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+ 2007

  1. Kazuharu Arakawa, Rintaro Saito, Masaru Tomita (2006), "Noise-reduction filtering for accurate detection of replication termini in bacterial genomes", FEBS Letters, 581(2):253-258.

  2. Rajeev K Azad, Jeffrey G Lawrence (2007), "Detecting laterally transferred genes: use of entropic clustering methods and genome position", Nucleic Acids Research, 35(14):4629-4639.
    [ abstract]

  3. Casey M. Bergman and Hadi Quesneville (2007), "Discovering and detecting transposable elements in genome sequences", Briefings in Bioinformatics, 8:382-392.
    [abstract]

  4. Giorgio Bernardi (2007), "The neoselectionist theory of genome evolution", Proceedings of National Academy of Sciences, 104(20):8385-8390.

  5. Guillaume Blanc, Hiroyuki Ogata, Catherine Robert, Stéphane Audic, Jean-Michel Claverie, and Didier Raoult (2007), "Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome", Genome Research, 17:1657-1664.
    [abstract]

  6. repeats
    Charles Bland, Teresa L Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos C Kyrpides, Philip Hugenholtz (2007), "CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats", BMC Bioinformatics, 8:209.
    [abstract]

  7. Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer (2007) "CpG island mapping by epigenome prediction", PLoS Computational Biology, 3(6):e110.
    [ abstract]

  8. Aurélia Boissin-Quillon, Didier Piau, Caroline Leroux (2007), "In silico segmentations of lentivirus envelope sequences", BMC Bioinformatics, 8:99.
    [abstract]

  9. sequence
    Kelly A Brayton, Audrey O T Lau, David R Herndon, Linda Hannick, Lowell S Kappmeyer, Shawn J Berens, Shelby L Bidwell, Wendy C Brown, Jonathan Crabtree, Doug Fadrosh, Tamara Feldblum, Heather A Forberger, Brian J Haas, Jeanne M Howell, Hoda Khouri, Hean Koo, David J Mann, Junzo Norimine, Ian T Paulsen, Diana Radune, Qinghu Ren, Roger K Smith, Jr¤a, Carlos E Suarez, Owen White, Jennifer R Wortman, Donald P Knowles Jr., Terry F McElwain, Vishvanath M Nene (2007), "Genome sequence of Babesia bovis and comparative analysis of Apicomplexan Hemoprotozoa", PLoS Pathology, 3(10):e148.
    [ abstract]

  10. Andrzej K. Brodzik (2007), "Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem", Bioinformatics, 23:694-700
    [abstract]

  11. sequence
    Jane M Carlton, Robert P Hirt, Joana C Silva, Arthur L Delcher, Michael Schatz, Qi Zhao, Jennifer R Wortman, Shelby L Bidwell, U Cecilia M Alsmark, Sébastien Besteiro, Thomas Sicheritz-Ponten, Christophe J Noel, Joel B Dacks, Peter G Foster, Cedric Simillion, Yves Van de Peer, Diego Miranda-Saavedra, Geoffrey J Barton, Gareth D Westrop, Sylke Müller, Daniele Dessi, Pier Luigi Fiori, Qinghu Ren, Ian Paulsen, Hanbang Zhang, Felix D Bastida-Corcuera, Augusto Simoes-Barbosa, Mark T Brown, Richard D Hayes, Mandira Mukherjee, Cheryl Y Okumura, Rachel Schneider, Alias J Smith, Stepanka Vanacova, Maria Villalvazo, Brian J Haas, Mihaela Pertea, Tamara V Feldblyum, Terry R Utterback, Chung-Li Shu, Kazutoyo Osoegawa, Pieter J de Jong, Ivan Hrdy, Lenka Horvathova, Zuzana Zubacova, Pavel Dolezal, Shehre-Banoo Malik, John M Logsdon, Jr, Katrin Henze, Arti Gupta, Ching C Wang, Rebecca L Dunne, Jacqueline A Upcroft, Peter Upcroft, Owen White, Steven L Salzberg, Petrus Tang, Cheng-Hsun Chiu, Ying-Shiung Lee, T Martin Embley, Graham H Coombs, Jeremy C Mottram, Jan Tachezy, Claire M Fraser-Liggett, Patricia J Johnson (2007), "Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis", Science, 315(5809):207-212.
    [ abstract]

  12. P Carpena, P Bernaola-Galvan, AV Coronado, M Hackenberg, JL Oliver (2007), "Identifying chracteristic scales in the human genome", Physical Review E, 75:032903.

