- and under-representation of short oligonucleotides in {DNA} sequences", AUTHOR = "Burge, C. and Campbell, A.M. and Karlin, S. ", JOURNAL = PNAS, VOLUME = 89, YEAR = 1992, PAGES = "1358--1362", KEYWORDS = "linguistics of DNA sequences") @BOOK (BHJ92, AUTHOR = "Barbour, A. D. and Holst, L. and Janson, S.", TITLE = "Poisson approximation", PUBLISHER = {Oxford-University Press} , YEAR = 1992, KEYWORDS = "Poisson approximation") @BOOK (Bil68, AUTHOR = "Billingsley, P.", TITLE = "Convergence of probability measures", PUBLISHER = {Wiley}, YEAR = 1968, KEYWORDS = "autre") @BOOK (Buc90, AUTHOR = "Bucklew, J. A.", TITLE = "Large deviation techniques in decision, simulation, and estimation", PUBLISHER = {Wiley} , YEAR = 1990, KEYWORDS = "autre") @ARTICLE (Che75 , TITLE = "Poisson approximation for dependent trials", AUTHOR = "Chen, L. H. Y.", JOURNAL = AP, VOLUME = 3, YEAR = 1975, PAGES = "534--545", KEYWORDS = "Poisson approximation") @ARTICLE (Che78 , TITLE = "Two central limit problems for dependent random variables", AUTHOR = "Chen, L. H. Y.", JOURNAL = "Z. Wahrscheinlichkeitstheorie verw. Gebiete", VOLUME = 43, YEAR = 1978, PAGES = "223--243", KEYWORDS = "autre") @ARTICLE (Chu89, TITLE = "Stochastic models for heterogeneous {DNA} sequences", AUTHOR = "Churchill, G. A.", JOURNAL = BMB, VOLUME = 51, YEAR = 1989, PAGES = "79--94", KEYWORDS = "heterogeneity") @ARTICLE (Chu92, TITLE = "Hidden {M}arkov chains and the analysis of genome structure", AUTHOR = "Churchill, G. A.", JOURNAL = "Computers Chem.", VOLUME = 16, YEAR = 1992, PAGES = "107--115", KEYWORDS = "heterogeneity") @ARTICLE (ChP88a, TITLE = "A limit theorem for the number of non-overlapping occurrences of a pattern in a sequence of independent trials", AUTHOR = "Chryssaphinou, O. and Papastavridis, S.", JOURNAL = JAP, VOLUME = 25, YEAR = 1988, PAGES = "428--431", KEYWORDS = "word counts") @ARTICLE (ChP88b, TITLE = "A limit theorem on the number of overlapping appearances of a pattern in a sequence of independent trials", AUTHOR = "Chryssaphinou, O. and Papastavridis, S.", JOURNAL = PTRF, VOLUME = 79, YEAR = 1988, PAGES = "129--143", KEYWORDS = "word counts") @ARTICLE (Cow91, TITLE = "Expected frequencies of {DNA} patterns using {W}hittle's formula", AUTHOR = "Cowan, R.", JOURNAL = JAP, VOLUME = 28, YEAR = 1991, PAGES = "886--892", KEYWORDS = "word counts, linguistics of DNA sequences") @ARTICLE (CPT93, TITLE = "On the number of overlapping success runs in a sequence of independent bernoulli trials", AUTHOR = "Chryssaphinou, O. and Papastavridis, S.", JOURNAL = AFN, VOLUME = 5, YEAR = 1993, PAGES = "103--112", KEYWORDS = "word counts") @BOOK (DCD83, AUTHOR = "Dacunha-Castelle, D. and Duflo, M.", TITLE = "Probabilit\'es et statistiques 2.{P}robl\`emes \`a temps mobile", PUBLISHER = {Masson} , YEAR = 1983, KEYWORDS = "autre") @ARTICLE (DeK92, TITLE = "Poisson approximations for $r$-scan processes", AUTHOR = "Dembo, A. and Karlin, S.", JOURNAL = AnAP, VOLUME = 2, YEAR = 1992, PAGES = "329-357", KEYWORDS = "Poisson process approximation, word locations") @BOOK (Duf90, AUTHOR = "Duflo, M.", TITLE = "M\'ethodes r\'ecursives al\'eatoires", PUBLISHER = {Masson} , YEAR = 1990, KEYWORDS = "autre") @PHDTHESIS (Erh97, TITLE = "Compound {P}oisson approximation for {M}arkov chains", AUTHOR = "Erhardsson, T.", SCHOOL = "Royal Institute of Technology, Stockholm", YEAR = 1997, KEYWORDS = "compound Poisson approximation, Markov chain models,word counts") @ARTICLE (Fu93, TITLE = "Poisson convergence in reliability of a large linearly connected system as related to coin tossing", AUTHOR = "Fu, J. C.", JOURNAL = SSI, VOLUME = 3, YEAR = 1993, PAGES = "261--275", KEYWORDS = "Poisson approximation") @ARTICLE (FuK94, TITLE = "Distribution theory of runs: {A} {M}arkov chain approach", AUTHOR = "Fu, J. C. and Koutras, V.", JOURNAL = JASA, VOLUME = 89, YEAR = 1994, PAGES = "1050--1058", KEYWORDS = "word counts, Markov chain models") @ARTICLE (FTW92, TITLE = "Base compositional structure of genomes", AUTHOR = "Fickett, J. W. and Torney, D. C. and Wolf, D. R.", JOURNAL = "Genomics", VOLUME = 13, YEAR = 1992, PAGES = "1056--1064", KEYWORDS = "DNA structure and biology") @ARTICLE (GGS95, TITLE = "Compound {P}oisson approximations for word patterns under {M}arkovian hypotheses", AUTHOR = "Geske, M. X. and Godbole, A. P. and Schaffner, A. A. and Skolnick, A. M. and Wallstrom, G. L.", JOURNAL = JAP, VOLUME = 32, YEAR = 1995, PAGES = "877--892", KEYWORDS = "compound Poisson approximation, word counts, Markov chain models, Chen-Stein method") @ARTICLE (GKP92, TITLE = "Extendable words in nucleotide sequences", AUTHOR = "Gelfand, M. S. and Kozhukhin, C. G. and Pevzner, P. A.", JOURNAL = CABIOS, VOLUME = 8, YEAR = 1992, PAGES = "129--135", KEYWORDS = "autre") @ARTICLE (God90, TITLE = "Specific formula for some success run distributions", AUTHOR = "Godbole, A. P.", JOURNAL = SPL, VOLUME = 10, YEAR = 1990, PAGES = "119--124", KEYWORDS = "word counts") @ARTICLE (God91, TITLE = "Poisson approximations for runs and patterns of rare events", AUTHOR = "Godbole, A. P.", JOURNAL = AdAP, VOLUME = 23, YEAR = 1991, PAGES = "851--865", KEYWORDS = "Poisson approximation, word counts") @ARTICLE (GoS93 , TITLE = "Improved poisson approximations for word patterns", AUTHOR = "Godbole, A. P. and Schaffner, A. A.", JOURNAL = AdAP, VOLUME = 25, YEAR = 1993, PAGES = "334--347", KEYWORDS = "Poisson approximation, word counts") @ARTICLE (GoW92 , TITLE = "Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons", AUTHOR = "Goldstein, L.. and Waterman, M.~S..", JOURNAL = BMB, VOLUME = 54, YEAR = 1992, PAGES = "785--812", KEYWORDS = "Poisson approximation, compound Poisson approximation, Poisson process approximation, alignment") @ARTICLE (GuO81a, TITLE = "Periods in strings", AUTHOR = "Guibas, L. J. and Odlyzko, A. M.", JOURNAL = JCTA, VOLUME = 30, YEAR = 1981, PAGES = "19--42", KEYWORDS = "combinatorics on words") @ARTICLE (GuO81b, TITLE = "String overlaps, pattern matching, and nontransitive games", AUTHOR = "Guibas, L. J. and Odlyzko, A. M.", JOURNAL = JCTA, VOLUME = 30, YEAR = 1981, PAGES = "183--208", KEYWORDS = "combinatorics on words") @ARTICLE (HiA93 , TITLE = "On number of occurrences of sucess runs of specified length in a two-state {M}arkov chain", AUTHOR = "Hirano, K. and Aki, S.", JOURNAL = SSI, VOLUME = 3, YEAR = 1993, PAGES = "313--320", KEYWORDS = "word counts, Markov chain models") @ARTICLE (KaA90, TITLE = "Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes", AUTHOR = "Karlin, S. and Altschul, S. F.", JOURNAL = PNAS, VOLUME = 87, YEAR = 1990, PAGES = "2264--2268", KEYWORDS = "alignment") @ARTICLE (KaM91a, TITLE = "Some statistical problems in the assessment of inhomogeneities of {DNA} sequence data", AUTHOR = "Karlin, S. and