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+ 2005

  1. repeats
    Tamanna Anwar, Asad U Khan (2005), "Mapping and analysis of Simple Sequence Repeats in the Arabidopsis thaliana Genome", Bioinformation, 1(2): 64-68.
    [abstract]

  2. Peter F Arndt, Terence Hwa (2005), "Identification and measurement of neighbor dependent nucleotide substitution processes", Bioinformatics, 21(10):2322-2328.
    [abstract]

  3. a/symmetry
    PJ Barral, L Cantini, A Hasmy, J Jimenez, A Marcano (2005), "Correlation between strand asymmetry and phylogeny in mitochondrial DNA", Journal of Theoretical Biology, 236(4):422-426.

  4. E Ben-Naim, PL Krapivsky (2005), "Chronological rank in biological evolution", Journal of Statistical Mechanics, Art. No. L10002.

  5. A Bergeron (2005), "A very elementary presentation of the Hannenhalli-Pevzner theory", Discrete Applied Mathematics, 146(2):134-145.

  6. G Bernardi (2005), "Lessons from a small, dispensable genome: the mitochondrial genome of yeast", Gene, 354:180-200.

  7. sequence
    M Berriman, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM (2005), "The genome of the African trypanosome Trypanosoma brucei", Science, 309(5733):416-422.

  8. MJ Berryman, A Allison, CR Wilkinson, D Abbott (2005), "Review of signal processing in genetics", Fluctuation and Noise Letters, 5(4):R13-R35.
    [PDF]

  9. repeats
    T Boby, AM Patch, and SJ Aves (2005), "TRbase: a database relating tandem repeats to disease genes for the human genome", Bioinformatics, 21(6):811-816.
    [abstract]

  10. Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M.R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwera (2005), "Evolutionary patterns of non-coding RNAs", Theory in Biosciences, 123(4):301-369.
    [ abstract]

  11. Hilary S. Booth, Conrad J. Burden, John H. Maindonald, Lucia Santoso, Matthew J. Wakefield, Susan R. Wilson (2005), "Discussion of 'A Bayesian approach to DNA sequence segmentation'", Biometrics, 61(2):635-637.
    [ abstract]

  12. B Borstnik, D Pumpernik (2005), "Evidence on DNA slippage step-length distribution", Physical Review E, 71(3):031913.
    [abstract]

  13. RJ Boys, DA Henderson (2005), "Discussion of 'A Bayesian approach to DNA sequence segmentation' - Reply", Biometrics, 61(2):637-639.
    [ abstract]

  14. EB Brodie of Brodie, S Nicolay, M Touchon, B Audit, Y d'Aubenton-Carafa, C Thermes, A Arneodo (2005), "From DNA sequence analysis to modeling replication in the human genome", Physical Review Letters, 94:248103.
    [abstract] [PDF]

  15. repeats
    AK Brodzik, O Peters (2005), "Symbol-balanced quaternionic periodicity transform for latent pattern detection in DNA sequences", in Proceedings of IEEE International Conference on Acoustics, Speech, and Signal Processing, 2005 (ICASSP '05), 5:18-23. (ISBN: 0-7803-8874-7)
    [ abstract]

  16. sequence
    CR Buell, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O'Shaughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S, Rice Chromosome 3 Sequencing Consortium (2005), "Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species", Genome Research, 15(9):1284-1291.

  17. repeats
    Davide Campagna, Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Matej Lexa, Nicola Cannata, and Giorgio Valle (2005), "RAP: a new computer program for de novo identification of repeated sequences in whole genomes", Bioinformatics, 21:582-588.
    [ abstract]

  18. Yinhe Cao, Wen-Wen Tung, JB Gao, Yan Qi (2005), "Recurrence time statistics: versatile tools for genomic DNA sequence analysis", Journal of Bioinformatics and Computational Biology, 3(3):677-696.
    [ abstract]

  19. A Carbone, F Kepes, A Zinovyev (2005), "Codon bias signatures, organisation of microorganisms in codon space and lifestyle", Molecular Biology and Evolution, 22(3):547-561.

  20. Enrico Carlon, Mehdi Lejard Malki, Ralf Blossey (2005), "Exons, introns, and DNA thermodynamics", Physical Review Letters, 94:178101.
    [abstract] [PDF]

  21. Peggy Cenac (2005), "Test on the structure of biological sequences via chaos game representation", Statistical Applications in Genetics and Molecular Biology, 4(1):27.
    [abstract]

  22. Chang-Heng Chang, Li-Ching Hsieh, Ta-Yuan Chen, Hong-Da Chen, Liaofu Luo, Hoong-Chien Lee (2005), "Shannon information in complete genomes", Journal of Bioinformatics and Computational Biology, 3(3):587-608.
    [ abstract]

  23. Hong-Da Chen, Chang-Heng Chang, Li-Ching Hsieh, Hoong-Chien Lee (2005), "Divergence and Shannon information in genomes", Physical Review Letters, 94:178103.
    [abstract] [PDF]

  24. a/symmetry
    Liang Chen and Hongyu Zhao (2005), "Negative correlation between compositional symmetries and local recombination rates", Bioinformatics, 21:3951-3958.
    [ abstract]

  25. TY Chen, LC Hsieh and HC Lee (2005), "Shannon information and self-similarity in complete genomes", Computer Physics Communications, 169:218-221.

