corr in DNA (2008)

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2008

sequence

Pierre Abad, Jérôme Gouzy, Jean-Marc Aury, Philippe Castagnone-Sereno, Etienne G J Danchin, Emeline Deleury, Laetitia Perfus-Barbeoch, Véronique Anthouard, François Artiguenave, Vivian C Blok, Marie-Cécile Caillaud, Pedro M Coutinho, Corinne Dasilva, Francesca De Luca, Florence Deau, Magali Esquibet, Timothé Flutre, Jared V Goldstone, Noureddine Hamamouch, Tarek Hewezi, Olivier Jaillon, Claire Jubin, Paola Leonetti, Marc Magliano, Tom R Maier, Gabriel V Markov, Paul McVeigh, Graziano Pesole, Julie Poulain, Marc Robinson-Rechavi, Erika Sallet, Béatrice Ségurens, Delphine Steinbach, Tom Tytgat, Edgardo Ugarte, Cyril van Ghelder, Pasqua Veronico, Thomas J Baum, Mark Blaxter, Teresa Bleve-Zacheo, Eric L Davis, Jonathan J Ewbank, Bruno Favery, Eric Grenier, Bernard Henrissat, John T Jones, Vincent Laudet, Aaron G Maule, Hadi Quesneville, Marie-Noëlle Rosso, Thomas Schiex, Geert Smant, Jean Weissenbach, Patrick Wincker (2008), "Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita", Nature Biotechnology, 26:909-915.
[ abstract]
sequence

MD Adams, Goglin K, Molyneaux N, Hujer KM, Lavender H, Jamison JJ, MacDonald IJ, Martin KM, Russo T, Campagnari AA, Hujer AM, Bonomo RA, Gill SR (2008), "Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii", Journal of Bacteriology, 190(24):8053-8064.
M Akhtar, J Epps, E Ambikairajah (2009), "Signal processing in sequence analysis: advances in eukaryotic gene prediction", IEEE Journal of Selected Topics in Signal Processing, 2(3):310-321.
[ abstract]
isochore

S Arhondakis, O Clay, G Bernardi (2008), "GC level and expression of human coding sequences", Biochemical and Biophysical Research Communications, 367(3):542-545.
R Arora, WA Sethares, JA Bucklew (2008), "Latent periodicities in genome sequences", IEEE Journal of Selected Topics in Signal Processing, 2(3):332-342.
[ abstract]
RH Baran, H Ko (2008), "Detecting horizontally transferred and essential genes based on dinucleotide relative abundance", DNA Research, 15(5):267-276.
Mark Bauer, Sheldon M Schuster, Khalid Sayood (2008), "The average mutual information profile as a genomic signature", BMC Bioinformatics, 9:48.
[abstract]
isochore

JM Bechtel, T Wittenschlaeger, T Dwyer, J Song, S Arunachalam, SK Ramakrishnan, S Shepard, A Fedorov (2008), "Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures", BMC Genomics, 9:284.
sequence

DR Bentley, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008), "Accurate whole human genome sequencing using reversible terminator chemistry", Nature, 456(7218):53-59.
Christoph Bock, Thomas Lengauer (2008) "Computational epigenetics", Bioinformatics, 24(1):1-10.
[abstract]
R Boekhorst, I Abnizova, C Nehaniv (2008), "Discriminating coding, non-coding and regulatory regions using rescaled range and detrended fluctuation analysis", Biosystems, 91:183-194.
Alexander Bolshoy (2008), "Revisiting the relationship between compositional sequence complexity and periodicity", Computational Biology and Chemistry, 32(1):17-28.
[ abstract]
N Bouaynaya, D Schonfeld (2008), "Nonstationary analysis of coding and noncoding regions in nucleotide sequences", IEEE Journal of Selected Topics in Signal Processing, 2(3):357-364.
[ abstract]
M Buiatti, M Buiatti (2008), "Chance vs. necessity in living systems: A false antinomy", Rivista di Biologia-Biology Forum, 101(1):29-65.
bending

Xiao-Qin Cao, Jia Zeng, Hong Yan (2008), "Structural properties of replication origins in yeast DNA sequences", Physical Biology, 5:036012.
[ abstract]
Z Ciao, B Liao, R Li (2008), "A group of 3D graphical representation of DNA sequences based on dual nucleotides", International Journal of Quantum Chemistry, 108:1485-1490.
sequence