Macken, C.", JOURNAL = JASA, VOLUME = 86, YEAR = 1991, PAGES = "27--35", KEYWORDS = "heterogeneity") @ARTICLE (KaM91b, TITLE = "Assessment of inhomogeneities in an \textit{E. coli} physical map", AUTHOR = "Karlin, S. and Macken, C.", JOURNAL = NAR, VOLUME = 19, YEAR = 1991, PAGES = "4241--4246", KEYWORDS = "distances between occurrences of pattern, heterogeneity") @ARTICLE (KaO87 , TITLE = "Counts of long aligned word matches among random letter sequences", AUTHOR = "Karlin, S. and Ost, F.", JOURNAL = AP, VOLUME = 19, YEAR = 1987, PAGES = "293--351", KEYWORDS = "alignment, Poisson approximation") @ARTICLE (KaO88, TITLE = "Maximal length of common words among random letter sequences", AUTHOR = "Karlin, S. and Ost, F.", JOURNAL = AP, VOLUME = 16, YEAR = 1988, PAGES = "535--563", KEYWORDS = "alignment") @ARTICLE (KlB92, TITLE = "First and second moment of counts of words in random texts generated by {M}arkov chains", AUTHOR = "Kleffe, J. and Borodovsky, M.", JOURNAL = CABIOS, VOLUME = 8, YEAR = 1992, PAGES = "433--441", KEYWORDS = "word counts, Markov chain models") @ARTICLE (KBC92, TITLE = "Statistical analyses of counts and distributions of restriction sites in {DNA} sequences", AUTHOR = "Karlin, S. and Burge, C. and Campbell, A. M.", JOURNAL = NAR, VOLUME = 20, YEAR = 1992, PAGES = "1363--1370", KEYWORDS = "word counts, linguistics of DNA sequences") @ARTICLE (KlG93, TITLE = "The joint distribution of patterns in random sequences with application to the {RC-}measure for expressivity", AUTHOR = "Kleffe, J. and Grau, E", JOURNAL = CABIOS, VOLUME = 9, YEAR = 1993, PAGES = "275--283", KEYWORDS = "autre") @ARTICLE (KlL90, TITLE = "Exact computation of pattern probabilities in random sequences generated by {M}arkov chains", AUTHOR = "Kleffe, J. and Langbecker, U.", JOURNAL = CABIOS, VOLUME = 6, YEAR = 1990, PAGES = "347--353", KEYWORDS = "word counts, Markov chain models, combinatorics on words") @Article (KNB99, author = {Krause, A. and Nicod\`eme, P. and Bornberg-Bauer, E. and Rehmsmeier, M. and Vingron, M.}, title = {{WWW}-Access to the {SYSTERS} Protein sequence Cluster set}, KEYWORDS = "clustering", journal = "Bioinformatics", year = 1999, note = {Application Note accepted for the GCB Special Issue of Bioinformatics} ) @ARTICLE (KoP91, TITLE = "Genome inhomogeneity is determined mainly by {WW} and {SS} dinucleotides", AUTHOR = "Kozhukhin, C. G. and Pevzner, P. A.", JOURNAL = CABIOS, VOLUME = 7, YEAR = 1991, PAGES = "39--49", KEYWORDS = "heterogeneity") @ARTICLE (LMS96, TITLE = "Over and underrepresentation of short {DNA} words in Herpesvirus genomes", AUTHOR = "Leung, M.~Y. Marsh, G.~M. and Speed, T.~P.", JOURNAL = JCB, VOLUME = 3, YEAR = 1996, PAGES = "345--360", KEYWORDS = "Markov chain models, Markov chain models") @BOOK (Lot83, AUTHOR = "Lothaire, M.", TITLE = "Combinatorics on words", PUBLISHER = {Addison-Wesley} , YEAR = 1983, KEYWORDS = "combinatorics on words") @ARTICLE (Lot92, TITLE = "{mRNA} periodical infrastructure complementary to the proof-reading site in the ribosome", AUTHOR = "Lagunez-Otero, J. and Trifonov, E. N.", JOURNAL = JBSD, VOLUME = 10, YEAR = 1992, PAGES = "455--464", KEYWORDS = "DNA structure and biology") @BOOK (MeT93, AUTHOR = "Meyn, S. P. and Tweedie, R. L.", TITLE = "Markov chains and stochastic stability", PUBLISHER = {Springer-Verlag} , YEAR = 1993, KEYWORDS = "Markov chain