corr in DNA (2004)

front page | preprints | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |
1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | 80s | 70s | 60s | 50s
[about] [links] [complete genomes] [gene duplication] [dna/protein music] [gene recognition] [mirror]

2004

sequence

Mitchell S Abrahamsen, Thomas J Templeton, Shinichiro Enomoto, Juan E Abrahante, Guan Zhu, Cheryl A Lancto, Mingqi Deng, Chang Liu, Giovanni Widmer, Saul Tzipori, Gregory A Buck, Ping Xu, Alan T Bankier, Paul H Dear, Bernard A Konfortov, Helen F Spriggs, Lakshminarayan Iyer, Vivek Anantharaman, L Aravind, Vivek Kapur (2004), "Complete genome sequence of the Apicomplexan, Cryptosporidium parvum", Science, 304(5669):441-445.
[ abstract]
C Acquisti, P Allegrini, P Bogani, M Buiatti, E Catanese, L Fronzoni, P Grigolini, G Mersi, L Palatella (2004), "In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures", Chaos, Solitons & Fractals, 20(1):127-137.
[abstract]
Vera Afreixo, Paulo JSG Ferreira, Dorabella Santos (2004), "Spectrum and symbol distribution of nucleotide sequences", Physical Review E, 70,031910.
[abstract]
protein

repeats

M Mar Alba, Roderic Guigo (2004), "Comparative analysis of amino acid repeats in rodents and humans", Genome Research, 14:549-554.
[abstract]
AE Allahverdyan, ZS Gevorkian, CK Hu, MC Wu (2004), "Unzipping of DNA with correlated base sequence", Physical Review E, 69(6):061908.
isochore

F Alvarez-Valin, O Clay, S Cruveiller, G Bernardi (2004), "Inaccurate reconstruction of ancestral GC levels creates a 'vanishing isochores' effect", Molecular Phylogenetics and Evolution, 31(2):788-793.
[abstract]
isochore

Stilianos Arhondakis, Fabio Auletta, Giuseppe Torelli and Giuseppe D'Onofrio (2004), "Base composition and expression level of human genes", Gene, 325:165-169.
[abstract]
Peter F Arndt (2004), "Identification and measurement of neighbor dependent nucleotide substitution processes", Lecture Notes in Informatics P-53, pp. 227-234.
Peter F Arndt, Terence Hwa (2004), "Regional and time-resolved mutation patterns of the human genome", Bioinformatics, 20:1482-1485.
B Audit, C Vaillant, A Arneodo, Y D'Aubenton-Carafa, C Thermes (2004), "Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences", Journal of Biological Physics, 30(1):33-81.
sequence

Nitin S Baliga, Richard Bonneau, Marc T Facciotti, Min Pan, Gustavo Glusman, Eric W Deutsch, Paul Shannon, Yulun Chiu, Rueyhung Sting Weng, Rueichi Richie Gan, Pingliang Hung, Shailesh V Date, Edward Marcotte, Leroy Hood, Wailap Victor Ng (2004), "Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea", Genome Research, 14:2221-2234.
G Battail (2004), "An engineer's view on genetic information and biological evolution", Biosystems, 76(1-3):279-290.
Gill Bejerano (2004), "Algorithms for variable length Markov chain modeling", Bioinformatics, 20(5):788-789.
[abstract]
Gill Bejerano, David Haussler, and Mathieu Blanchette (2004), "Into the heart of darkness: large-scale clustering of human non-coding DNA", Bioinformatics, 20:i40-i48.
isochore

EM Belle, L Duret, N Galtier, A Eyre-Walker (2004), "The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny", Journal of Molecular Evolution, 58(6):653-660.
SD Bentley, J Parkhill (2004), "Comparative genomic structure of prokaryotes", Annual Review of Genetics, 38:771-792.
John A Berger , Sanjit K Mitra , Marco Carli, Alessandro Neri (2004), "Visualization and analysis of DNA sequences using DNA walks", Journal of the Franklin Institute, 341(1-2):37-55.
[abstract]
isochore

P Bernaola-Galvan, JL Oliver, P Carpena, O Clay, G Bernardi (2004), "Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes", Gene, 333:121-133.
[abstract] [PDF]
MJ Berryman, A Allison, D Abbott (2004), "Mutual information for examinig correlations in DNA", Fluctuation and Noise Letters, 4(2):L237-L246.
arXiv preprint, q-bio.PE/0404010.
abstract
Mehmet Bilgen, Mehmet Karaca, A. Naci Onus, and Ayse Gül Ince (2004), "A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences", Bioinformatics, 20:3379-3386.
Mathieu Blanchette, Eric D. Green, Webb Miller, David Haussler (2004), "Reconstructing large regions of an ancestral mammalian genome in silico", Genome Research, 14:2412-2423.
repeats

