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+ 2002

  1. Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yuta Ichiba, Tokio Kozuki, Toshimichi Ikemura (2002), "A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency", Genome Informatics, 13:12-20.

  2. repeats
    G Achaz, EP Rocha, P Netter, E Coissac (2002), "Origin and fate of repeats in bacteria", Nucleic Acids Research, 30(13):2987-2994.
    [abstract]

  3. sequence
    L Akman, A Yamashita, H Watanabe, K Oshima, T Shiba, M Hattori, S Aksoy (2002), "Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia", Nature Genetics, 32(3):335-336.

  4. Jonas Almeida, Susana Vinga (2002), "Universal sequence map (USM) or arbitrary discrete sequences", BMC Bioinformatics, 3:6.
    [abstract] [PDF ]

  5. V V Anh, K S Lau, and Z G Yu (2002), "Recognition of an organism from fragments of its complete genome", Physical Review E, 66:031910.
    [ abstract]

  6. isochore
    Fernando Alvarez-Valin, Guillermo Lamolle, Giorgio Bernardi (2002), "Isochores, GC3 and mutation biases in the human genome", Gene, 300(1-2):161-168.

  7. Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi (2002), "Monotony of surprise and large-scale quest for unusual words", Proceedings of the Sixth International Conference on Research in Computational Molecular Biology , pp. 22-31.

  8. Peter F Arndt, Christopher B Burge, Terence Hwa (2002), "DNA sequence evolution with neighbor-dependent mutation", Proceedings of the Sixth International Conference on Research in Computational Molecular Biology , 32-38.

  9. bending
    B Audit, C Vaillant, A Arneodo, Y d'Aubenton-Carafa, C Thermes (2002), "Long-range correlations between DNA bending sites" Journal of Molecular Biology, 316(4):903-918.
    [ abstract]

  10. bending
    B Audit, C Vaillant, A Arneodo, Y d'Aubenton-Carafa, C Thermes (2002), "Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences", Journal of Biological Physics, 30(1):33-81.
    [abstract]

  11. PJ Avery (2002), "Fitting interconnected Markov Chain models - DNA sequences and cricket test matches", Journal of the Royal Statistical Society Series D - The Statistician, 51:267-278.

  12. Rajeev K Azad, Pedro Bernaola-Galván, Ramakrishna Ramaswamy, J. Subba Rao (2002), "Segmentation of genomic DNA through entropic divergence: power laws and scaling", Physical Review E, 65(5):051909
    [ abstract]

  13. sequence
    T Baba, F Takeuchi, M Kuroda, H Yuzawa, K Aoki, A Oguchi, Y Nagai, N Iwama, K Asano, T Naimi, H Kuroda, L Cui, K Yamamoto, K Hiramatsu (2002), "Genome and virulence determinants of high virulence community-acquired MRSA", Lancet, 359:1819-1827.

  14. a/symmetry
    Pierre-François Baisnée, Steve Hampson, and Pierre Baldi (2002), "Why are complementary DNA strands symmetric?", Bioinformatics, 18:1021-1033.
    [PDF ]

  15. J Balakrishnan (2002), "Symmetry scheme for amino acid codons", Physical Review E, 65:021912.

  16. Ian Bancroft (2002), "Insights into cereal genomes from two draft genome sequences of rice", Genome Biology , 3(6):reviews1015.

  17. Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano (2002), "A string pattern regression algorithm and its application to pattern discovery in long introns", Genome Informatics, 13:3-11.

  18. sequence
    Q Bao, Y Tian, W Li, Z Xu, Z Xuan, S Hu, W Dong, J Yang, Y Chen, Y Xue, Y Xu, X Lai, L Huang, X Dong, Y Ma, L Ling, H Tan, R Chen, J Wang, J Yu, H Yang (2002), "A complete sequence of the T. tengcongensis genome", Genome Research, 12:689-700.
    [ abstract]

  19. repeats
    Zhirong Bao, and Sean R. Eddy (2002), "Automated De Novo identification of repeat sequence families in sequenced genomes", Genome Research, 12(8):1269-1276.

  20. repeats
    Mark A Batzer, Prescott L Deininger (2002), "Alu repeats and human genomic diversity" Nature Reviews Genetics, 3:370-380.
    [abstract] [PDF]

  21. isochore
    E Belle, N Smith, A Eyre-Walker (2002), "Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis", Journal of Molecular Evolution, 55:356-363.

  22. sequence
    SD Bentley, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA. (2002), "Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)", Nature, 417:141-147.

  23. sequence
    SB Beres, Sylva GL, Barbian KD, Lei B, Hoff JS, Mammarella ND, Liu MY, Smoot JC, Porcella SF, Parkins LD, Campbell DS, Smith TM, McCormick JK, Leung DY, Schlievert PM, Musser JM. (2002), "Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence", Proceedings of the National Academy of Sciences, 99:10078-10083.

  24. B Berkhout, A Grigoriev, M Bakker, VV Lukashov (2002), "Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure", AIDS Research and Human Retroviruses, 18(2):133-141.

  25. Pedro Bernaola-Galván, Pedro Carpena (2002), "Comment on 'Factorial moments analyses show a characteristic length scale in DNA sequences'", Physical Review Letters, 88(21):219803.
    [PDF ]

  26. Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán, Jose L Oliver (2002), "Study of statistical correlations in DNA sequences", Gene, 300(1-2):105-115.
    [ abstract] [PDF ]

  27. JA Birdsell (2002), "Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution", Molecular Biology and Evolution, 19(7):1181-1197.