  26. YH Chen, SL Nyeo, JP Yu (2005), "Power-laws in the complete sequences of human genome", Journal of Biological Systems, 13(2):105-115.

  27. Yaw-Hwang Chen, Su-Long Nyeo, Chiung-Yuh Yeh (2005), "Model for the distributions of k-mers in DNA sequences", Physical Review E, 72:011908.
    [abstract]

  28. Jun Cheng, Lin-Xi Zhang (2005), "Statistical properties of nucleotide clusters in DNA sequences", Journal of Zhejiang University Science B, 6(5):408-412.
    [abstract]

  29. Jun Cheng, Lin-Xi Zhang (2005), "Scaling behaviors of CG clusters for chromosomes", Chaos, Solitons & Fractals, 25(2):339-346.

  30. DSH Chew, KP Choi, MY Cheung (2005), "Scoring schemes of palindrome clusters for mode sensitive prediction of replication origins in herpesviruses", Nucleic Acids Research, 33(15):e134.

  31. Dominique Chu, HC Paul Lee, Tom Lenaerts (2005), "Emergence of uptake sequence in bacterial DNA", Artificial Life, 11(3):?-?.

  32. isochore
    O Clay, G Bernardi (2005), "How not to search for isochores: A reply to Cohen et al.", Molecular Biology and Evolution, 22(12):2315-2317.

  33. repeats
    Tom Coenye and Peter Vandamme (2005), "Characterization of mononucleotide repeats in sequenced prokaryotic genomes", DNA Research, 12(4):221-233.
    [ abstract]

  34. Amir B. Cohanim, Yechezkel Kashi, Edward N. Trifonov (2005), "Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae", Journal of Biomolecular Structure and Dynamics 22(6):687-694.
    [abstract]

  35. isochore
    N Cohen, T Dagan, L Stone, D Graur (2005), "GC composition of the human genome: In search of isochores", Molecular Biology and Evolution, 22(5):1260-1272.

  36. AV Coronado, P Carpena (2005), "Size effects on correlation measures ", Journal of Biological Physics, 31(1):121-133.

  37. M Costa, AL Goldberger, CK Peng (2005), "Multiscale entropy analysis of biological signals", Physical Review E, 71(2):021906.
    [abstract]

  38. L da Fontoura Costa (2005), "Biological sequence analysis through the one-dimensional percolation transform and its enhanced version", Bioinformatics, 21(5):608-616.
    [abstract]

  39. Yamini Dalal, Tomara J. Fleury, Alfred Cioffi and Arnold Stein (2005), "Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation", Nucleic Acids Research, 33(3):934-945.
    [ abstract]

  40. protein
    G D'Avenio, M Grigioni, G Orefici, R Creti (2005), "SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence", Bioinformatics, 21(13):2943-2949.
    [abstract]

  41. M Dehnert, R Plaumann, WE Helm, MT Hutt (2005), "Genome phylogeny based on short-range correlations in DNA sequences", Journal of Computational Biology, 12(5):545-553.

  42. Manuel Dehnert, Werner E. Helm and Marc-Thorsten Hutt (2005), "Information theory reveals large-scale synchronisation of statistical correlations in eukaryote genomes", Gene, 345(1):81-90.

  43. Ralph A Dean, Nicholas J Talbot, Daniel J Ebbole, Mark L Farman, Thomas K Mitchell, Marc J Orbach, Michael Thon, Resham Kulkarni, Jin-Rong Xu, Huaqin Pan, Nick D Read, Yong-Hwan Lee, Ignazio Carbone, Doug Brown, Yeon Yee Oh, Nicole Donofrio, Jun Seop Jeong, Darren M Soanes, Slavica Djonovic, Elena Kolomiets, Cathryn Rehmeyer, Weixi Li, Michael Harding, Soonok Kim, Marc-Henri Lebrun, Heidi Bohnert, Sean Coughlan, Jonathan Butler, Sarah Calvo, Li-Jun Ma, Robert Nicol, Seth Purcell, Chad Nusbaum, James E Galagan and Bruce W Birren (2005), "The genome sequence of the rice blast fungus Magnaporthe grisea", Nature, 434:980-986.
    [ abstract]

  44. Albert DG de Roos (2005), "Origin of introns based on the definition of exon modules and their conserved interfaces", Bioinformatics, 21(1):2-9.
    [abstract]

  45. Emmanouil T Dermitzakis, Alexandre Reymond & Stylianos E Antonarakis (2005), "Conserved non-genic sequences - an unexpected feature of mammalian genomes" Nature Reviews Genetics, 6:151-157.
    [abstract]

