corr in DNA (2003)

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2003

Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yuta Ichiba, Tokio Kozuki, Toshimichi Ikemura (2003), "Informatics for unveiling hidden genome signatures", Genome Research, 13(4):693-702.
[ abstract]
repeats

Guillaume Achaza, Eric Coissaca, Pierre Nettera, Eduardo P. C. Rochac (2003), "Associations between inverted repeats and the structural evolution of bacterial genomes", Genetics, 164:1279-1289.
[abstract]
database

Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, Philipp Bucher (2003), "Signal search analysis server", Nucleic Acids Research, 31:3618-3620.
[PDF] [webpage from the authors: signal search analysis]
Peter F Arndt, Christopher B Burge, Terence Hwa (2003), "DNA sequence evolution with neighbor-dependent mutation", Journal of Computatioal Biology, 10:313-322.
isochore

PF Arndt, DA Petrov, T Hwa (2003), "Distinct changes of genomic biases in nucleotide substitution at the time of mammalian radiation" Molecular Biology and Evolution, 20:1887-1896.
[abstract] [PDF]
B Audit, CA Ouzounis (2003), "From genes to genomes: universal, scale-invariant properties of microbial chromosome organisation", Journal of Molecular Biology, 332(3):617-633.
[abstract] [PDF]
sequence

Alan T Bankier, Helen F Spriggs, Berthold Fartmann, Bernard A Konfortov, Martin Madera, Christine Vogel, Sarah A Teichmann, Al Ivens, Paul H Dear (2003), "Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum", Genome Research, 13:1787-1799.
[abstract]
Endre Barta, Laszlo Kajan, Sandor Pong (2003), "IS: a web-site for intron statistics", Bioinformatics,19:543.
[ abstract]
S Basu, DP Burma, P Chaudhuri (2003), "Words in DNA sequences: some case studies based on their frequency statistics", Journal of Mathematical Biology, 46(6):479-503.
Vieri Benci, Giulia Menconi (2003), "Computable information content and a simple application to the study of DNA", Progress in Nonlinear Differential Equation and Their Applications, Vol.54, Nonlinear Equations: Methods, Models and Applications, eds. Daniela Lupo, Carlo D Pagani, Berhard Ruf, pp.19-31 (Birkhauser).
Gary Benson (2003), "Composition alignment", In G Benson, R Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 447-461 (Springer).
repeats

Jeff W Bizzaro, Kenneth A Marx (2003), "Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA", BMC Bioinformatics, 4:22.
[html]
Alix Boc, Vladimir Makarenkov (2003), "New efficient algorithm for detection of horizontal gene transfer events", In G Benson, R Page, ed., Algorithms and Bioinformatics: 3rd International Workshop (WABI), Lecture Notes in Bioinformatics, volume 2812. pp. 190-201 (Springer).
Alexander Bolshoy (2003), "DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity", Applied Bioinformatics, 2(2):103-112.
[abstract]
repeats

Nathan J Bowen, I King Jordan, Jonathan A Epstein, Valerie Wood, Henry L Levin (2003), "Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe", Genome Research, 13:1984-1997.
[abstract]
sequence

Brazilian National Genome Project Consortium: Ana Tereza Ribeiro de Vasconcelos, Darcy F de Almeida, Mariangela Hungria, Claudia Teixeira Guimarães, Regina Vasconcellos Antônio, Francisca Cunha Almeida, Luiz G P de Almeida, Rosana de Almeida, José Antonio Alves-Gomes, Elizabeth Mazoni Andrade, Julia Araripe, Magnólia Fernandes Florêncio de Araújo, Spartaco Astolfi-Filho, Vasco Azevedo, Alessandra Jorge Baptista, Luiz Artur Mendes Bataus, Jacqueline da Silva Batista, André Beló, Cássio van den Berg, Maurício Bogo, Sandro Bonatto, Juliano Bordignon, Marcelo Macedo Brigido, Cristiana Alves Brito, Marcelo Brocchi, Helio Almeida Burity, Anamaria Aranha Camargo, Divina das Dores de Paula Cardoso, Newton Portilho Carneiro, Dirce Maria Carraro, Cláudia Márcia Benedetto Carvalho, Júlio Cézar de Mattos Cascardo, Benildo Sousa Cavada, Ligia Maria O Chueire, Tânia Beatriz Creczynski-Pasa, Nivaldo Costa da Cunha-Junior, Nelson Fagundes, Clarissa Lima Falcão, Fabiana Fantinatti, Izeni Pires Farias, Maria Sueli Soares Felipe, Lilian Pereira Ferrari, Jesus Aparecido Ferro, Maria Inês Tiraboschi Ferro, Gloria Regina Franco, Nara Suzy Aguiar de Freitas, Luiz Roberto Furlan, Ricardo Tostes Gazzinelli, Eliane Aparecida Gomes, Pablo Rodrigues Gonçalves, Thalles Barbosa Grangeiro, Dario Grattapaglia, Edmundo Carlos Grisard, Ebert Seixas Hanna, Sílvia Neto Jardim, Jomar Laurino, Lélia Cristina Tenório Leoi, Lucymara Fassarella Agnez Lima, Maria de Fatima Loureiro, Maria do Carmo Catanho Pereira de Lyra, Humberto Maciel França Madeira, Gilson Paulo Manfio, Andrea Queiroz Maranhão, Wellington Santos Martins, Sônia Marli Zingaretti di Mauro, Silvia Regina Batistuzzo de Medeiros, Rosely de Vasconcellos Meissner, Miguel Angelo Martins Moreira, Fabrícia Ferreira do Nascimento, Marisa Fabiana Nicolás, Jaquelline Germano Oliveira, Sergio Costa Oliveira, Roger Ferreira Cury Paixão, Juliana Alves Parente, Fabio de Oliveira Pedrosa, Sergio Danilo Junho Pena, José Odair Pereira, Maristela Pereira, Luciana Santos Rodrigues Costa Pinto, Luciano da Silva Pinto, Jorge Ivan Rebelo Porto, Deise Porto Potrich, Cicero Eduardo Ramalho-Neto, Alessandra Maria Moreira Reis, Liu Um Rigo, Edson Rondinelli, Elen Bethleen Pedraça do Santos, Fabrício R Santos, Maria Paula Cruz Schneider, Hector N Seuanez, Ana Maria Rodrigues Silva, Artur Luiz da Costa da Silva, Denise Wanderlei Silva, Rosane Silva, Isabella de Carmo Simões, Daniel Simon, Célia Maria de Almeida Soares, Renata de Bastos Ascenço Soares, Emanuel Maltempi Souza, Kelly Rose Lobo de Souza, Rangel Celso Souza, Maria Berenice Reynaud Steffens, Mário Steindel, Santuza Ribeiro Teixeira, Turan Urmenyi, André Vettore, Roseli Wassem, Arnaldo Zaha, and Andrew John George Simpson (2003), "The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability", Proceedings of National Academy of Sciences, 100(20):11660-11665.
[ abstract]
RJ Britten, L Rowen, J Williams, RA Cameron (2003), "Majority of divergence between closely related DNA samples is due to indels", Proceedings of National Academy of Sciences, 100(8):4661-4665.
[abstract]
Jurgen Brosius (2003), "How significant is 98.5% 'junk' in mammalian genomes?", Bioinformatics,19:ii35.
[ abstract]
M Buchner, S Janjarasjitt (2003), "Detection and visualization of tandem repeats in DNA sequences", IEEE Transactions on Signal Processing, 51(9):2280-2287.
[ abstract]
sequence