  28. database
    Ewan Birney, Michele Clamp, Tim Hubbard (2002) "Databases and tools for browsing genomes", Annual Review of Genomics and Human Genetics, 3:293-310.

  29. Claudio Bonanno, Stefano Galatolo, Giulia Menconi (2002), "Information of sequences and applications", Physica A, 305(1-2):196-199.
    [ abstract]

  30. repeats
    Branko Borstnik, Danilo Pumpernik (2002), "Tandem repeats in protein coding regions of primate genes", Genome Research, 12:909-915.
    [abstract]

  31. RJ Boys, DA Henderson (2002), "A comparison of reversible jump MCMC algorithms for DNA sequence segmentation using hidden Markov models", Computing Science & Statistics, 33:1-15.

  32. Cedric O Buckley, Desmond Stephens, Patricia A Herring, Julius H Jackson (2002), "%(G+C) variation and prediction by a model of bacterial gene transfer and codon adaptation", Omics: A Journal of Integrative Biology, 6(3):259-272.

  33. Marcello Buiatti, Claudia Acquisti, Giuseppe Mersi, Patrizia Bogani, Marco Buiatti (2002), "The biological meaning of DNA correlations," in Fractals in Biology and Medicine, Volume III, Mathematics and Biosciences in interaction, eds. GA Losa, D Merlini, TF Nonnenmacher, ER Weibel (Birkhauser).

  34. sequence
    JM Carlton, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ (2002), "Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii", Nature, 419:512-519.

  35. repeats
    Adalberto T Castelo, Wellington Martins, Guang R. Gao (2002), "TROLL-Tandem Repeat Occurrence Locator", Bioinformatics, 18:634-636.

  36. isochore
    J Castresana (2003), "Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content", Nucleic Acids Research, 30(8):1751-1756.

  37. AM Campbell, S Karlin (2002), "Evolution of genome structure", Theoretical Population Biology, 61(4):365-366.

  38. S Chattopadhyay, WA Kanner, J Chakrabarti (2002), "DNA nucleotides: A case study of evolution", European Physics Journal B, 26(3):393-398.

  39. P Chaudhuri, S Das (2002), "SWORDS: A statistical tool for analysing large DNA sequences", Journal of Biosciences, 27(suppl 1):1-6.
    [PDF ]

  40. repeats
    C Chen, A Gentles, J Jurka, S Karlin (2002), "Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22", Proceedings of the National Academy of Sciences, 99:2930-2935.

  41. Xin Chen, Ming Li, Bin Ma, John Tromp (2002), "DNACompress: fast and effective DNA sequence compression", Bioinformatics, 18:1696-1698.

  42. Jeong-Hyeon Choi, Hwan-Gue Cho (2002), "Analysis of common k-mers for whole genome sequences using SSB-tree", Genome Informatics, 13:30-41.

  43. isochore
    Oliver Clay, Giorgio Bernardi (2002), "Isochores: dream or reality?" (Letters), Trends in Biotechnology, 20(6):237.

  44. PD Cristea (2002), "Conversion of nucleotides sequences into genomic signals", J Cell Mol Med., 6(2):279-303.

  45. sequence
    AC da Silva, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, do Amaral AM, Bertolini MC, Camargo LE, Camarotte G, Cannavan F, Cardozo J, Chambergo F, Ciapina LP, Cicarelli RM, Coutinho LL, Cursino-Santos JR, El-Dorry H, Faria JB, Ferreira AJ, Ferreira RC, Ferro MI, Formighieri EF, Franco MC, Greggio CC, Gruber A, Katsuyama AM, Kishi LT, Leite RP, Lemos EG, Lemos MV, Locali EC, Machado MA, Madeira AM, Martinez-Rossi NM, Martins EC, Meidanis J, Menck CF, Miyaki CY, Moon DH, Moreira LM, Novo MT, Okura VK, Oliveira MC, Oliveira VR, Pereira HA, Rossi A, Sena JA, Silva C, de Souza RF, Spinola LA, Takita MA, Tamura RE, Teixeira EC, Tezza RI, Trindade dos Santos M, Truffi D, Tsai SM, White FF, Setubal JC, Kitajima JP. (2002), "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities", Nature, 417:459-463.

  46. sequence
    Paramvir Dehal, Yutaka Satou, Robert K Campbell, Jarrod Chapman, Bernard Degnan, Anthony De Tomaso, Brad Davidson, Anna Di Gregorio, Maarten Gelpke, David M Goodstein, Naoe Harafuji, Kenneth E M Hastings, Isaac Ho, Kohji Hotta, Wayne Huang, Takeshi Kawashima, Patrick Lemaire, Diego Martinez, Ian A Meinertzhagen, Simona Necula, Masaru Nonaka, Nik Putnam, Sam Rash, Hidetoshi Saiga, Masanobu Satake, Astrid Terry, Lixy Yamada, Hong-Gang Wang, Satoko Awazu, Kaoru Azumi, Jeffrey Boore, Margherita Branno, Stephen Chin-bow, Rosaria DeSantis, Sharon Doyle, Pilar Francino, David N. Keys, Shinobu Haga, Hiroko Hayashi, Kyosuke Hino, Kaoru S. Imai, Kazuo Inaba, Shungo Kano, Kenji Kobayashi, Mari Kobayashi, Byung-In Lee, Kazuhiro W. Makabe, Chitra Manohar, Giorgio Matassi, Monica Medina, Yasuaki Mochizuki, Steve Mount, Tomomi Morishita, Sachiko Miura, Akie Nakayama, Satoko Nishizaka, Hisayo Nomoto, Fumiko Ohta, Kazuko Oishi, Isidore Rigoutsos, Masako Sano, Akane Sasaki, Yasunori Sasakura, Eiichi Shoguchi, Tadasu Shin-i, Antoinetta Spagnuolo, Didier Stainier, Miho M. Suzuki, Olivier Tassy, Naohito Takatori, Miki Tokuoka, Kasumi Yagi, Fumiko Yoshizaki, Shuichi Wada, Cindy Zhang, P. Douglas Hyatt, Frank Larimer, Chris Detter, Norman Doggett, Tijana Glavina, Trevor Hawkins, Paul Richardson, Susan Lucas, Yuji Kohara,dagger Michael Levine,dagger Nori Satoh,dagger Daniel S. Rokhsardagger (2002), "The draft genome of Ciona intestinalis: insights into Chordate and Vertebrate origins", Science, 298:2157-2167.