models") @ARTICLE (Mot92, TITLE = "Maximum-likelihood estimation of the statistical distribution of {S}mith-{W}aterman local sequence similarity scores", AUTHOR = "R. Mott", JOURNAL = "BMB", YEAR = 1992, PAGES = "59--75", KEYWORDS = "alignment") @ARTICLE (MRV91, TITLE = "Evidence for horizontal gene transfer in {E}scherichia coli speciation", AUTHOR = "M\'edigue, C. and Rouxel, T. and Vigier, P. and H\'enaut, A. and Danchin, A.", JOURNAL = JMB, VOLUME = 222, YEAR = 1991, PAGES = "851--856", KEYWORDS = "DNA structure and biology") @ARTICLE (MTr99, TITLE = "Approximate {S}tatistics of {G}apped {A}lignments", AUTHOR = "R. Mott and R. Tribes", JOURNAL = "JCB", VOLUME = 6, NUMBER = 1, YEAR = 1999, PAGES = "91--112", KEYWORDS = "alignment") @Article{Nic98, author = {Pierre Nicod\`eme}, title = {{SSMAL}: similarity searching with alignment graphs}, KEYWORDS = {alignment}, journal = {Bioinformatics}, year = 1998, volume = 14, number = 6, pages = "508--515" } @Inproceedings{NiS97, author = "P. Nicod\`eme and J. M. Steyaert", title = {Selecting Optimal Oligonucleotide Primers for Multiplex {PCR}}, KEYWORDS = { {PCR} Multiplex}, booktitle = {Fifth International Conference on Intelligent Systems for Molecular Biology}, year = 1997, publisher = {{AAAI} Press}, pages = {210--213} } @UNPUBLISHED{NSF00, author = "Pierre Nicod{\`e}me and Bruno Salvy and Philippe Flajolet", title = "Motif Statistics", KEYWORDS = "motif counts, regular expressions, automatas" , year = 2000, note = "To appear in Theoretical Computer Science"} @ARTICLE (Nus81, TITLE = "The universal dinucleotide asymmetry rules in {DNA} and the amino acid codon choice", AUTHOR = "Nussinov, R.", JOURNAL = JME, VOLUME = 17, YEAR = 1981, PAGES = "237--244", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (OBH99, TITLE = "Rapid {A}ssessment of {E}xtremal {S}tatistics for {G}apped {L}ocal {A}lignment", AUTHOR = "R. Olsen and R. Bundschuh and T. Hwa", JOURNAL = "American Association for Artificial Intelligence", YEAR = 1999, PAGES = "?", KEYWORDS = "alignment") @ARTICLE (Pev92, TITLE = "Nucleotide sequences versus {M}arkov models", AUTHOR = "Pevzner, P. A.", JOURNAL = "Computers Chem.", VOLUME = 16, YEAR = 1992, PAGES = "103--106", KEYWORDS = "Markov chain models") @ARTICLE (PBM89a, TITLE = "Linguistics of nucleotides sequences {I:} {T}he significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words", AUTHOR = "Pevzner, P. A. and Borodovsky, M. Y. and Mironov, A. A.", JOURNAL = JBSD, VOLUME = 6, YEAR = 1989, PAGES = "1013--1026", KEYWORDS = "linguistics of DNA sequences, word counts") @ARTICLE (PBM89b , TITLE = "Linguistics of nucleotides sequences {II:} {S}tationary words in genetic texts and the zonal structure of {DNA}", AUTHOR = "Pevzner, P. A. and Borodovsky, M. Y. and Mironov, A. A.", JOURNAL = JBSD, VOLUME = 6, YEAR = 1989, PAGES = "1027--1038", KEYWORDS = "linguistics of DNA sequences, DNA structure and biology") @ARTICLE (PAI87a , TITLE = "The effect of codon usage on the oligonucleotide composition of the {\it {E}. coli} genome and identification of over- and underrepresented sequences by {M}arkov chain analysis", AUTHOR = "Phillips, G. J. and Arnold, J. and Ivarie, R.", JOURNAL = NAR, VOLUME = 15, YEAR = 1987, PAGES = "2627--2638", KEYWORDS = "linguistics of DNA sequences, Markov chain models") @ARTICLE (PAI87b , TITLE = "Mono- through hexanucleotide composition