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+ 2006

  1. Mateo Aboy, Roberto Hornero, Daniel Abasolo, Daniel Alvarez (2006), "Interpretation of the Lempel-Ziv complexity measure in the context of biomedical signal analysis", IEEE Transactions on Biomedical Engineering, 53(11):2282-2288.

  2. György Abrusán, Hans-Jürgen Krambeck (2006), "The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model", Journal of Molecular Evolution, 63(4):484-492.

  3. a/symmetry
    Guenter Albrecht-Buehler (2006), "Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions", Proceedings of National Academy of Sciences, 103(47):17828-17833.
    [abstract] [PDF]

  4. Timothy E. Allen, Nathan D Price, Andrew R Joyce, Bernhard Ř Palsson (2006), "Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization", PLoS Computational Biology, 2(1):e2.
    [html] [PDF]

  5. S Arhondakis, O Clay, G Bernardi (2006), "Compositional properties of human cDNA libraries: practical implications", FEBS Letters, 580(24):5772-5778.

  6. sequence
    JM Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Ségurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Câmara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouël A, Lepčre G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Bétermier M, Weissenbach J, Scarpelli C, Schächter V, Sperling L, Meyer E, Cohen J, Wincker P (2006), "Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia", Nature, 444(7116):171-178.

  7. sequence
    Yoshinao Azuma, Hideki Hirakawa, Atsushi Yamashita, Yan Cai, Mohd Akhlakur Rahman, Harumi Suzuki, Shigeki Mitaku, Hidehiro Toh, Susumu Goto, Tomoyuki Murakami, Kazuro Sugi, Hideo Hayashi, Hideto Fukushi, Masahira Hattori, Satoru Kuhara, and Mutsunori Shirai (2006), "Genome Sequence of the Cat Pathogen, Chlamydophila felis", DNA Research, 13:15-23.
    [abstract]

  8. Andrew TM Bagshaw, Joel PW Pitt, Neil J Gemmell (2006), "Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots", BMC Genomics, 7:179.
    [abstract]

  9. protein
    Fenglan Bai, Tianming Wang (2006), "On graphical and numerical representation of protein sequences", Journal of Biomolecular Structure and Dynamics, 23(5):537-546.
    [abstract]

  10. Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola (2006), "Codon usage domains over bacterial chromosomes", PLoS Computational Biology, 2(4):e37.
    [abstract]

  11. A Benecke (2006), "Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs", European Physical Journal E, 19(3):353-366.

  12. Tim T. Binnewies, Yair Motro, Peter F. Hallin, Ole Lund, David Dunn, Tom La, David J. Hampson, Matthew Bellgard, Trudy M. Wassenaar and David W. Ussery (2006), "Ten years of bacterial genome sequencing: comparative-genomics-based discoveries", Functional & Integrative Genomics, 6(3):165-185.
    [abstract]

  13. Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, Jörn Walter (2006), "CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure", PLoS Genetics, 2(3): e26.
    [abstract]

  14. repeats
    Valentina Boeva, Mireille Regnier, Dmitri Papatsenko, and Vsevolod Makeev (2006), "Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression", Bioinformatics, 22(6):676-684.
    [abstract]

  15. Sergey V Buldyrev (2006), "Power law correlations in DNA sequences", in Power Laws, Scale-Free Networks and Genome Biology, eds. Eugene V Koonin, Yuri I Wolf, Georgy P Karev, pp.123-164 (Springer).

  16. Emanuele Bultrini and Elisabetta Pizzi (2006), "A new parameter to study compositional properties of non-coding regions in eukaryotic genomes", Gene, 385:75-82.
    [abstract]

  17. repeats
    Anat Caspi and Lior Pachter (2006), "Identification of transposable elements using multiple alignments of related genomes", Genome Research, 16(2):260-270.
    [abstract]

  18. sequence
    Patrick S G Chain, Vincent J Denef, Konstantinos T Konstantinidis, Lisa M Vergez, Loreine Agulló, Valeria Latorre Reyes, Loren Hauser, Macarena Córdova, Luis Gómez, Myriam González, Miriam Land, Victoria Lao, Frank Larimer, John J LiPuma, Eshwar Mahenthiralingam, Stephanie A Malfatti, Christopher J Marx, J Jacob Parnell, Alban Ramette, Paul Richardson, Michael Seeger, Daryl Smith, Theodore Spilker, Woo Jun Sul, Tamara V Tsoi, Luke E Ulrich, Igor B Zhulin, and James M Tiedje (2005), "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility" Proceedings of National Academy of Sciences, 103(42):15280-15287.

  19. V R Chechetkin, V V Lobzin (2006), "Anticodons, frameshifts, and hidden periodicities in tRNA sequences", Journal of Biomolecular Structure and Dynamics, 24(2):189-202.
    [abstract]

  20. isochore
    JF Chen, F Lu, SS Chen, SH Tao (2006), "Significant positive correlation between the recombination rate and GC content in the human pseudoautosomal region", Genome, 49(5):413-419.

  21. P. Christoph Champ, Tim T. Binnewies, Natasja Nielsen, Guy Zinman, Kristoffer Kiil, Heng Wu, Jon Bohlin, and David W. Ussery (2006), "Genome update: purine strand bias in 280 bacterial genomes", Microbiology, 152:579-583.
    [html]

  22. Dominique Chu, Jonathan Rowe, and Hoong-Chien Lee (2006), "Evaluation of the current models for the evolution of bacterial DNA uptake signal sequences", Journal of Theoretical Biology, 238:157-166.

  23. period:10-11
    AB Cohanim, Y Kashi, EN Trifonov (2006), "Three sequence rules for chromatin", Journal of Biomolecular Structure and Dynamics, 23(5):559-566.
    [abstract]

  24. Richard Cordaux, Jungnam Lee, Liv Dinoso, Mark A Batzer (2006), "Recent integrated Alu retrosposons are essentially neutral residents of the human genome" Gene, 373:138-144.