  47. sequence
    VG del Vecchio, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R. (2002), "The genome sequence of the facultative intracellular pathogen Brucella melitensis", Proceedings of the National Academy of Sciences, 99:443-448.

  48. sequence
    W Deng, Burland V, Plunkett G 3rd, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S, Schwartz DC, Fetherston JD, Lindler LE, Brubaker RR, Plano GV, Straley SC, McDonough KA, Nilles ML, Matson JS, Blattner FR, Perry RD. (2002), "Genome sequence of Yersinia pestis KIM", Journal of Bacteriology, 184:4601-4611.
    [ abstract]

  49. sequence
    U Deppenmeier, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G. (2002), "The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea", Journal of Molecular Microbiology and Biotechnology, 4:453-461.

  50. Emmanouil T Dermitzakis, Alexandre Reymond, Robert Lyle, Nathalie Scamuffa, Catherine Ucla, Samuel Deutsch, Brian J Stevenson, Volker Flegel, Philipp Bucher, C Victor Jongeneel, Stylianos E Antonarakis (2002), "Numerous potentially functional but non-genic conserved sequences on human chromosome 21", Nature , 420:578-582.

  51. isochore
    Giuseppe D'Onofrio (2002), "Expression patterns and gene distribution in the human genome", Gene, 300(1-2):155-160.
    [ abstract] [PDF]

  52. isochore
    L Duret, M Semon, G Piganeau, D Mouchiroud, N Galtier (2002), "Vanishing GC-Rich isochores in mammalian genomes", Genetics, 162(4):1837-1847.

  53. sequence
    Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM. (2002) "The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium", Proceedings of the National Academy of Sciences, 99:9509-9514

  54. J Filipski, M Mucha (2002), "Structure, function and DNA composition of Saccharomyces cerevisiae chromatin loops", Gene, 300:63-68.

  55. sequence
    ST Fitz-Gibbon, H Ladner, UJ Kim, KO Stetter, MI Simon, JH Miller (2002), "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum", Proceedings of the National Academy of Sciences, 99:984-989.

  56. a/symmetry
    DR Forsdyke (2002), "Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia", Bioinformatics, 18:215-217.

  57. repeats
    AC Frank, H Amiri, SGE Andersson (2002), "Genome deterioration: loss of repeated sequences and accumulation of junk DNA", Genetica, 115(1):1-12.
    [ abstract]

  58. M Frisch, K Frech, A Klingenhoff, K Cartharius, I Liebich, T Werner (2002), "A new tool for the in silico prediction of matrix attachment regions in large genomic sequences", Genome Research, 12:349-354.

  59. period
    Atsushi Fukushima, Toshimichi Ikemura, Makoto Kinouchi, Taku Oshima, Yoshihiro Kudo, Hirotada Mori, Shigehiko Kanaya (2002), "Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis", Gene, 300(1-2):203-211.
    [ abstract] [PDF]

  60. period
    Atsushi Fukushima, Toshimichi Ikemura, Taku Oshima, Hirotada Mori, Shigehiko Kanaya (2002), "Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis", in Genome Informatics 2002 (Universal Academy Press, Japan), pp.?-?.
    [PDF]

  61. sequence
    Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B. (2002), "The genome of M. acetivorans reveals extensive metabolic and physiological diversity", Genome Research, 12:532-542.
    [abstract]

  62. sequence
    MJ Gardner, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B (2002), "Genome sequence of the human malaria parasite Plasmodium falciparum", Nature, 419:498-511.
    [PDF]

  63. sequence
    MJ Gardner, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, Granger D, Fujii C, Hansen C, Pederson J, Feldblyum T, Peterson J, Suh B, Angiuoli S, Pertea M, Allen J, Selengut J, White O, Cummings LM, Smith HO, Adams MD, Venter JC, Carucci DJ, Hoffman SL, Fraser CM. "Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14" (2002), Nature, 419(6906):531-534.

  64. protein
    A Giuliani, R Benigni, JP Zbilut, CL Webber, P Sirabella, A Colosimo (2002), "Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships", Chemical Reviews, 102(5):1471-1491.

  65. sequence
    P Glaser, Rusniok C, Buchrieser C, Chevalier F, Frangeul L, Msadek T, Zouine M, Couve E, Lalioui L, Poyart C, Trieu-Cuot P, Kunst F. (2002), "Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease", Molecular Microbiology, 45:1499-1513.