of the {\it {E}scherichia coli} genome : a {M}arkov chain analysis", AUTHOR = "Phillips, G. J. and Arnold, J. and Ivarie, R.", JOURNAL = NAR, VOLUME = 15, YEAR = 1987, PAGES = "2611--2626", KEYWORDS = "linguistics of DNA sequences, Markov chain models") @ARTICLE (PHT90, TITLE = "Linguistic measure of taxonomic and functional relatedness of nucleotides sequences", AUTHOR = "Pietrokovsky, S. and Hirshon, J. and Trifonov, E. N.", JOURNAL = JBSD, VOLUME = 7, YEAR = 1990, PAGES = "1251--1268", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (PiT92, TITLE = "Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics", AUTHOR = "Pietrokovski, S. and Trifonov, E. N.", JOURNAL = "Gene", VOLUME = 122, YEAR = 1992, PAGES = "129--137", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (Raf85, TITLE = "A model for high-order {M}arkov chains", AUTHOR = "Raftery, A. E.", JOURNAL = JRSSB, VOLUME = 47, YEAR = 1985, PAGES = "528--539", KEYWORDS = "Markov chain models") @ARTICLE ( Raj74, TITLE = "Success runs in a two-state {M}arkov chain", AUTHOR = "Rajarshi, M. B.", JOURNAL = JAP, VOLUME = 11, YEAR = 1974, PAGES = "190--192", KEYWORDS = "Markov chain models, word counts") @ARTICLE (RaT94, TITLE = "Estimation and modelling repeated patterns in high order {M}arkov chains with the {M}ixture {T}ransition {D}istribution {M}odel", AUTHOR = " Raftery, A. and Tavar\'e, Simon", JOURNAL = ApS, VOLUME = 43, YEAR = 1994, PAGES = "179-199", KEYWORDS = "Markov chain models") @INCOLLECTION(ReS99, TITLE = "Compound {P}oisson approximations for occurrences of multiple words", AUTHOR = "Reinert, G. and Schbath, S.", BOOKTITLE = "Statistics in Genetics and Molecular Biology", YEAR = 1999, PUBLISHER = "IMS Lecture Notes-Monograph Series", EDITOR = "Seillier, F.", NOTE = "Vol. 33", KEYWORDS = "word counts, Chen-Stein method, compound Poisson approximation") @ARTICLE(ReS98, TITLE = "Compound {P}oisson and {P}oisson process approximations for occurrences of multiple words in Markov Chains", AUTHOR = "Reinert, G. and Schbath, S.", YEAR = 1998, JOURNAL = JCB, VOLUME = 5, PAGES = "223--254.", KEYWORDS = "word counts, Markov chain models, Chen-Stein method, compound Poisson approximation") @ARTICLE (Roo94, TITLE = "Stein's method for compound {P}oisson approximation : the local approach", AUTHOR = " Roos, M.", JOURNAL = AAP, VOLUME = 4, YEAR = 1994, PAGES = "1177-1187", KEYWORDS = "compound Poisson approximation, Stein method") @ARTICLE(Sch97b, TITLE = "An efficient statistic to detect over- and under-represented words in {DNA} sequences", AUTHOR = "Schbath, S.", YEAR = 1997, JOURNAL = JCB, VOLUME = 4, PAGES = "189--192.", KEYWORDS = "linguistics of DNA sequences, word counts") @ARTICLE(Sch97a, TITLE = "Coverage processes in physical mapping by anchoring random clones", AUTHOR = "Schbath, S.", JOURNAL = JCB, VOLUME = 4, YEAR = 1997, PAGES = "61--82.", KEYWORDS = "physical mapping") @ARTICLE(Sch95a, TITLE = "Compound {P}oisson approximation of word counts in {DNA} sequences ", AUTHOR = "Schbath, S.", JOURNAL = ESAIM, VOLUME = 1, YEAR = 1995, PAGES = "1--16.", HTTP = "http://www.edpsciences.org/ps/OnlinePS.fr.html", KEYWORDS = "word counts, Chen-Stein method, compound Poisson approximation") @PHDTHESIS (Sch95b, AUTHOR = "Schbath, S. ", TITLE = "{É}tude asymptotique du nombre d'occurrences d'un mot dans une chaîne de {M}arkov et application à la recherche