Jane M Carlton, John H Adams, Joana C Silva, Shelby L Bidwell, Hernan Lorenzi, Elisabet Caler, Jonathan Crabtree, Samuel V Angiuoli, Emilio F Merino, Paolo Amedeo, Qin Cheng, Richard M R Coulson, Brendan S Crabb, Hernando A del Portillo, Kobby Essien, Tamara V Feldblyum, Carmen Fernandez-Becerra, Paul R Gilson, Amy H Gueye, Xiang Guo, Simon Kang'a, Taco W A Kooij, Michael Korsinczky, Esmeralda V-S Meyer, Vish Nene, Ian Paulsen, Owen White, Stuart A Ralph, Qinghu Ren, Tobias J Sargeant, Steven L Salzberg, Christian J Stoeckert, Steven A Sullivan, Marcio M Yamamoto, Stephen L Hoffman, Jennifer R Wortman, Malcolm J Gardner, Mary R Galinski, John W Barnwell, Claire M Fraser-Liggett (2008), "Comparative genomics of the neglected human malaria parasite Plasmodium vivax", Nature, 455:757-763.
[ abstract]
protein

K Chen, J T Huzil, H Freedman, P Ramachandran, A Antoniou, J A Tuszynski, L Kurgan (2008), "Identification of tubulin drug binding sites and prediction of relative differences in binding affinities to tubulin isotypes using digital signal processing", Journal of Molecular Graphics and Modelling, 27:497-505.
isochore

M Costantini, M Di Filippo, G Bernardi (2008), "Extrapolating ENCODE data to the whole human genome", Gene, 419(1-2):66-69.
isochore

M Costantini, G Bernardi (2008), "Correlations between coding and contiguous non-coding sequences in isochore families from vertebrate genomes", Gene, 410(2):241-248.
isochore

M Costantini, G Bernardi (2008), "The short-sequence designs of isochores from the human genome", Proceedings of National Academy of Sciences, 105(37):13971-13976.
isochore

M Costantini, G Bernardi (2008), "Replication timing, chromosomal bands, and isochores", Proceedings of National Academy of Sciences, 105(9):3433-3437.
Qi Dai, Yanchun Yang, Tianming Wang (2008) "Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison", Bioinformatics, 24(20):2296-2302.
[abstract]
E Darai-Ramqvist, A Sandlund, S Müller, G Klein, S Imreh, M Kost-Alimova (2008), "Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions", Genome Research, 18(3):370-379.
isochore

M Di Filippo, G Bernardi (2008), "Mapping DNase-I hypersensitive sites on human isochores", Gene, 419(1-2):62-65.
sequence

Christoph Dieterich, Sandra W Clifton, Lisa N Schuster, Asif Chinwalla, Kimberly Delehaunty, Iris Dinkelacker, Lucinda Fulton, Robert Fulton, Jennifer Godfrey, Pat Minx, Makedonka Mitreva, Waltraud Roeseler, Huiyu Tian, Hanh Witte, Shiaw-Pyng Yang, Richard K Wilson, Ralf J Sommer (2008), "The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism", Nature Genetics, 40:1193-1198.
[ abstract]
isochore

L Duret, PF Arndt (2008), "The impact of recombination on nucleotide substitutions in the human genome", PLoS Genetics, 4(5):e1000071.
a/symmetry

KJ Evans (2008), "Genomic DNA from animals shows contrasting strand bias in large and small subsequences", BMC Genomics, 9(1):43.
sequence

Simon J Foote, Janine T Bossé, Anne B Bouevitch, Paul R Langford, N Martin Young, and John HE Nash (2008), "The complete genome sequence of Actinobacillus pleuropneumoniae L20 (serotype 5b)", Journal of Bacteriology, to appear.
F Gao, CT Zhang (2008), "Prediction of replication time zones at single nucleotide resolution in the human genome", FEBS Letters, 582:2441-2445.
JAL Garcia, F Bartumeus, D Roche, et al. (2008), "Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses", Genomics, 91(6):538-543.
Simon Gog, Martin Bader, and Enno Ohlebusch (2008), "GENESIS: genome evolution scenarios", Bioinformatics, 24(5):711-712.
[abstract]
Bailin Hao, Lei Gao (2008), "Prokaryotic branch of the tree of life: a composition vector approach", Journal of Systematics & Evolution, 46(6):258-262.
sequence