  66. sequence
    G Glockner, L Eichinger, K Szafranski, JA Pachebat, AT Bankier, PH Dear, R Lehmann, C Baumgart, G Parra, JF Abril, R Guigo, K Kumpf, B Tunggal, E Cox, MA Quail, M Platzer, A Rosenthal, AA Noegel; Dictyostelium Genome Sequencing Consortium (2002), "Sequence and analysis of chromosome 2 of Dictyostelium discoideum", Nature, 418:79-85.

  67. sequence
    Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. (2002), "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)", Science, 296:92-100.

  68. repeats
    John M Greally (2002), "Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome", Proceedings of the National Academy of Sciences, 99(1):327-332.
    [ abstract]

  69. T Ryan Gregory (2002), "Genome size and developmental complexity", Genetica, 115(1):131-146.
    [ abstract]

  70. I Gross, P Bernaola-Galvan, P Carpena, R Roman-Roldan, JL Oliver, HE Stanley (2002), "Analysis of symbolic sequences using the Jense-Shannon divergence", Physical Review E, 65, 041905.
    [PDF] [ abstract]

  71. S Hamspon, D Kibler, P Baldi (2002), "Distribution patterns of over-represented k-mers in non-coding yeast DNA", Bioinformatics, 18:513-528.

  72. John M Hancock (2002), "Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects", Genetica, 115(1):93-103.
    [ abstract]

  73. Bailin Hao (2002), "'Spatial-temporal' patterns in prokaryote genomes", International Journal of Bifurcation and Chaos, 12(11):2625-2630.
    [ abstract]

  74. repeats
    Yu-hua Hao and Zheng Tan (2002), "The generation of long telomere overhangs in human cells: a model and its implication", Bioinformatics, 18:666-671.

  75. PA He, J Wang (2002), "Characteristic sequences for DNA primary sequence", Journal of Chemical Information and Computer Sciences, 42:1080-1085.

  76. sequence
    JF Heidelberg, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, DeBoy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM (2002), "Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis", Nature Biotechnology, 20(11):1118-1123.

  77. repeats
    Steven Henikoff (2002), "Near the edge of a chromosome's 'black hoe'", Trends in Genetics, 18(4):165-167.
    [PDF]

  78. sequence
    RA Holt, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chatuverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL (2002), "The genome sequence of the malaria mosquito Anopheles gambiae", Science, 298:129-149.

  79. LS Hsieh, HC Lee (2002), "Model for growth of bacterial genomes", Modern Physics Letters, 16:821-827.

  80. isochore
    S Hughes, O Clay, G Bernardi (2003), "Compositional patterns in reptilian genomes", Gene, 295(2):323-329.

  81. Dirk Husmeier and Frank Wright (2002), "A Bayesian approach to discriminate between alternative DNA sequence segmentations", Bioinformatics, 18(2):226-234.

  82. TS Ilyina, Yu. M Romanova (2002), "Bacterial genomic islands: organization, function, and evolutionary role", Molecular Biology (Molekulyarnaya Biologiya), 36(2):171-179.

  83. Julius H Jackson, Scott H Harrison, Patricia A Herring (2002), "A theoretical limit to coding space in chromosomes of bacteria", Omics: A Journal of Integrative Biology, 6(2):115-121.

  84. repeats
    Rund Jansen, Jam DA van Embden, Wim Gaastra, Leo M Schouls (2002), "Identification of a novel family of sequence repeats among prokaryotes", Omics: A Journal of Integrative Biology, 6(1):23-33.

  85. Robert W Jernigan, Robert H Baran (2002), "Pervasive properties of the genomic signature", BMC Genomics, 3:23.

  86. Samuel Karlin, Luciano Brocchieria, Jonathan Trentb, B Edwin Blaisdella, Jan Mrázeka (2002), "Heterogeneity of genome and proteome content in bacteria, archaea, and eukaryotes", Theoretical Population Biology, 61(4):367-390.

  87. Henrik Kaessmann, Sebastian Zöllner, Anton Nekrutenko, Wen-Hsiung Li (2002), "Signatures of domain shuffling in the human genome", Genome Research, 12:1642-1650.
    [abstract]

  88. sequence
    Takakazu Kaneko, Yasukazu Nakamura, Shusei Sato, Erika Asamizu, Tomohiko Kato, Shigemi Sasamoto, Akiko Watanabe, Kumi Idesawa, Atsuko Ishikawa, Kumiko Kawashima, Takaharu Kimura, Yoshie Kishida, Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Yoko Mochizuki, Shinobu Nakayama, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada and Satoshi Tabata (2002), "Complete genome structure of the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110", DNA Research, 9(6):189-197.
    [ abstract]

  89. sequence
    Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vasieva O, Chu L, Kogan Y, Chaga O, Goltsman E, Bernal A, Larsen N, D'Souza M, Walunas T, Pusch G, Haselkorn R, Fonstein M, Kyrpides N, Overbeek R. (2002), "Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586", Journal of Bacteriology, 184:2005-2018.
    [ abstract]

  90. P Katsaloulis, T Theoharis, A Provata (2002), "Statistical distributions of oligonucleotide combinations: applications in human chromosomes 21 and 22", Physica A, 316:380-396.
    [ abstract]

  91. repeats
    M Kawano, S Kanaya, T Oshima, Y Masuda, T Ara, H Mori (2002), "Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of long direct repeat (LDR) sequences", DNA Research, 9:1-10.

  92. Stephen Kearsey (2002), "Surveying genome replication", Genome Biology, 3(6):review1016.

  93. repeats
    Margaret G Kidwell (2002), "Transposable elements and the evolution of genome size in eukaryotes", Genetica, 115(1):49-63.
    [ abstract]

  94. Valery M Kirzhner, Abraham B Korol, Alexander Bolshoy, Eviatar Nevo (2002), "Compositional spectrum - revealing patterns for genomic sequence characterization and comparison", Physica A, 312(3-4):447-457.