C Robin Buell, Vinita Joardar, Magdalen Lindeberg, Jeremy Selengut, Ian T Paulsen, Michelle L Gwinn, Robert J Dodson, Robert T Deboy, A Scott Durkin, James F Kolonay, Ramana Madupu, Sean Daugherty, Lauren Brinkac, Maureen J Beanan, Daniel H Haft, William C Nelson, Tanja Davidsen, Nikhat Zafar, Liwei Zhou, Jia Liu, Qiaoping Yuan, Hoda Khouri, Nadia Fedorova, Bao Tran, Daniel Russell, Kristi Berry, Teresa Utterback, Susan E Van Aken, Tamara V Feldblyum, Mark D'Ascenzo, Wen-Ling Deng, Adela R Ramos, James R Alfano, Samuel Cartinhour, Arun K Chatterjee, Terrence P Delaney, Sondra G Lazarowitz, Gregory B Martin, David J Schneider, Xiaoyan Tang, Carol L Bender, Owen White, Claire M Fraser, Alan Collmer (2003), "The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000", Proceedings of National Academy of Sciences, 100(18):10181-10186.
[ abstract]
Emanuele Bultrini, Elisabetta Pizzi, Paolo Del Giudice, Clara Frontali (2003), "Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster", Gene, 304:183-192.
[PDF ]
sequence

Susan E Celniker, Gerry Rubin (2003), "Fly genome", Annual Review of Genomics and Human Genetics, 4:?-?.
sequence

A M Cerdeño-Tárraga, A Efstratiou, L G Dover, M T G Holden, M Pallen, S D Bentley, G S Besra, C Churcher, K D James, A De Zoysa, T Chillingworth, A Cronin, L Dowd, T Feltwell, N Hamlin, S Holroyd, K Jagels, S Moule, M A Quail, E Rabbinowitsch, K M Rutherford, N R Thomson, L Unwin, S Whitehead, B G Barrell, and J Parkhill (2003), "The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129", Nucleic Acids Research, 31(22):6516-6523.
[ abstract]
MB Chaley, EV Korotkov, NA Kudryashov (2003), "Latent periodicity of 21 bases typical for MCP II gene is widely present in various genes", DNA Sequence, 14:33-52.
S Chattopadhyay, J Chakrabarti (2003), "Temporal changes in phosphoglycerate kinase coding sequences: a quantitative measure", Journal of Computational Biology, 10(1):83-93.
[abstract]
J Chen, H Li, KH Sun, B Kim (2003), "How will bioinformatics impact signal processing research?", IEEE Signal Processing Magazine, 20(6):16-26.
[ abstract]
XY Chen, LJ Bao, JY Mo, PX Cai (2003), "Study on DNA sequences fractal characteristics by Mexican hat wavelet" (in Chinese), Acta Chimica Sinica, 61(2):273-278.
XY Chen, LJ Bao, JY Mo, Y Wang (2003), "Characterizing long-range correlation properties in nucleotide sequences", Chinese Chemical Letters, 14(5):503-504.
isochore

O Clay, CJ Douady, N Carels, S Hughes, G Bucciarelli, G Bernardi (2003), "Using analytical ultracentrifugation to study compositional variation in vertebrate genomes", European Biophysics Journal, 32(5):418-426.
J Conde (2003), "Twofold symmetries in nucleotide distribution in large domains of Saccharomyces cerevisiae Chromosome I", Molecular Genetics and Genomics, 270(4):287-295.
Paul Dan Cristea (2003), "Large scale features in DNA genomic signals", Signal Processing, 83(4):871-888.
S Cruveiller, K Jabbari, O Clay, G Bernardi (2003), "Compositional features of eukaryotic genomes for checking predicted genes", Briefing in Bioinformatics, 4(1):31-42.
Cibele Q da-Silva (2003), "Hidden Markov models applied to a subsequence of the Xylella fastidiosa genome", Genetics and Molecular Biology, 26(4):529-535.
[PDF]
Vincent Daubin, Emmanuelle Lerat, Guy Perriere (2003), "The source of laterally transferred genes in bacterial genomes", Genome Biology, 4:R57.
[html]
M Dehnert, WE Helm, MT Hutt (2003), "A discrete autoregressive process as a model for short-range correlations in DNA sequences", Physica A, 327(304):535-553.
[abstract]
ET Dermitzakis, A Reymond, N Scamuffa, C Ucla, E Kirkness, C Rossier, SE Antonarakis (2004), "Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)", Science, 302(5647):1033-1035.
repeats

