corr in DNA (2000)

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2000

sequence

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor Miklos GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC (2000), "The genome sequence of Drosophila melanogaster", Science, 287:2185-2195.
L Allison, L Stern, T Edgoose, TI Dix (2000), "Sequence complexity for biological sequence analysis", Computers & Chemistry, 24(1):43-55.
Dimitris Anastassiou (2000), "Frequency-domain analysis of biomolecular sequences", Bioinformatics, 16:1073-1081.
[PDF]
Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi, Xuyan Xu (2000), "Effecient detection of unusual words", Journal of Computational Biology, 7(1-2):71-94.
[ abstract]
sequence

The Arabidopsis Genome Initiative (2000), "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature, 408:796-815.
[PDF]
P Baldi, P-F Baisnee (2000), "Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths", Bioinformatics, 16(10):865-889.
J Barral P., A Hasmy, J Jiménez, and A Marcano (2000), "Nonlinear modeling technique for the analysis of DNA chains", Physical Review E, 61(2):1812-1815.
[PDF]
Stephen Beck, John Trowsdale (2000), "The human major histocompatibility complex: lessons from the DNA sequence", Annual Review of Genomics and Human Genetics, 1:117-137.
[PDF]
repeats

Joseph A. Bedell, Ian Korf, and Warren Gish (2000), "MaskerAid : a performance enhancement to RepeatMasker", Bioinformatics, 16(11):1040-1041.
[abstract]
a/symmetry

A Beletskill, A Grigorie, S Joyce, AS Bhagwat (2000), "Mutation induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome", Journal of Molecular Biology, 300:1057-1065.
[ abstract] [PDF]
Pedro Bernaola-Galván, Ivo Grosse, Pedro Carpena, Jose L Oliver, Ramón Román-Roldán, H Eugene Stanley (2000), "Finding borders between coding and non-coding regions by an entropic segmentation method", Physical Review Letters, 85(6):1342-1345.
[abstract] [PDF]
G Bernardi (2000), "Isochores and the evolutionary genomics of vertebrates", Gene, 241:3-17.
G Bernardi (2000), "The compositional evolution of vertebrate genomes", Gene, 259:31-43.
RJ Boys, DA Henderson, DW Wilkinson (2000), "Detecting homogeneous segments in DNA sequences by using hidden Markov models", Journal of the Royal Statistical Society, Series C (Applied Statistics), 49:269-285.
JV Braun, RK Bruan, HG Muller (2000), "Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation", Biometrika , 87(2):301-314.
[abstract] [PDF]
Harmen Bussemaker, Hao Li, Eric Siggia (2000), "Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis", Proceedings of the National Academy of Sciences, 97:10096-10100.
[PDF]
N Carels, G Bernardi (2000), "The compositional organization and the expression of the Arabidopsis genome", FEBS Letters, 472(2-3):302-306.
N Carels, G Bernardi (2000), "Two classes of genes in plants", Genetics, 154:1819-1825.
[abstract]
dna-music

T Delatour (2000), "Molecular music: the acoustic conversion of molecular vibrational spectra", Computer Music Journal, 24(3):48-68.
G Dodin, P Vandergheynst, P Levoir, C Cordier, L Marcourt (2000), "Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences", Journal of Theoretical Biology, 206(3):323-326.
NV Dokholyan, SV Buldyrev, S Havlin, HE Stanley (2000), "Distributions of dimeric tandem repeats in non-coding and coding DNA sequences", Journal of Theoretical Biology, 202(4):273-282.
L Duret, N Galtier (2000), "The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact", Molecular Biology and Evolution, 17(11):1620-1625.
a/symmetry

Jonathan A Eisen, John F Heidelberg, Owen White, Steven L Salzberg (2000), "Evidence for symmetric chromosomal inversions around the replication origin in bacteria", Genome Biology, 1(6): research0011.1-0011.9.
[PDF]
DR Forsdyke, JR Mortimer (2000), "Chargaff's legacy", Gene, 261:127-137.
isochore

KJ Fryxell, E Zuckerkandl (2000), "Cytosine deamination plays a primary role in the evolution of mammalian isochores", Molecular Biology and Evolution, 17(9):1371-1383.
[abstract]
a/symmetry