  95. bending
    R Kiyama, EN Trifonov (2002), "What positions nucleosomes?--A model", FEBS Letters, 523(1-3):7-11.

  96. RJ Klein, Z Misulovin, SR Eddy (2002), "Noncoding RNA genes identified in AT-rich hyperthermophiles", Proceedings of the National Academy of Sciences, 99(11):7542-7547.
    [PDF]

  97. Michal Kolar, Frantisek Slanina (2002), "How the quasispecies evolution depends on the topology of the genome space", Physica A, 313:549-568.

  98. protein
    A Laskin, E Korotkov, N Kudryashov (2002), "New method of latent periodicity detection may determine structurally related proteins and protein families", Proceedings of the Third Conference on Bioinformatics of Genome Regulation and Structure, 3:97-99 Novosibirsk.

  99. JG Lawrence, H Ochman (2002), "Reconciling the many faces of lateral gene transfer", Trends in Microbiology, 10:1-4.

  100. MJ Lercher, LD Hurst (2002), "Human SNP variability and mutation rate are higher in regions of high recombination", Trends in Genetics, 18:337-340.

  101. isochore
    MJ Lercher, NGC Smith, A Eyre-Walker, LD Hurst (2002), "The evolution of isochores: evidence from SNP frequency distributions", Genetics, 162(4):1805-1810.

  102. isochore
    W Li (2002), "Are isochore sequences homogeneous?" Gene, 300(1-2):129-139.
    [ abstract] [PDF]

  103. W Li, P Bernaola-Galvan, F Haghighi, I Grosse (2002) , "Applications of recursive segmentation to the analysis of DNA sequences", Computers & Chemistry (genome and informatics special issue), 26(5):491-510.
    [ abstract] [PDF]

  104. I Liebich, J Bode, M Frisch, E Wingender (2002), "S/MARt DB: a database on scaffold/matrix attached regions", Nucleic Acids Research, 30:372-374.
    [abstract] [PDF]

  105. I Liebich, J Bode, I Reuter, E Wingender (2002), "Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs)", Nucleic Acids Research, 30(15):3433-3442.
    [PDF]

  106. F Lillo, S Basile, RN Mantegna (2002), "Comparative genomics study of inverted repeats in bacteria", Bioinformatics, 18:971-979.

  107. P Lio (2002), "Investigating the relationship between genome structure, composition, and ecology in prokaryotes", Molecular Biology and Evolution, 19(6):789-800.

  108. Rong Liu, Zhen Qi, Xiao-peng Zhu, Lun-jiang Ling, Ru-shan Han (2002), "Genome-scale compositional comparisons in noncoding regions of eukaryotes", Progress in Biochemistry and Biophysics (in Chinese), 29(4):583-587.

  109. protein
    Xin Liu, Di Liu, Ji Qi, Wei-Mou Zheng (2002), "Simplified amino acid alphabets based on deviation of conditional probability from random background", Physical Review E, 66:021906.
    [ abstract]

  110. a/symmetry
    Jean R Lobry, Noboru Sueoka (2002), "Asymmetric directional mutation pressures in bacteria", Genome Biology, 3(10):research0058.1-0058.14.

  111. Michael Z. Ludwig (2002), "Functional evolution of noncoding DNA", Current Opinion in Genetics & Development, 12(6):634-639.

  112. Michael Lynch (2002), "Intron evolution as a population-genetic process ", Proceedings of the National Academy of Sciences, 99(9):6118-6123.
    [abstract]

  113. Mary F Lyon (2002), "A personal history of the mouse genome", Annual Review of Genomics and Human Genetics, 3:1-16.

  114. P Mackiewicz, M Kowalczuk, D Mackiewicz, A Nowicka, M Dudkiewicz, A Laszkiewicz, MR Dudek, S Cebrat (2002), "Replication, associated mutational pressure generating long-range correlation in DNA", Physica A, 314(1-4):646-654.
    [ abstract]

  115. Jacek Majewski, Jurg Ott (2002), "Distribution and characterization of regulatory elements in the human genome", Genome Research, 12:1827-1836.
    [abstract]

  116. CH Makhoul, EN Trifonov (2002), "Distribution of rare triplets along mRNA and their relation to protein folding", Journal of Biomolecular Structure and Dynamics, 20(3):413-420.

  117. repeats
    Harmit S Malik, Steven Henikoff (2002), "Conflict begets complexity: the evolution of centromeres", Current Opinion in Genetics & Development, 12(6):711-718.

  118. repeats
    Heather C Mefford, Barbara J Trask (2002), "The complex structure and dynamic evolution of human subtelomeres", Nature Review Genetics, 3(2):91-102.
    [abstract]

  119. AK Mohanty, AVSS Narayana Rao (2002), "Reply", Physical Review Letters, 88(21):219804.
    [PDF]

  120. J Mrazek, LH Gaynon, S Karlin (2002), "Frequent oligonucleotide motifs in genomes of three streptococci", Nucleic Acids Research, 30(19):4216-4221.

  121. protein
    KB Murray, D Gorse, JM Thornton (2002), "Wavelet Transforms for the detection and characterization of repeating motifs", Journal of Molecular Biology, 316(2):341-363.
    [ abstract]

  122. A Musio, T Mariani, P Vezzoni, A Frattini (2002), "Heterogeneous gene distribution reflects human genome complexity as detected at the cytogenetic level", Cancer Genetics and Cytogenetics, 134(2):168-171.