  13. a/symmetry
    David SH Chew, Ming-Ying Leung, Kwok Pui Choi (2007), "AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions", BMC Bioinformatics, 8:163
    [abstract]

  14. isochore
    Jena L Chojnowski, James Franklin, Yoshinao Katsu, Taisen Iguchi, Louis J Guillette Jr, Rebecca T Kimball, Edward L Braun (2007), "Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes", Journal of Molecular Evolution, 65(3):259-266.
    [ abstract]

  15. protein
    Irena Cosic, Elena Pirogova (2007), "Bioactive peptide design using the Resonant Recognition Model", Nonlinear Biomedical Physics, 1:7.
    [ abstract]

  16. M Costantini, O Clay, C Federico, S Saccone, F Auletta, G Bernardi (2007), "Human chromosomal bands: nested structure, high-definition map and molecular basis", Chromosoma, 116(1):29-40.
    [ abstract]

  17. Maria Costantini, Miriam Di Filippo, Fabio Auletta, Giorgio Bernardi (2007), "Isochore pattern and gene distribution in the chicken genome", Gene, 400(1-2):9-15.

  18. M Costantini, F Auletta, G Bernardi (2007), "Isochore patterns and gene distributions in fish genomes", Genomics, 90(3):364-371.
    [ abstract]

  19. Miklos Csuros, Laurent Noe, Gregory Kucherov (2007), "Reconsidering the significance of genomic word frequencies", Trends in Genetics, 23(11):543-546.
    [ abstract]

  20. N Day, A Hemmaplardh, RE Thurman, JA Stamatoyannopoulos, WS Noble (2007), "Unsupervised segmentation of continuous genomic data", Bioinformatics, 23(11):1424-1426.

  21. a/symmetry
    Xuegong Deng, Xuemei Deng, Ilkka Havukkala (2007), "Strong GC and AT skew correlation in chicken genome", in Pattern Recognition in Bioinformatics (Lecture Notes in Computer Science, Volume 4774), pp.51-59 (Springer).

  22. a/symmetry
    Xuegong Deng, Ilkka Havukkala, Xuemei Deng (2007), "Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes", BMC Evolutionary Biology, 7:234.

  23. repeats
    Nevzat Onur Domaniç, Franco P. Preparata (2007), "A novel approach to the detection of genomic approximate tandem repeats in the Levenshtein metric", Journal of Computational Biology, 14(7):873-891.
    [abstract]

  24. isochore
    Giuseppe D'Onofrio, Tapash Chandra Ghosh, Salvatore Saccone (2007), "Different functional classes of genes are characterized by different compositional properties", FEBS Letters, 581(30):5819-5824.
    [ abstract]

  25. isochore
    Timothy R Dreszer, Gregory D Wall, David Haussler, Katherine S Pollard (2007), "Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion", Genome Research, 17:1420-1430.
    [abstract]

  26. repeats
    Robert A Edgar (2007), "PILER-CR: Fast and accurate identification of CRISPR repeats", BMC Bioinformatics, 8(1):18.
    [abstract]

  27. AWF Edwards (2007), "Picturing the genetic code", Nature Precedings preprint, 682
    [ abstract]

  28. isochore
    H Ellegren (2007), "Molecular evolutionary genomics of birds", Cytogenetics and Genome Research, 117(1-4):120-130.

  29. C. Daniel Eller, Moira Regelson, Barry Merriman, Stan Nelson, Steve Horvath, York Marahrens (2007), "Repetitive sequence environment distinguishes housekeeping genes", Gene, 390(1-2):153-165.
    [ abstract]

  30. DNA-loop
    Kenneth Evans, Sascha Ott, Annika Hansen, Georgy Koentges, Lorenz Wernisch (2007), "A comparative study of S/MAR prediction tools", BMC Bioinformatics, 8:71
    [abstract]

  31. Hao Fan, Jia-You Chu (2007), "A brief review of short tandem repeat mutation", Genomics, Proteomics & Bioinformatics, 5(1):7-14.
    [ abstract]

  32. isochore
    GG Fortes, C Bouza, P Martínez, L Sánchez (2007), "Diversity in isochore structure among cold-blooded vertebrates based on GC content of coding and non-coding sequences", Genetica, 129(3):281-289.