  25. M Costantini, O Clay, F Auletta, G Bernardi (2006), "An isochore map of human chromosomes", Genome Research, 16(4):536-541.
    [abstract] [PDF]

  26. Miklos Csuros, Ming-Te Cheng, Andreas Grimm, Amine Halawani and Perrine Landreau (2006), "Segmentation with an isochore distribution", Lecture Notes in Computer Science Vol 4175, pp. 388-399 (Springer)
    [PDF]

  27. Daniel Dalevi, Devdatt Dubhashi, Malte Hermansson (2006), "A new order estimator for fixed and variable length Markov models with applications to DNA sequence similarity", Statistical Applications in Genetics and Molecular Biology, 5(1):8.
    [abstract]

  28. Rajdeep Das, Nevenka Dimitrova, Zhenyu Xuan, Robert A. Rollins, Fatemah Haghighi, John R. Edwards, Jingyue Ju, Timothy H Bestor, Michael Q Zhang (2006), "Computational prediction of methylation status in human genomic sequences", Proceedings of National Academy of Sciences, 103(28):10713-10716.

  29. Grégory Deceliere, Yann Letrillard, Sandrine Charles, and Christian Biémont (2006), "TESD: a transposable element dynamics simulation environment", Bioinformatics, 22(21):2702-2703.
    [abstract]

  30. Manuel Dehnert, Werner E. Helm, and Marc-Thorsten Hütt (2006), "Informational structure of two closely related eukaryotic genomes", Physical Review E, 74:021913.
    [abstract]

  31. sequence
    Evelyne Derelle, Conchita Ferraz, Stephane Rombauts, Pierre Rouzé, Alexandra Z Worden, Steven Robbens, Frédéric Partensky, Sven Degroeve, Sophie Echeynié, Richard Cooke, Yvan Saeys, Jan Wuyts, Kamel Jabbari, Chris Bowler, Olivier Panaud, Benoît Piégu, Steven G. Ball, Jean-Philippe Ral, François-Yves Bouget, Gwenael Piganeau, Bernard De Baets, André Picard, Michel Delseny, Jacques Demaille, Yves Van de Peer, and Hervé Moreau (2006), "Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features", Proceedings of National Academy of Sciences, 103(31):11647-11652.
    [abstract]

  32. binding-energy
    bending
    DNA-loop
    Surjit B. Dixit and David L. Beveridge (2006), "Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction", Bioinformatics, 22(8):1007-1009.
    [abstract]

  33. JA Drake, C Bird, J Nemesh, DJ Thomas, C Newton-Cheh, A Reymond, L Excoffier, H Attar, SE Antonarakis, ET Dermitzakis, JN Hirschhorn (2006), "Conserved noncoding sequences are selectively constrained and not mutation cold spots", Nature Genetics, 38(2):223-227.

  34. Laurent Duret, Adam Eyre-Walker and Nicolas Galtier (2006), "A new perspective on isochore evolution", Gene, 385:71-74
    [abstract]

  35. sequence
    Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, Jonathan H. Badger, Qinghu Ren, Paolo Amedeo, Kristie M. Jones, Luke J. Tallon, Arthur L. Delcher, Steven L. Salzberg, Joana C. Silva, Brian J. Haas, William H. Majoros, Maryam Farzad, Jane M. Carlton, Roger K. Smith Jr., Jyoti Garg, Ronald E. Pearlman, Kathleen M. Karrer, Lei Sun, Gerard Manning, Nels C. Elde, Aaron P. Turkewitz, David J. Asai, David E. Wilkes, Yufeng Wang, Hong Cai, Kathleen Collins, B. Andrew Stewart, Suzanne R. Lee, Katarzyna Wilamowska, Zasha Weinberg, Walter L. Ruzzo, Dorota Wloga, Jacek Gaertig, Joseph Frankel, Che-Chia Tsao, Martin A. Gorovsky, Patrick J. Keeling, Ross F. Waller, Nicola J. Patron, J. Michael Cherry, Nicholas A. Stover, Cynthia J. Krieger, Christina del Toro, Hilary F. Ryder, Sondra C. Williamson, Rebecca A. Barbeau, Eileen P. Hamilton, Eduardo Orias (2006), "Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote", PLoS Biology, 4(9):e286.
    [abstract]

  36. A Fadiel, K D Eichenbaum, A Hamza (2006), "'Genomemark': detecting word periodicity in biological sequences", Journal of Biomolecular Structure and Dynamics, 23(4):457-464.
    [abstract]

  37. Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang (2006), "Predicting methylation status of CpG islands in the human brain", Bioinformatics, 22(18):2204-2209.

  38. period:10-11
    A Fire, R Alcazar, F Tan (2006), "Unusual DNA structures associated with germline genetic activity in Caenorhabditis elegans", Genetics, 173(3):1259-1273.

  39. bending
    Claire Gaillard and François Strauss (2006), "DNA topology and genome organization in higher eukaryotes: A model", Journal of Theoretical Biology, 243:604-607.
    [abstract]

  40. Feng Gao, Chun-Ting Zhang (2006), "GC-profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences", Nucleic Acids Research, 34(web server issue):W686-W691.

  41. sequence
    Paul R. Gilson, Vanessa Su, Claudio H. Slamovits, Michael E. Reith, Patrick J. Keeling, and Geoffrey I. McFadden (2006), "Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature's smallest nucleus", Proceedings of National Academy of Sciences, 103(25):9566-9571.

  42. Richard E. Green, Johannes Krause, Susan E. Ptak, Adrian W. Briggs, Michael T. Ronan, Jan F. Simons, Lei Du, Michael Egholm, Jonathan M. Rothberg, Maja Paunovic, and Svante Pääbo (2006), "Analysis of one million base pairs of Neanderthal DNA", Nature, 444:330-336.