B Borstnik, D Pumpernik (2004), "Mutational dynamics of short tandem repeats in human genome", Europhysics Letters, 65(2):290-296.
G Bourque, P Pevzner, G Tesler (2004), "Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes", Genome Research, 14(4):507-516.
RJ Boys, DA Henderson (2004), "A Bayesian approach to DNA sequence segmentation" (with discussion), Biometrics, 60(3):573-581.
[abstract]
Charles Lawrence, Ivan Auger (2004), "Discussions on 'A Bayesian Approach to DNA Sequence Segmentation'" Biometrics, 60(3):581-582.
Mayetri Gupta, Jun S. Liu (2004), "Discussions on 'A Bayesian Approach to DNA Sequence Segmentation'" Biometrics, 60(3):582-583.
Terey Speed (2004), "Discussions on 'A Bayesian Approach to DNA Sequence Segmentation'" Biometrics, 60(3):583-584.
Jeffrey L. Thorne (2004), "Discussions on 'A Bayesian Approach to DNA Sequence Segmentation'" Biometrics, 60(3):584-585.
RJ Boys, DA Henderson (2004), "Rejoinder to 'A Bayesian Approach to DNA Sequence Segmentation'", Biometrics, 60(3):585-588.
[PDF]
Adam M Breier, Sourav Chatterji, Nicholas R Cozzarelli (2004), "Prediction of Saccharomyces cerevisiae replication origins", Genome Biology, 5:R22.
[html]
RJ Britten (2004), "Coding sequences of functioning human genes derived entirely from mobile element sequences", Proceedings of National Academy of Sciences, 101(48):16825-16830.
[abstract]
M Buiatti, M Buiatti (2004), "Towards a statistical characterisation of the living state of matter", Chaos, Solitons & Fractals, 20(1):55-61.
[abstract]
J Castresana, R Guigo, MM Alba (2004), "Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome ", Journal of Molecular Evolution, 59(1):72-79.
Niranjan Chakravarthy, A Spanias, LD Iasemidis, K Tsakalis (2004), "Autoregressive modeling and feature analysis of DNA sequences", EURASIP Journal on Applied Signal Processing, 2004(1):13-28.
[abstract]
D Charif, J Thioulouse, JR Lobry, G Perriere (2004), "Online synonymous codon usage analyses with the ade4 and seqinR package", Bioinformatics, 20:?-?.
VR Chechetkin, VV Lobzin "Spectral entropy criteria for structural segmentation in genomic DNA sequences", Physics Letters A, 328(1):79-86.
Swaine L Chen (2004), "Codon usage between genomes is constrained by genome-wide mutational processes", Proceedings of National Academy of Sciences, 101(10):3480-3485.
[abstract]
TY Chen, LC Hsieh, CH Chang, LF Luo, FM Jia, HC Lee (2004), "Universal lengths in complete microbial genomes", International Journal of Modern Physics B, 18:2448-2454.
DSH Chew, KP Choi, H Heidner, MY Cheung (2004), "Palindromes in SARS and coronaviruses", INFORMS Journal on Computing, 16(4):331-340.
sequence

Minchen Chien, Irina Morozova, Shundi Shi, Huitao Sheng, Jing Chen, Shawn M. Gomez, Gifty Asamani, Kendra Hill, John Nuara, Marc Feder, Justin Rineer, Joseph J. Greenberg, Valeria Steshenko, Samantha H. Park, Baohui Zhao, Elita Teplitskaya, John R. Edwards, Sergey Pampou, Anthi Georghiou, I.-Chun Chou, William Iannuccilli, Michael E. Ulz, Dae H. Kim, Alex Geringer-Sameth, Curtis Goldsberry, Pavel Morozov, Stuart G. Fischer, Gil Segal, Xiaoyan Qu, Andrey Rzhetsky, Peisen Zhang, Eftihia Cayanis, Pieter J. De Jong, Jingyue Ju, Sergey Kalachikov, Howard A. Shuman, James J. Russo (2004), "The genomic sequence of the accidental pathogen Legionella pneumophila", Science, 305(5692):1966-1968.
Paul Dan Cristea (2004), "Genomic signals of reoriented ORFs", EURASIP Journal on Applied Signal Processing, 2004(1):132-137.
[abstract]
protein

Gavin E. Crooks, Steven E. Brenner (2004), "Protein secondary structure: entropy, correlations and prediction", Bioinformatics, 20:1603-1611.
[abstract]
Stéphane Cruveiller, Kamel Jabbari, Oliver Clay, Giorgio Bernardi (2004), "Compositional gene landscapes in vertebrates", Genome Research, 14:886-892.
[abstract]
repeats

Olivier Delgrange, Eric Rivals (2004), "STAR: an algorithm to Search for Tandem Approximate Repeats", Bioinformatics, 20(16):2812-2820.
[abstract]
sequence

P Deloukas, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C, Howe K, Hunt SE, Andrews TD, Gilbert JG, Swarbreck D, Ashurst JL, Taylor A, Battles J, Bird CP, Ainscough R, Almeida JP, Ashwell RI, Ambrose KD, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Bates K, Beasley H, Bray-Allen S, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Cahill P, Camire D, Carter NP, Chapman JC, Clark SY, Clarke G, Clee CM, Clegg S, Corby N, Coulson A, Dhami P, Dutta I, Dunn M, Faulkner L, Frankish A, Frankland JA, Garner P, Garnett J, Gribble S, Griffiths C, Grocock R, Gustafson E, Hammond S, Harley JL, Hart E, Heath PD, Ho TP, Hopkins B, Horne J, Howden PJ, Huckle E, Hynds C, Johnson C, Johnson D, Kana A, Kay M, Kimberley AM, Kershaw JK, Kokkinaki M, Laird GK, Lawlor S, Lee HM, Leongamornlert DA, Laird G, Lloyd C, Lloyd DM, Loveland J, Lovell J, McLaren S, McLay KE, McMurray A, Mashreghi-Mohammadi M, Matthews L, Milne S, Nickerson T, Nguyen M, Overton-Larty E, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter K, Rice CM, Rogosin A, Ross MT, Sarafidou T, Sehra HK, Shownkeen R, Skuce CD, Smith M, Standring L, Sycamore N, Tester J, Thorpe A, Torcasso W, Tracey A, Tromans A, Tsolas J, Wall M, Walsh J, Wang H, Weinstock K, West AP, Willey DL, Whitehead SL, Wilming L, Wray PW, Young L, Chen Y, Lovering RC, Moschonas NK, Siebert R, Fechtel K, Bentley D, Durbin R, Hubbard T, Doucette-Stamm L, Beck S, Smith DR, Rogers J. (2004), "The DNA sequence and comparative analysis of human chromosome 10", Nature, 429(6990):375-381.
ET Dermitzakis, E Kirkness, S Schwarz, E Birney, A Reymond, SE Antonarakis (2004), "Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment", Genome Research, 14(5):852-859.
sequence