  33. protein
    Zakharia M Frenkel, Edward N Trifonov (2007), "Walking through protein sequence space", Journal of Theoretical Biology, 244:77-80.

  34. Lei Gao, Ji Qi, Jiandong Sun, Bailin Hao (2007), "Prkaryote phylogeny meets taxonomy: comparasion of composition vector trees with systematic bacteriology", Science in China (Series C Life Science), 50(5):587-599. Supplementary material: 37(4):389-401 (in Chinese).

  35. Robert A Gatenby, B Roy Frieden (2007), "Information theory in living systems, methods, applications, and challenges", Bulletin of Mathematical Biology, 69(2):635-657,
    [ abstract]

  36. Derek Gatherer (2007), "Peptide vovabulary analysis reveals ultra-conservation and homonymity in protein sequences", Bioinformatics and Biology Insights, 1:101-126.
    [abstract]

  37. sequence
    (Rhesus Macaque Genome Sequencing and Analysis Consortium) RA Gibbs, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS (2007) "Evolutionary and biomedical insights from the rhesus macaque genome", Science, 316(5822):222-234.

  38. Jacob L Glass, Reid F Thompson, Batbayar Khulan, Maria E Figueroa, Emmanuel N Olivier, Erin J Oakley, Gary Van Zant, Eric E Bouhassira, Ari Melnick, Aaron Golden, Melissa J Fazzari and John M Greally (2007), "CG dinucleotide clustering is a species-specific property of the genome", Nucleic Acids Research, 35:6798-6807.
    [ abstract]

  39. L Gordon, S Yang, M Tran-Gyamfi, D Baggott, M Christensen, A Hamilton, R Crooijmans, M Groenen, S Lucas, I Ovcharenko, L Stubbs (2007), "Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions", Genome Research, 17(11):1603-1613.

  40. Liang Goh, Susan K. Murphy, Sayan Muhkerjee, and Terrence S. Furey (2007), "Genomic sweeping for hypermethylated genes", Bioinformatics, 23:281-288.
    [abstract]

  41. Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel (2007), "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats", BMC Bioinformatics, 8:172
    [abstract]

  42. Liza Gross (2007), "Are 'Ultraconserved' genetic elements really indispensable?", PLoS Biology, 5(9):e253.
    [ abstract]

  43. Ravi Gupta, Divya Sarthi, Ankush Mittal, and Kuldip Singh (2007), "A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences", EURASIP Journal on Bioinformatics and Systems Biology, article ID 43596.

  44. isochore
    Niina Haiminen, Heikki Mannila (2007), "Discovering isochores by least-squares optimal segmentation", Gene, 394(1-2):53-60.

  45. N Haiminen, H Mannila, E Terzi (2007), "Comparing segmentations by applying randomization techniques", BMC Bioinformatics, 8:171.
    [abstract]

  46. Bailin Hao (2007), "Combinatorics from bacterial genomes", in Combinatorial Optimization and Applications (Lecture Notes in Computer Science, Volume 4616), pp.1611-3349 (Springer).

  47. Joan Hérisson, Guillaume Payen, and Rachid Gherbi (2007), "A 3D pattern matching algorithm for DNA sequences", Bioinformatics, 23:680-686
    [abstract]

  48. isochore
    Ryan D Hernandez, Scott H Williamson, Lan Zhu, Carlos D Bustamante (2007), "Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans", Molecular Biology and Evolution, 24(10):2196-2202.
    [abstract]

  49. sequence
    Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B. Hilton, Baltazar A. Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Antonio Costa de Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T. Hiraki, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue Hsing, Hiroshi Ikawa, Kazuho Ikeo, Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hiroaki Kawashima, Jitendra P. Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O Koyanagi, Hiromi Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W. Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O'Donovan, Hajime Ohyanagi, Toshihisa Okido, Satoshi OOta, Naoki Osato, Lance E. Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K. Singh, Brian Smith-White, Jun-ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Mika Tsugane, Akhilesh K. Tyagi, Apichart Vanavichit, Aihui Wang, Rod A. Wing, Kaori Yamaguchi, Mayu Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Gojobori, Takuji Sasaki, for the Rice Annotation Project (2007), "Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana", Genome Research, 17:175-183.
    [ abstract]

  50. isochore
    Frank Gronlund Jorgensen, Mikkel Heide Schierup, Andrew G Clark (2007), "Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera", Molecular Biology and Evolution, 24(2):611-619.