  46. sequence
    L Eichinger, J A Pachebat, G Glöckner, M-A Rajandream, R Sucgang, M Berriman, J Song, R Olsen, K Szafranski, Q Xu, B Tunggal, S Kummerfeld, M Madera, B A Konfortov, F Rivero, A T Bankier, R Lehmann, N Hamlin, R Davies, P Gaudet, P Fey, K Pilcher, G Chen, D Saunders, E Sodergren, P Davis, A Kerhornou, X Nie, N Hall, C Anjard, L Hemphill, N Bason, P Farbrother, B Desany, E Just, T Morio, R Rost, C Churcher, J Cooper, S Haydock, N van Driessche, A Cronin, I Goodhead, D Muzny, T Mourier, A Pain, M Lu, D Harper, R Lindsay, H Hauser, K James, M Quiles, M Madan Babu, T Saito, C Buchrieser, A Wardroper, M Felder, M Thangavelu, D Johnson, A Knights, H Loulseged, K Mungall, K Oliver, C Price, M A Quail, H Urushihara, J Hernandez, E Rabbinowitsch, D Steffen, M Sanders, J Ma, Y Kohara, S Sharp, M Simmonds, S Spiegler, A Tivey, S Sugano, B White, D Walker, J Woodward, T Winckler, Y Tanaka, G Shaulsky, M Schleicher, G Weinstock, A Rosenthal, E C Cox, R L Chisholm, R Gibbs, W F Loomis, M Platzer, R R Kay, J Williams, P H Dear, A A Noegel, B Barrell and A Kuspa (2005), "The genome of the social amoeba Dictyostelium discoideum", Nature, 435:43-57.
    [ abstract]

  47. sequence
    NM El-Sayed, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, Anupama A, Arner E, Aslund L, Attipoe P, Bontempi E, Bringaud F, Burton P, Cadag E, Campbell DA, Carrington M, Crabtree J, Darban H, da Silveira JF, de Jong P, Edwards K, Englund PT, Fazelina G, Feldblyum T, Ferella M, Frasch AC, Gull K, Horn D, Hou L, Huang Y, Kindlund E, Klingbeil M, Kluge S, Koo H, Lacerda D, Levin MJ, Lorenzi H, Louie T, Machado CR, McCulloch R, McKenna A, Mizuno Y, Mottram JC, Nelson S, Ochaya S, Osoegawa K, Pai G, Parsons M, Pentony M, Pettersson U, Pop M, Ramirez JL, Rinta J, Robertson L, Salzberg SL, Sanchez DO, Seyler A, Sharma R, Shetty J, Simpson AJ, Sisk E, Tammi MT, Tarleton R, Teixeira S, Van Aken S, Vogt C, Ward PN, Wickstead B, Wortman J, White O, Fraser CM, Stuart KD, Andersson B (2005), "The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease", Science, 309(5733):409-415.

  48. sequence
    Derrick E Fouts, Emmanuel F. Mongodin, Robert E. Mandrell, William G. Miller, David A. Rasko, Jacques Ravel, Lauren M. Brinkac, Robert T. DeBoy, Craig T. Parker, Sean C. Daugherty, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, Steven A. Sullivan, Jyoti U. Shetty, Mobolanle A. Ayodeji, Alla Shvartsbeyn, Michael C. Schatz, Jonathan H. Badger, Claire M. Fraser, Karen E. Nelson (2005), "Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species", PLoS Biology, 3(1):e15.
    [ abstract]

  49. sequence
    JE Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Ba?türkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peńalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005), "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae", Nature, 438(7071):1105-1115.
    [ abstract]

  50. Mythily Ganapathi , Pragya Srivastava , Sushanta K Das Sutar , Kaushal Kumar , Dipayan Dasgupta , Gajinder P Singh , Vani Brahmachari, Samir K Brahmachari (2005), "Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes", BMC Bioinformatics, 6:126.
    [abstract]

  51. Madhavi Ganapathiraju, N Balakrishnan, Raj Reddy, Judith Klein-Seetharaman (2005), "Computational biology and language", in Ambient Intelligence for Scientific Discovery, ed. Y Cai, Lecture Notes in Artificial Intelligence (LNAI), vol 3345, pp.25-47.

  52. JB Gao, Y Qi, YH Cao, WW Tung (2005), "Protein coding sequence identification by simultaneously characterizing the periodic and random features of DNA sequences", Journal of Biomedicine and Biotechnology, 2:139-146.

  53. JA Garcia, MV Jose (2005), "Mathematical properties of DNA sequences from coding and noncoding regions", Revista Mexicana de Fisica, 51(2):122-130.

  54. sequence
    MJ Gardner, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, Shallom SJ, Weidman J, Jiang L, Lynn J, Weaver B, Shoaibi A, Domingo AR, Wasawo D, Crabtree J, Wortman JR, Haas B, Angiuoli SV, Creasy TH, Lu C, Suh B, Silva JC, Utterback TR, Feldblyum TV, Pertea M, Allen J, Nierman WC, Taracha EL, Salzberg SL, White OR, Fitzhugh HA, Morzaria S, Venter JC, Fraser CM, Nene V (2005), "Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes", Science, 309(5731):134-137.

  55. sequence
    E Ghedin, NA Sengamalay, M Shumway, J Zaborsky, T Feldblyum, V Subbu, DJ Spiro, J Sitz, H Koo, P Bolotov, D Dernovoy, T Tatusova, Y Bao, K St George, J Taylor, DJ Lipman, CM Fraser, JK Taubenberger, SL Salzberg (2005), "Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution", Nature, 437:1162-1166.

  56. A Gibson, V Gowri-Shankar, PG Higgs, M Rattray (2005), "A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods", Molecular Biology and Evolution, 22(2):251-264.