M Dewannieux, C Esnault, T Heidmann (2003), "LINE-mediated retrotransposition of marked Alu sequences", Nature Genetics, 35(1):41-48.
sequence

Eric Duchaud, Christophe Rusniok, Lionel Frangeul, Carmen Buchrieser, Alain Givaudan, Séad Taourit, Stéphanie Bocs, Caroline Boursaux-Eude, Michael Chandler, Jean-François Charles, Elie Dassa, Richard Derose, Sylviane Derzelle, Georges Freyssinet, Sophie Gaudriault, Claudine Médigue, Anne Lanois, Kerrie Powell, Patricia Siguier, Rachel Vincent, Vincent Wingate, Mohamed Zouine, Philippe Glaser, Noël Boemare, Antoine Danchin, Frank Kunst (2003), "The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens" Nature Biotechnology, 21(11):1307-1313.
Dannie Durand, David Sankoff (2003), "Tests for gene clustering", Journal of Computational Biology, 10(3/4):453-482.
[abstract]
Ahmed Fadiel, Stuart Lithwick, Gopi Ganji, Stephen W Scherer (2003), "Remarkable sequence signatures in archaeal genomes", Archaea, 1:185-190.
L Frappat, C Minichini, A Sciarrino, P Sorba (2003), "Universality and Shannon entropy of codon usage", Physical Review E, 68(6):061910.
[ abstract]
L Frappat, A Sciarrino, P Sorba (2003), "Sum rules for codon usage probabilities", Physics Letters A, 311:264-269.
[ abstract]
Kelly A Frazer, Xiyin Chen, David A Hinds, PV Krishna Pant, Nila Patil, David R Cox (2003), "Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates", Genome Research, 13(3):341-346.
[ abstract]
isochore

TS Furey, D Haussler (2003), "Integration of the cytogenetic map with the draft human genome sequence", Human Molecular Genetics, 12(9):1037-1044.
[abstract]
database

Moshe Gal, Tzvi Katz, Amir Ovadia, Gad Yagil (2003), "TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts", Nucleic Acids Research, 31: 3682-3685.
[webpage from the authors: TRACTS]
JB Gao, Yinhe Cao, Jae-Min Lee (2003), "Principal component analysis of 1/f^a noise ", Physics Letters A, 314(5-6):392-400.
[abstract]
sequence

R Gil, FJ Silva, E Zientz, F Delmotte, F Gonzalez-Candelas, A Latorre, C Rausell, J Kamerbeek, J Gadau, B Holldobler, RC van Ham, R Gross, A Moya (2003), "The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes", Proceedings of National Academy of Sciences, 100(16):9388-9393.
[ abstract]
Aristides Gionis, Heikki Mannila (2003), "Finding recurrent sources in sequences", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp. 123-130.
Alexander N Gorban, Andrei Y Zinovyev, Tatyana G Popova (2003), "Seven clusters in genomic triplet distributions", In Silico Biology, 3:0039.
a/symmetry

P Green, B Ewing, W Miller, PJ Thomas, NISC Comparative Sequencing Program , ED Green (2003), "Transcription-associated mutational asymmetry in mammalian evolution", Nature Genetics, 33(4):514-517.
[abstract]
database

Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Graziano Pesole (2003), "PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences", Nucleic Acids Research, 31:3608-3612.
[webpage from the authors: PatSearch]
repeats

D Grover, PP Majumder, CB Rao, SK Brahmachari, M Mukerji (2003), "Nonrandom distribution of Alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22", Molecular Biology and Evolution, 20(9):1420-1424.
[abstract]
XF Guo, A Nandy (2003), "Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy", Chemical Physics Letters, 369(3-4):361-366.
Mayetri Gupta, Jun S Liu (2003), "Discovery of conserved sequence patterns using a stochastic dictionary model", Journal of American Statistical Association, 98:55-66.
LV Gusev, VV Vasilevskaya, VJ Makeev, PG Khalatur, AR Khokhlov (2003), "Segmentation of heteropolymer sequences specifying subsequences with different composition and statistical properties", Macromolecular Theory and Simulations, 12(8):604-613.
repeats

Sarah E. Hall, Gregory Kettler, and Daphne Preuss (2003), "Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains", Genome Research, 13(2):195-205.
[ abstract]
isochore

Kazuo Hamada, Tokumasa Horiike, Hidetoshi Ota, Keiko Mizuno, Takao Shinozawa "Presence of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions", Genes & Genetic Systems, 2:195-198.
[abstract]
Bailin Hao, Ji Qi (2003), "Vertical heredity vs. horizontal gene transfer: a challenge to bacterial classification", Journal of Systems Science and Complexity, 16(3):307-314.
Bailin Hao, Ji Qi, B Wang (2003), "Prokaryotic phylogeny based on complete genomes without sequence alignment", Modern Physics Letters, B17:91-94.
RC Hardison, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D (2003), "Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution", Genome Research, 13(1):13-26.
[ abstract]
protein

Paul M Harrison, Mark Gerstein (2003), "A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes", Genome Biology, 4(6):R40.
[ html]
J Healy, EE Thomas, JT Schwartz, M Wigler (2003), "Annotating large genomes with exact word matches", Genome Research, 13(10):2306-2315.
Andreas Heger, Michael Lappe, Lisa Holm (2003), "Accurate detection of very sparse sequence motifs", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp. ?-?.
sequence