  51. Olivier Jaillon, Jean-Marc Aury, Benjamin Noel, Alberto Policriti, Christian Clepet, Alberto Casagrande, Nathalie Choisne, Sébastien Aubourg, Nicola Vitulo, Claire Jubin, Alessandro Vezzi, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner, Erica Mica, Delphine Jublot, Julie Poulain, Clémence Bruyère, Alain Billault, Béatrice Segurens, Michel Gouyvenoux, Edgardo Ugarte, Federica Cattonaro, Véronique Anthouard, Virginie Vico, Cristian Del Fabbro, Michaël Alaux, Gabriele Di Gaspero, Vincent Dumas, Nicoletta Felice, Sophie Paillard, Irena Juman, Marco Moroldo, Simone Scalabrin, Aurélie Canaguier, Isabelle Le Clainche, Giorgio Malacrida, Eléonore Durand, Graziano Pesole, Valérie Laucou, Philippe Chatelet, Didier Merdinoglu, Massimo Delledonne, Mario Pezzotti, Alain Lecharny, Claude Scarpelli, François Artiguenave, M. Enrico Pè, Giorgio Valle, Michele Morgante, Michel Caboche, Anne-Françoise Adam-Blondon, Jean Weissenbach, Francis Quétier, Patrick Wincker, for The French-Italian Public Consortium for Grapevine Genome Characterization (2007), "The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla", Nature, 449:463-467.
    [ abstract]

  52. sequence
    M Kasahara, K Naruse, S Sasaki, Y Nakatani, W Qu, B Ahsan, T Yamada, Y Nagayasu, K Doi, Y Kasai, T Jindo, D Kobayashi, A Shimada, A Toyoda, Y Kuroki, A Fujiyama, T Sasaki, A Shimizu, S Asakawa, N Shimizu, S Hashimoto, J Yang, Y Lee, K Matsushima, S Sugano, M Sakaizumi, T Narita, K Ohishi, S Haga, F Ohta, H Nomoto, K Nogata, T Morishita, T Endo, T Shin-I, H Takeda, S Morishita, Y Kohara (2007), The medaka draft genome and insights into vertebrate genome evolution, Nature, 447(7145):714-719.

  53. Wayne S Kendal (2007), "Scale invariant correlations between genes and SNPs on human chromosome 1 reveal potential evolutionary mechanisms", Journal of Theoretical Biology, 245:329-340.

  54. Erik Larsson, Per Lindahl, Petter Mostad (2007), "HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing", BMC Bioinformatics, 8:418.
    [abstract]

  55. protein
    AA Laskin, KG Skryabin, EV Korotkov (2007), "Latent periodicity of protein families, identified with the indel-aware algorithm", Journal of Proteome Research, 6:862-868.

  56. repeats
    Sébastien Leclercq, Eric Rivals, Philippe Jarne (2007), "Detecting microsatellites within genomes: significant variation among algorithms", BMC Bioinformatics, 8:125
    [abstract]

  57. P Licinio, JCO Guerra (2007), "Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets", Biophysical Journal, 92:2000-2006.

  58. Fabrizio Lillo, Marco Spano (2007), "Inverted and mirror repeats in model nucleotide sequences", Physical Review E, 76:041914.
    [abstract]

  59. Fang Liu, Eivind Tøstesen, Jostein K. Sundet, Tor-Kristian Jenssen, Christoph Bock, Geir Ivar Jerstad, William G. Thilly, Eivind Hovig (2007), "The human genomic melting map", PLoS Computational Biology, 3(5):e93.