  123. sequence
    Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Masahiko Ikeuchi, Hiroshi Katoh, Shigemi Sasamoto, Akiko Watanabe, Mayumi Iriguchi, Kumiko Kawashima, Takaharu Kimura, Yoshie Kishida, Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Masako Sugimoto, Chie Takeuchi, Manabu Yamada and Satoshi Tabata (2002), "Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1", DNA Research, 9:123-130.
    [ abstract]

  124. A Nandy (2002), "Investigations on evolutionary changes in base distributions in gene sequences", Internet Eletronic Journal of Molecular Design, 1(10):545-558.

  125. Hugo Naya, Héctor Romero, Alejandro Zavala, Beatriz Alvarez, Héctor Musto (2002), "Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes", Journal of Molecular Evolution, 55(3):260-264.
    [ abstract]

  126. sequence
    K Nelson, I Paulsen, C Weinel, R Dodson, H Hilbert, D Fouts, S Gill, M Pop, V Martins Dos Santos, M Holmes, L Brinkac, M Beanan, R DeBoy, S Daugherty, J Kolonay, R Madupu, W Nelson, O White, J Peterson, H Khouri, I Hance, P Lee, E Holtzapple, D Scanlan, K Tran, A Moazzez, T Utterback, M Rizzo, K Lee, D Kosack, D Moestl, H Wedler, J Lauber, J Hoheisel, M Straetz, S Heim, C Kiewitz, J Eisen, K Timmis, A Duesterhoft, B Tummler, CM Fraser (2002), "Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440", Journal of Environmental Microbiology, 4(12):799-808.

  127. P Nicolas, L Bize, F Muri, M Hoebeke, F Rodolphe, SD Ehrlich, B Prum, P Bessieres (2002), "Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models", Nucleic Acids Research, 30(6):1418-1426.
    [PDF]

  128. isochore
    Yoshihito Niimura, Takashi Gojobori (2002), "In silico chromosome staining: Reconstruction of Giemsa bands from the whole human genome sequence", Proceedings of the National Academy of Sciences, 99(2):797-802.
    [ abstract]

  129. C Nikolaou, Y Almirantis (2002), "A study of the middle-scale nucleotide clustering in DNA sequences of various origin and functionality, by means of a method based on a modified standard deviation", Journal of Theoretical Biology, 217(4):479-492.

  130. Su-Long Nyeo, I-Ching Yang (2002), "Codon distributions in DNA sequence of Escherichia Coli", Journal of Biological Systems, 10(1):47-60.
    [ abstract]

  131. period:3
    period:10-11
    SL Nyeo, IC Yang, CH Wu (2002), "Spectral classification of archaeal and bacterial genomes", Journal of Biological Systems, 10(3):233-241.
    [ abstract]

  132. repeats
    Ikuo Ogiwara, Masaki Miya, Kazuhiko Ohshima, Norihiro Okada (2002), "V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit", Genome Research, 12:316-324.
    [abstract]

  133. NN Oiwa, JA Glazier (2002), "The fractal structure of the mitochondrial genomes", Physica A, 311(1-2):221-230.

  134. isochore
    Jose L Oliver Pedro Carpena, Ramón Román-Roldán, Trinidad Mata-Balaguer, Andres Mejias-Romero, Michael Hackenberg, Pedro Bernaola-Galván (2002), "Isochore chromosome maps of the human genome", Gene, 300(1-2):117-127.
    [ abstract] [PDF]

  135. M Ortuno, P Carpena, P Bernaola-Galvan, E Munoz, AM Somoza (2002), "Keyword detection in natural languages and DNA", Europhysics Letters, 57(5):759-764.
    [PDF]

  136. sequence
    IT Paulsen, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM (2002), "The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts", Proceedings of the National Academy of Sciences, 99:13148-13153.

  137. repeats
    Adam Pavlicek, Oliver Clay, Giorgio Bernardi (2002), "Transposable elements encoding functional proteins: pitfalls in unprocessed genomic data?" FEBS Letters, 523(1-3):252-253.
    [ abstract]

  138. isochore
    A Pavlicek, J Paces, O Clay, G Bernardi (2002), "A compact view of isochores in the draft human genome sequence", FEBS Letters, 511(1-3):165-169.
    [PDF]

  139. repeats
    Adam Pavlicek, Jan Paces, Radek Zika, Jiri Hejnar (2002), "Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection", Gene, 300(1-2):189-194.
    [PDF]

  140. S Paxia, A Rudra, Y Zhou, B Mishra (2002), "A random walk down the genomes: DNA evolution in valis", Computer, 35(7):73.

  141. Bret A Payseur, Michael W Nachman (2002), "Gene density and human nucleotide polymorphism", Molecular Biology and Evolution, 19:336-340.
    [html]

  142. Jerome K Percus (2002), Mathematics of Genome Analysis (Cambridge University Press).

  143. Dmitri A Petrov (2002), "Mutational equilibrium model of genome size evolution", Theoretical Population Biology, 61(4):531-544.

  144. isochore
    G Piganeau, D Mouchiroud, L Duret, C Gautier (2002), "Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores", Journal of Molecular Evolution, 54(1):129-133.
    [PDF]

  145. L Ponger, D Mouchiroud (2002), "CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequence", Bioinformatics, 18(4):631-633.

  146. A Provata, Y Almirantis (2002), "Statistical dynamics of clustering in the genome structure", Journal of Statistical Physics, 106(1-2):23-56.