  57. sequence
    Steven R Gill, Derrick E Fouts, Gordon L Archer, Emmanuel F Mongodin, Robert T. DeBoy, Jacques Ravel, Ian T. Paulsen, James F. Kolonay, Lauren Brinkac, Mauren Beanan, Robert J. Dodson, Sean C. Daugherty, Ramana Madupu, Samuel V. Angiuoli, A. Scott Durkin, Daniel H. Haft, Jessica Vamathevan, Hoda Khouri, Terry Utterback, Chris Lee, George Dimitrov, Lingxia Jiang, Haiying Qin, Jan Weidman, Kevin Tran, Kathy Kang, Ioana R. Hance, Karen E. Nelson, Claire M. Fraser (2005), "Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant staphylococcus aureus strain and a biofilm-producing methicillin-Resistant Staphylococcus epidermidis strain", Journal of Bacteriology, 187(7):2426-2438.

  58. A Gorban, T Popova, A Zinovyev (2005), "Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences", Physica A, 353:365-387.

  59. AN Gorban, TG Popova, AY Zinovyev (2005), "Four basic symmetry types in the universal 7-cluster structure of microbial genomic sequences", In Silico Biology, 5(3):265-282.

  60. T Ryan Gregory (2005), "Synergy between sequence and size in large-scale genomics", Nature Reviews Genetics, 6:699-708.
    [abstract]

  61. L Gueguen (2005), "Sarment: Python modules for HMM analysis and partitioning of sequences", Bioinformatics, 21(16):3427-3428.
    [abstract]

  62. Michael Hackenberg, Pedro Bernaola-Galván, Pedro Carpena, José L. Oliver (2005), "The biased distribution of Alus in human isochores might be driven by recombination", Journal of Molecular Evolution, 60(3):365-377.

  63. Bernhard Haubold , Nora Pierstorff , Friedrich Moeller and Thomas Wiehe (2005), "Genome comparison without alignment using shortest unique substrings", BMC Bioinformatics, 6:123.
    [abstract]

  64. sequence
    LW Hillier, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK (2005), "Generation and annotation of the DNA sequences of human chromosomes 2 and 4", Nature, 434(7034):724-731.
    [PDF]

  65. Tobias Hindemitt and Klaus F. X. Mayer (2005), "CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences", Bioinformatics, 21:4304-4306.
    [ abstract]

  66. CH Hwang, D Chiu, I Sohn (2005), "Exon structure analysis via PCA and ICA of short-time Fourier transform", Lecture Notes in Computer Science, vol 3611, pp.306-315.

  67. Y Isohata, M Hayashi (2005), "Analyses of DNA base sequences for eukaryotes in terms of power spectrum method", Japanese Journal of Applied Physics, 44(2):1143-1146.

  68. Alasdair C Ivens, Christopher S Peacock, Elizabeth A Worthey, Lee Murphy, Gautam Aggarwal, Matthew Berriman, Ellen Sisk, Marie-Adele Rajandream, Ellen Adlem, Rita Aert, Atashi Anupama, Zina Apostolou, Philip Attipoe, Nathalie Bason, Christopher Bauser, Alfred Beck, Stephen M Beverley, Gabriella Bianchettin, Katja Borzym, Gordana Bothe, Carlo V Bruschi, Matt Collins, Eithon Cadag, Laura Ciarloni, Christine Clayton, Richard M R Coulson, Ann Cronin, Angela K Cruz, Robert M Davies, Javier De Gaudenzi, Deborah E Dobson, Andreas Duesterhoeft, Gholam Fazelina, Nigel Fosker, Alberto Carlos Frasch, Audrey Fraser, Monika Fuchs, Claudia Gabel, Arlette Goble, André Goffeau, David Harris, Christiane Hertz-Fowler, Helmut Hilbert, David Horn, Yiting Huang, Sven Klages, Andrew Knights, Michael Kube, Natasha Larke, Lyudmila Litvin, Angela Lord, Tin Louie, Marco Marra, David Masuy, Keith Matthews, Shulamit Michaeli, Jeremy C Mottram, Silke Müller-Auer, Heather Munden, Siri Nelson, Halina Norbertczak, Karen Oliver, Susan O'Neil, Martin Pentony, Thomas M Pohl, Claire Price, Bénédicte Purnelle, Michael A Quail, Ester Rabbinowitsch, Richard Reinhardt, Michael Rieger, Joel Rinta, Johan Robben, Laura Robertson, Jeronimo C Ruiz, Simon Rutter, David Saunders, Melanie Schäfer, Jacquie Schein, David C Schwartz, Kathy Seeger, Amber Seyler, Sarah Sharp, Heesun Shin, Dhileep Sivam, Rob Squares, Steve Squares, Valentina Tosato, Christy Vogt, Guido Volckaert, Rolf Wambutt, Tim Warren, Holger Wedler, John Woodward, Shiguo Zhou, Wolfgang Zimmermann, Deborah F Smith, Jenefer M Blackwell, Kenneth D Stuart, Bart Barrell, Peter J Myler (2005), "The genome of the kinetoplastid parasite, Leishmania major", Science, 309(5733):436-442.
    [ abstract]

  69. WS Kendal, BP Suomela (2005), "Large-scale genomic correlations in Arabidopsis thaliana relate to chromosomal structure", BMC Genomics, 6(1):82.
    [PDF]

  70. binding-energy
    Ryan T. Koehler and Nicolas Peyret (2005), "Thermodynamic properties of DNA sequences: characteristic values for the human genome", Bioinformatics, 21(16):3333-3339.
    [abstract]

  71. Alan Wee-Chung Liew, Yonghui Wu, Hong Yan, Mengsu Yang (2005), "Effective statistical features for coding and non-coding DNA sequence classification for yeast, C. elegans and human", International Journal of Bioinformatics Research and Applications, 1(2):181-201.