  43. sequence
    SG Gregory, KF Barlow, KE McLay, R Kaul, D Swarbreck, A Dunham, CE Scott, KL Howe, K Woodfine, CCA Spencer, MC Jones, C Gillson, S Searle, Y Zhou, F Kokocinski, L McDonald, R Evans, K Phillips, A Atkinson, R Cooper, C Jones, RE Hall, TD Andrews, C Lloyd, R Ainscough, JP Almeida, KD Ambrose, F Anderson, RW Andrew, RIS Ashwell, K Aubin, AK Babbage, CL Bagguley, J Bailey, H Beasley, G Bethel, CP Bird, S Bray-Allen, JY Brown, AJ Brown, D Buckley, J Burton, J Bye, C Carder, JC Chapman, SY Clark, G Clarke, C Clee, V Cobley, RE Collier, N Corby, GJ Coville, J Davies, R Deadman, M Dunn, M Earthrowl, AG Ellington, H Errington, A Frankish, J Frankland, L French, P Garner, J Garnett, L Gay, MRJ Ghori, R Gibson, LM Gilby, W Gillett, RJ Glithero, DV Grafham, C Griffiths, S Griffiths-Jones, R Grocock, S Hammond, ESI Harrison, E Hart, E Haugen, PD Heath, S Holmes, K Holt, PJ Howden, AR Hunt, SE Hunt, G Hunter, J Isherwood, R James, C Johnson, D Johnson, A Joy, M Kay, JK Kershaw, M Kibukawa, AM Kimberley, A King, AJ Knights, H Lad, G Laird, S Lawlor, DA Leongamornlert, DM Lloyd, J Loveland, J Lovell, MJ Lush, R Lyne, S Martin, M Mashreghi-Mohammadi, L Matthews, NSW Matthews, S McLaren, S Milne, S Mistry, MJF M oore, T Nickerson, CN O'Dell, K Oliver, A Palmeiri, SA Palmer, A Parker, D Patel, AV Pearce, AI Peck, S Pelan, K Phelps, BJ Phillimore, R Plumb, J Rajan, C Raymond, G Rouse, C Saenphimmachak, HK Sehra, E Sheridan, R Shownkeen, S Sims, CD Skuce, M Smith, C Steward, S Subramanian, N Sycamore, A Tracey, A Tromans, Z Van Helmond, M Wall, JM Wallis, S White, SL Whitehead, JE Wilkinson, DL Willey, H Williams, L Wilming, PW Wray, Z Wu, A Coulson, M Vaudin, JE Sulston, R Durbin, T Hubbard, R Wooster, I Dunham, NP Carter, G McVean, MT Ross, J Harrow, MV Olson, S Beck, J Rogers and DR Bentley (2006), "The DNA sequence and biological annotation of human chromosome 1", Nature, 441:315-321.
    [abstract] [PDF]

  44. Jianying Gu and Wen-Hsiung Li (2006), "Are GC-rich isochores vanishing in mammals?", Gene, 385:50-56.
    [abstract]

  45. P Katsaloulis, T Theoharis, WM Zheng, BL Hao, A Bountis, Y Almirantis, A Provata (2006), "Long-range correlations of RNA polymerase II promoter sequences across organisms", Physica A, 366:308-322.

  46. Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza, José L Oliver (2006), "CpGcluster: a distance-based algorithm for CpG-island detection", BMC Bioinformatics, 7:446.
    [abstract]

  47. Adrian D. Haimovich, Bruce Byrne, Ramakrishna Ramaswamy, William J. Welsh (2006), "Wavelet analysis of DNA walks", Journal of Computational Biology, 13(7):1289-1298.
    [abstract]

  48. Anne E. Hall, Gregory C. Kettler, and Daphne Preuss (2006), "Dynamic evolution at pericentromeres", Genome Research, 16(3):355-364.
    [abstract]

  49. Weilong Hao and G. Brian Golding (2006), "The fate of laterally transferred genes: Life in the fast lane to adaptation or death", Genome Research, 16(5):636-643.
    [abstract]

  50. repeats
    Bernhard Haubold, Thomas Wiehe (2006), "How repetitive are genomes?", BMC Bioinformatics, 7:541.
    [abstract]

  51. MF Higareda, H Hernández-Saldana, RA Méndez-Sánchez (2006), "Nearest-neighbor spacing distribution of basis in some in tron-less and intron-containing coding DNA sequences", Physica A, 372(2):368-373.
    [abstract]

  52. Koichiro Higasa, Kenshi Hayashi (2006), "Periodicity of SNP distribution around transcription start sites", BMC Genomics, 7:88.
    [abstract]

  53. a/symmetry
    Wen-Ru Hou, Hai-Fang Wang, Deng-Ke Niu (2006), "Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication orgin, and termination", Biomchemical and Biophysical Research Communications, 344:1258-1262.

  54. sequence
    Jörg Kämper, Regine Kahmann, Michael Bölker, Li-Jun Ma, Thomas Brefort, Barry J. Saville, Flora Banuett, James W. Kronstad, Scott E. Gold, Olaf Müller, Michael H. Perlin, Han A. B. Wösten, Ronald de Vries, José Ruiz-Herrera, Cristina G. Reynaga-Peńa, Karen Snetselaar, Michael McCann, José Pérez-Martín, Michael Feldbrügge, Christoph W. Basse, Gero Steinberg, Jose I. Ibeas, William Holloman, Plinio Guzman, Mark Farman, Jason E. Stajich, Rafael Sentandreu, Juan M. González-Prieto, John C. Kennell, Lazaro Molina, Jan Schirawski, Artemio Mendoza-Mendoza, Doris Greilinger, Karin Münch, Nicole Rössel, Mario Scherer, Miroslav Vranes, Oliver Ladendorf, Volker Vincon, Uta Fuchs, Björn Sandrock, Shaowu Meng, Eric C. H. Ho, Matt J. Cahill, Kylie J. Boyce, Jana Klose, Steven J. Klosterman, Heine J. Deelstra, Lucila Ortiz-Castellanos, Weixi Li, Patricia Sanchez-Alonso, Peter H. Schreier, Isolde Häuser-Hahn, Martin Vaupel, Edda Koopmann, Gabi Friedrich, Hartmut Voss, Thomas Schlüter, Jonathan Margolis, Darren Platt, Candace Swimmer, Andreas Gnirke, Feng Chen, Valentina Vysotskaia, Gertrud Mannhaupt, Ulrich Güldener, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Hans-Werner Mewes, Evan W. Mauceli, David DeCaprio, Claire M. Wade, Jonathan Butler, Sarah Young, David B. Jaffe, Sarah Calvo, Chad Nusbaum, James Galagan, and Bruce W. Birren (2006), "Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis", Nature, 444:97-101.