  60. Ying-zhao Liu, Yan-chun Yang, Tian-ming Wang (2007), "Characteristic distribution of L-tuple for DNA primary sequence", Journal of Biomolecular Structure and Dynamics, 25(1):85-92.
    [abstract]

  61. CB Lowe, G Bejerano, D Haussler (2007), "Thousands of human mobile element fragments undergo strong purifying selection near developmental genes", Proceedings of National Academy of Sciences, 104(19):8005-8010.

  62. Bin-Guang Ma (2007), "How to describe genes: enlightenment from the quaternary number system", Biosystems, 90:20-27.

  63. Bo Eskerod Madsen, Palle Villesen, & Carsten Wiuf (2007), "A periodic pattern of SNPs in the human genome", Nature Precedings preprint, 435
    [ abstract]

  64. L Martignetti, M Caselle (2007), "Universal power law behaviors in genomic sequences and evolutionary models", Physical Review E, 76(2):021902.

  65. C Melodelima, C Gautier, D Piau (2007), "A markovian approach for the prediction of mouse isochores", Journal of Mathematical Biology, 55(3):353-364.

  66. PW Messer, PF Arndt (2007), "The majority of recent short DNA insertions in the human genome are tandem duplications", Molecular Biology and Evolution, 24(5):1190-1197.

  67. PW Messer, R Bundschuh, M Vingron, PF Arndt (2007), "Effects of long-range correlations in DNA on sequence alignment score statistics", Journal of Computational Biology, 14(5):655-668.
    [abstract]

  68. protein
    Christopher Michael Hemmerich and Sun Kim (2007), "A study of residue correlation within protein sequences and its application to sequence classification", EURASIP Journal on Bioinformatics and Systems Biology, 2007:87356.
    [html]

  69. sequence
    Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M J Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E Deakin, Melissa J Fazzari, Jacob L Glass, Manfred Grabherr, John M Greally, Wanjun Gu, Timothy A Hore, Gavin A Huttley, Michael Kleber, Randy L Jirtle, Edda Koina, Jeannie T Lee, Shaun Mahony, Marco A Marra, Robert D Miller, Robert D Nicholls, Mayumi Oda, Anthony T Papenfuss, Zuly E Parra, David D Pollock, David A Ray, Jacqueline E Schein, Terence P Speed, Katherine Thompson, John L VandeBerg, Claire M Wade, Jerilyn A Walker, Paul D Waters, Caleb Webber, Jennifer R Weidman, Xiaohui Xie, Michael C Zody, Broad Institute Genome Sequencing Platform and Broad Institute Whole Genome Assembly Team and, Jennifer A Marshall Graves, Chris P Ponting, Matthew Breen, Paul B Samollow, Eric S Lander, Kerstin Lindblad-Toh (2007), "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences", Nature, 447:167-177.
    [ abstract]

  70. a/symmetry
    Xiang Jia Min and Donal A. Hickey (2007), "DNA asymmetric strand bias affects the amino acid composition of mitochondrial proteins", DNA Research, 14:201-206.
    [ abstract]

  71. a/symmetry
    D Mitchell (2007), "GC content and genome length in Chargaff compliant genomes", Biochemical and Biophysical Research Communications, 353(1):207-210.
    [ abstract]

  72. Richard A Morton, Brian R Morton (2007), "Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes", BMC Genomics, 8:369.
    [abstract]

  73. S Nicolay, EB Brodie of Brodie, M Touchon, B Audit, Y d'Aubenton-Carafa, C Thermes, A Arneodo (2007), "Bifractality of human DNA strand-asymmetry profiles results from transcription", Physical Review E, 75:032902.
    [abstract]

  74. Nidhal Bouaynaya, Dan Schonfeld (2007), "Non-stationary analysis of DNA sequences", in Proceedings of IEEE 14th Workshop onn Statistical Signal Processing, pp.200-204 (IEEE).
    [abstract]

  75. Nestor Norio Oiwa (2007), "The nucleotide sequence and the local electronic structure", Journal of Physics: Condensed Matter, 19:181001.
    [abstract]

  76. a/symmetry
    Kohji Okamura, John Wei, Stephen W Scherer (2007), "Evolutionary implications of inversions that have caused intra-strand parity in DNA", BMC Genomics, 8:160.
    [abstract]