  72. sequence
    V Joardar, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR. (2005), "Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition", Journal of Bacteriology, 187(18):6488-6498.

  73. Marco V Jose, Tzipe Govezensky, Juan R Bobadilla (2005), "Statistical properties of DNA sequences revisited: the role of inverse bilateral symmetry in bacterial chromosomes", Physica A, 351:477-498.

  74. S Karlin (2005), "Colloquium perspective: Statistical signals in bioinformatics", Proceedings of National Academy of Sciences, 102(38):13355-13362.
    [ abstract]

  75. period:10-11
    Etienne Larsabal, Antoine Danchin (2005), "Genomes are covered with ubiquitous 11 bp periodic patterns, the 'class A flexible patterns'", BMC Bioinformatics, 6:206.
    [abstract]

  76. protein
    Andrew A Laskin, Nikolay A Kudryashovb, Konstantin G Skryabina, Eugene V Korotkov (2005), "Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families", Computational Biology and Chemistry, 29(3):229-243.
    [ abstract]

  77. protein
    H Leonov, IT Arkin (2005), "A periodicity analysis of transmembrane helices", Bioinformatics, 21(11):2604-2610.
    [abstract]

  78. MY Leung, KP Choi, A Xia, LHY Chen (2004), "Nonrandom clusters of palindromes in herpesvirus genomes", Journal of Computational Biology, 12(3):331-354.

  79. VG Levitsky, AV Katokhin, OA Podkolodnaya, DP Furman, NA Kolchanov (2005), "NPRD: Nucleosome Positioning Region Database", Nucleic Acids Research, 33(Database issue):D67-D70.

  80. W Li, D Holste (2005), "Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome", Physical Review E, 71:041910.
    [abstract] [PDF]

  81. sequence
    K Lindblad-Toh, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. (2005), "Genome sequence, comparative analysis and haplotype structure of the domestic dog", Nature, 438(7069):803-819.
    [PDF]

  82. sequence
    B Loftus, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N. (2005), "The genome of the protist parasite Entamoeba histolytica", Nature, 433(7028):865-868.

  83. sequence
    BJ Loftus, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW. (2005), "The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans", Science, 307(5713):1321-1324.

  84. SRC Lopes, MA Nunes (2005), "Long memory analysis in DNA sequences", Physica A, 361(2):569-588.
    [ abstract]

  85. PL Luque-Escamilla, J Martinez-Aroza, JL Oliver, JF Gomez-Lopera, R Roman-Roldan (2005), "Compositional searching of CpG islands in the human genome", Physical Review E, 71(6):061925.
    [abstract]

  86. Bin-Guang Ma, Ling-Ling Chen (2005), "The most deviated codon position in AT-rich bacterial genomes: a function related analysis", Journal of Biomolecular Structure and Dynamics 23(2):113-232.
    [abstract]

  87. sequence
    Masayuki Machida, Kiyoshi Asai, Motoaki Sano, Toshihiro Tanaka, Toshitaka Kumagai, Goro Terai, Ken-Ichi Kusumoto, Toshihide Arima, Osamu Akita, Yutaka Kashiwagi, Keietsu Abe, Katsuya Gomi, Hiroyuki Horiuchi, Katsuhiko Kitamoto, Tetsuo Kobayashi, Michio Takeuchi, David W Denning, James E Galagan, William C Nierman, Jiujiang Yu, David B Archer, Joan W Bennett, Deepak Bhatnagar, Thomas E Cleveland, Natalie D Fedorova, Osamu Gotoh, Hiroshi Horikawa, Akira Hosoyama, Masayuki Ichinomiya, Rie Igarashi, Kazuhiro Iwashita, Praveen Rao Juvvadi, Masashi Kato, Yumiko Kato, Taishin Kin, Akira Kokubun, Hiroshi Maeda, Noriko Maeyama, Jun-ichi Maruyama, Hideki Nagasaki, Tasuku Nakajima, Ken Oda, Kinya Okada, Ian Paulsen, Kazutoshi Sakamoto, Toshihiko Sawano, Mikio Takahashi, Kumiko Takase, Yasunobu Terabayashi, Jennifer R Wortman, Osamu Yamada, Youhei Yamagata, Hideharu Anazawa, Yoji Hata, Yoshinao Koide, Takashi Komori, Yasuji Koyama, Toshitaka Minetoki, Sivasundaram Suharnan, Akimitsu Tanaka, Katsumi Isono, Satoru Kuhara, Naotake Ogasawara and Hisashi Kikuchi (2005), "Genome sequencing and analysis of Aspergillus oryzae", Nature, 438:1157-1161.
    [ abstract]

  88. sequence
    Tadashi Matsunaga, Yoshiko Okamura, Yorikane Fukuda, Aris Tri Wahyudi, Yaeko Murase, and Haruko Takeyama (2005), "Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1", DNA Research, 12:157-166.
    [ abstract]

  89. SS Melnyk, OV Usatenko, VA Yampol'skii, VA Golick (2005), "Competition between two kinds of correlations in literary texts", Physical Review E, 72(2):026140.