  55. Jonathan M. Keith (2006), "Segmenting eukaryotic genomes with the generalized Gibbs sampler", Journal of Computational Biology, 13(7):1369-1383.
    [abstract]

  56. isochore
    A Khelifi, J Meunier, L Duret, D Mouchiroud (2006), "GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates", Journal of Molecular Evolution, 62(2):745-752.
    [abstract]

  57. SB Kogan, M Kato, R Kiyama, EN Trifonov (2006), "Sequence structure of human nucleosome DNA", Journal of Biomolecular Structure and Dynamics, 24(1):43-48
    [abstract]

  58. isochore
    Fyodor A. Kondrashov, Aleksey Y. Ogurtsov and Alexey S. Kondrashov (2006), "Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites", Journal of Theoretical Biology, 240:616-626.
    [abstract]

  59. Daniel Kotlar, Yizhar Lavner (2006), "The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids", BMC Genomics, 7:67.
    [abstract]

  60. sequence
    Andrea Krause, Adarsh Ramakumar, Daniela Bartels, Federico Battistoni, Thomas Bekel, Jens Boch, Melanie Böhm, Frauke Friedrich, Thomas Hurek, Lutz Krause, Burkhard Linke, Alice C McHardy, Abhijit Sarkar, Susanne Schneiker, Arshad Ali Syed, Rudolf Thauer, Frank-Jörg Vorhölter, Stefan Weidner, Alfred Pühler, Barbara Reinhold-Hurek, Olaf Kaiser, and Alexander Goesmann (2006), "Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72", Nature Biotechnology, 24:1385-1391.

  61. period:10-11
    Lokesh Kumar, Matthias Futschik, Hanspeter Herzel (2006), "DNA motifs and sequence periodicities", In Silico Biology, 6:0008.

  62. protein
    Igor B. Kuznetsov and Seungwoo Hwang (2006), "A novel sensitive method for the detection of user-defined compositional bias in biological sequences", Bioinformatics, 22(9):1055-1063.
    [abstract]

  63. Ngai-Fong Law, Kin-On Cheng, Wan-Chi Siu (2006), "On relationship of Z-curve and Fourier approaches for DNA coding sequence classification", Bioinformation, 1(7): 242-246.
    [abstract]

  64. Chun Li, Nannan Tang, Jun Wan (2006), "Directed graphs of DNA sequences and their numerical characterization", Journal of Theoretical Biology, 241:173-177.
    [abstract]

  65. Wentian Li, Pedro Miramontes (2006), "Large-scale oscillation of structure-related DNA sequence features in human chromosome 21", Physical Review E, 74:021912.
    [abstract]

  66. Xiao Qing Liu, Qi Dai, Zhilong Xu, Tianming Wang (2006), "PNN-curve: a new 2D graphical representation of DNA sequences and its application", Journal of Theoretical Biology, 243:555-561.
    [abstract]

  67. repeats
    Xiaowen Liu, Lusheng Wang (2006), "Finding the region of pseudo-periodic tandem repeats in biological sequences", Algorithms for Molecular Biology, 1:2.
    [abstract]

  68. JR Lobry and A Necsulea (2006), "Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes", Gene, 385:128-136.
    [abstract]

  69. S.R.C. Lopes and M.A. Nunes (2006), "Long memory analysis in DNA sequences", Physica A, 361(2):569-588.

  70. sequence
    K Makarova, A Slesarev, Y Wolf, A Sorokin, B Mirkin, E Koonin, A Pavlov, N Pavlova, V Karamychev, N Polouchine, V Shakhova, I Grigoriev, Y Lou, D Rohksar, S Lucas, K Huang, D M Goodstein, T Hawkins, V Plengvidhya, D Welker, J Hughes, Y Goh, A Benson, K Baldwin, J -H Lee, I Díaz-Muńiz, B Dosti, V Smeianov, W Wechter, R Barabote, G Lorca, E Altermann, R Barrangou, B Ganesan, Y Xie, H Rawsthorne, D Tamir, C Parker, F Breidt, J Broadbent, R Hutkins, D O'Sullivan, J Steele, G Unlu, M Saier, T Klaenhammer, P Richardson, S Kozyavkin, B Weimer, and D Mills (2006), "Comparative genomics of the lactic acid bacteria", Proceedings of National Academy of Sciences, 103(42):15611-15616

  71. repeats
    Ketil Malde, Korbinian Schneeberger, Eivind Coward, and Inge Jonassen (2006), "RBR: library-less repeat detection for ESTs", Bioinformatics, 22(18):2232-2236.
    [abstract]

  72. Matthew Mazowita, Lani Haque, David Sankoff (2006), "Stability of rearrangement measures in the comparison of genome sequences", Journal of Computational Biology, 13(2):554-566.
    [abstract]

  73. sequence
    Michael P. McLeod, René L. Warren, William W. L. Hsiao, Naoto Araki, Matthew Myhre, Clinton Fernandes, Daisuke Miyazawa, Wendy Wong, Anita L. Lillquist, Dennis Wang, Manisha Dosanjh, Hirofumi Hara, Anca Petrescu, Ryan D. Morin, George Yang, Jeff M. Stott, Jacqueline E. Schein, Heesun Shin, Duane Smailus, Asim S. Siddiqui, Marco A. Marra, Steven J. M. Jones, Robert Holt, Fiona S. L. Brinkman, Keisuke Miyauchi, Masao Fukuda, Julian E. Davies, William W. Mohn, and Lindsay D. Eltis (2006), "The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse", Proceedings of National Academy of Sciences, 103(42):15582-15587.

  74. John A. McNeil, Kelly P. Smith, Lisa L. Hall, and Jeanne B. Lawrence (2006), "Word frequency analysis reveals enrichment of dinucleotide repeats on the human X chromosome and [GATA]n in the X escape region", Genome Research, 16(4):477-484.
    [abstract]

  75. Christelle Melodelima, Laurent Guéguen, Didier Piau and Christian Gautier (2006), "A computational prediction of isochores based on hidden Markov models", Gene, 385:41-49.
    [abstract]

  76. Giulia Menconi, Roberto Marangoni (2006), "A compression-based approach for coding sequences identification. I. application to prokaryotic genomes", Journal of Computational Biology, 13(8):1477-1488.
    [abstract]

  77. Philipp W Messer, Peter F Arndt (2006), "CorGen -- measuring and generating long-range correlations for DNA sequence analysis", Nucleic Acids Research, 34(Web Server issue):W692-W695.
    [abstract]

  78. Philipp W Messer, Ralf Bundschuh, Martin Vingron, Peter F Arndt (2006), "Alignment statistics for long-range correlated genomic sequences", Proceedings of the Tenth International Conference on Research in Computational Molecular Biology , pp.?-?

  79. D Mitchell, R Bridge (2006), "A test of Chargaff's second rule", Biochemical and Biophysical Research Communications, 340:90-94.

  80. D Mitchell, R Bridge (2006), "An investigation of genomic base distribution", Biochemical and Biophysical Research Communications, 344(2):612-616.