Y Hongoh, Sharma VK, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M (2008), "Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut", Science, 322(5904):1108-1109.
Iva Hrabcova, Jaroslav Kypr (2008), "The longest (A+T) and (G+C) blocks in the human and other genomes", Journal of Biomolecular Structure and Dynamics, 25(4):337-346.
[abstract]
Kun-Lin Hsieh, I-Ching Yang (2008), "Incorporating PCA and fuzzy-ART techniques into achieve organism classification based on codon usage consideration", Computers in Biology and Medicine, 38(8):886-893.
[ abstract]
protein

Christopher JR Illingworth, Kevin E Parkes, Christopher R Snell, Philip M Mullineaux, Christopher A Reynolds (2008), "Criteria for confirming sequence periodicity identified by Fourier transform analysis: Application to GCR2, a candidate plant GPCR?", Biophysical Chemistry, 133(1-3):28-35.
[ abstract]
R Jiang, H Yan (2008), "Studies of spectral properties of short genes using the wavelet subspace Hilbert-Huang transform (WSHHT)", Physica A, 387(16-17):4223-4247.
XY Jiang, D Lavenier, SST Yau (2008), "Coding region prediction based on a universal DNA sequence representation method", Journal of Computational Biology, 15(10):1237-1256.
JE Karro, M Peifer, RC Hardison, M Kollmann, HH von Grünberg (2008), "Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure", Molecular Biology and Evolution, 25(2):362-374.
JM Keith, P Adams, S Stephen, et al. "Delineating slowly and rapidly evolving fractions of the Drosophila genome", Journal of Computational Biology, 15(4):407-430.
repeats

YD Kelkar, S Tyekucheva, F Chiaromonte, KD Makova (2008), "The genome-wide determinants of human and chimpanzee microsatellite evolution", Genome Research, 18(1):30-38.
sequence

Nicole King, M Jody Westbrook, Susan L Young, Alan Kuo, Monika Abedin, Jarrod Chapman, Stephen Fairclough, Uffe Hellsten, Yoh Isogai, Ivica Letunic, Michael Marr, David Pincus, Nicholas Putnam, Antonis Rokas, Kevin J Wright, Richard Zuzow, William Dirks, Matthew Good, David Goodstein, Derek Lemons, Wanqing Li, Jessica B Lyons, Andrea Morris, Scott Nichols, Daniel J Richter, Asaf Salamov, JGI Sequencing, Peer Bork, Wendell A Lim, Gerard Manning, W Todd Miller, William McGinnis, Harris Shapiro, Robert Tjian, Igor V Grigoriev, Daniel Rokhsar, (2008), "The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans", Nature, 451:783-788.
[ abstract]
Sudhir Kumar, Masatoshi Nei, Joel Dudley, Koichiro Tamura (2008), "MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences", Briefings in Bioinformatics, 9(4):299-306.
[abstract]
sequence

HS Lee, Kang SG, Bae SS, Lim JK, Cho Y, Kim YJ, Jeon JH, Cha SS, Kwon KK, Kim HT, Park CJ, Lee HW, Kim SI, Chun J, Colwell RR, Kim SJ, Lee JH (2008), "The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism", Journal of Bacteriology, 190(22):7491-7499.
isochore

MK Li, L Gu, SS Chen, JQ Dai, SH Tao (2008), "Evolution of the isochore structure in the scale of chromosome: insight from the mutation bias and fixation bias", Journal of Evolutionary Biology, 21(1):173-182.
repeats

Xuehui Li, Tamer Kahveci, A Mark Settles (2008), "A novel genome-scale repeat finder geared towards transposons", Bioinformatics, 24(4):468-476.
[abstract]
sequence

Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, Nikos C Kyrpides (2008), "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata", Nucleic Acids Research, 36(Database issue):D475-D479.
[ abstract]
Zhi-Hua Liu, Xiao Sun (2008), "Coronavirus phylogeny based on base-base correlation", International Journal of Bioinformatics Research and Applications, 4(2):211-220.
[ abstract]
sequence

Eric Lyons, Michael Freeling (2008), "How to usefully compare homologous plant genes and chromosomes as DNA sequences", The Plant Journal, 53(4):661-673.
[ abstract]
Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Webb Miller, David Haussler (2008), "The infinite sites model of genome evolution", Proceedings of National Academy of Sciences, 105(38):14254-14261.
[ abstract]
isochore