  90. Philipp W Messer, Peter F Arndt, Michael Lässig (2005), "Solvable sequence evolution models and genomic correlations", Physical Review Letters, 94:138103.
    [ abstract] [PDF]

  91. PW Messer, M Lassig, PF Arndt (2005), "Universality of long-range correlations in expansion-randomization systems", Journal of Statistical Mechanics, Art No. P10004.

  92. sequence
    Barbara A Methe, Karen E Nelson, Jody W Deming, Bahram Momen, Eugene Melamud, Xijun Zhang, John Moult, Ramana Madupu, William C. Nelson, Robert J. Dodson, Lauren M. Brinkac, Sean C. Daugherty, Anthony S. Durkin, Robert T. DeBoy, James F. Kolonay, Steven A. Sullivan, Liwei Zhou, Tanja M. Davidsen, Martin Wu, Adrienne L. Huston, Matthew Lewis, Bruce Weaver, Janice F. Weidman, Hoda Khouri, Terry R. Utterback, Tamara V. Feldblyum and Claire M. Fraser (2005), "The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses", Proceedings of National Academy of Sciences, 102(3):10913-10918.
    [ abstract]

  93. V Miele, PY Bourguignon, D Robelin, G Nuel, H Richard (2005), "seq++: analyzing biological sequences with a range of Markov-related models", Bioinformatics, 21(11):2783-2784.
    [abstract]

  94. sequence
    S Tarjei Mikkelsen, LaDeana W. Hillier, Evan E. Eichler, Michael C. Zody, David B. Jaffe, Shiaw-Pyng Yang, Wolfgang Enard, Ines Hellmann, Kerstin Lindblad-Toh, Tasha K. Altheide, Nicoletta Archidiacono, Peer Bork, Jonathan Butler, Jean L. Chang, Ze Cheng, Asif T. Chinwalla, Pieter deJong, Kimberley D. Delehaunty, Catrina C. Fronick, Lucinda L. Fulton, Yoav Gilad, Gustavo Glusman, Sante Gnerre, Tina A. Graves, Toshiyuki Hayakawa, Karen E. Hayden, Xiaoqiu Huang, Hongkai Ji, W. James Kent, Mary-Claire King, Edward J. Kulbokas, III, Ming K. Lee, Ge Liu, Carlos Lopez-Otin, Kateryna D. Makova, Orna Man, Elaine R. Mardis, Evan Mauceli, Tracie L. Miner, William E. Nash, Joanne O. Nelson, Svante Pääbo, Nick J. Patterson, Craig S. Pohl, Katherine S. Pollard, Kay Prüfer, Xose S. Puente, David Reich, Mariano Rocchi, Kate Rosenbloom, Maryellen Ruvolo, Daniel J. Richter, Stephen F. Schaffner, Arian F. A. Smit, Scott M. Smith, Mikita Suyama, James Taylor, David Torrents, Eray Tuzun, Ajit Varki, Gloria Velasco, Mario Ventura, John W. Wallis, Michael C. Wendl, Richard K. Wilson, Eric S. Lander, Robert H. Waterston (The Chimpanzee Sequencing and Analysis Consortium) (2005), "Initial sequence of the chimpanzee genome and comparison with the human genome", Nature, 437(7055):69-87.
    [PDF]

  95. I Miklos, P Ittzes, J Hein (2005), "ParIS Genome Rearrangement server", Bioinformatics, 21(6):817-820.
    [abstract]

  96. WJ Murphy, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA (2005), "Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps", Science, 309(5734):613-617.

  97. H Musto, H Naya, A Zavala, H Romero, F Alvarez-Valin, G Bernardi (2005), "The correlation between genomic G+C and optimal growth temperature of prokaryotes is robust: a reply to Marashi and Ghalanbor", Biochemical and Biophysical Research Communications, 330(2):357-360.

  98. Jacques Nicolas, Patrick Durand, Grégory Ranchy, Sébastien Tempel, and Anne-Sophie Valin (2005), "Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes", Bioinformatics, 21:4408-4410.
    [ abstract]

  99. sequence
    WC Nierman, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer PS, Farman M, Fedorova N, Fedorova N, Feldblyum TV, Fischer R, Fosker N, Fraser A, García JL, García MJ, Goble A, Goldman GH, Gomi K, Griffith-Jones S, Gwilliam R, Haas B, Haas H, Harris D, Horiuchi H, Huang J, Humphray S, Jiménez J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Konzack S, Kulkarni R, Kumagai T, Lafon A, Latgé JP, Li W, Lord A, Lu C, Majoros WH, May GS, Miller BL, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Peńalva MA, Pertea M, Price C, Pritchard BL, Quail MA, Rabbinowitsch E, Rawlins N, Rajandream MA, Reichard U, Renauld H, Robson GD, Rodriguez de Córdoba S, Rodríguez-Peńa JM, Ronning CM, Rutter S, Salzberg SL, Sanchez M, Sánchez-Ferrero JC, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vazquez de Aldana CR, Weidman J, White O, Woodward J, Yu JH, Fraser C, Galagan JE, Asai K, Machida M, Hall N, Barrell B, Denning DW (2005), "Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus", Nature, 438:1151-1156.
    [ abstract]

  100. a/symmetry
    Christoforos Nikolaou, Yannis Almirantis (2005), "A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species", Nucleic Acids Research, 33(21):6816-6822.