de mots de fréquence exceptionnelle dans les séquences d'{ADN}", SCHOOL = "Université René Descartes, Paris V", YEAR = 1995, KEYWORDS = "word counts, Markov chain models, Chen-Stein method, linguistics of DNA sequences, compound Poisson approximation") @ARTICLE (Sen90, TITLE = "Statistique asymptotique presque-s\^ure de modèles statistiques convexes", AUTHOR = "Senoussi, R.", JOURNAL = AIHP, VOLUME = 26, YEAR = 1990, PAGES = "19--44", KEYWORDS = "autre") @ARTICLE (She81, TITLE = "Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification", AUTHOR = "Shepherd, J. C. W.", JOURNAL = PNAS, VOLUME = 78, YEAR = 1981, PAGES = "1596--1600", KEYWORDS = "DNA structure and biology") @ARTICLE (Ste72, TITLE = "A bound for the error in the normal approximation to the distribution of a sum of dependent random variables", AUTHOR = "Stein, C.", JOURNAL = "Proc. 6th Berkeley Sympos. Math. Statist. Probab.", VOLUME = 2, YEAR = 1972, PAGES = "583--602", KEYWORDS = "Stein method") @ARTICLE (SEG90, TITLE = "Statistical analysis of nucleotide sequences", AUTHOR = "St\H{u}ckle, E. E. and Emmrich, C. and Grob, U. and Nielsen, P. J.", JOURNAL = NAR, VOLUME = 18, YEAR = 1990, PAGES = "6641--6647", KEYWORDS = "word counts, linguistics of DNA sequences") @ARTICLE (SPT95, TITLE = "Exceptional motifs in different {M}arkov chain models for a statistical analysis of {DNA} sequences ", AUTHOR = "Schbath, S. and Prum, B. and Turckheim, E.~de ", JOURNAL = JCB, VOLUME = 2, YEAR = 1995, PAGES = "417--437", KEYWORDS = "word counts, Markov chain models, linguistics of DNA sequences") @ARTICLE (Tri87, TITLE = "Translation framing code and frame-monitoring mechanism as suggested by the analysis of {mRNA} and 16{S} {rRNA} nucleotide sequences", AUTHOR = "Trifonov, E. N.", JOURNAL = JMB, VOLUME = 194, YEAR = 1987, PAGES = "643--652", KEYWORDS = "DNA structure and biology") @ARTICLE (Tri89, TITLE = "The multiple codes of nucleotide sequences", AUTHOR = "Trifonov, E. N.", JOURNAL = BMB, VOLUME = 51, YEAR = 1989, PAGES = "417--432", KEYWORDS = "DNA structure and biology") @ARTICLE (Tri92, TITLE = "Recognition of correct reading frame by the ribosome", AUTHOR = "Trifonov, E. N.", JOURNAL = "Biochimie", VOLUME = 74, YEAR = 1992, PAGES = "357--362", KEYWORDS = "DNA structure and biology") @BOOK (Wat89, AUTHOR = "Waterman, M.S.", TITLE = "Mathematical methods for {DNA} sequences", PUBLISHER = {CRC Press} , YEAR = 1989, KEYWORDS = "general DNA sequence analysis") @BOOK (Wat95, AUTHOR = "Waterman, M.S.", TITLE = "Introduction to computational biology", PUBLISHER = {Chapman \& Hall} , YEAR = 1995, KEYWORDS = "general DNA sequence analysis") @ARTICLE (Whi55, TITLE = "Some distribution and moment formulae for the {M}arkov chain", AUTHOR = "Whittle, P.", JOURNAL = JRSSB, VOLUME = 17, YEAR = 1955, PAGES = "235--242", KEYWORDS = "Markov chain models") @ARTICLE (YoO89, TITLE = "Concordant evolution of coding and noncoding regions of {DNA} made possible by the universal rule of {TA/CG} deficiency-{TG/CT} excess", AUTHOR = "Yomo, T. and Ohno, S.", JOURNAL = PNAS, VOLUME = 86, YEAR = 1989, PAGES = "8452--8456", KEYWORDS = "DNA structure and biology, linguistics of DNA sequences") @ARTICLE (ArW85, TITLE = "Critical phenomena in sequence matching", AUTHOR = "Arratia, R. and Waterman, M. S.", JOURNAL = AP, VOLUME = 13, YEAR = 1985, PAGES = "1236--1249", KEYWORDS = "length of