AA Mahmud, G Amore, G Bernardi (2008), "Compositional genome contexts affect gene expression control in sea urchin embryo", PLoS ONE, 3(12):e4025.
isochore

C Melodelima, C Gautier (2008), "The GC-heterogeneity of teleost fishes", BMC Genomics, 9(1):632.
JP Mena-Chalco, H Carrer, Y Zana, et al. (2008), "Identification of protein coding regions using the modified Gabor-wavelet transform", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(2):198-207.
G Menconi, V Benci, M Buiatti (2008), "Data compression and genomes: A two-dimensional life domain map", Journal of Theoretical Biology, 253(2):281-288
repeats

Angelika Merkel and Neil Gemmell (2008), "Detecting short tandem repeats from genome data: opening the software black box", Briefings in Bioinformatics, 9(5):355-366.
[abstract]
sequence

WG Miller, Wang G, Binnewies TT, Parker CT (2009), "The complete genome sequence and analysis of the human pathogen Campylobacter lari", Foodborne Pathogens and Disease, 5(4):371-386.
Atulya K. Nagar, Dilbag Sokhi (2008), "On wavelet-based adaptive approach for gene comparison", International Journal of Intelligent Systems Technologies and Applications 5(1-2):104-114.
repeats

CT O'Dushlaine, DC Shields (2008), "Marked variation in predicted and observed variability of tandem repeat loci across the human genome", BMC Genomics, 9:175.
isochore

JL Oliver, P Bernaola-Galván, M Hackenberg, P Carpena (2008), "Phylogenetic distribution of large-scale genome patchiness", BMC Evolutionary Biology, 8:107.
sequence

Charles H Opperman, David M Bird, Valerie M Williamson, Dan S Rokhsar, Mark Burke, Jonathan Cohn, John Cromer, Steve Diener, Jim Gajan, Steve Graham, T D Houfek, Qingli Liu, Therese Mitros, Jennifer Schaff, Reenah Schaffer, Elizabeth Scholl, Bryon R Sosinski, Varghese P Thomas, Eric Windham (2008), "Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism", Proceedings of National Academy of Sciences, 105(39):14802-14807.
[ abstract]
Kenshiro Oshima, Hidehiro Toh, Yoshitoshi Ogura, Hiroyuki Sasamoto, Hidetoshi Morita, Sang-Hee Park, Tadasuke Ooka, Sunao Iyoda, Todd D Taylor, Tetsuya Hayashi, Kikuji Itoh, Masahira Hattori (2008), "Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult", DNA Research, 15(6):375-386.
[ abstract]
Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandic', Matko Gluncic', Nils Paar (2008), "Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats", BMC Bioinformatics, 9:466.
sequence

A Pain, U Böhme, A E Berry, K Mungall, R D Finn, A P Jackson, T Mourier, J Mistry, E M Pasini, M A Aslett, S Balasubrammaniam, K Borgwardt, K Brooks, C Carret, T J Carver, I Cherevach, T Chillingworth, T G Clark, M R Galinski, N Hall, D Harper, D Harris, H Hauser, A Ivens, C S Janssen, T Keane, N Larke, S Lapp, M Marti, S Moule, I M Meyer, D Ormond, N Peters, M Sanders, S Sanders, T J Sargeant, M Simmonds, F Smith, R Squares, S Thurston, A R Tivey, D Walker, B White, E Zuiderwijk, C Churcher, M A Quail, A F Cowman, C M R Turner, M A Rajandream, C H M Kocken, A W Thomas, C I Newbold, B G Barrell, M Berriman (2008), "The genome of the simian and human malaria parasite Plasmodium knowlesi", Nature, 455:799-803.
[ abstract]
sequence

D Paul, S Bridges, SC Burgess, Y Dandass, ML Lawrence (2008), "Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T", Journal of Bacteriology, 190(15):5531-5532.
isochore

U Pozzoli, G Menozzi, M Fumagalli, M Cereda, GP Comi, R Cagliani, N Bresolin, M Sironi (2008), "Both selective and neutral processes drive GC content evolution in the human genome", BMC Evolutionary Biology, 8:99.
sequence