  81. repeats
    Satoshi Mizuta, Hikaru Munakata, Abulimiti Aimaiti, Ichitaro Oya, Kenji Oosawa and Toshio Shimizu (2006), "Analysis of tandem repeats found in 44 prokaryotic genomes", In Silico Biology, 6:0014.

  82. period:10-11
    Fernando Moreno-Herrero, Ralf Seidel, Steven M Johnson, Andrew Fire, Nynke H. Dekker (2006), "Structural analysis of hyperperiodic DNA from Caenorhabditis elegans", Nucleic Acids Research, 34(1):3057-3066.
    [abstract]

  83. repeats
    Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, and Richa Agarwala (2006), "WindowMasker: window-based masker for sequenced genomes", Bioinformatics, 22(2):134-141.
    [abstract]

  84. Jan Mrázek and Shaohua Xie (2006), "Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences", Bioinformatics, 22(24):3099-3100.
    [abstract]

  85. Indranil Mukhopadhyay, Anup Som, Satyabrata Sahoo (2006), "Word organization in coding DNA: a mathematical model", Theory in Biosciences, 125:1-17.

  86. H Musto, H Naya, A Zavala, H Romero, F Alvarez-Valin, G Bernardi (2006), "Genomic GC level, optimal growth temperature, and genome size in prokaryotes", Biochemical and Biophysical Research Communications, 347(1):1-3.

  87. sequence
    Donna M. Muzny, Steven E. Scherer, Rajinder Kaul, Jing Wang, Jun Yu, Ralf Sudbrak, Christian J. Buhay, Rui Chen, Andrew Cree, Yan Ding, Shannon Dugan-Rocha, Rachel Gill, Preethi Gunaratne, R. Alan Harris, Alicia C. Hawes, Judith Hernandez, Anne V. Hodgson, Jennifer Hume, Andrew Jackson, Ziad Mohid Khan, Christie Kovar-Smith, Lora R. Lewis, Ryan J. Lozado, Michael L. Metzker, Aleksandar Milosavljevic, George R. Miner, Margaret B. Morgan, Lynne V. Nazareth, Graham Scott, Erica Sodergren, Xing-Zhi Song, David Steffen, Sharon Wei, David A. Wheeler, Mathew W. Wright, Kim C. Worley, Ye Yuan, Zhengdong Zhang, Charles Q. Adams, M. Ali Ansari-Lari, Mulu Ayele, Mary J. Brown, Guan Chen, Zhijian Chen, James Clendenning, Kerstin P. Clerc-Blankenburg, Runsheng Chen, Zhu Chen, Clay Davis, Oliver Delgado, Huyen H. Dinh, Wei Dong, Heather Draper, Stephen Ernst, Gang Fu, Manuel L. Gonzalez-Garay, Dawn K. Garcia, Will Gillett, Jun Gu, Bailin Hao, Eric Haugen, Paul Havlak, Xin He, Steffen Hennig, Songnian Hu, Wei Huang, Laronda R. Jackson, Leni S. Jacob, Susan H. Kelly, Michael Kube, Ruth Levy, Zhangwan Li, Bin Liu, Jing Liu, Wen Liu, Jing Lu, Manjula Maheshwari, Bao-Viet Nguyen, Geoffrey O. Okwuonu, Anthony Palmeiri, Shiran Pasternak, Lesette M. Perez, Karen A. Phelps, Farah J. H. Plopper, Boqin Qiang, Christopher Raymond, Ruben Rodriguez, Channakhone Saenphimmachak, Jireh Santibanez, Hua Shen, Yan Shen, Sandhya Subramanian, Paul E. Tabor, Daniel Verduzco, Lenee Waldron, Jian Wang, Jun Wang, Qiaoyan Wang, Gabrielle A. Williams, Gane K.-S. Wong, Zhijian Yao, JingKun Zhang, Xiuqing Zhang, Guoping Zhao, Jianling Zhou, Yang Zhou, further contributors, David Nelson, Hans Lehrach, Richard Reinhardt, Susan L. Naylor, Huanming Yang, Maynard Olson, George Weinstock and Richard A. Gibbs (2006), "The DNA sequence, annotation and analysis of human chromosome 3", Nature, 440:1194-1198.
    [abstract] [PDF]

  88. R Nagarajan, M Upreti (2006), "Impact of tandem repeats on the scaling of nucleotide sequences", International Journal of Bifurcation and Chaos, 16(10):3103-3108.

  89. repeats
    Hidenori Nishihara, Arian F.A. Smit, and Norihiro Okada (2006), "Functional noncoding sequences derived from SINEs in the mammalian genome", Genome Research, 16(6):864-874.
    [abstract]

  90. sequence
    James P Noonan, Graham Coop, Sridhar Kudaravalli, Doug Smith, Johannes Krause, Joe Alessi, Feng Chen, Darren Platt, Svante Pääbo, Jonathan K. Pritchard, and Edward M. Rubin (2006), "Sequencing and analysis of Neanderthal genomic DNA", Science, 314:1113-1118.

  91. Gregory Nuel (2006), "Numerical solutions for patterns statistics on Markov chains", Statistical Applications in Genetics and Molecular Biology, 5(1):26.
    [abstract]

  92. sequence
    Jung D. Oh, Helene Kling-Bäckhed, Marios Giannakis, Jian Xu, Robert S. Fulton, Lucinda A. Fulton, Holland S. Cordum, Chunyan Wang, Glendoria Elliott, Jennifer Edwards, Elaine R. Mardis, Lars G. Engstrand, and Jeffrey I. Gordon (2006), "The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: Evolution during disease progression", Proceedings of National Academy of Sciences, 103(26):9999-10004.

  93. T Oikonomou, A Provata (2006), "Non-extensive trends in the size distribution of coding and non-coding DNA sequences in the human genome", European Physical Journal B, 50(1-2):259-264.
    [abstract]

  94. Yuriy L Orlov, Rene te Boekhorst, Irina I Abnizova (2006), "Statistical measures of the structure of genomic sequences: entropy, complexity, and position information", Journal of Bioinformatics and Computational Biology, 4(2):523-536.
    [abstract]

  95. Mauro Petrillo, Giustina Silvestro, Pier Paolo Di Nocera, Angelo Boccia, Giovanni Paolella (2006), "Stem-loop structures in prokaryotic genomes", BMC Genomics, 7:170.
    [abstract]

  96. KS Pollard, SR Salama, B King, AD Kern, T Dreszer, S Katzman, A Siepel, JS Pedersen, G Bejerano, R Baertsch, KR Rosenbloom, J Kent, D Haussler (2006), "Forces shaping the fastest evolving regions in the human genome", PLoS Genetics, 2(10):e168.