Bernard Dujon, David Sherman, Gilles Fischer, Pascal Durrens, Serge Casaregola, Ingrid Lafontaine, Jacky de Montigny, Christian Marck, Cécile Neuvéglise, Emmanuel Talla, Nicolas Goffard, Lionel Frangeul, Michel Aigle, Véronique Anthouard, Anna Babour, Valérie Barbe, Stéphanie Barnay, Sylvie Blanchin, Jean-Marie Beckerich, Emmanuelle Beyne, Claudine Bleykasten, Anita Boisramé, Jeanne Boyer, Laurence Cattolico, Fabrice Confanioleri, Antoine de Daruvar, Laurence Despons, Emmanuelle Fabre, Cécile Fairhead, Hélène Ferry-Dumazet, Alexis Groppi, Florence Hantraye, Christophe Hennequin, Nicolas Jauniaux, Philippe Joyet, Rym Kachouri, Alix Kerrest, Romain Koszul, Marc Lemaire, Isabelle Lesur, Laurence Ma, Héloïse Muller, Jean-Marc Nicaud, Macha Nikolski, Sophie Oztas, Odile Ozier-Kalogeropoulos, Stefan Pellenz, Serge Potier, Guy-Franck Richard, Marie-Laure Straub, Audrey Suleau, Dominique Swennen, Fredj Tekaia, Micheline Wésolowski-Louvel, Eric Westhof, Bénédicte Wirth, Maria Zeniou-Meyer, Ivan Zivanovic, Monique Bolotin-Fukuhara, Agnès Thierry, Christiane Bouchier, Bernard Caudron, Claude Scarpelli, Claude Gaillardin, Jean Weissenbach, Patrick Wincker, Jean-Luc Souciet (2004), "Genome evolution in yeasts", Nature, 430:35-44.
[abstract]
sequence

A Dunham, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SC, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JG, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJ, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, Ross MT (2004), "The DNA sequence and analysis of human chromosome 13", Nature, 428(6982):522-528.
[abstract] [PDF]
Stephen T Eskesen, Frank N Eskesen, Brian Kinghorn, Anatoly Ruvinsky (2004), "Periodicity of DNA in exons", BMC Molecular Biology, 5:12.
MJ Fazzari, JM Greally (2004), "Epigenomics: beyond CpG islands", Nature Reviews Genetics, 5(6):467-474.
C Federico, S Saccone, L Andreozzi, S Motta, V Russo, N Carels, G Bernardi (2004), "The pig genome: compositional analysis and identification of the gene-richest regions in chromosomes and nuclei", Gene, 343(2):245-251.
Yuriy Fofanov, Yi Luo, Charles Katili, Jim Wang, Yuri Belosludtsev, Thomas Powdrill, Chetan Belapurkar, Viacheslav Fofanov, Tong-Bin Li, Sergey Chumakov, and B. Montgomery Pettitt (2004), "How independent are the appearances of n-mers in different genomes? ", Bioinformatics, 20(15):2421-2428.
isochore

DR Forsdyke (2004), "Regions of relative GC% uniformity are recombinational isolators", Journal of Biological Systems, 12(3):261-271.
DR Forsdyke (2004), "Purine-loading, stem-loops, and Chargaff's second parity rule: a discussion of the application of elementary principles to early chemical observations", Applied Bioinformatics, 3(1):3-8.
[abstract]
Anders Fuglsang (2004), "Compositional nonrandomness upstream of start codons in archaebacteria", Gene, 332:89-95.
[abstract]
Madhavi Ganapathiraju, Vijayalaxmi Manoharan, Judith Klein-Seetharaman, (2004), "BLMT: Statistical sequence analysis using n-grams", Journal of Applied Bioinformatics, 3(2):?-?.
José A García, Samantha Alvarez, Alejandro Flores, Tzipe Govezensky, Juan R Bobadillaa, Marco V José (2004), "Statistical analysis of the distribution of amino acids in Borrelia burgdorferi genome under different genetic codes", Physica A, 342:288-293.
Seymour Garte (2004), "Fractal properties of the human genome", Journal of Theoretical Biology, 230(2):251-260.
[ abstract]
N. Gheldof and J. Dekker (2004), "Spatial organization of genomes", Current Genomics, 5(2):?-?.
sequence

RA Gibbs, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Alba M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hubner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, Lopez-Otin C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium (2004), "Genome sequence of the Brown Norway rat yields insights into mammalian evolution", Nature, 428(6982):493-521.
[abstract] [PDF]
T Ryan Gregory (2004), "Insertion–deletion biases and the evolution of genome size", Gene, 324:15-34.
[abstract]
sequence