J Garcia-Lara, M Picardeau, BJ Hinnebusch, WM Huang, S Casjens (2000), "The role of genomics in approaching the study of Borrelia DNA replication", Journal of Molecular Microbiology and Biotechnology, 2(4):447-454.
C Gautier (2000), "Compositional bias in DNA", Current Opinion in Genetics & Development, 10(6):656-661.
JL Gerton, J DeRisi, R Shroff, M Lichten, PO Brown, TD Petes (2000), "Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae", Proceedings of the National Academy of Sciences, 97:11383-11390.
[PDF]
a/symmetry

A Gierlik, M Kowalczuk, P Mackiewicz, M R Dudek, S Cebrat (2000), "Is there a replication-associated mutational pressure in the Saccharomyces cerevisae Genome?", Journal of Theoretical Biology, 202(4):305-314.
sequence

JI Glass, EJ Lefkowitz, JS Glass, CR Heiner, EY Chen, GH Cassell (2000), "The complete sequence of the mucosal pathogen Ureaplasma urealyticum", Nature, 407:757-762.
AN Gorban, TG Popova, MG Sadovsky (2000), "Classification of symbol sequences over their frequency dictionaries: towards the connection between structure and natural taxonomy", Open System and Information Dynamics, 7:1-17.
[PDF]
a/symmetry

A Grigorie (2000), "Graphical genome comparison: rearrangements and replication origin of Helicobacter pylori", Trends in Genetics, 16(9):376-378. [PDF ]
I Grosse, H Herzel, SV Buldyrev, HE Stanley (2000), "Species independence of mutual information in coding and noncoding DNA",
Physical Review E, 61(5):5624-5629.
[abstract ] [PDF ]
I Grosse, SV Buldyrev, HE Stanley, D Holste, H Herzel (2000), "Average mutual information of coding and noncoding DNA", Proceedings of Pacific Symposium on Bioinformatics, 5:611-620.
[webpage of PSB'00 ], [PDF]
S Guharay, BR Hunt, JA York, OR White (2000), "Correlations in DNA sequences across the three domains of life", Physica D, 146(1-4):388-396.
[PDF ]
Riva Gur-Arie, Cyril J Cohen, Yuyal Eitan, Leora Shelef, Eric M Hallerman, Yechezkel Kashi (2000), "Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism", Genome Research, 10(1):62-71.
[abstract]
AL Halpern (2000), "Multiple-changepoint testing for an alternating segments model of a binary sequence", Biometrics, 56(3):903-908.
Bailin Hao (2000), "Fractals from genomes", Modern Physics Letters B, 14(25-26):871-875.
Bailin Hao (2000), "Fractals from genomes: exact solutions of a biology-inspired problem", Physica A, 282:225-246.
[abstract] [PDF]
Bailin Hao, Hoongchien Lee, Shuyu Zhang (2000), "Fractals related to long DNA sequences and complete genomes", Chaos, Solitons & Fractals, 11(6):825-836.
[PDF]
Bailin Hao, Huiming Xie, Zuguo Yu, Guoyi Chen (2000), "Factorizable language: from dynamics to bacterial complete genomes", Physica A, 288(1-4):10-20.
[PDF]
Bailin Hao, Huiming Xie, Zuguo Yu, Guoyi Chen (2000), "Avoided strings in bacterial complete genomes and a related combinatorial problem", Annals of Combinatorics, 4:247-255.
[PDF]
D Haring, J Kypr (2000), "Escherichia coli genome is composed of two distinct types of nucleotide sequences", Biochemical and Biophysical Research Communications, 272(2):571-575.
sequence

Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Groner Y, Soeda E, Ohki M, Takagi T, Sakaki Y, Taudien S, Blechschmidt K, Polley A, Menzel U, Delabar J, Kumpf K, Lehmann R, Patterson D, Reichwald K, Rump A, Schillhabel M, Schudy A, Zimmermann W, Rosenthal A, Kudoh J, Schibuya K, Kawasaki K, Asakawa S, Shintani A, Sasaki T, Nagamine K, Mitsuyama S, Antonarakis SE, Minoshima S, Shimizu N, Nordsiek G, Hornischer K, Brant P, Scharfe M, Schon O, Desario A, Reichelt J, Kauer G, Blocker H, Ramser J, Beck A, Klages S, Hennig S, Riesselmann L, Dagand E, Haaf T, Wehrmeyer S, Borzym K, Gardiner K, Nizetic D, Francis F, Lehrach H, Reinhardt R, Yaspo ML, Chromosome 21 mapping and sequencing consortium (2000), "The DNA sequence of human chromosome 21", Nature, 405(6784):311-319. Erratum in: Nature, 407(6800):110 (2000).
[PDF]
sequence

Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Umayam, L., Gill, S.R., Nelson, K.E., Read, T.D., Tettelin, H., Richardson, D., Ermolaeva, M.D., Vamathevan, J., Bass, S., Qin, H., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Fleishmann, R.D., Nierman, W.C. White, O. (2000), "DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae", Nature, 406:477-483
Dirk Holste, Olaf Weiss, Ivo Grosse, Hanspeter Herzel (2000), "Are noncoding sequences of Rickettsia prowazekii remnants of 'neutralized' genes?" Journal of Molecular Evolution, 51:353-362.
Jenny Hsieh, Andrew Fire (2000), "Recognition and silencing of repeated DNA", Annual Review of Genetics, 34:187-204. [PDF ]
protein

A Irback (2000), "Sequence design in coarse-grained protein models", Progress of Theoretical Physics Supplement, 138:273-281.
protein

A Irback, E Sandelin (2000), "On hydrophobicity correlations in protein chains", Biophysical Journal, 79(5):2252-2258.
Kamel Jabbari, Giorgio Bernardi (2000), "The distribution of genes in the Drosophila genome", Gene, 247(1-2):287-292.
JH Jackson, R George, PA Herring (2000), "Vectors of Shannon information from Fourier signals characterizing base periodicity in genes and genomes", Biochemical and Biophysical Research Communications, 268(2):289-292.
[ abstract]
repeats

database

J Jurka (2000), "Repbase update: a database and an electronic journal of repetitive elements", Trends in Genetics, 8(5):277-288.
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 (2000), "Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti", DNA Research, 7(6):331-338. (supplement, 7(6):381-406)
sequence

Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M. (2000), "Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium", Proceedings of the National Academy of Sciences, 97:14257-14262.
Lily E Kay (2000), Who Wrote the Book of Life? A History of the Genetic Code (Stanford University Press)
OV Kirillova (2000), "Entropy concepts and DNA investigations", Physics Letters A, 274:247-253.
Maude Klaerr-Blanchard, He´le`ne Chiapello, Eivind Coward (2001), "Detecting localized repeats in genomic sequences: A new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences", Computers & Chemistry, 24(1): 57-70.
Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich (2000), "Computation and visualization of degenerate repeats in complete genomes", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, pp.?-?.
[webpage of ISMB'00 ]
Dorothy M Lang (2000), "Net nearest neighbor analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences", Bioinformatics, 16(3):212-221.
[PDF ]
protein

Pietro Lio, Marina Vannucci (2000), "Wavelet change-point prediction of transmembrane proteins", Bioinformatics, 16(4):376-382.
[PDF ]
P Lio, M Vannucci (2000), "Finding pathogenicity islands and gene transfer events in genome data", Bioinformatics,16(10):932-940.
repeats

KS Lobachev, JE Stenger, OG Kozyreva, J Jurka, DA Gordenin, MA Resnick (2000), "Inverted Alu repeats unstable in yeast are excluded from the human genome", EMBO Journal, 19(14):3822-3830.
VV Lobzin, VR Chechetkin (2000), "Order and correlations in genomic DNA sequences. The spectral approach", Uspekhi Fizicheskikh Nauk, 170(1):57-81.
a/symmetry

P Lopez, P Forterre, H Le Guyader, H Phillipe (2000), "Origin of replication of Thermotoga Maritima", Trends In Genetics, 16:59-60.
Ricardo Mansilla, Germinal Cocho (2000), "Multiscaling in expansion-modification systems: an explanation for long range correlation in DNA", Complex Systems, 12:207-240.
AK Mohanty, AVSS Rao (2000), "Factorial moments analyses show a characteristic length scale in DNA sequences", Physical Review Letters, 84:1832-1835.
[abstract] [PDF ]
A Mooers, EC Holmes (2000), "The evolution of base composition and phylogenetic inference", Trends in Ecology & Evolution, 9:365-369.
Anton Nekrutenko and Wen-Hsiung Li (2000), "Assessment of compositional heterogeneity within and between eukaryotic genomes", Genome Research, 10:1986-1995.
[abstract] [PDF]
sequence