  147. sequence
    FT Robb, DL Maeder, JR Brown, J DiRuggiero, MD Stump, RK Yeh, RB Weiss, DM Dunn (2002), "Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology", Methods in Enzymology, 330:134-157.

  148. S Robin, JJ Daudin, H Richard, MF Sagot, S Schbath (2002) "Occurrence probability of structured motifs in random sequences" Journal of Computational Biology , 9(6):761-773.
    [ abstract]

  149. Stephane Robin (2002), "A compound Poisson model for word occurrences in DNA sequences", Journal of Royal Statistical Society: Series C (Applied Statistics) , 51(4):437-451.

  150. EPC Rocha (2002), "Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?" Trends in Microbiology, 10:393-396.

  151. repeats
    EP Rocha, A Blanchard (2002), "Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution", Nucleic Acids Research, 30(9):2031-2042.

  152. EP Rocha, A Danchin (2002), "Base composition bias might result from competition for metabolic resources", Trends in Genetics, 18(6):291-294.

  153. repeats
    EP Rocha, I Matic, F Taddei (2002), "Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?", Nucleic Acids Research, 30(9):1886-1894.

  154. Alexandre Rosas, Edvaldo Nogueira, Jr., Jose F Fontanari (2002), "Multifractal analysis of DNA walks and trails", Physical Review E, 66:061906.
    [ abstract]

  155. a/symmetry
    Claude-Alain H Roten, Patrick Gamba, Jean-Luc Barblan, Dimitri Karamata (2004), "Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes", Nucleic Acids Research, 30(1):142-144.

  156. C Sabatti, K Lange (2002), "Genomewise motif identification using a dictionary model", IEEE Proceedings, 90:1803-1810.

  157. isochore
    S Saccone, C Frederico, G Bernardi (2002), "Localization of the gene-richest and the gene-poorest isochores in the interphase nucleic of mammals and birds", Gene, 300(1-2):169-178.
    [PDF]

  158. A Sakurai, S Fujimori, H Kochiwa, S Kitamura-Abe, T Washio, R Saito, The RIKEN Genome Exploration Research Group Phase II Team, P Carninci, Y Hayashizaki, M Tomita (2002), "On biased distribution of introns in various eukaryotes", Gene, 300(1-2):89-95.
    [ abstract] [PDF]

  159. sequence
    Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thebault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA. (2002), "Genome sequence of the plant pathogen Ralstonia solanacearum", Nature, 415:497-502.

  160. Marko Salmenkivi, Juha Kere, Heikki Mannila (2002), "Genome segmentation using piecewise constant intensity models and reversible jump MCMC", Bioinformatics, 18:S211-S218.

  161. a/symmetry
    J Sanchez, MV Jose (2002), "Analysis of bilateral inverse symmetry in whole bacterial chromosomes", Biochemical and Biophysical Research Communications, 299(1):126-134.
    [PDF]

  162. David Sankoff, Melanie Deneault, Pascal Turbis, Chris Allen (2002), "Chromosomal distributions of breakpoints in cancer, infertility, and evolution", Theoretical Population Biology, 61(4):497-501.

  163. Nicola Scafetta, Vito Latora, Paolo Grigolini (2002), "Levy scaling: the diffusion entropy analysis applied to DNA sequences", Physical Review E, 66:031906.
    [ abstract]
    also, arXiv preprint, cond-mat/0205525.
    [abstract]

  164. N Scafetta, V Latora, P Grigolini (2002), "Levy statistics in coding and non-coding nucleotide sequences", Physics Letters A, 299(5-6):565-570.
    [ abstract]

  165. P Schattner (2002), "Searching for RNA genes using base-composition statistics", Nucleic Acids Research, 30(9):2076-2082.

  166. sequence
    MA Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F. (2002), "The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract", Proceedings of the National Academy of Sciences, 99:14422-14427.

  167. Mark Schreiber and Chris Brown (2002), "Compensation for nucleotide bias in a genome by representation as a discrete channel with noise", Bioinformatics, 18:507-512.

  168. David B Searls (2002), "The language of genes", Nature, 420:211-217.

  169. AM Selvam (2002), "Quantumlike chaos in the frequency distributions of the bases A, C, G, T in drosophila DNA", Apeiron, 9(4):103-148.
    [html]

  170. repeats
    James A Shapiro (2002), "Repetitive DNA, genome system architecture and genome reorganization", Research in Microbiology, 153:447-453.

  171. protein
    repeats
    Kiyotaka Shiba, Yuki Takahashi, Tetsuo Noda (2002), "On the role of periodism in the origin of proteins", Journal of Molecular Biology, 320(4):833-840.
    [ abstract]

  172. protein
    CT Shih, ZY Su, JF Gwan, BL Hao, CH Hsieh, JL Lo, HC Lee (2002), "Geometric and statistical properties of the nean-field HP model, the LS model and real protein sequences", Physical Review E, 65:041923.
    [ abstract]

  173. sequence
    T Shimizu, K Ohtani, H Hirakawa, K Ohshima, A Yamashita, T Shiba, N Ogasawara, M Hattori, S Kuhara, H Hayashi (2002), "Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater", Proceedings of the National Academy of Sciences, 99:996-1001.

  174. Alastair G B Simpson, Erin K MacQuarrie, Andrew J Roger (2002), "Eukaryotic evolution: early origin of canonical introns", Nature, 419:270.

  175. M Skovgaard, LJ Jensen, C Friis, HH Staerfeldt, P Worning, S Brunak, D Ussery (2002), "The atlas visualization of genomewide information", Methods in Microbiology, 33:49-66.