  97. isochore
    William H. Press, Harlan Robins (2006), "Isochores exhibit evidence of genes interacting with the large-scale genomic environment", Genetics, 174:1029-1040.
    [abstract]

  98. Hui-Qi Qu, Steve G Lawrence, Fan Guo, Jacek Majewski, Constantin Polychronakos (2006), "Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms", BMC Genomics, 7:213.
    [abstract]

  99. A. M. Quirke, F. Jerry Reen, Marcus J. Claesson, and E. Fidelma Boyd (2006), "Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen", Bioinformatics, 22(8):905-910.
    [abstract]

  100. E Rayko, K Jabbari, G Bernardi (2006), "The evolution of introns in human duplicated genes", Gene, 365:41-47.

  101. TS Rekha, CK Mitra (2006), "1/f correlations in viral genomes - a Fast-Fourier Tranformation (FFT) study", Indian Journal of Biochemistry & Biophysics, 43(3):137-142.

  102. Eduardo P.C. Rocha, Marie Touchon, and Edward J. Feil (2006), "Similar compositional biases are caused by very different mutational effects", Genome Research, 16:1537-1547.
    [abstract]

  103. Robert A. Rollins, Fatemeh Haghighi, John R. Edwards, Rajdeep Das, Michael Q. Zhang, Jingyue Ju, and Timothy H. Bestor (2006), "Large-scale structure of genomic methylation patterns", Genome Research, 16(2):157-163.
    [abstract]

  104. Gail Rosen (2006), "Examining coding structure and redundancy in DNA. How does DNA protect itself from life's uncertainty?", IEEE Engineering in Medicine and Biology Magazine, 25(1):62-68.

  105. MG Sadovsky (2006), "Information capacity of nucleotide sequences and Its applications", Bulletin of Mathematical Biology, 68(4):785-806.
    [abstract]

  106. William Salerno, Paul Havlak, Jonathan Miller (2006), "Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments", Proceedings of National Academy of Sciences, 103(35):13121-13125.
    [abstract]

  107. Joaquin Sanchez, Imelda Lopez-Villasenor (2006), "A simple model to explain three-base periodicity in coding DNA", FEBS Letters, 580:6413-6422.
    [abstract]

  108. S Saxonov, P Berg, DL Brutlag (2006), "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters", Proceedings of National Academy of Sciences, 103(5):1412-1417.
    [abstract]

  109. sequence
    Steven E. Scherer, Donna M. Muzny, Christian J. Buhay, Rui Chen, Andrew Cree, Yan Ding, Shannon Dugan-Rocha, Rachel Gill, Preethi Gunaratne, R. Alan Harris, Alicia C. Hawes, Judith Hernandez, Anne V. Hodgson, Jennifer Hume, Andrew Jackson, Ziad Mohid Khan, Christie Kovar-Smith, Lora R. Lewis, Ryan J. Lozado, Michael L. Metzker, Aleksandar Milosavljevic, George R. Miner, Kate T. Montgomery, Margaret B. Morgan, Lynne V. Nazareth, Graham Scott, Erica Sodergren, Xing-Zhi Song, David Steffen, Ruth C. Lovering, David A. Wheeler, Kim C. Worley, Yi Yuan, Zhengdong Zhang, Charles Q. Adams, M. Ali Ansari-Lari, Mulu Ayele, Mary J. Brown, Guan Chen, Zhijian Chen, Kerstin P. Clerc-Blankenburg, Clay Davis, Oliver Delgado, Huyen H. Dinh, Heather Draper, Manuel L. Gonzalez-Garay, Paul Havlak, Laronda R. Jackson, Leni S. Jacob, Susan H. Kelly, Li Li, Zhangwan Li, Jing Liu, Wen Liu, Jing Lu, Manjula Maheshwari, Bao-Viet Nguyen, Geoffrey O. Okwuonu, Shiran Pasternak, Lesette M. Perez, Farah J. H. Plopper, Jireh Santibanez, Hua Shen, Paul E. Tabor, Daniel Verduzco, Lenee Waldron, Qiaoyan Wang, Gabrielle A. Williams, JingKun Zhang, Jianling Zhou (2006), "The finished DNA sequence of human chromosome 12", Nature, 440:346-351.
    [abstract] [PDF]

  110. Eran Segal, Yvonne Fondufe-Mittendorf, Lingyi Chen, AnnChristine Thĺström, Yair Field, Irene K Moore, Ji-Ping Z Wang, Jonathan Widom (2006), "A genomic code for nucleosome positioning", Nature, 442:772-778.
    [abstract]

  111. Mark R. Segal (2006), "Validation in genomics: CpG island methylation revisited", Statistical Applications in Genetics and Molecular Biology, 5(1):29.
    [abstract]

  112. Shurjo K Sen, Kyudong Han, Jianxin Wang, Jungnam Lee, Hui Wang, Pauline A Callinan, Matthew Dyer, Richard Cordaux, Ping Liang, and Mark A Batzer (2006), "Human genomic deletions mediated by recombination between Alu elements", American Journal of Human Genetics, 79:41-53.

  113. Svetlana A Shabalina, Aleksey Y Ogurtsov, Nikolay A Spiridonov (2006), "A periodic pattern of mRNA secondary structure created by the genetic code", Nucleic Acids Research, 34(8):2428-2437.

  114. Xiaoli Shi, Huimin Xie, Shuyu Zhang, Bailin Hao (2007), "Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language", Journal of the Korean Physical Society, 50(1):118-123.

  115. Cas Simons, Michael Pheasant, Igor V. Makunin, and John S. Mattick (2006), "Transposon-free regions in mammalian genomes", Genome Research, 16(2):164-172.
    [abstract]

  116. Sagi Snir, Lior Pachter (2006), "Phylogenetic profiling of insertions and deletions in vertebrate genomes", Proceedings of the Tenth International Conference on Research in Computational Molecular Biology , pp.?-?