Nicholas H Putnam, Thomas Butts, David E K Ferrier, Rebecca F Furlong, Uffe Hellsten, Takeshi Kawashima, Marc Robinson-Rechavi, Eiichi Shoguchi, Astrid Terry, Jr-Kai Yu, Elia Benito-Gutiérrez, Inna Dubchak, Jordi Garcia-Fernàndez, Jeremy J Gibson-Brown, Igor V Grigoriev, Amy C Horton, Pieter J de Jong, Jerzy Jurka, Vladimir V Kapitonov, Yuji Kohara, Yoko Kuroki, Erika Lindquist, Susan Lucas, Kazutoyo Osoegawa, Len A Pennacchio, Asaf A Salamov, Yutaka Satou, Tatjana Sauka-Spengler, Jeremy Schmutz, Tadasu Shin-I, Atsushi Toyoda, Marianne Bronner-Fraser, Asao Fujiyama, Linda Z Holland, Peter W H Holland, Nori Satoh, Daniel S Rokhsar (2008), "The amphioxus genome and the evolution of the chordate karyotype", Nature, 453:1064-1071.
[ abstract]
protein

P Ramachandran, A Antoniou (2008), "A new technique for the identification of hot spot locations in proteins using digital filters," IEEE Journal of Selected Topics in Signal Processing, 2(3):378-389.
sequence

SA Rensing, D Lang, A Zimmer, A Terry, A Salamov, H Shapiro, T Nishiyama, F P-Perroud, E Lindquist, Y Kamisugi, T Tanahashi, K Sakakibara, T Fujita, K Oishi, T Shin-I, Y Kuroki, A Toyoda, Y Suzuki, I S-Hashimoto, K Yamaguchi, S Sugano, Y Kohara, A Fujiyama, N Ashton, A Anterola, S Aoki, WB Barbazuk, E Barker, J Bennetzen, R Blankenship, SH Cho, S Dutcher, M Estelle, J Fawcett, H Gundlach, K Hanada, A Heyl, KA Hicks, J Hughes, M Lohr, K Mayer, A Melkozernov, T Murata, DR Nelson, B Pils, M Prigge, B Reiss, T Renner, S Rombauts, P Rushton, A Sanderfoot, G Schween, H S-Shiu, K Stueber, FL Theodoulou, H Tu, Y Van de Peer, PJ Verrier, E Waters, A Wood, G Yang, D Cove, AC Cuming, M Hasebe, S Lucas, BD Mishler, R Reski, I Grigoriev, RS Quatrano, JL Boore (2008), "The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants", Science, 319:64-69.
[ abstract]
A Riva, AS Carpentier, F Barloy-Hubler, A Cheron, A Henaut (2008), "Analyzing stochastic transcription to elucidate the nucleoid's organization", BMC Genomics, 9:125.
repeats

M Rosandic', M Gluncic', V Paar, I Basar (2008), "The role of alphoid higher order repeats (HORs) in the centromere folding", Journal of Theoretical Biology, 254(3):555-560.
DB Saakian (2008), "Evolution models with base substitutions, insertions, deletions, and selection", Physical Review E, 78(6):061920.
repeats

Surya Saha, Susan Bridges, Zenaida V Magbanua, Daniel G Peterson (2008), "Computational approaches and tools used in identification of dispersed repetitive DNA sequences", Tropical Plant Biology, 1(1):85-96.
[ abstract]
repeats

Surya Saha, Susan Bridges, Zenaida V Magbanua, Daniel G Peterson (2008), "Empirical comparison of ab initio repeat finding programs", Nucleic Acids Research, to appear.
[ abstract]
sequence

JH Saw, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M (2008), "Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1", Genome Biology, 9(11):R161.
isochore

T Schmidt, D Frishman (2008), "Assignment of isochores for all completely sequenced vertebrate genomes using a consensus", Genome Biology, 9(6):R104.
Dustin E Schones, Keji Zhao (2008), "Genome-wide approaches to studying chromatin modifications", Nature Reviews Genetics, 9:179-191.
[abstract]
sequence

DA Sela, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA (2008), "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome", Proceedings of National Academy of Sciences, 105(48):18964-18969.
a/symmetry

Natalia V. Sernova and Mikhail S. Gelfand (2008), "Identification of replication origins in prokaryotic genomes", Briefings in Bioinformatics, 9(5):376-391.
[abstract]
sequence