WV Ng, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S (2000), "Genome sequence of Halobacterium species NRC-1", Proceedings of the National Academy of Sciences, 97:12176-12181.
repeats

Kenichi Noma, Hisako Ohtsubo, Eiichi Ohtsubo (2000), "ATLN Elements, LINEs from Arabidopsis thaliana: Identification and Characterization", DNA Research, 7(5):291-303.
A Nowicka, MR Dudek, S Cebrat, M Kowalczuk, P Mackiewicz, M Dudkiewicz, D Szczepanik (2000) "Long-tail feature of DNA words over- and under-representation in coding sequences", Computational Methods in Science and Technology, 6:65-71.
H Ochman, JG Lawrence, EA Groisman (2000), "Lateral gene transfer and the nature of bacterial innovation", Nature, 405:299-304.
NN Oiwa, C Goldman (2000), "Phylogenetic study of the spatial distribution of protein-coding and control segments in DNA chains", Physical Review Letters, 85(11):2396-2399.
sequence

Parkhill, J., Achtman, M., James, K.D., Bentley, S.D., Churcher, C., Klee, S.R., Morelli, G., Basham, D., Brown, D., Chillingworth, T., Davies, R.M., Davis, P., Devlin, K., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Leather, S., Moule, S., Mungall, K., Quail, M.A., Rajandream, M.A., Rutherford, K.M., Simmonds, M., Skelton, J., Whitehead, S., Spratt, B.G. Barrell, B.G. (2000), "Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491", Nature, 404:502-506.
sequence

Parkhill, J., Wren, B.W., Mungall, K., Ketley, J.M., Churcher, C., Basham, D., Chillingworth, T., Davies, R.M., Feltwell, T., Holroyd, S., Jagels, K., Karlyshev, A.V., Moule, S., Pallen, M.J., Penn, C.W., Quail, M.A., Rajandream, M.A., Rutherford, K.M., van Vliet, A.H., Whitehead, S., Barrell, B.G. (2000), "The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences", Nature, 403:665-668.
P Perani, S Caccio, S Saccone, L Andreozzi, G Bernardi (2000), "Telomeres in warm-blooded vertebrates are composed of GC-rich isochores", Biochem Geneics, 38(7-8):227-239.
a/symmetry

M Picardeau, JR Lobry, BJ Hinnebusch (2000), "Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and cicular plasmids", Genome Research, 10(10):1594-1604.
[abstract] [PDF ]
E Pizzi, C Frontali (2000), "Divergence of noncoding sequences and of insertions encoding nonglobular domains at a genomic region well conserved in plasmodia", Journal of Molecular Evolution, 50(5):474-480.
A Provata, Y Almirantis (2000), "Fractal Cantor patterns in the sequences structure of DNA", Fractals, 8(1):15-27.
[abstract]
A Provata, Y Almirantis (2000), "Statistical dynamics of clustering in the genome structure", (abstract) Journal of Statistical Physics, 101(1-2):709-709.
VE Ramensky, V Ju Makeev, MA Roytberg, VG Tumanyan (2000), "DNA segmentation through the Bayesian approach", Journal of Computational Biology, 7(1-2):215-231.
[ abstract]
M Randic (2000), "Condensed representation of DNA primary sequences", Journal of Chemical Information and Computer Sciences, 40(1):50-56.
M Randic (2000), "On characterization of DNA primary sequences by a condensed matrix", Chemical Physics Letters, 317(1-2):29-34.
M Randic, M Vracko, A Nandy, SC Basak (2000), "On 3-D graphical representation of DNA primary sequences and their numerical characterization", Journal of Chemical Information and Computer Sciences, 40(5):1235-1244.
sequence