  101. G Nuel (2005), "S-SPatt: simple statistics for patterns on Markov chains", Bioinformatics, 21(13):3051-3052.
    [abstract]

  102. sequence
    C Nusbaum, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, DeCaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, O'Neill K, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES. (2005), "DNA sequence and analysis of human chromosome 18", Nature, 437(7058):551-555.
    [PDF]

  103. NN Oiwa, C Goldman (2005), "On the analysis of large-scale genomic structures", Cell Biochemistry and Biophysics, 42(2):145-165.

  104. ZQ Ouyang, JK Liu, ZS She (2005), "Hierarchical structure analysis describing abnormal base composition of genomes", Physical Review E, 72(4):041915.

  105. repeats
    V Paar, N Pavin, M Rosandic, M Gluncic, I Basar, R Pezer, SD Zinic (2005), "ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome", Bioinformatics, 21(7):846-852.
    [abstract]

  106. binding-energy
    Alejandro Panjkovich, Francisco Melo (2005), "Comparison of different melting temperature calculation methods for short DNA sequences", Bioinformatics, 21:711-722.
    [ abstract] [PDF]

  107. Apoorva Patel (2005), "The triplet genetic code had a doublet predecessor", Journal of Theoretical Biology, 233:527-532.

  108. sequence
    IT Paulsen, Press CM, Ravel J, Kobayashi DY, Myers GS, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson LS 3rd, Thomashow LS, Loper JE. (2005), "Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5", Nature Biotechnology, 23(7):873-878.

  109. Francesco Piazza, Pietro Lio (2005), "Statistical analysis of simple repeats in the human genome", Physica A, 347:472-488.

  110. repeats
    AL Price, NC Jones, PA Pevzner (2005), "De novo identification of repeat families in large genomes", Bioinformatics, 21(Suppl 1):i351-i358.
    [abstract]

  111. Oleg N Reva, Burkhard Tümmler (2005), "Differentiation of regions with atypical oligonucleotide composition in bacterial genomes", BMC Bioinformatics, 6:251.
    [abstract]

  112. S Robin, F Rodolphe, S Schbath (2005), DNA, Words and Models: Statistics of Exceptional Words (Cambridge University Press).

  113. isochore
    Harlan Robins, William H Press (2005), "Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs", Proceedings of National Academy of Sciences, 102(43):15557-15562.
    [abstract]

  114. sequence
    MT Ross, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RI, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Emery-Cohen A, Errington H, Evans KL, Faulkner L, Francis F, Frankland J, Fraser AE, Galgoczy P, Gilbert J, Gill R, Glockner G, Gregory SG, Gribble S, Griffiths C, Grocock R, Gu Y, Gwilliam R, Hamilton C, Hart EA, Hawes A, Heath PD, Heitmann K, Hennig S, Hernandez J, Hinzmann B, Ho S, Hoffs M, Howden PJ, Huckle EJ, Hume J, Hunt PJ, Hunt AR, Isherwood J, Jacob L, Johnson D, Jones S, de Jong PJ, Joseph SS, Keenan S, Kelly S, Kershaw JK, Khan Z, Kioschis P, Klages S, Knights AJ, Kosiura A, Kovar-Smith C, Laird GK, Langford C, Lawlor S, Leversha M, Lewis L, Liu W, Lloyd C, Lloyd DM, Loulseged H, Loveland JE, Lovell JD, Lozado R, Lu J, Lyne R, Ma J, Maheshwari M, Matthews LH, McDowall J, McLaren S, McMurray A, Meidl P, Meitinger T, Milne S, Miner G, Mistry SL, Morgan M, Morris S, Muller I, Mullikin JC, Nguyen N, Nordsiek G, Nyakatura G, O'Dell CN, Okwuonu G, Palmer S, Pandian R, Parker D, Parrish J, Pasternak S, Patel D, Pearce AV, Pearson DM, Pelan SE, Perez L, Porter KM, Ramsey Y, Reichwald K, Rhodes S, Ridler KA, Schlessinger D, Schueler MG, Sehra HK, Shaw-Smith C, Shen H, Sheridan EM, Shownkeen R, Skuce CD, Smith ML, Sotheran EC, Steingruber HE, Steward CA, Storey R, Swann RM, Swarbreck D, Tabor PE, Taudien S, Taylor T, Teague B, Thomas K, Thorpe A, Timms K, Tracey A, Trevanion S, Tromans AC, d'Urso M, Verduzco D, Villasana D, Waldron L, Wall M, Wang Q, Warren J, Warry GL, Wei X, West A, Whitehead SL, Whiteley MN, Wilkinson JE, Willey DL, Williams G, Williams L, Williamson A, Williamson H, Wilming L, Woodmansey RL, Wray PW, Yen J, Zhang J, Zhou J, Zoghbi H, Zorilla S, Buck D, Reinhardt R, Poustka A, Rosenthal A, Lehrach H, Meindl A, Minx PJ, Hillier LW, Willard HF, Wilson RK, Waterston RH, Rice CM, Vaudin M, Coulson A, Nelson DL, Weinstock G, Sulston JE, Durbin R, Hubbard T, Gibbs RA, Beck S, Rogers J, Bentley DR (2005), "The DNA sequence of the human X chromosome", Nature, 434(7031):325-337.
    [PDF]

  115. S Santini, G Bernardi (2005), "Organization and base composition of tilapia Hox genes: implications for the evolution of Hox clusters in fish", Gene, 346:51-61.

  116. sequence
    R Seshadri, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF. (2005), "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes", Science, 307:105-108.