Stefan M Sievert, Kathleen M Scott, Martin G Klotz, Patrick S G Chain, Loren J Hauser, James Hemp, Michael Hügler, Miriam Land, Alla Lapidus, Frank W Larimer, Susan Lucas, Stephanie A Malfatti, Folker Meyer, Ian T Paulsen, Qinghu Ren, Jörg Simon, and the USF Genomics Class (2008), "The genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans", Applied and Environmental Microbiology, to appear.
repeats

Abanish Singh, Cedric Feschotte, Nikola Stojanovic (2008), "A study of the repetitive structure and distribution of short motifs in human genomic sequences", International Journal of Bioinformatics Research and Applications, 3(4):523-535.
[ abstract]
H Sun, G Skogerbo, Z Wang, W Liu, Y Li (2008), "Structural relationships between highly conserved elements and genes in vertebrate genomes", PLoS ONE, 3(11):e3727.
RE Thurman, WS Noble, JA Stamatoyannopoulos (2008), "Multi-scale correlations in continuous genomic data", Proceedings of Pacific Symposium on Bioinformatics, 13:201-215.
M Tumminello, F Lillo, RN Mantegna (2008), "Generation of hierarchically correlated multivariate symbolic sequences with an application to the assessment of bootstrap confidence in phylogenetic analysis", European Physical Journal B, 65(3):333-340.
J Tuqan, A Rushdi (2008), "A DSP approach for finding the codon bias in DNA sequences", IEEE Journal of Selected Topics in Signal Processing, 2(3):343-356
[ abstract]
OV Usatenko, SS Melnik, L Kroon, et al. (2008), "Spectral analysis and synthesis of 1D dichotomous long-range correlated systems: from diffraction gratings to quantum wires", Physica A, 387(19-20):4733-4739.
repeats

Karen Usdin (2008), "The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases", Genome Research, 18(7):1011-1019.
[abstract]
isochore

A Varriale, G Torelli, G Bernardi (2008), "Compositional properties and thermal adaptation of 18S rRNA in vertebrates", RNA, 14(8):1492-1500.
protein

N Veljkovic, S Glisic, J Prljic, V Perovic, M Botta, V Veljkovic (2008), "Discovery of new therapeutic targets by the informational spectrum method", Current Protein & Peptide Science, 9(5):493-506.
GS Vernikos, J Parkhill (2008), "Resolving the structural features of genomic islands: A machine learning approach", Genome Research, to appear.
sequence

F Wang, Wang J, Jian H, Zhang B, Li S, Wang F, Zeng X, Gao L, Bartlett DH, Yu J, Hu S, Xiao X. (2008), "Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3", PLoS ONE, 3(4):e1937.
sequence

J Wang, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GK, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J (2008), "The diploid genome sequence of an Asian individual", Nature, 456(7218):60-65.
SC Wang, PC Li, HC Tseng (2008), "Long range correlation and possible electron conduction through DNA sequences", Physica A, 387(21):5159-5168.
Y Wang, FC Leung (2008), "Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites", Genomics, Proteomics, and Bioinformatics, 6(3-4):144-154.
Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi, David M Gilbert (2008), "ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data", BMC Bioinformatics, 9:530
[ abstract]
a/symmetry

Jianyu Wen, Brian J Parker, Georg F Weiller (2008), "Analysis of structural strand asymmetry in non-coding RNAs", Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.187-198 (Imperial College Press).
protein

Yang Yang, Bao-Liang Lu, Wen-Yun Yang (2008), "Classification of protein sequences based on word segmentation methods", Proceedings of the 6th Asia-Pacific Bioinformatics Conference eds. A Brazma, S Miyano, T Akutsu, pp.177-186 (Imperial College Press).
isochore

Wen-Xin Zheng, Chun-Ting Zhang (2008), "Biological implications of isochore boundaries in the human genome", Journal of Biomolecular Structure and Dynamics, 25(4):327-336.
[abstract]
Fengfeng Zhou, Victor Olman, Ying Xu (2008), "Barcodes for genomes and applications", BMC Bioinformatics, 9:546
[ abstract]
Jerzy S Zielinski, Nidhal Bouaynaya, Dan Schonfeld, William O'Neill (2008), "Time-dependent ARMA modeling of genomic sequences", BMC Bioinformatics, 9(suppl 9):S14.
[ abstract]