R Heilig, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Bruls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Segurens B, Aniere F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Menard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufosse-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guerin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier L, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quetier F, Waterston R, Hood L, Weissenbach J. (2003), "The DNA sequence and analysis of human chromosome 14", Nature, 421:601-607.
[ PDF]
sequence

LW Hillier, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. (2003), "The DNA sequence of human chromosome 7", Nature, 424(6945):157-164.
[abstract] [PDF]
D Holste, I Grosse, S Beirer, P Schieg, H Herzel (2003), "Repeats and correlations in human DNA sequences", Physical Review E, 67(6):061913.
[PDF] [ abstract]
Li-Ching Hsieh, Liaofu Luo, Fengmin Ji, HC Lee (2003), "Minimal model for genome evolution and growth", Physical Review Letters, 90:018101.
[PDF]
also arXiv preprint, physics/0206024.
[abstract]
LS Hsieh, LF Luo, HC Lee (2003), "Short segmental duplication: parsimony in growth of microbial genomes", Genome Biology, 4:P7.
LS Hsieh, LF Luo, HC Lee (2003), "Genomes are large systems with small-system statistics: segmental duplication in the growth of microbial genomes", AAPPS Bulletin, 13:22-27.
Tai-Hsin Hsu, Su-long Nyeo (2003), "Diffusion coefficients of two-dimensional viral DNA walks", Physical Review E, 67(5):051911.
[ abstract]
Tai-Hsin Hsu, Su-long Nyeo (2003), "Simple deviation analysis of two-dimensional viral DNA walks", Journal of Biological Systems, 11(3):221-243
[abstract]
database

bending

Yanlin Huang, David Kowalski (2003), "WEB-THERMODYN: sequence analysis software for profiling DNA helical stability", Nucleic Acids Research, 31:3819-3821.
[PDF] [webpage from the authors: WEB-THERMODYN ]
database

Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, Tetsuo Shibuya (2003), "The web server of IBM's Bioinformatics and Pattern Discovery group", Nucleic Acids Research, 31: 3645-3650.
[webpage from the authors: IBM bioinformatics group ]
Y Isohata, M Hayashi (2003), "Power spectrum and mutual information analyses of DNA base (nucleotide) sequences", Journal of The Physical Society of Japan, 72(3):735-742.
isochore

binding-energy

K Jabbari, O Clay, G Bernardi G (2003), "GC(3) heterogeneity and body temperature in vertebrates", Gene, 317:161-163.
isochore

K Jabbari, S Cruveiller, O Clay, G Bernardi G (2003), "The correlation between GC(3) and hydropathy in human genes", Gene, 317:137-140.
sequence

P Janssen, B Audit, I Cases, N Darzentas, L Goldovsky, V Kunin, N Lopez-Bigas, JM Peregrin-Alvarez, JB Pereira-Leal, S Tsoka, CA Ouzounis (2003), "Beyond 100 genomes" (correspondence), Genome Biology, 4(5):402.
[PDF]
repeats

K Johanning, CA Stevenson, OO Oyeniran, YM Gozal, AM Roy-Engel, J Jurka, PL Deininger (2003), "Potential for retroposition by old Alu subfamilies", Journal of Molecular Evolution, 56(6):658-664.
bending

Aditi Kanhere, Manju Bansal (2003), "An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data", Nucleic Acids Research, 31:2647-2658.
repeats

VV Kapitonov, J Jurka (2003), "A novel class of SINE elements derived from 5S rRNA", Molecular Biology and Evolution, 20(5):694-702.
[abstract]
Gerhard Kauer, Helmut Blocker (2003), "Applying signal theory to the analysis of biomolecules", Bioinformatics,19:2016-2021.
[ abstract]
WS Kendal (2003), "An exponential dispersion model for the distribution of human single nucleotide polymorphisms", Molecular Biology and Evolution, 20(4):579-590.
[abstract]
sequence

EF Kirkness, V Bafna, AL Halpern, S Levy, K Remington, DB Rusch, AL Delcher, M Pop, W Wang, CM Fraser, JC Venter (2003), "The dog genome: survey sequencing and comparative analysis", Science, 301(5641):1898-1903.
Valery Kirzhner, Eviatar Nevo, Abraham Korol, Alexander Bolshoy (2003), "A large-scale comparison of genomic sequences: one promising approach", Acta Biotheoretica, 51(2):73-89.
database

repeats

Roman Kolpakov, Ghizlane Bana, Gregory Kucherov (2003), "mreps: efficient and flexible detection of tandem repeats in DNA", Nucleic Acids Research, 31:3672-3678.
[PDF] [webpage from the authors: mreps]
Eugene V Koonin, Michael Y Galperin (2003), Sequence - Evolution - Function Computational Approaches in Comparative Genomics (Kluwer Academic Publishers).
[ table of contents ]
EV Korotkov, MA Korotkova, FE Frenkel, NA Kudryashov (2003), "The informational concept of searching for periodicity in symbol sequences", Molecular Biology (Molekulyarnaya Biologiya) , 37(2):372-386.
EV Korotkov, MA Korotkova, NA Kudryashov (2003), "Information decomposition method to analyse symbolical sequences", Physics Letters A, 312(3-4):198-210.
[abstract]
repeats

I Yu Khitrinskaya, VA Stepanov, VP Puzyrev (2003), "Alu Repeats in the Human Genome", Molecular Biology (Molekulyarnaya Biologiya) , 37(2):325-333.
NS Kupriyanova, DV Shibalev, AS Voronov, OV Muravenko, AV Zelenin, AP Ryskov (2003), "Segmental duplications in subtelomeric regions of human chromosome 13", Molecular Biology (Molekulyarnaya Biologiya) , 37(2):194-199.
MH Lacroix, N Yu Oparina, TD Mashkova (2003), "Segmental duplications in the human genome", Molecular Biology (Molekulyarnaya Biologiya) , 37(2):186-193.
protein