  117. sequence
    Erica Sodergren, George M Weinstock, Eric H Davidson, R Andrew Cameron, Richard A Gibbs, Robert C Angerer, Lynne M Angerer, Maria Ina Arnone, David R Burgess, Robert D Burke, James A Coffman, Michael Dean, Maurice R Elphick, Charles A Ettensohn, Kathy R Foltz, Amro Hamdoun, Richard O Hynes, William H Klein, William Marzluff, David R McClay, Robert L Morris, Arcady Mushegian, Jonathan P Rast, L Courtney Smith, Michael C Thorndyke, Victor D Vacquier, Gary M Wessel, Greg Wray, Lan Zhang, Christine G Elsik, Olga Ermolaeva, Wratko Hlavina, Gretchen Hofmann, Paul Kitts, Melissa J Landrum, Aaron J Mackey, Donna Maglott, Georgia Panopoulou, Albert J Poustka, Kim Pruitt, Victor Sapojnikov, Xingzhi Song, Alexandre Souvorov, Victor Solovyev, Zheng Wei, Charles A Whittaker, Kim Worley, K James Durbin, Yufeng Shen, Olivier Fedrigo, David Garfield, Ralph Haygood, Alexander Primus, Rahul Satija, Tonya Severson, Manuel L Gonzalez-Garay, Andrew R Jackson, Aleksandar Milosavljevic, Mark Tong, Christopher E Killian, Brian T Livingston, Fred H Wilt, Nikki Adams, Robert Bellé, Seth Carbonneau, Rocky Cheung, Patrick Cormier, Bertrand Cosson, Jenifer Croce, Antonio Fernandez-Guerra, Anne-Marie Genevičre, Manisha Goel, Hemant Kelkar, Julia Morales, Odile Mulner-Lorillon, Anthony J Robertson, Jared V Goldstone, Bryan Cole, David Epel, Bert Gold, Mark E Hahn, Meredith Howard-Ashby, Mark Scally, John J Stegeman, Erin L Allgood, Jonah Cool, Kyle M Judkins, Shawn S McCafferty, Ashlan M Musante, Robert A Obar, Amanda P Rawson, Blair J Rossetti, Ian R Gibbons, Matthew P Hoffman, Andrew Leone, Sorin Istrail, Stefan C Materna, Manoj P Samanta, Viktor Stolc, Waraporn Tongprasit, Qiang Tu, Karl-Frederik Bergeron, Bruce P Brandhorst, James Whittle, Kevin Berney, David J Bottjer, Cristina Calestani, Kevin Peterson, Elly Chow, Qiu Autumn Yuan, Eran Elhaik, Dan Graur, Justin T Reese, Ian Bosdet, Shin Heesun, Marco A Marra, Jacqueline Schein, Michele K Anderson, Virginia Brockton, Katherine M Buckley, Avis H Cohen, Sebastian D Fugmann, Taku Hibino, Mariano Loza-Coll, Audrey J Majeske, Cynthia Messier, Sham V Nair, Zeev Pancer, David P Terwilliger, Cavit Agca, Enrique Arboleda, Nansheng Chen, Allison M Churcher, F Hallböök, Glen W Humphrey, Mohammed M Idris, Takae Kiyama, Shuguang Liang, Dan Mellott, Xiuqian Mu, Greg Murray, Robert P Olinski, Florian Raible, Matthew Rowe, John S Taylor, Kristin Tessmar-Raible, D Wang, Karen H Wilson, Shunsuke Yaguchi, Terry Gaasterland, Blanca E Galindo, Herath J Gunaratne, Celina Juliano, Masashi Kinukawa, Gary W Moy, Anna T Neill, Mamoru Nomura, Michael Raisch, Anna Reade, Michelle M Roux, Jia L Song, Yi-Hsien Su, Ian K Townley, Ekaterina Voronina, Julian L Wong, Gabriele Amore, Margherita Branno, Euan R Brown, Vincenzo Cavalieri, Véronique Duboc, Louise Duloquin, Constantin Flytzanis, Christian Gache, François Lapraz, Thierry Lepage, Annamaria Locascio, Pedro Martinez, Giorgio Matassi, Valeria Matranga, Ryan Range, Francesca Rizzo, Eric Röttinger, Wendy Beane, Cynthia Bradham, Christine Byrum, Tom Glenn, Sofia Hussain, Gerard Manning, Esther Miranda, Rebecca Thomason, Katherine Walton, Athula Wikramanayke, Shu-Yu Wu, Ronghui Xu, C Titus Brown, Lili Chen, Rachel F Gray, Pei Yun Lee, Jongmin Nam, Paola Oliveri, Joel Smith, Donna Muzny, Stephanie Bell, Joseph Chacko, Andrew Cree, Stacey Curry, Clay Davis, Huyen Dinh, Shannon Dugan-Rocha, Jerry Fowler, Rachel Gill, Cerrissa Hamilton, Judith Hernandez, Sandra Hines, Jennifer Hume, LaRonda Jackson, Angela Jolivet, Christie Kovar, Sandra Lee, Lora Lewis, George Miner, Margaret Morgan, Lynne V Nazareth, Geoffrey Okwuonu, David Parker, Ling-Ling Pu, Rachel Thorn, Rita Wright (Sea Urchin Genome Sequencing Consortium) (2006) "The Genome of the Sea Urchin Strongylocentrotus purpuratus", Science, 314(5801):941-952.

  118. Naoki Takahashi and Hiroshi Nakashima (2006), "Negative correlation of G+C content at silent substitution sites between orthologous human and mouse protein-coding sequences", DNA Research, 13(3):135-140.
    [abstract]

  119. repeats
    Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, Ivan Couée, Abdelhak El Amrani, and Jacques Nicolas (2006), "Domain organization within repeated DNA sequences: application to the study of a family of transposable elements", Bioinformatics, 22(16):1948-1954.
    [abstract]

  120. protein
    VP Turutina, AA Laskin, NA Kudryashov, KG Skryabin, EV Korotkov (2006), "Identification of latent periodicity in amino acid sequences of protein families", Biochemistry (Moscow), 71(1):18-31.
    [abstract]

  121. protein
    Vera P Turutina, Andrew A Laskin, Nikolay A Kudryashov, Konstantin G Skryabin, Eugene V Korotkov (2006), "Identification of amino acid latent periodicity within 94 protein families", Journal of Computational Biology, 13(4):946-964.