the longest run") @ARTICLE (Ban88, TITLE = "On some statistics connected with runs in Markov chains", AUTHOR = "Banjevic, D.", JOURNAL = JAP, VOLUME = 25, YEAR = 1988, PAGES = "815--821", KEYWORDS = "Markov chain models, waiting time for first occurrences of patterns ") @ARTICLE (Ben84, TITLE = "The occurrence of sequence patterns in ergodic Markov chains", AUTHOR = "Benevento, R.", JOURNAL = SPA, VOLUME = 17, YEAR = 1984, PAGES = "369--373", KEYWORDS = "Markov chain models, waiting time for first occurrences of patterns") @ARTICLE (BiC87, TITLE = "Markov renewal processes, counters and repeated sequences in Markov chains", AUTHOR = "Biggins, J. D. and Cannings, C.", JOURNAL = AdAP, VOLUME = 19, YEAR = 1987, PAGES = "521--545", KEYWORDS = "autre") @ARTICLE (Blo82, TITLE = "On the mean number of random digits until a given sequence occurs", AUTHOR = "Blom, G.", JOURNAL = JAP, VOLUME = 19, YEAR = 1982, PAGES = "136--143", KEYWORDS = "waiting time for first occurrences of patterns, distances between occurrences of patterns, word locations ") @ARTICLE (BlT82, TITLE = "How many random digits are required until given sequences are obtained ?", AUTHOR = "Blom, G. and Thorburn, D.", JOURNAL = JAP, VOLUME = 19, YEAR = 1982, PAGES = "518--531", KEYWORDS = "waiting time for first occurrences of patterns, distances between occurrences of patterns, word locations") @ARTICLE (BWZ85 , TITLE = "Renewal theory for several patterns", AUTHOR = "Breen, S. and Waterman, M.~S. and Zhang, N.", JOURNAL = JAP, VOLUME = 22, YEAR = 1985, PAGES = "228--234", KEYWORDS = "waiting time for first occurrences of patterns") @ARTICLE (ErR70, TITLE = "On a new law of large numbers", AUTHOR = "Erd{\"o}s, P. and {Ré}nyi, A.", JOURNAL = JAM, VOLUME = 23, YEAR = 1970, PAGES = "103--111", KEYWORDS = "length of the longest run") @ARTICLE (DDL86, TITLE = "Exact convergence rate in the limit theorems of {E}rd{\"o}s-{Ré}nyi and {Shepp}", AUTHOR = "Deheuvels, P. and Devroye, L. and Lynch, J.", JOURNAL = AP, VOLUME = 14, YEAR = 1986, PAGES = "209-223", KEYWORDS = "length of the longest run") @BOOK (Fel68, TITLE = "An introduction to Probability Theory and its Applications", AUTHOR = "Feller, W.", PUBLISHER = {Wiley, New York} , YEAR = 1968, KEYWORDS = "waiting time for first occurrences of patterns") @ARTICLE (GeL81, TITLE = "The occurrence of sequence patterns in repeated experiments and hitting times in a Markov chain", AUTHOR = "Gerber, H. U. and Li, S.-Y.", JOURNAL = SPA, VOLUME = 11, YEAR = 1981, PAGES = "101--108", KEYWORDS = "Markov chain models, waiting time for first occurrences of patterns") @ARTICLE (GuO80, TITLE = "Long repetitive patterns in random sequences", AUTHOR = "Guibas, L. J. and Odlyzko, A. M.", JOURNAL = ZW, VOLUME = 53, YEAR = 1980, PAGES = "241--262", KEYWORDS = "length of the longest run") @ARTICLE (Kus82, TITLE = "Longest runs in Markov chains", AUTHOR = "Kusolitsch, N.", JOURNAL = PSI, YEAR = 1982, PAGES = "223--230", KEYWORDS = "length of the longest run") @ARTICLE (Li80, TITLE = "A martingale approach to the study of occurrence of sequences patterns in repeated experiments", AUTHOR = "Li, S.", JOURNAL = AP, YEAR = 1980, VOLUME = 8, PAGES = "1171--1176", KEYWORDS = "waiting time for first occurrences of patterns") @PHDTHESIS (Lun90, TITLE = "Stochastic models and statistical methods for DNA sequence data", AUTHOR = "Lundstrom, R.", SCHOOL = "University of Utah", YEAR = 1990, KEYWORDS = "word counts, Markov chain models") @ARTICLE (NeK82, TITLE = "On the longest run of coincidences", AUTHOR = "Nemetz, T. and Kusolitsch, N.", JOURNAL = ZW, VOLUME = 61, YEAR = 1982, PAGES = "59--73", KEYWORDS = "length of the longest run") @UNPUBLISHED(ReS96, TITLE = " A last word on frequency of pattern occurrences in a Markovian sequence", AUTHOR = "Régnier, M. and Szpankowski, W.", YEAR = 1996, NOTE = "\textit{Submitted to IEEE Transactions on Information Theory }", KEYWORDS = "word counts") @PHDTHESIS (Rud96, TITLE = "On the first occurrence of a given pattern in a semi-Markov process", AUTHOR = " Rudander, J.", SCHOOL = "University of Uppsala", YEAR = 1996, KEYWORDS = "Markov chain models, waiting time for first occurrences of patterns") @ARTICLE (Sam81, TITLE = "On the length of the longest head run for a Markov chain with two states", AUTHOR = " Samarova, S.", JOURNAL = TPA, VOLUME = 26, YEAR = 1981, PAGES = "498-509", KEYWORDS = "Markov chain models, length of the longest run") @ARTICLE (Sch83, TITLE = "Run probabilities in sequences of Markov-dependent trials", AUTHOR = "Schwager", JOURNAL = JASA, VOLUME = 78, YEAR = 1983, PAGES = "168--175", KEYWORDS = "Markov chain models, waiting time for first occurrences of patterns") @ARTICLE (TaA97, TITLE = "Central limit theorem for renewal theory for several patterns", AUTHOR = "Tanushev, M. S. and Arratia, R.", JOURNAL = JCB, VOLUME = 4, YEAR = 1997, PAGES = "35--44", KEYWORDS = "renewals, word counts") @UNPUBLISHED(Tan96, TITLE = "Central limit theorem for several patterns in a Markov chain sequence of letters.", AUTHOR = "Tanushev, M. S.", YEAR = 1996, NOTE = "Preprint", KEYWORDS = "Markov chain models, renewals, word counts") @ARTICLE (Tho83, TITLE = "On the mean number of trials until the last trials satisfy a given condition", AUTHOR = "Thorburn, D.", JOURNAL = SPA, VOLUME = 16, YEAR = 1983, PAGES = "211--217", KEYWORDS = "waiting time for first occurrences of patterns") @ARTICLE (BEG98, TITLE = "Codon usage can explain {GT}-rich islands surrounding {C}hi sites on the \textsl{Escherichia coli\/} genome", AUTHOR = "Biaudet, V. and El Karoui, M. and Gruss, A.", JOURNAL = "Mol. Microbiol.", VOLUME = 29, YEAR = 1998, PAGES = "666--669", KEYWORDS = "DNA structure and biology, linguistics of DNA sequences") @ARTICLE (CNB98, TITLE = "A five-nucleotide sequence protects {DNA} from exonucleolytic degradation by {A}dd{AB}, the {R}ec{BCD} analogue of \textsl{Bacillus subtilis\/}", AUTHOR = "Chedin, F. and Noirot, P. and Biaudet, V. and Ehrlich, S.D.", JOURNAL = "Mol. Microbiol.", VOLUME = 31, YEAR = 1998, PAGES = "1369--1377", KEYWORDS = "DNA structure and biology") @ARTICLE (RVD98, TITLE = " Oligonucleotide bias in \textit{Bacillus subtilis}: general trends and taxonomic comparisons", AUTHOR = " Rocha, E.P.C. and Viari, A. and Danchin, A.", JOURNAL = NAR, VOLUME = 26, YEAR = 1998, PAGES = "2971-2980", KEYWORDS = "linguistics of DNA sequences") @ARTICLE (SBK98, TITLE = "Identification of the {C}hi site of \textsl{Haemophilus influenzae\/} as several sequences related to the \textsl{Escherichia coli\/} {C}hi site", AUTHOR = "Sourice, S. and Biaudet, V. and El Karoui, M. and Ehrlich, S.D. and Gruss, A.", JOURNAL = "Mol. Microbiol.", VOLUME = 27, YEAR = 1998, PAGES = "1021--1029", KEYWORDS = "DNA structure and biology")