AA Laskin, MB Chaley, EV Korotkov, NA Kudryashov (2003), "Identification of NAD+ regions in the amino acid sequences of different proteins", Molecular Biology (Molekulyarnaya Biologiya) , 37(4):663-673.
repeats

A Lefebvre, T Lecroq, H Dauchel, J Alexandre (2003), "FORRepeats: detects repeats on entire chromosomes and between genomes", Bioinformatics, 19(3):319-326.
[abstract]
MJ Lercher, AO Urrutia, A Pavlicek, LD Hurst (2003), "A unification of mosaic structures in the human genome", Human Molecular Genetics, 12:2411-2415.
SP Li, KL Ng, MC Chung (2003), "Quantitative linguistic study of DNA sequences", Physica A, 321:189-192.
isochore

W Li, P Bernaola-Galvan, P Carpena, JL Oliver (2003), "Isochores merit the prefix 'iso'", Computational Biology and Chemistry, 27(1):5-10.
[abstract] [ PDF]
Pietro Lio (2003), "Wavelets in bioinformatics and computational biology: state of art and perspectives", Bioinformatics,19:2-9.
[ abstract
Ge Liu, NISC Comparative Sequencing Program, Shaying Zhao, Jeffrey A Bailey, S Cenk Sahinalp, Can Alkan, Eray Tuzun, Eric D Green, Evan E. Eichler (2003), "Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome", Genome Research, 13(3):358-368.
[ abstract]
JR Lobry, D Chessel (2003), "Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria", Journal of Applied Genetics, 44:235-261.
JR Lobry, JM Louarn (2003), "Polarization of prokaryotic chromosomes", Current Opinion in Microbiology, 6:101-108.
[PDF]
a/symmetry

Elizabeth Louie, Jurg Ott and Jacek Majewski (2003), "Nucleotide frequency variation across human genes", Genome Research, 13(12):2594-2601.
[abstract] [PDF]
M Lynch, JS Conery (2003), "The origins of genome complexity", Science, 302(5649):1401-1404.
(Commented by AE Vinogradov, 304(5669):389-390. Authors' response: 304(5669):389-390.)
a/symmetry

D Mackiewicz, P Mackiewicz, M Kowalczuk, M Dudkiewicz, MR Dudek, S Cebrat (2003), "Rearrangements between differently replicating DNA strands in asymmetric bacterial genomes", Acta Microbiol Pol., 52(3):245-260.
a/symmetry

D Mackiewicz, P Mackiewicz, M Kowalczuk, M Dudkiewicz, MR Dudek, S Cebrat (2003), "High divergence rate of sequences located on different DNA strands in closely related bacterial genomes", Journal of Applied Genetics, 44(4):561-584.
VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko (2003), "Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information", Nucleic Acids Research, 31:6016-6026.
Antonio Marin, Jose L Oliver (2003), "GC-biased mutation pressure and ORF lengthening", Journal of Molecular Evolution, 56(3):371-372.
repeats

RA Martienssen (2003), "Maintenance of heterochromatin by RNA interference of tandem repeats" (perspective), Nature Genetics, 35(3):213-214.
sequence

BA Methe, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM. (2003), "Genome of Geobacter sulfurreducens: metal reduction in subsurface environments", Science, 302(5652):1967-1969.
Dirk Metzler (2003), "Statistical alignment based on fragment insertion and deletion models", Bioinformatics, 19:490-499.
[ abstract]
Pedro Miramontes, Germinal Cocho (2003), "DNA dimer correlations reflect in vivo conditions and discriminate among nearest-neighbor base pair free energy parameter measures", Physica A, 321:577-586.
[abstract]
Boris G Mirkin, Trevor I Fenner, Michael Y Galperin, Eugene V Koonin (2003), "Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes", BMC Evolutionary Biology, 3:2
isochore

JI Montoya-Burgos, P Boursot, N Galtier (2003), "Recombination explains isochores in mammalian genomes", Trends in Genetics, 19:128-130.
James R Mortimer, Donald R Forsdyke (2003), "Comparison of responses by bacteriophages and bacteria to pressures on the base composition of open reading frames", Applied Bioinformatics , 2(1):47-62.
sequence

AJ Mungall, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S. (2003), "The DNA sequence and analysis of human chromosome 6", Nature, 425(6960):805-811.
[abstract] [PDF]
sequence

Yasukazu Nakamura, Takakazu Kaneko, Shusei Sato, Mamoru Mimuro, Hideaki Miyashita, Tohru Tsuchiya, Shigemi Sasamoto, Akiko Watanabe, Kumiko Kawashima, Yoshie Kishida, Chiaki Kiyokawa, Mitsuyo Kohara, Midori Matsumoto, Ai Matsuno, Naomi Nakazaki, Sayaka Shimpo, Chie Takeuchi, Manabu Yamada, Satoshi Tabata (2003), "Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids", DNA Research, 10(4):137-145.
[abstract]
protein

T Nandi, D Dash, R Ghai, C B-Rao, K Kannan, SK Brahmachari, C Ramakrishnan, S Ramachandran (2003), "A novel complexity measure for comparative analysis of protein sequences from complete genomes", Journal of Biomolecular Structure & Dynamics, 20(5):657-667.
A Nandy, P Nandy (2003), "On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models", Chemical Physics Letters, 368:102-107.
AG Nazina, DA Papatsenko (2003), "Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency", BMC Bioinformatics, 4:65.
sequence