  176. NG Smith, A Eyre-Walker (2003), "The compositional evolution of the murid genome", Journal of Molecular Evolution, 55:197-201.

  177. a/symmetry
    Noboru Sueoka (2002), "Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses", Gene, 300(1-2):141-154.
    [PDF]

  178. Daiya Takai, Peter A Jones (2002), "Comprehensive analysis of CpG islands in human chromosomes 21 and 22", Proceedings of the National Academy of Sciences, 99(6):3740-3745.

  179. sequence
    H Takami, Y Takaki, I Uchiyama (2002), "Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments", Nucleic Acids Research, 30(18):3927-3935.
    [abstract]

  180. sequence
    I Tamas, L Klasson, B Canback, AK Naslund, AS Eriksson, JJ Wernegreen, JP Sandstrom, NA Moran, SG Andersson (2002), "50 million years of genomic stasis in endosymbiotic bacteria", Science, 296:2376-2379.

  181. sequence
    H Tettelin , Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM. (2002), "Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae", Proceedings of the National Academy of Sciences, 99:12391-12396.

  182. EN Trifonov (2002), "Segmented genome: elementary units of genome structure" (in Russian), Genetika, 38(6):793-798.

  183. EN Trifonov (2002), "Evolution of the genetic code and earliest proteins. Reconstruction from the current sequences" (in Russian). Biofizika, 47(4):581-586.

  184. protein
    EN Trifonov, IN Berezovsky (2002), "Proteomic code" (in Russian), Mol Biol (Mosk), 36(2):315-319.

  185. Olga G Troyanskaya, Ora Arbell, Yair Koren, Gad M Landau, and Alexander Bolshoy (2002), "Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity", Bioinformatics, 18:679-688.
    [ webpage from the authors]

  186. Anastasios A Tsonis, Fred L Heller, Panagiotis A Tsonis (2002), "Probing the linearity and nonlinearity in DNA sequences", Physica A, 312(3-4):458-468.

  187. Panagiotis A Tsonis, Anastasios A Tsonis (2002), "Linguistic features in eukaryotic genomes", Complexity, 7(4):13-15.

  188. David Ussery, Dikeos Mario Soumpasis, Soren Brunak, Hans Henrik Starfeldt, Peder Worning, Anders Krogh (2002), "Bias of purine stretches in sequenced chromosomes", Computers & Chemistry (genome and informatics special issue), 26(5):531-541.

  189. Erik van Nimwegen, Mihaela Zavolan, Nikolaus Rajewsky, Eric D Siggia (2002), "Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics", Proceedings of the National Academy of Sciences, 99:7323-7328.

  190. sequence
    Robert H Waterston, Kerstin Lindblad-Toh, et al. (Mouse Genome Sequencing Consortium) (2002), "Initial sequencing and comparative analysis of the mouse genome", Nature , 420:520-562.
    [PDF]

  191. Gane Ka-Shu Wong, Jun Wang, Lin Tao, Jun Tan, JianGuo Zhang, Douglas A Passey, Jun Yu (2002), "Compositional gradients in Gramineae genes", Genome Research, 12(6):851-856.
    [abstract]

  192. Kim Wong, Turlough M. Finan, Brian G. Golding (2002), "Dinucleotide compositional analysis of {\sl Sinorhizobium meliloti} using the genome signature: distinguishing chromosomes and plasmids", Functional & Integrative Genomics, 2(6):274-281.

  193. sequence
    Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Benito J, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P. (2002), "The genome sequence of Schizosaccharomyces pombe", Nature, 415:871-880.

  194. F Wu, WM Zheng (2002), "Which are more random: Coding or noncoding DNA sequences?", Communications in Theoretical Physics, 37(5):637-640.

  195. Huijie Yang, Fangcui Zhao, Yizhong Zhuo, Xizhen Wu, Zhuxia Li (2002), "Analysis of DNA chains by means of factorial moments ", Physics Letters A, 292(6):349-356.

  196. period
    IC Yang, CH Wu (2002), "A model for the periodicities of nucleotides in DNA sequences", Chinese Journal of Physics, 40(4):456-461.

  197. sequence
    Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H. (2002) "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)", Science, 296:79-92.

  198. Jun Yu, Zhiyong Yang, Miho Kibukawa, Marcia Paddock, Douglas A Passey, Gane Ka-Shu Wong (2002), "Minimal introns are not 'junk' ", Genome Research, 12:1185-1189.
    [abstract]

  199. ZG Yu, A Vo, ZM Gong, SC Long (2002), "Fractals in DNA sequence analysis", Chinese Physics, 11(12):1313-1318.

  200. Barry Zeeberg (2002), "Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes", Genome Research, 12:944-955.
    [abstract]

  201. J Zhang (2002), "Analysis of information content for biological sequences", Journal of Computational Biology, 9(3):487-504.
    [ abstract]

  202. period:3
    J Zhang, XF Shi (2002), "Tentative study of the coding sequences without 3-base periodicity" (in Chinese), Progress in Biochemistry and Biophysics, 29(2):267-272.

  203. a/symmetry
    R Zhang, CT Zhang (2002), "Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method", Biochemical and Biophysical Research Communications, 297(2):396-400.

  204. Olga Zhaxybayeva, J Peter Gogarten (2002), "Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses ", BMC Genomics, 3:4.
    [abstract]

  205. E Zuckerkandl (2002), "Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine", Genetica, 115(1):105-129.
    [ abstract]
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