  122. sequence
    G A Tuskan, S DiFazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, S Ralph, S Rombauts, A Salamov, J Schein, L Sterck, A Aerts, R R Bhalerao, R P Bhalerao, D Blaudez, W Boerjan, A Brun, A Brunner, V Busov, M Campbell, J Carlson, M Chalot, J Chapman, G-L Chen, D Cooper, P M Coutinho, J Couturier, S Covert, Q Cronk, R Cunningham, J Davis, S Degroeve, A Déjardin, C dePamphilis, J Detter, B Dirks, I Dubchak, S Duplessis, J Ehlting, B Ellis, K Gendler, D Goodstein, M Gribskov, J Grimwood, A Groover, L Gunter, B Hamberger, B Heinze, Y Helariutta, B Henrissat, D Holligan, R Holt, W Huang, N Islam-Faridi, S Jones, M Jones-Rhoades, R Jorgensen, C Joshi, J Kangasjärvi, J Karlsson, C Kelleher, R Kirkpatrick, M Kirst, A Kohler, U Kalluri, F Larimer, J Leebens-Mack, J-C Leplé, P Locascio, Y Lou, S Lucas, F Martin, B Montanini, C Napoli, D R Nelson, C Nelson, K Nieminen, O Nilsson, V Pereda, G Peter, R Philippe, G Pilate, A Poliakov, J Razumovskaya, P Richardson, C Rinaldi, K Ritland, P Rouzé, D Ryaboy, J Schmutz, J Schrader, B Segerman, H Shin, A Siddiqui, F Sterky, A Terry, C-J Tsai, E Uberbacher, P Unneberg, J Vahala, K Wall, S Wessler, G Yang, T Yin, C Douglas, M Marra, G Sandberg, Y Van de Peer, D Rokhsar (2006), "The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)", Science, 313(5793):1596-1604.
    [abstract]

  123. C Vaillant, B Audit, C Thermes, A Arnéodo (2006), "Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder", European Physical Journal E, 1993):263-277.
    [abstract]

  124. Mark WJ van Passel, Aldert Bart, Angela CM Luyf, Antoine HC van Kampen, Arie van der Ende (2006), "Compositional discordance between prokaryotic plasmids and host chromosomes", BMC Genomics, 7:26.
    [abstract]

  125. Georgios S. Vernikos and Julian Parkhill (2006), "Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands", Bioinformatics, 22(18):2196-2203.
    [abstract]

  126. Kalin Vetsigian, Carl Woese, Nigel Goldenfeld (2006), "Collective evolution and the genetic code", Proceedings of National Academy of Sciences, 103(28):10696-10701.
    [abstract]

  127. AE Vinogradov (2006), "'Genome design' model: evidence from conserved intronic sequence in human-mouse comparison", Genome Research, 16(3):347-354.
    [abstract]

  128. AE Vinogradov (2006), "'Genome design' model and multicellular complexity: golden middle ", Nucleic Acids Research, 34(20):5906-5914.
    [abstract]

  129. Yuhong Wang, Wei Li, Tongtong Zhang, Chuanfang Ding, Zhibin Lu, Nanye Long, John P. Rose, Bi-Cheng Wang and Dawei Lin (2006), "Reconstruction of ancient genome and gene order from complete microbial genome sequences", Journal of Theoretical Biology, 239:494-498.
    [abstract]

  130. sequence
    George M. Weinstock et. al (The Honeybee Genome Sequencing Consortium) (2006), "Insights into social insects from the genome of the honeybee Apis mellifera", Nature, 443(7114):931-949.
    [abstract]

  131. a/symmetry
    Peder Worning, Lars J. Jensen, Peter F. Hallin, Hans-Henrik Stćrfeldt, David W. Ussery (2006), "Origin of replication in circular prokaryotic chromosomes", Environmental Microbiology, 8(2):353-361.
    [abstract]

  132. Huijie Yang, Fangcui Zhao, Jianzhong Gu, Binghong Wang (2006), "Nonlinear modelling approach to human promoter sequences", Journal of Theoretical Biology, 241(4):765-773.

  133. repeats
    Shihua Zhang, Yi Xiao (2006), "Quasiperiodic property in Alu repeats", Physical Review E, 74:022901.
    [abstract]

  134. Yusen Zhang, Wei Chen (2006), "Invariants of DNA sequences based on 2DD-curves", Journal of Theoretical Biology, 242:382-388.
    [abstract]

  135. Olga Zhaxybayeva, J. Peter Gogarten, Robert L. Charlebois, W. Ford Doolittle, and R. Thane Papke (2006), "Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events", Genome Reseach, 16(9):1099-1108.
    [abstract]

  136. repeats
    D Zhi, BJ Raphael, AL Price, H Tang, PA Pevzner (2006), "Identifying repeat domains in large genomes", Genome Biology, 7(1):R7.

  137. sequence
    Michael C. Zody, Manuel Garber, Ted Sharpe, Sarah K. Young, Lee Rowen, Keith O'Neill, Charles A. Whittaker, Michael Kamal, Jean L. Chang, Christina A. Cuomo, Ken Dewar, Michael G. FitzGerald, Chinnappa D. Kodira, Anup Madan, Shizhen Qin, Xiaoping Yang, Nissa Abbasi, Amr Abouelleil, Harindra M. Arachchi, Lida Baradarani, Brian Birditt, Scott Bloom, Toby Bloom, Mark L. Borowsky, Jeremy Burke, Jonathan Butler, April Cook, Kurt DeArellano, David DeCaprio, Lester Dorris, III, Monica Dors, Evan E. Eichler, Reinhard Engels, Jessica Fahey, Peter Fleetwood, Cynthia Friedman, Gary Gearin, Jennifer L. Hall, Grace Hensley, Ericka Johnson, Charlien Jones, Asha Kamat, Amardeep Kaur, Devin P. Locke, Anuradha Madan, Glen Munson, David B. Jaffe, Annie Lui, Pendexter Macdonald, Evan Mauceli, Jerome W. Naylor, Ryan Nesbitt, Robert Nicol, Sinéad B. O'Leary, Amber Ratcliffe, Steven Rounsley, Xinwei She, Katherine M. B. Sneddon, Sandra Stewart, Carrie Sougnez, Sabrina M. Stone, Kerri Topham, Dascena Vincent, Shunguang Wang, Andrew R. Zimmer, Bruce W. Birren, Leroy Hood, Eric S. Lander and Chad Nusbaum (2006), "Analysis of the DNA sequence and duplication history of human chromosome 15", Nature, 440:671-675.
    [abstract] [PDF]
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