KE Nelson, RD Fleischmann, RT DeBoy, IT Paulsen, DE Fouts, JA Eisen, SC Daugherty, RJ Dodson, AS Durkin, M Gwinn, DH Haft, JF Kolonay, WC Nelson, T Mason, L Tallon, J Gray, D Granger, H Tettelin, H Dong, JL Galvin, MJ Duncan, FE Dewhirst, CM Fraser(2003), "Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83", Journal of Bacteriology, 185(18):5591-5601.
[ abstract]
C Nikolaou, Y Almirantis (2003), "Mutually symmetric and complementary triplets: differences in their use distinguish systematically between coding and non-coding genomic sequences", Journal of Theoretical Biology, 223(4):477-487.
[abstract]
Vera van Noort, Peder Worning, David W Ussery, William A Rosche, Richard R Sinden (2003), "Strand misalignments lead to quasipalindrome", Trends in Genetics, 19(7):365-369.
repeats

N Yu Oparina, MH Lacroix, AA Rychkov, TD Mashkova (2003), "Tandem and interspersed repeats contribute to the mosaic structure of segmental duplications in the human genome", Molecular Biology (Molekulyarnaya Biologiya) , 37(2):200-204
Hasan H. Otu, Khalid Sayood (2003), "A new sequence distance measure for phylogenetic tree construction", Bioinformatics, 19(16):2122-2130.
[
HY Ou, FB Guo, CT Zhang (2003), "Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method", FEBS Letters, 540(1-3):188-194.
M Ozery-Flato, R Shamir (2003), "Two notes on genome rearrangement", Journal of Bioinformatics and Computational Biology, 1(1):71-94.
[abstract]
repeats

Valerio Parisi, Valeria De Fonzo, Filippo Aluffi-Pentini (2003), "STRING: finding tandem repeats in DNA sequences", Bioinformatics, 19:1733-1738.
[ abstract]
sequence

J Parkhill, M Sebaihia, A Preston, L D Murphy, N Thomson, D E Harris, M T G Holden, C M Churcher, S D Bentley, K L Mungall, A M Cerdeño-Tárraga, L Temple, K James, B Harris, M A Quail, M Achtman, R Atkin, S Baker, D Basham, N Bason, I Cherevach, T Chillingworth, M Collins, A Cronin, P Davis, J Doggett, T Feltwell, A Goble, N Hamlin, H Hauser, S Holroyd, K Jagels, S Leather, S Moule, H Norberczak, S O'Neil, D Ormond, C Price, E Rabbinowitsch, S Rutter, M Sanders, D Saunders, K Seeger, S Sharp, M Simmonds, J Skelton, R Squares, S Squares, K Stevens, L Unwin, S Whitehead, B G Barrell, D J Maskell (2003), "Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica", Nature Genetics, 35(1):32-40.
sequence

IT Paulsen, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003), "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis", Science, 299(5615):2071-2074.
David T Pride, Richard J Meinersmann, Trudy M Wassenaar, Martin J Blaser (2003), "Evolutionary implications of microbial genome tetranucleotide frequency biases", Genome Research, 13(2):145-158.
[ abstract]
Ramakrishna Ramaswamy, Rajeev K Azad (2003), "Analysis of DNA sequences through segmentation: exploring the mosaic via statistical measures", Physica Scripta, T106:21-25.
sequence

TD Read, GSA Myers, RC Brunham, WC Nelson, IT Paulsen, J Heidelberg, E Holtzapple, H Khouri, NB Federova, HA Carty, LA Umayam, DH Haft, J Peterson, MJ Beanan, O White, SL Salzberg, RC Hsia, G McClarty, RG Rank, PM Bavoil, CM Fraser, (2003), "Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae", Nucleic Acids Research, 31(8):2134-2147.
sequence

TD Read, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC, Hazen A, Cline R, Redmond C, Thwaite JE, White O, Salzberg SL, Thomason B, Friedlander AM, Koehler TM, Hanna PC, Kolsto AB, Fraser CM. (2003), "The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria", Nature, 423(6935):81-86.
isochore

Rachael A Ream, Glenn C Johns, George N Somero (2003), "Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G+C content", Molecular Biology and Evolution, 20(1):105-110.
[abstract]
database

H Richard, G Nuel (2003), "SPA: simple web tool to assess statistical significance of DNA patterns", Nucleic Acids Research, 31:3679-3681.
[PDF] [webpage from the authors: SPA]
database

David Robelin, Hugues Richard, Bernard Prum (2003), "SIC: a tool to detect short inverted segments in a biological sequence", Nucleic Acids Research, 31:3669-3671.
[PDF] [webpage from the authors: SIC ]
Eduardo PC Rocha (2003), "An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction", Genome Research, 13(6a):1123-1132.
[ abstract]
EPC Rocha, A Danchin (2003), "Essentiality, not expressiveness, drives gene strand bias in bacteria", Nature Genetics, 34:377-378.
S Roche, D Bicout, E Macia, E Kats (2003), "Long range correlations in DNA: scaling properties and charge transfer efficiency", Physical Review Letters, 91(22):228101.
repeats

M Rosandic, V Paar, I Basar (2003), "Key-string segmentation algorithm and higher-order repeat 16mer (54 copies) in human alpha satellite DNA in chromosome 7", Journal of Theoretical Biology, 221(1):29-37.
[abstract]
repeats

M Rosandic, V Paar, M Gluncic, I Basar, N Pavin (2003), "Key-string algorithm - novel approach to computational analysis of repetitive sequences in human centromeric DNA", Croatian Medical Journal, 44(4):386-406.
repeats