  117. repeats
    JA Shapiro (2005), "A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering", Gene, 345:91-100.

  118. repeats
    JA Shapiro, RV Sternberg (2005), "Why repetitive DNA is essential to genome function", Biological Reviews, 80:227-250.

  119. protein
    Sung W. Shin, Sam M. Kim (2005), "A new algorithm for detecting low-complexity regions in protein sequences", Bioinformatics, 21:160-170.
    [ abstract]

  120. protein
    B. David Silverman (2005), "Underlying hydrophobic sequence periodicity of protein tertiary structure", Journal of Biomolecular Structure and Dynamics 22(4):411-424.
    [abstract]

  121. Nadia D Singh, Peter F Arndt, Dmitri A Petrov (2005), "Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster", Genetics, 169:709-722.

  122. Wojciech Szpankowski, Wenhui Ren, Lukasz Szpankowski (2005), "An optimal DNA segmentation based on the MDL principle", International Journal of Bioinformatics Research and Applications, 1:?-?.

  123. sequence
    H Tettelin, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM. (2005), "Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome' ", Proceedings of National Academy of Sciences, 102(39):13950-13955.

  124. YX Tian, C Chen, XY Zou, JD Qiu, PX Cai, JY Mo (2005), "Fourier power spectrum analysis of exons for the period-3 behavior", Chinese Chemical Letters, 16(7):939-942.

  125. YX Tian, C Chen, XY Zou, et al. (2005), "Study on period-3 behavior of exons", Acta Chimica Sinica, 63(13):1215-1219.

  126. a/symmetry
    M Touchon, S Nicolay, B Audit, EB Brodie of Brodie, Y d'Aubenton-Carafa, A Arneodo, C Thermes (2005), "Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins", Proceedings of National Academy of Sciences, 102(28):9836-9841,
    [ abstract] [PDF]

  127. C Vaillant, B Audit, A Arneodo (2005), "Thermodynamics of DNA loops with long-range correlated structural disorder", Physical Review Letters, 95:068101.
    [abstract] [PDF]

  128. MW van Passel, AC Luyf, AH van Kampen, A Bart, A van der Ende (2005), "-web, an online tool to assess composition similarity of individual nucleic acid sequences", Bioinformatics, 21(13):3053-3055.
    [abstract]

  129. AE Vinogradov (2005), "Noncoding DNA, isochores and gene expression: nucleosome formation potential", Nucleic Acids Research, 33(2):559-563.
    [PDF]

  130. AE Vinogradov (2005), "Dualism of gene GC content and CpG pattern in regard to expression in the human genome: magnitude versus breadth", Trends in Genetics, 21(12):639-643.
    [PDF]

  131. Klaudia Walter, Irina Abnizova, Greg Elgar, Walter R. Gilks (2005), "Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences", Trends in Genetics, 21(8):436-440.
    [ abstract]

  132. period:10-11
    Ji-Ping Z Wang, Jonathan Widom (2005), "Improved alignment of nucleosome DNA sequences using a mixture model", Nucleic Acids Research, 33(21):6743-6755.

  133. Junwen Wang, Sridhar Hannenhalli (2005), "Generalizations of Markov model to characterize biological sequences", BMC Bioinformatics, 6:219.
    [abstract]

  134. Yingwei Wang, Kathleen Hill, Shiva Singh and Lila Kari (2005), "The spectrum of genomic signatures: from dinucleotides to chaos game representation", Gene, 346:173-185.

  135. Matthew T Webster, Nick G C Smith, Lina Hultin-Rosenberg, Peter F Arndt, Hans Ellegren (2005), "Male-driven biased gene conversion governs the evolution of base composition in human Alu repeats", Molecular Biolology and Evolution, 22:1468-1474.

  136. repeats
    Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger (2005), "Finding approximate tandem repeats in genomic sequences", Journal of Computational Biology, 12(7):928-942.

  137. repeats
    Thomas Wicker, Jon S. Robertson, Stefan R. Schulze, F. Alex Feltus, Vincent Magrini, Jason A. Morrison, Elaine R. Mardis, Richard K. Wilson, Daniel G. Peterson, Andrew H. Paterson, and Robert Ivarie (2005), "The repetitive landscape of the chicken genome", Genome Research, 15:126-136.

  138. Tiee-Jian Wu, Ying-Hsueh Huang, Lung-An Li (2005), "Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences", Bioinformatics, 21(22):4125-4132.
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  139. Albert CC Yang , Ary L Goldberger, CK Peng (2005), "Genomic classification using an information-based similarity index: application to the SARS coronavirus", Journal of Computational Biology, 12(8):1103-1116.

  140. a/symmetry
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  141. CT Zhang, F Gao, R Zhang (2005), "Segmentation algorithm for DNA sequences", Physical Review E, 72(4):041917.
    [abstract]

  142. Linxi Zhang, Tingting Sun (2005), "Statistical properties of nucleotides in human chromosomes 21 and 22", Chaos, Solitons & Fractals, 23(3):1077-1085.
    [ abstract]

  143. Li-Qian Zhou, Zu-Guo Yu, Ji-Qing Deng, Vo Anh, Shun-Chao Long (2005), "A fractal method to distinguish coding and non-coding sequences in a complete genome based on a number sequence", Journal of Theoretical Biology, 232(4):559-567.
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