Read, T.D., Brunham, R.C., Shen, C., Gill, S.R., Heidelberg, J.F., White, O., Hickey, E.K., Peterson, J., Utterback, T., Berry, K., Bass, S., Linher, K., Weidman, J., Khouri, H., Craven, B., Bowman, C., Dodson, R., Gwinn, M., Nelson, W., DeBoy, R., Kolonay, J., McClarty, G., Salzberg, S.L., Eisen, J., Fraser, C.M. (2000), "Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39", Nucleic Acids Research, 28:1397-1406.
M Regnier (2000), "A unified approach to word occurrence probabilities ", Discrete Applied Mathematics, 104(1-3):259-280.
[ abstract]
Gesine Reinert, Sophie Schbath, Michael S Waterman (2000), "Probabilistic and statistical properties of words: an overview", Journal of Computational Biology, 7(1-2):1-46.
[ abstract]
Hector Romero, Alejandro Zavala, Hector Musto (2000), "Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces ", Nucleic Acids Research, 28(10):2084-2090.
sequence

Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W (2000), "The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum", Nature, 407:508-513.
H Salgado, G Moreno-Hagelsieb, TF Smith, J Collado-Vides (2000), "Operons in Escherichia coli: genomic analyses and predictions", Proceedings of the National Academy of Sciences, 97:6652-6657.
[abstract]
Sophie Schbath (2000), "An overview on the distribution of word counts in Markov chains", Journal of Computational Biology, 7(1-2):193-201.
[ abstract]
protein

SC Schmidler, JS Liu, DL Brutlag (2000), "Bayesian segmentation of protein secondary structure", Journal of Computational Biology, 7(1-2):233-248.
[ abstract] [PDF ]
Andrew M. Shedlock, Norihiro Okada (2000), "SINE insertions: powerful tools for molecular systematics", BioEssays, 22(2):148-160.
sequence

S Shigenobu, H Watanabe, M Hattori, Y Sakaki, H Ishikawa (2000), "Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS", Nature, 407:81-86.
sequence

Shirai, M., Hirakawa, H., Kimoto, M., Tabuchi, M., Kishi, F., Ouchi, K., Shiba, T., Ishii, K., Hattori, M., Kuhara, S. Nakazawa, T. (2000), "Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA", Nucleic Acids Research, 28:2311-2314.
sequence

Silvestri, M.L., Siqueira, W.J., de Souza, A.A., de Souza, A.P., Terenzi, M.F., Truffi, D., Tsai, S.M., Tsuhako, M.H., Vallada, H., Van Sluys, M.A., Verjovski-Almeida, S., Vettore, A.L., Zago, M.A., Zatz, M., Meidanis, J. and Setubai, J.C. (2000), "The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis", Nature, 406:151-157.
David S Stoffer, David E Tyler, David A Wendt (2000), "The spectral envelope and its applications", Statistical Science, 15(3):224-253. [abstract]
sequence

Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S., Hufnagle, W.O., Kowalik, D.J., Lagrou, M., Garber, R.L., Goltry, L., Tolentino. E., Westbrock-Wadman, S., Yuan, Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, G.K., Wu, Z. and Paulsen, I.T. (2000), "Complete genome sequence of Pseudomonas aeruginosa A01, an opportunistic pathogen", Nature, 406:959-964.
N Sueoka, Y Kawanishi (2000), "DNA G+C content of the third codon position and codon usage biases of human genes", Gene, 261(1):53-62.
sequence

H Takami, K Horikoshi (2000), "Analysis of the genome of an alkaliphilic Bacillus strain from an industrial point of view", Extremophiles, 4:99-108.
sequence

Tettelin, H., Saunders, N.J., Heidelberg, J., Jeffries, A.C., Nelson, K.E., Eisen, J.A., Ketchum, K.A., Hood, D.W., Peden, J.F., Dodson, R.J., Nelson, W.C., Gwinn, M.L., DeBoy, R., Peterson, J.D., Hickey, E.K., Haft, D.H., Salzberg, S.L., White, O., Fleischmann, R.D., Dougherty, B.A., Mason, T., Ciecko, A., Parksey, D.S., Blair, E., Cittone, H., Clark, E.B., Cotton, M.D., Utterback, T.R., Khouri, H., Qin, H., Vamathevan, J., Gill, J., Scarlato, V., Masignani, V., Pizza, M., Grandi, G., Sun, L., Smith, H.O., Fraser, C.M., Moxon, E.R., Rappuoli, R.. Venter J.C. (2000), "Complete genome sequence of Neisseria meningitidis serogroup B strain MC58", Science, 287:1809-1815.
sequence