J Grimwood, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM (2004), "The DNA sequence and biology of human chromosome 19", Nature, 428(6982):529-535.
[abstract] [PDF]
repeats

Deepak Grover, Mitali Mukerji, Pankaj Bhatnagar, K. Kannan, Samir K Brahmachari (2004), "Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition", Bioinformatics, 20:813-817.
[abstract]
R. Hall, L. Stern (2004), "A rapid method for illustrating features in both coding and non-coding regions of a genome", Bioinformatics, 20:982-983.
[abstract]
Daniel L Halligan, Adam Eyre-Walker, Peter Andolfatto, and Peter D. Keightley (2004), "Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila", Genome Research, 14(2):273-279.
[ abstract]
Bailin Hao, Ji Qi (2004), "Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance", Journal of Bioinformatics and Computational Biology, 2(1):1-19.
JH He (2004), "Mysterious Pi and a possible link to DNA sequencing", International Journal of Nonlinear Sciences and Numerical Simulation, 5(3):263-274.
sequence

JF Heidelberg, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM. (2004), "The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough", Nature Biotechnology, 22(5):554-559.
sequence

LW Hillier, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SM, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betran E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK; International Chicken Genome Sequencing Consortium (2004), "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution", Nature, 432:695-716.
[PDF]
period:10-11

S Hosid, EN Trifonov, A Bolshoy (2004), "Sequence periodicity of Escherichia coli is concentrated in intergenic regions", BMC Molecular Biology, 5(1):14.
LS Hsieh, Ta-Yuan Chen, Chang-Heng Chang, Wen-Lan Fan, HC Lee (2004), "Universality in large-scale structure of complete genomes", Genome Biology, 5:P7.
sequence

SJ Humphray, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blocker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I (2004), "DNA sequence and analysis of human chromosome 9", Nature, 429(6990):369-374.
Laurence D Hurst, Csaba Pál, Martin J Lercher (2004), "The evolutionary dynamics of eukaryotic gene order", Nature Reviews Genetics, 5:299-310.
[abstract]
sequence

International Human Genome Sequencing Consortium (2004), "Finishing the euchromatic sequence of the human genome", Nature, 431:931-945.
[abstract]
K Jabbari, G Bernardi (2004), "Cytosine methylation and CpG, TpG (CpA) and TpA frequencies", Gene, 333:143-149.
Michael I Jensen-Seaman, Terrence S Furey, Bret A Payseur, Yontao Lu, Krishna M Roskin, Chin-Fu Chen, Michael A Thomas, David Haussler, Howard J Jacob (2004), "Comparative recombination rates in the rat, mouse, and human genomes", Genome Research, 14(4):528-538.
[abstract]
Jerzy Jurka (2004), "Evolutionary impact of human Alu repetitive elements", Current Opinion in Genetics & Development, 14(6):603-608.
repeats

J Jurka, O Kohany, A Pavlicek, VV Kapitonov, MV Jurka (2004), "Duplication, coclustering, and selection of human Alu retrotransposons", Proceedings of National Academy of Sciences, 101(5):1268-1272.
[abstract]
WS Kendal (2004), "A scale invariant clustering of genes on human chromosome 7", BMC Evolutionary Biology, 4:3.
[abstract] [PDF]
repeats

Dennis DY Kim, Thomas TY Kim, Thomas Walsh, Yoshifumi Kobayashi, Tara C Matise, Steven Buyske, Abram Gabrie (2004), "Widespread RNA editing of embedded Alu elements in the human transcriptome", Genome Research, 14:1719-1725.
K Krishnamachari, A Krishnamachari (2004), "Sequence variability and long-range dependence in DNA: An information theoretic perspective", Lecture Notes in Computer Science Vol 3316, pp. 1354-1361.
repeats

Arun Krishnan, Francis Tang (2004), "Exhaustive whole-genome tandem repeats search", Bioinformatics, 20(16):2702-2710.
[abstract]
isochore

G Kudla, A Helwak, L Lipinski (2004), "Gene conversion and GC-content evolution in mammalian Hsp70", Molecular Biology and Evolution, 21(7):1438-1444.
D Kugiumtzisa, A Provata (2004), "Statistical analysis of gene and intergenic DNA sequences", Physica A, 342(3-4):623-638.
sequence

Frank W Larimer, Patrick Chain, Loren Hauser, Jane Lamerdin, Stephanie Malfatti, Long Do, Miriam L Land, Dale A Pelletier, J Thomas Beatty, Andrew S Lang, F Robert Tabita, Janet L Gibson, Thomas E Hanson, Cedric Bobst, Janelle L Torres y Torres, Caroline Peres, Faith H Harrison, Jane Gibson, Caroline S Harwood (2004), "Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris", Nature Biotechnology, 22:55-61.
F. Lazzarato, G. Franceschinis, M. Botta, F. Cordero, and R. A. Calogero (2004), "RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets", Bioinformatics, 20(16):2848-2850.
[abstract]
isochore

SJ Lee, JR Mortimer, DR Forsdyke (2004), "Genomic conflict settled in favour of the species rather than of the gene at extreme GC% values", Applied Bioinformatics, 3(4):219-228.
repeats