Roman Roset, Juan A. Subirana, and Xavier Messeguer (2003), "MREPATT: detection and analysis of exact consecutive repeats in genomic sequences", Bioinformatics, 19:2475-2476.
[ abstract]
MG Sadovsky (2003), "Comparison of real frequencies of strings vs. the expected ones reveals the information capacity of macromoleculae", Journal of Biological Physics, 29(1):23-28.
DC Samuels, RJ Boys, DA Henderson, PF Chinnery (2003), ``A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate", Nucleic Acids Research, 31:6043-6052.
David Sankoff (2003), "Genome rearrangements", Annual Review of Genetics, ?:?-?.
Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita (2003), "Computational analysis of stop codon readthrough in D.melanogaster", Bioinformatics, 19:1371-1380.
[ abstract]
sequence

SW Scherer, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HH, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GA, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJ, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Dohner H, Dohner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC. (2003), "Human chromosome 7: DNA sequence and biology", Science, 300(5620):767-772.
sequence

Rekha Seshadri, Ian T. Paulsen, Jonathan A. Eisen, Timothy D. Read, Karen E. Nelson, William C. Nelson, Naomi L. Ward, Hervé Tettelin, Tanja M. Davidsen, Maureen J. Beanan, Robert T. Deboy, Sean C. Daugherty, Lauren M. Brinkac, Ramana Madupu, Robert J. Dodson, Hoda M. Khouri, Kathy H. Lee, Heather A. Carty, David Scanlan, Robert A. Heinzen, Herbert A. Thompson, James E. Samuel, Claire M. Fraser, John F. Heidelberg, (2003), "Complete genome sequence of the Q-fever pathogen Coxiella burnetii", Proceedings of National Academy of Sciences, 100(9):5455-5460.
G Ch Sirakoulis, I Karafyllidis, Ch Mizas, V Mardiris, A Thanailakis, Ph Tsalides (2003), "A cellular automaton model for the study of DNA sequence evolution", Computers in Biology and Medicine, 33(5):439-453.
[ abstract]
sequence

H Skaletsky, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC. (2003), "The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes", Nature, 423(6942):825-837.
[abstract] [PDF]
A Som, S Sahoo, J Chakrabarti (2003), "Coding DNA sequences: statistical distributions", Mathematical Biosciences, 183:49-61.
[abstract]
A Som, S Sahoo, I Mukhopadhyay, J Chakrabarti, R Chaudhury (2003), "Scaling violations in coding DNA", Europhysics Letters, 62(2):271-277.
JZ Song, A Ware, SL Liu (2003), "Wavelet to predict bacterial ori and ter: a tendency towards a physical balance", BMC Genomics, 4:17.
Gino Spinelli (2003), "Heterochromatin and complexity: a theoretical appraoch", Nonlinear Dynamics, Psychology and Life Science, 7:?-?.
sequence

Lincoln D Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris Clee, Avril Coghlan, Alan Coulson, Peter D'Eustachio, David H A Fitch, Lucinda A Fulton, Robert E Fulton, Sam Griffiths-Jones, Todd W Harris, LaDeana W Hillier, Ravi Kamath, Patricia E Kuwabara, Elaine R Mardis, Marco A Marra, Tracie L Miner, Patrick Minx, James C Mullikin, Robert W Plumb, Jane Rogers, Jacqueline E Schein, Marc Sohrmann, John Spieth, Jason E Stajich, Chaochun Wei, David Willey, Richard K Wilson, Richard Durbin, Robert H Waterston (2003), "The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics", PLoS Biology, 1(2):166-192.
Willen P Stemmer (2003), "DNA shuffling", Annual Review of Genetics,?:?-?
Eors Szathmary (2003), "Why are there four letters in the genetic alphabet?", Nature Reviews Genetics, 4(12):995-1001.
J Szczepanski, T Michalek (2003), "Random fields approach to the study of DNA chains", Journal of Biological Physics, 29(1):39-54.
Sankar Subramanian, Sudhir Kumar (2003), "Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes", Genome Research, 13(5):838-844.
[ abstract]
repeats

Subbaya Subramanian, Vamsi M Madgula, Ranjan George, Rakesh K Mishra, Madhusudhan W Pandit, Chanderashekar S Kumar, Lalji Singh (2003), "Triplet repeats in human genome: distribution and their association with genes and other genomic regions", Bioinformatics, 19:549-552.
[ abstract]
repeats

Xiaoping Sun, Hiep D. Le, Janice M. Wahlstrom, Gary H. Karpen (2003), "Sequence analysis of a functional Drosophila centromere", Genome Research, 13(2):182-194.
[ abstract]
D Takai, PA Jones (2003), "The CpG island searcher: a new WWW resource", In Silico Biology, 3(3):0021.
[webpage from the authors: http://www.cpgislands.com , or http://www.uscnorris.com/cpgislands/cpg.cgi ]
F Takeuchi, Y Futamura, H Yoshikura, K Yamamoto (2003), "Statistics of trinucleotides in coding sequences and evolution", Journal of Theoretical Biology, 222(2):139-149.
Tatiana Tatarinova, Vyacheslav Brover, Maxim Troukhan, Nickolai Alexandrov (2003), "Skew in CG content near the transcription start site in Arabidopsis thaliana", Bioinformatics, 19 (suppl 1):i313-i314.
[ abstract]
a/symmetry

M Touchon, S Nicolay, A Arneodo, Y d'Aubenton-Carafa, C Thermes (2003), "Transcription-coupled TA and GC strand asymmetries in the human genome", FEBS Letters, 555(3):579-582.
[abstract]
OV Usatenko, VA Yampol'skii (2003), "Binary N-step Markov chain and long-range correlated systems", Physical Review Letters, 90(11):110601.
[PDF]
arXiv preprint, physics/0211053.
[abstract]
OV Usatenko, VA Yampol'skii, SS Mel'nyk, KE Kechedzhy (2003), "Symbolic stochastic dynamical systems viewed as binary N-step Markov chains", Physical Review E, 68:061107.
[ abstract]
C Vaillant, B Audit, C Thermes, A Arneodo (2003), "Influence of the sequence on the elastic properties of long DNA chains", Physical Review E, 67:032901.
[ abstract]
sequence