  77. sequence
    B Palenik, Grimwood, J, Aerts, A, Rouzé, P, Salamov, A, Putnam, N, Zhou, K, Jorgensen, R, Derelle, E, Rombauts, S, Otillar, R, Merchant, S, Podell, S, Gaasterland, T, Manuell, A, Napoli, C, Gendler, K, Vallon, O, Peyretaillade, E, Jancek, S, Piganeau, G, Heijde, M, Lohr, M, Jabbari, K, Bowler, C, Werner, G, Robbens, S, Pazour, G, Dubchak, I, Ren, Q, Delwiche, C, Paulsen, I, De Boever, P, Schmutz, J, Rokhsar, D, Van de Peer, Y, Moreau, H, Grigoriev, I (2007), "The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation", Proceedings of National Academy of Sciences, 104:7705-7710

  78. repeats
    V Paar, I Basar, M Rosandic', M Gluncic' (2007), "Consensus higher order repeats and frequency of string distributions in human genome", Current Genomics, 8(2):93-111.

  79. HE Peckham, RE Thurman, Y Fu, JA Stamatoyannopoulos, WS Noble, K Struhl, Z Weng (2007), Nucleosome positioning signals in genomic DNA. Genome Research, 17(8):1170-1177.

  80. sequence
    HJ Pel, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wösten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H (2007), "Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88", Nature Biotechnology, 25(2):221-231.
    [ abstract]

  81. Boris Podobnik, Jia Shao, Nikolay V. Dokholyan, Vinko Zlatic, H. Eugene Stanley, Ivo Grosse (2006), "Similarity and dissimilarity in correlations of genomic DNA", Physica A, 373:497-502.
    [ abstract]

  82. sequence
    Joan U. Pontius, James C. Mullikin, Douglas R. Smith, Agencourt Sequencing Team, Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro A. Schäffer, Richa Agarwala, Kristina Narfström, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-Slattery, Warren E. Johnson, Guillaume Bourque, Glenn Tesler, NISC Comparative Sequencing Program, and Stephen J. O?Brien (2007), "Initial sequence and comparative analysis of the cat genome", Genome Research, 17:1675-1689.
    [abstract]

  83. A Provata, Th Oikonomou (2007), "Power law exponents characterizing human DNA", Physical Review E, 75:056102.
    [abstract]

  84. Issaac Rajan, Sarang Aravamuthan, Sharmila S Mande (2007), "Identification of compositionally distinct regions in genomes using the centroid method", Bioinformatics, 23(20):2672-2677.
    [abstract]

  85. repeats
    Passoupathy Rajendrakumar, Akshaya Kumar Biswal, Sena M. Balachandran, Kommoju Srinivasarao, and Raman M. Sundaram (2007), "Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions", Bioinformatics, 23(1):1-4.
    [abstract]

  86. DB Saakian (2007), "A new method for the solution of models of biological evolution: derivation of exact steady-state distributions", Journal of Statistical Physics, 128(3):781-798.

  87. F Salih, B. Salih, E. N. Trifonov (2007), "Sequence-directed mapping of nucleosome positions", Journal of Biomolecular Structure and Dynamics, 24(5):489-494.
    [abstract]

  88. isochore
    C Schmegner, H Hameister, W Vogel, G Assum (2007), "Isochores and replication time zones: a perfect match", Cytogenetic and Genome Research, 116:167-172.

  89. isochore
    Claudia Schmegner, Josef Hoegel, Walther Vogel, Günter Assum (2007), "The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: implications for the evolution of the mammalian genome structure", Genetics, 175:421-428.
    [abstract]

  90. D Sellis, A Provata, Y Almirantis (2007), "Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws", Molecular Biology and Evolution, 24(11):2385-2399.