Sun-Hee Leem, Natalay Kouprina, Jane Grimwood, Jung-Hyun Kim, Michael Mullokandov, Young-Ho Yoon, Ji-Youn Chae, Jenna Morgan, Susan Lucas, Paul Richardson, Chris Detter, Tijana Glavina, Eddy Rubin, J. Carl Barrett, Vladimir Larionov (2004), "Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements ", Genome Research, 14(2):239-246.
[ abstract]
repeats

Lugang Li, Renchao Jin, Poh-Lin Kok, and Honghui Wan (2004), "Pseudo-periodic partitions of biological sequences", Bioinformatics, 20(3):295-306.
[ abstract]
W Li, D Holste (2004), "An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21", Computational Biology and Chemistry, 28(5-6):393-399.
[PDF]
W Li, D Holste (2004), "Spectral analysis of guanine and cytosine fluctuation of mouse genomic DNA", Fluctuation and Noise Letters, 4(3):L453-L464.
[ abstract] [PDF]
Bo Liao, Tian-Ming Wang (2004), "New 2D graphical representation of DNA sequences", Journal of Computational Chemistry, 25(11):1364-1368.
[ abstract]
Bo Liao, Tian-Ming Wang (2004), "3-D graphical representation of DNA sequences and their numerical characterization", Journal of Molecular Structure: THEOCHEM, 681(1-3):209-212.
[ abstract]
P Licinio, RB Caligiome (2004), "Inference of phylogenetic distances from DNA-walk divergences", Physica A, 341:471-481.
JR Lobry (2004), "Life history traits and genome structure: aerobiosis and G+C content in bacteria", Lecture Notes in Computer Sciences, Vol.3039, pp.679-?.
[abstract]
period:3

Imelda Lopez-Villasenor, Marco V Jose, Joaquin Sanchez (2004), "Three-base periodicity patterns and self-similarity in whole bacterial chromosomes", Biochemical and Biophysical Research Communications, 325(2):467-478.
Gerton Lunter and Jotun Hein (2004), "A nucleotide substitution model with nearest-neighbour interactions", Bioinformatics, 20:i216-i223.
P Mackiewicz, J Zakrzewska-Czerwinska, A Zawilak, MR Dudek, S Cebrat (2004), "Where does bacterial replication start? Rules for predicting the oriC region", Nucleic Acids Research, 32(13):3781-3791.
A Marin, MN Wang, G Gutierrez (2004), "Short-range compositional correlation in the yeast genome depends on transcriptional orientation", Gene, 333:151-155.
sequence

Joel Martin, Cliff Han, Laurie A. Gordon, Astrid Terry, Shyam Prabhakar, Xinwei She, Gary Xie,, Uffe Hellsten, Yee Man Chan, Michael Altherr,, Olivier Couronne, Andrea Aerts, Eva Bajorek, Stacey Black, Heather Blumer, Elbert Branscomb,, Nancy C. Brown, William J. Bruno, Judith M. Buckingham, David F. Callen, Connie S. Campbell, Mary L. Campbell, Evelyn W. Campbell, Chenier Caoile, Jean F. Challacombe, Leslie A. Chasteen, Olga Chertkov, Han C. Chi, Mari Christensen, Lynn M. Clark, Judith D. Cohn, Mirian Denys, John C. Detter, Mark Dickson, Mira Dimitrijevic-Bussod, Julio Escobar, Joseph J. Fawcett, Dave Flowers, Dea Fotopulos, Tijana Glavina, Maria Gomez, Eidelyn Gonzales, David Goodstein, Lynne A. Goodwin, Deborah L. Grady, Igor Grigoriev, Matthew Groza, Nancy Hammon, Trevor Hawkins, Lauren Haydu, Carl E. Hildebrand, Wayne Huang, Sanjay Israni, Jamie Jett, Phillip B. Jewett, Kristen Kadner, Heather Kimball, Arthur Kobayashi,, Marie-Claude Krawczyk, Tina Leyba, Jonathan L. Longmire, Frederick Lopez, Yunian Lou, Steve Lowry, Thom Ludeman, Chitra F. Manohar, Graham A. Mark, Kimberly L. McMurray, Linda J. Meincke, Jenna Morgan, Robert K. Moyzis, Mark O. Mundt, A. Christine Munk, Richard D. Nandkeshwar, Sam Pitluck, Martin Pollard, Paul Predki, Beverly Parson-Quintana, Lucia Ramirez, Sam Rash, James Retterer, Darryl O. Ricke, Donna L. Robinson, Alex Rodriguez, Asaf Salamov, Elizabeth H. Saunders, Duncan Scott, Timothy Shough, Raymond L. Stallings, Malinda Stalvey, Robert D. Sutherland, Roxanne Tapia, Judith G. Tesmer, Nina Thayer,, Linda S. Thompson, Hope Tice, David C. Torney, Mary Tran-Gyamfi, Ming Tsai, Levy E. Ulanovsky, Anna Ustaszewska, Nu Vo, P. Scott White, Albert L. Williams, Patricia L. Wills, Jung-Rung Wu, Kevin Wu, Joan Yang, Pieter DeJong, David Bruce, Norman A. Doggett, Larry Deaven, Jeremy Schmutz, Jane Grimwood, Paul Richardson, Daniel S. Rokhsar, Evan E. Eichler, Paul Gilna, Susan M. Lucas, Richard M. Myers, Edward M. Rubin, and Len A. Pennacchio, (2004), "The sequence and analysis of duplication-rich human chromosome 16", Nature, 432:988-994.
[PDF]
sequence