M A van Sluys, M C de Oliveira, C B Monteiro-Vitorello, C Y Miyaki, L R Furlan, L E A Camargo, A C R da Silva, D H Moon, M A Takita, E G M Lemos, M A Machado, M I T Ferro, F R da Silva, M H S Goldman, G H Goldman, M V F Lemos, H El-Dorry, S M Tsai, H Carrer, D M Carraro, R C de Oliveira, L R Nunes, W J Siqueira, L L Coutinho, E T Kimura, E S Ferro, R Harakava, E E Kuramae, C L Marino, E Giglioti, I L Abreu, L M C Alves, A M do Amaral, G S Baia, S R Blanco, M S Brito, F S Cannavan, A V Celestino, A F da Cunha, R C Fenille, J A Ferro, E F Formighieri, L T Kishi, S G Leoni, A R Oliveira, V E Rosa, Jr, F T Sassaki, J A D Sena, A A de Souza, D Truffi, F Tsukumo, G M Yanai, L G Zaros, E L Civerolo, A J G Simpson, N F Almeida, Jr, J C Setubal, J P Kitajima (2003), "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa", Journal of Bacteriology, 185(3):1018-1026.
[ abstract]
sequence

JC Venter, S Levy, T Stockwell, K Remington, A Halpern (2003), "Massive parallelism, randomness and genomic advances", Nature Genetics, 33(suppl):219-227.
Susana Vinga, Jonas Almeida (2003), "Alignment-free sequence comparison-a review", Bioinformatics, 19:513-523.
[ abstract]
isochore

binding-energy

bending

AE Vinogradov (2003), "DNA helix: the importance of being GC-rich", Nucleic Acids Research, 31:1838-1844. [PDF]
isochore

AE Vinogradov (2003), "Isochores and tissue-specificity", Nucleic Acids Research, 31:5212-5220.
[abstract] [PDF]
bending

database

Kristian Vlahovicek, László Kaján, and Sándor Pongor (2003), "DNA analysis servers: plot.it, bend.it, model.it and IS", Nucleic Acids Research, 31:3686-3687.
[PDF] [webpage from the authors: DNA tools]
MT Webster, NGC Smith, H Ellegren (2003), "Compositional evolution of noncoding DNA in the human and chimpanzee genomes", Molecular Biology and Evolution, 20(2):278-286.
[abstract]
sequence

J Wei, M B Goldberg, V Burland, M M Venkatesan, W Deng, G Fournier, G F Mayhew, G Plunkett III, D J Rose, A Darling, B Mau, N T Perna, S M Payne, L J Runyen-Janecky, S Zhou, D C Schwartz, and F R Blattner (2003), "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T", Infection and Immunity, 71(5):2775-2786.
[abstract]
isochore

SY Wen, CT Zhang (2003), "Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis", Biochemical and Biophysical Research Communications, 311(1):215-222.
KH Wolfe, WH Li (2003), "Molecular evolution meets the genomics revolution", Nature Genetics, 33(suppl):255-265.
[PDF]
Yonghui Wu, Alan Wee-Chung Liew, Hong Yan, and Mengsu Yang (2003), "Classification of short human exons and introns based on statistical features", Physical Review E, 67(6): 061915.
[abstract]
Zuo-Bing Wu (2003), "Self-similarity limits of genomic signatures", Fractals, 11(1):19-25.
[abstract]
Xuhua Xia, Zheng Xie, Wen-Hsiung Li (2003), "Effects of GC content and mutational pressure on the lengths of exons and coding sequences", Journal of Molecular Evolution, 56(3):362-370.
[abstract]
repeats

Y Xiao, YZ Huang, MF Li, RZ Xu, SF Xiao (2003), "Nonlinear analysis of correlations in Alu repeat sequences in DNA", Physical Review E, 68(6):061913.
repeats

J Xing, AH Salem, DJ Hedges, GE Kilroy, WS Watkins, JE Schienman, CB Stewart, J Jurka, LB Jorde, MA Batzer (2003), "Comprehensive analysis of two Alu Yd subfamilies", Journal of Molecular Evolution, 57(Suppl 1):S76-S89.
sequence

Zhenyu Xuan, Jinhua Wang, Michael Q Zhang (2003), "Computational comparison of two mouse draft genomes and the human golden path", Genome Biology, 4(1):R1.
Edourard Yeramian, Louis Jones (2003), "GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives", Nucleic Acids Research, 31(13):3843-3849.
ZG Yu, V Anh, KS Lau (2003), "Multifractal and correlation analyses of protein sequences from complete genomes", Physical Review E, 68(2):021913.
[ abstract]
ZG Yu, V Anh, KS Lau (2003), "Iterated function system and multifractal analysis of biological sequences", International Journal of Modern Physics B, 17(22-24):4367-4375.
CT Zhang, R Zhang (2003), "An isochore map of the human genome based on the Z curve method", Gene, 317(1-2):127-135.
[abstract]
database

CT Zhang, R Zhang, HY Ou (2003), "The Z curve database: a graphic representation of genome sequences", Bioinformatics, 19:593-599.
[webpage from the authors: Zcurve_B]
Louxin Zhang, Bin Ma, Lusheng Wang, Ying Xu (2003), "Greedy method for inferring tandem duplication history", Bioinformatics, 19:1497-1504.
[ abstract]
R Zhang, CT Zhang (2003), "Multiple replication origins of the archaeon Halobacterium species NRC-1", Biochemical and Biophysical Research Communications, 302:728-734.