Theologis,A., Ecker,J.R., Palm,C.J., Federspiel,N.A., Kaul,S., White,O., Alonso,J., Altafi,H., Araujo,R., Bowman,C.L., Brooks,S.Y., Buehler,E., Chan,A., Chao,Q., Chen,H., Cheuk,R.F., Chin,C.W., Chung,M.K., Conn,L., Conway,A.B., Conway,A.R., Creasy,T.H., Dewar,K., Dunn,P., Etgu,P., Feldblyum,T.V., Feng,J., Fong,B., Fujii,C.Y., Gill,J.E., Goldsmith,A.D., Haas,B., Hansen,N.F., Hughes,B., Huizar,L., Hunter,J.L., Jenkins,J., Johnson-Hopson,C., Khan,S., Khaykin,E., Kim,C.J., Koo,H.L., Kremenetskaia,I., Kurtz,D.B., Kwan,A., Lam,B., Langin-Hooper,S., Lee,A., Lee,J.M., Lenz,C.A., Li,J.H., Li,Y., Lin,X., Liu,S.X., Liu,Z.A., Luros,J.S., Maiti,R., Marziali,A., Militscher,J., Miranda,M., Nguyen,M., Nierman,W.C., Osborne,B.I., Pai,G., Peterson,J., Pham,P.K., Rizzo,M., Rooney,T., Rowley,D., Sakano,H., Salzberg,S.L., Schwartz,J.R., Shinn,P., Southwick,A.M., Sun,H., Tallon,L.J., Tambunga,G., Toriumi,M.J., Town,C.D., Utterback,T., Van Aken,S., Vaysberg,M., Vysotskaia,V.S., Walker,M., Wu,D., Yu,G., Fraser,C.M., Venter,J.C. and Davis,R.W. (2000), "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana", Nature, 408:816-820.
[PDF]
a/symmetry

Elisabath RM Tillier, Richard A Collins (2000), "The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes", Journal of Molecular Evolution, 50:249-257.
[abstract ]
repeats

G Toth, Z Gaspari, J Jurka (2000), "Microsatellites in different eukaryotic genomes: survey and analysis", Genome Research, 10(7):967-981.
protein

EN Trifonov (2000), "Consensus temporal order of amino acids and evolution of the triplet code", Gene, 261(1):139-151.
Honghui Wan, John C. Wootton (2000), "A global compositional complexity measure for biological sequences: AT-rich and GC-rich genomes encode less complex proteins". Computers & Chemistry, 24(1):71-94.
[PDF ]
protein

O Weiss, MA Jimenez-Montano, H Herzel (2000), "Information content of protein sequences", Journal of Theoretical Biology, 206(3):379-386.
ZB Wu (2000), "Metric representation of DNA sequences", Electrophoresis,21(12):2321-2326.
BJ West, P Allegrini, M Buiatti, P Grigolini (2000), "Non-normal statistics of DNA sequences of prokaryotes", Journal of Biological Physics, 26(1):17-25.
Itai Yanai, Carlos J. Camacho, and Charles DeLisi (2000), "Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification", Physical Review Letters, 85(12):2641-2644.
[PDF ]
E Yeramian (2000), "Genes and the physics of the DNA double-helix", Gene, 255:139-150.
[PDF]
E Yeramian (2000), "The physics of DNA and the annotation of the Plasmodium falciparum genome", Gene, 255:151-168.
[PDF]
repeats

T Yoshida, N Obata, K Oosawa (2000), "Color-coding reveals tandem repeats in the Escherichia coli genome", Journal of Molecular Biology, 298(3):343-349.
Zuguo Yu, Bailin Hao, Huimin Xie, Guoyi Chen (2000), "Dimension of fractals related to language defined by tagged strings in complete genome", Chaos, Solitons & Fractals, 11(14):2215-2222.
Zuguo Yu, Bin Wang (2000), "A time series model of CDS sequences on complete genome", Chaos, Solitons & Fractals, 12(3):519-526.
ZG Yu, GY Chen (2000), "Rescaled range and transition matrix analysis of DNA sequences", Communications in Theoretical Physics, 33(4):673-678.

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