MP McLeod, Qin X, Karpathy SE, Gioia J, Highlander SK, Fox GE, McNeill TZ, Jiang H, Muzny D, Jacob LS, Hawes AC, Sodergren E, Gill R, Hume J, Morgan M, Fan G, Amin AG, Gibbs RA, Hong C, Yu XJ, Walker DH, Weinstock GM. (2004), "Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae", Journal of Bacteriology, 186(17):5842-5855.
Giulia Menconi (2004), "Sublinear Growth of Information in DNA Sequences", Bulletin of Mathematical Biology, 67(4):737-759.
[abstract]
isochore

J Meunier, L Duret (2004), "Recombination drives the evolution of GC-content in the human genome", Molecular Biology and Evolution, 21(6):984-990.
sequence

Kazuei Mita, Masahiro Kasahara, Shin Sasaki, Yukinobu Nagayasu, Tomoyuki Yamada, Hiroyuki Kanamori, Nobukazu Namiki, Masanari Kitagawa, Hidetoshi Yamashita, Yuji Yasukochi, Keiko Kadono-Okuda, Kimiko Yamamoto, Masahiro Ajimura, Gopalapillai Ravikumar, Michihiko Shimomura, Yoshiaki Nagamura, Tadasu Shin-i, Hiroaki Abe, Toru Shimada, Shinichi Morishita and Takuji Sasaki (2004), "The genome sequence of silkworm, Bombyx mori", DNA Research, 11(1):27-35.
[abstract]
sequence

MA Moran, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C, Brinkac L, Lewis M, Johri S, Weaver B, Pai G, Eisen JA, Rahe E, Sheldon WM, Ye W, Miller TR, Carlton J, Rasko DA, Paulsen IT, Ren Q, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Rosovitz MJ, Haft DH, Selengut J, Ward N. (2004), "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment", Nature, 432(7019):910-913.
repeats

Hiroo Murakami, Nobuyoshi Sugaya, Makihiko Sato, Akira Imaizumi, Sachiyo Aburatani, Katsuhisa Horimoto (2004), "Detection of inter-spread repeat sequence in genomic DNA sequence", Genome Informatics, 15(1):170-179.
binding-energy

H Musto, H Naya, A Zavala, H Romero, F Alvarez-Valin, G Bernardi (2004), "Correlations between genomic GC levels and optimal growth temperatures in prokaryotes", FEBS Letters, 573(1-3):73-77.
sequence

KE Nelson, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM. (2004), "Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species", Nucleic Acids Research, 32(8):2386-2395.
sequence

WC Nierman, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM. (2004), "Structural flexibility in the Burkholderia mallei genome", Proceedings of National Academy of Sciences, 101(39):14246-14251.
[abstract]
S Nicolay, F Argoul, M Touchon, Y d'Aubenton-Carafa, C Thermes, A Arneodo (2004), "Low frequency rhythms in human DNA sequences: A key to the organization of gene location and orientation? " Physical Review Letters, 93:108101.
[abstract] [PDF]
S Nicolay, EB Brodie, M Touchon, Y d'Aubenton-Carafa, C Thermes, A Arneodo (2004), "From scale invariance to deterministic chaos in DNA sequences: towards a deterministic description of gene organization in the human genome", Physica A, 342:270-280.
Daniel Nicorici and Jaakko Astola (2004), "Segmentation of DNA into coding and noncoding regions based on recursive entropic segmentation and stop-codon statistics", EURASIP Journal on Applied Signal Processing, 2004(1):81-91.
[abstract]
C Nikolaou, Y Almirantis (2004), "Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference", Journal of Molecular Evolution, 59(3):309-316.
G Nuel (2004), "LD-SPatt: large deviations statistics for patterns on Markov chains", Journal of Computational Biology, 11(6):1023-1033.
Aleksey Y Ogurtsov1, Shamil Sunyaev, Alexey S Kondrashov (2004), "Indel-based evolutionary distance and mouse-human divergence", Genome Research, 14:1610-1616.
Nestor N. Oiwa, James A. Glazier (2004), "Self-similar mitochondrial DNA", Cell Biochemistry and Biophysics, 41(1):41-62.
[ abstract]
isochore

JL Oliver, P Carpena, M Hackenberg, P Bernaola-Galvan (2004), "IsoFinder: computational prediction of isochores in genome sequences", Nucleic Acids Research, 32:W287-W292.
Nicolas Omont and François Képès "Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication", Bioinformatics, 20(16):2719-2725.
[abstract]
YL Orlov, VN Potapov (2004), "Complexity: an internet resource for analysis of DNA sequence complexity", Nucleic Acids Research, 32(web server issue):W628-W633.
[abstract]
Zhengqing Ouyang, Chao Wang, and Zhen-Su She (2004), "Scaling and hierarchical structures in DNA sequences", Physical Review Letters, 93(7):078103.
repeats

V Paar, N Pavin, I Basar, M Rosandic, I Luketin, SD Zinic (2004), "Spectral densities and frequencies in the power spectrum of higher order repeat alpha satellite in human DNA molecule", Croatica Chemica Acta, 77(1-2):73-81.
J Paces, R Zika, V Paces, A Pavlicek, O Clay, G Bernardi (2004), "Representing GC variation along eukaryotic chromosomes", Gene, 333:135-141.
[PDF]
protein

Evanthia E Pashou, Zoi I Litou, Theodore D Liakopoulos, Stavros J Hamodrakas (2004), "waveTM: wavelet-based transmembrane segment prediction", In Silico Biology, 4(2):127-131.
A Paz, D Mester, I Baca, E Nevo, A Korol (2004), "Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes", Proceedings of National Academy of Sciences, 101(9):2951-2956.
[abstract]
repeats