  91. Xiaoli Shi, Xiyin Wang, Zhe Li, Qihui Zhu, Ji Yang, Song Ge, Jingchu Luo (2007), "Evidence that natural selection is the primary cause of the guanine-cytosine content variation in rice genes", Journal of Integrative Plant Biology, 49:1393-1399.
    [ abstract]

  92. sequence
    Kerrin S Small, Michael Brudno, Matthew M Hill, and Arend Sidow (2007), "A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome", Genome Biology, 8(3):R41.
    [ abstract]

  93. Jie Song (2007), "Analysis of similarity/dissimilarity DNA sequences by a new 3D graphical representation", Journal of Biological Systems, 15(3):287-297.
    [ abstract]

  94. Haruo Suzuki, Rintaro Saito, and Masaru Tomita (2007), "Variation in the correlation of G+C composition with synonymous codon usage bias among bacteria", EURASIP Journal on Bioinformatics and Systems Biology, 2007:61374.
    [abstract]

  95. D Swati (2007), "In silico comparison of bacterial strains using mutual information", Journal of Biosciences, 32(6):1169-1184.
    [PDF]

  96. Vivek Thakur, Rajeev K. Azad, and Ram Ramaswamy (2007), "Markov models of genome segmentation", Physical Review E, 75:011915.
    [abstract]

  97. Cuong Than, Derek Ruths, Hideki Innan, Luay Nakhleh (2007), "Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions" Journal of Computational Biology, 14(4):517-535.
    [abstract]

  98. Jamie M Thomas, Daniel Horspool, Gordon Brown, Vasily Tcherepanov, Chris Upton (2007), "GraphDNA: a Java program for graphical display of DNA composition analyses", BMC Bioinformatics, 8:21
    [abstract]

  99. Vetrivel Umashankar, Vijayakumar Arunkumar, Sudarsanam Dorairaj (2007), "ACUA: A software tool for automated codon usage analysis", Bioinformation, 2(2):62-63.
    [PDF]

  100. sequence
    Riccardo Velasco, Andrey Zharkikh, Michela Troggio, Dustin A Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, Lisa M FitzGerald, Silvia Vezzulli, Julia Reid, Giulia Malacarne, Diana Iliev, Giuseppina Coppola, Bryan Wardell, Diego Micheletti, Teresita Macalma, Marco Facci, Jeff T Mitchell, Michele Perazzolli, Glenn Eldredge, Pamela Gatto, Rozan Oyzerski, Marco Moretto, Natalia Gutin, Marco Stefanini, Yang Chen, Cinzia Segala, Christine Davenport, Lorenzo Demattè, Amy Mraz, Juri Battilana, Keith Stormo, Fabrizio Costa, Quanzhou Tao, Azeddine Si-Ammour, Tim Harkins, Angie Lackey, Clotilde Perbost, Bruce Taillon, Alessandra Stella, Victor Solovyev, Jeffrey A Fawcett, Lieven Sterck, Klaas Vandepoele, Stella M Grando, Stefano Toppo, Claudio Moser, Jerry Lanchbury, Robert Bogden, Mark Skolnick, Vittorio Sgaramella, Satish K Bhatnagar, Paolo Fontana, Alexander Gutin, Yves Van de Peer, Francesco Salamini, and Roberto Viola (2007), "A high quality draft consensus sequence of the genome of a heterozygous grapevine variety", PLoS ONE, 2:e1326

  101. Susana Vinga, Jonas S Almeida (2007), "Local Renyi entropic profiles of DNA sequences", BMC Bioinformatics, 8:393.
    [abstract]

  102. protein
    Zhimeng Wang, Lin Jiang, Menglong Li, Lina Sun, Rongying Lin (2007), "Fast Fourier transform-based support vector machine for subcellular localization prediction using different substitution models", Acta Biochimica et Biophysica Sinica, 39(9):715-721.
    [ abstract]

  103. protein
    Liu Xiang, Wang Yifei (2007), "A modified resonant recognition model to predict protein-protein interaction", Frontiers of Biology in China, 2(3):268-271.
    [ abstract]

  104. period:3
    C Yin, SST Yau (2007), "Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence", Journal of Theoretical Biology, 247:687-694.

  105. Byung-Jun Yoon, PP Vaidyanathan (2007), "Computational identification and analysis of noncoding RNAs -- Unearthing the buried treasures in the genome", IEEE Signal Processing Magazine, 24(1):64-74.

  106. Jun Yu (2007), "A content-centric organization of the genetic code", Genomics, Proteomics & Bioinformatics, 5(1):1-6.
    [ abstract]
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