PA Pevzner, H Tang, G Tesler (2004), "De novo repeat classification and fragment assembly", Genome Research, 14:1786-1796.
Michel Peyrard (2004), "Nonlinear dynamics and statistical physics of DNA", Nonlinearity, 17:R1-R40.
Douglas Poland (2004), "The persistence exponent of DNA", Biophysical Chemistry, 110(1-2):59-72.
[abstract]
repeats

Alkes L Price, Eleazar Eskin, Pavel A Pevzner (2004), "Whole-genome analysis of Alu repeat elements reveals complex evolutionary history", Genome Research, 14:2245-2252.
Ji Qi, Hong Luo, Bailin Hao (2004), "CVTree: a phylogenetic tree reconstruction tool based on whole gemomes", Nucleic Acids Research, 32:W45-W47.
Ji Qi, Bin Wang, Bailin Hao (2004), "Whole genome prokaryote phylogeny without sequence alignment: a K-string composition approach", Journal of Molecular Evolution, 58(1):1-11.
sequence

DA Rasko, Ravel J, Okstad OA, Helgason E, Cer RZ, Jiang L, Shores KA, Fouts DE, Tourasse NJ, Angiuoli SV, Kolonay J, Nelson WC, Kolsto AB, Fraser CM, Read TD. (2004), "The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1", Nucleic Acids Research, 32(3):977-988.
Harold Riethman, Anthony Ambrosini, Carlos Castaneda, Jeffrey Finklestein, Xue-Lan Hu, Uma Mudunuri, Sheila Paul, Jun Wei (2004) "Mapping and initial analysis of human subtelomeric sequence assemblies", Genome Research, 14(1):18-28.
[ abstract]
Igor B Rogozin, Kira S Makarova, Yuri I Wolf, Eugene V Koonin (2004), "Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes", Briefings in Bioinformatics, 5(2):131-149.
A Sandelin, P Bailey, S Bruce, PG Engström, JM Klos, WW Wasserman, J Ericson, B Lenhard (2004), "Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes", BMC Genomics, 5(1):99.
R Seshadri, Myers GS, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, Ayodeji B, Shatsman S, McLeod MP, Smajs D, Howell JK, Pal S, Amin A, Vashisth P, McNeill TZ, Xiang Q, Sodergren E, Baca E, Weinstock GM, Norris SJ, Fraser CM, Paulsen IT. (2004), "Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes", Proceedings of National Academy of Sciences, 101(15):5646-5651.
[abstract]
period:10-11

Patrick Schieg, Hanspeter Herzel (2004), "Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA", Journal of Molecular Biology, 343(4):891-901.
[abstract]
sequence

J Schmutz, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. (2004), "The DNA sequence and comparative analysis of human chromosome 5", Nature, 431(7006):268-274.
[PDF]
repeats

Christian Schönbach (2004), "From masking repeats to identifying functional repeats in the mouse transcriptome", Briefings in Bioinformatics, 5(2):107-117.
repeats

Deepak Sharma, Biju Issac, GPS Raghava, R Ramaswamy (2004), "Spectral Repeat Finder(SRF): identification of repetitive sequences using Fourier transformation", Bioinformatics, 20(9):1405-1412.
Jiuzhou Song, Tony Ware, Shu-Lin Liu, M Surette (2004), "Comparative genomics via wavelet analysis for closely related bacteria", EURASIP Journal on Applied Signal Processing, 2004(1):5-12.
[abstract]
TT Sun, LX Zhang, J Chen, ZT Jiang (2004), "Statistical properties and fractals of nucleotide clusters in DNA sequences", Chaos, Solitons & Fractals, 20(5):1075-1084.
David Sussillo, Anshul Kundaje, Dimitris Anastassiou (2004), "Spectrogram analysis of genomics", EURASIP Journal on Applied Signal Processing, 2004(1):29-42.
[abstract] [PDF] [supplement material from the authors: http://www.ee.columbia.edu/~sussillo/spectrofish/]
repeats

Radek Szklarczyk and Jaap Heringa (2004), "Tracking repeats using significance and transitivity", Bioinformatics, 20:i311-i317.
Akito Taneda (2004), "Adplot: detection and visualization of repetitive patterns in complete genomes ", Bioinformatics, 20(5):701-708.
[abstract]
repeats

Thomas EE, Srebro N, Sebat J, Navin N, Healy J, Mishra B, Wigler M. "Distribution of short paired duplications in mammalian genomes", Proceedings of National Academy of Sciences, 101(28):10349-10354.
[abstract]
a/symmetry

Marie Touchon, Alain Arneodo, Yves d'Aubenton-Carafa, Claude Thermes (2004), "Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes", Nucleic Acids Research, 32(17):4969-4978.
repeats

Y Xiao, YZ Huang (2004), "Roles of genes and Alu repeats in nonlinear correlations of HUMHBB DNA sequence", Chaos, Solitons & Fractals, 20(3):497-502.
PP Vaidyanathan (2004), "Genomics and proteomics: a signal processor's tour", IEEE Circuits and Systems Magazine, 4(4):6-29.
PP Vaidyanathan, Byung-Jun Yoon (2004), "The role of signal-processing concepts in genomics and proteomics", Journal of the Franklin Institute, 341(1-2):111-135.
[abstract]
S Vinga, JS Almeida (2004), "Rényi continuous entropy of DNA sequences", Journal of Theoretical Biology, 231(3) 377-388.
A.E. Vinogradov (2004), "Evolution of genome size: multilevel selection mutation bias or dynamical chaos?", Current Opinion in Genetics & Development, 14:620-626.
Yong Wang, Frederick C.C. Leung (2004), "An evaluation of new criteria for CpG islands in the human genome as gene markers", Bioinformatics, 20:1170-1177.
[abstract]
Yong Wang, Frederick C.C. Leung (2004), "DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria", Bioinformatics, 20:3336-3345.
repeats

Peter E Warburton, Joti Giordano, Fanny Cheung, Yefgeniy Gelfand, Gary Benson (2004), "Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes", Genome Research, 14:1861-1869.
[abstract]
sequence

N Ward, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS, Dimitrov G, Jiang L, Scanlan D, Kang KH, Lewis M, Nelson KE, Methe B, Wu M, Heidelberg JF, Paulsen IT, Fouts D, Ravel J, Tettelin H, Ren Q, Read T, DeBoy RT, Seshadri R, Salzberg SL, Jensen HB, Birkeland NK, Nelson WC, Dodson RJ, Grindhaug SH, Holt I, Eidhammer I, Jonasen I, Vanaken S, Utterback T, Feldblyum TV, Fraser CM, Lillehaug JR, Eisen JA. (2005), "Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)", PLoS Biology, 2(10):e303.
sequence

H Watanabe, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blocker H, Hellmann I, Khaitovich P, Paabo S, Reinhardt R, Zheng HJ, Zhang XL, Zhu GF, Wang BF, Fu G, Ren SX, Zhao GP, Chen Z, Lee YS, Cheong JE, Choi SH, Wu KM, Liu TT, Hsiao KJ, Tsai SF, Kim CG, OOta S, Kitano T, Kohara Y, Saitou N, Park HS, Wang SY, Yaspo ML, Sakaki Y (2004), "DNA sequence and comparative analysis of chimpanzee chromosome 22", Nature, 429(6990):382-388.
[abstract] [PDF]
repeats

Ydo Wexler, Zohar Yakhini, Yechezkel Kashi, Dan Geiger (2004), "Finding approximate tandem repeats in genomic sequences", Proceedings of the Eighth International Conference on Research in Computational Molecular Biology , pp.?-?
sequence

Martin Wu, Ling V Sun, Jessica Vamathevan, Markus Riegler, Robert Deboy, Jeremy C Brownlie, Elizabeth A McGraw, William Martin, Christian Esser, Nahal Ahmadinejad, Christian Wiegand, Ramana Madupu, Maureen J Beanan, Lauren M Brinkac, Sean C Daugherty, A. Scott Durkin, James F Kolonay, William C Nelson, Yasmin Mohamoud, Perris Lee, Kristi Berry, M. Brook Young, Teresa Utterback, Janice Weidman, William C Nierman, Ian T Paulsen, Karen E Nelson, Hervé Tettelin, Scott L O'Neill, Jonathan A Eisen (2004), "Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements", PLoS Biology, 2(3):e69.
Z.B. Wu (2004), "Recurrence plot analysis of DNA sequences", Physics Letters A, 332:250-255.
sequence

Ping Xu, Giovanni Widmer, Yingping Wang, Luiz S Ozaki, Joao M Alves, Myrna G Serrano, Daniela Puiu, Patricio Manque, Donna Akiyoshi, Aaron J Mackey, William R Pearson, Paul H Dear, Alan T Bankier, Darrell L Peterson, Mitchell S Abrahamsen, Vivek Kapur, Saul Tzipori, Gregory A Buck (2004), "The genome of Cryptosporidium hominis", Nature, 431:1107-1112.
[ abstract]
Soojin Yi, Tyrone J. Summers, Nathaniel M. Pearson, Wen-Hsiung Li (2004), "Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes", Genome Research, 14(1):37-43.
[ abstract]
protein

ZG Yu, V Anh, KS Lau (2004), "Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses", Journal of Theoretical Biology, 226(3):341-348.
isochore

CT Zhang, R Zhang (2004), "Isochore structures in the mouse genome", Genomics, 83(3):384-394.
[abstract]
CT Zhang, R Zhang (2004), "A nucleotide composition constraint of genome sequences", Computational Biology and Chemistry, 28:149-153.
[abstract]
repeats

Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, Kexuan Tang (2004), "Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana", Bioinformatics, 20:1081-1086.
[abstract]
isochore

Lingang Zhang, Simon Kasif, Charles R Cantor, Natalia E Broude (2004), "GC/AT-content spikes as genomics punctuation marks", Proceedings of National Academy of Sciences, 101(48):16855-16860.
[abstract]
Linxi Zhang and Zhouting Jiang (2004), "Long-range correlations in DNA sequences using 2D DNA walk based on pairs of sequential nucleotides", Chaos, Solitons & Fractals, 22(4):947-955.
[abstract]
Ren Zhang, Chun-Ting Zhang (2004), "A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I", Bioinformatics, 20(5):612-622.
[abstract]
isochore

Ren Zhang, Chun-Ting Zhang (2004), "Isochore structures in the genome of the plant Arabidopsis thaliana", Journal of Molecular Evolution, 59:227-238.
Ren Zhang, Chun-Ting Zhang (2004), "Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii", Extremophiles, 8(3):253-258.
[ abstract]