corr in DNA (1997)

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1997

Yannis Almirantis, Astero Provata (1997), "The 'clustered structure' of the purine/pyrimidines distribution in DNA distinguishes systematically between coding and non-coding sequences", Bulletin of Mathematical Biology, 59(5):975-992. [ abstract] [ Medline entry]
GI Bell, J Jurka (1997), "The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process", Journal of Molecular Evolution, 44(4):414-421.
G Bernardi, S Hughes, D Mouchiroud (1997), "The major compositional transitions in the vertebrate genome", Journal of Molecular Evolution, 44:S44-S51.
[ abstract ]
sequence

Blattner, F.R., Plunkett, G. III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997), "The complete genome sequence of Escherichia coli K-12", Science, 277:1453-1474.
B Borstnik, D Pumpernik, D Lukman (1997), "Computer simulation of DNA sequential correlations", International Journal of Quantum Chemistry, 64(3):387-392.
LY Cao (1997), "Testing predictability of symbolic sequences using time-delay embedding", Physica A, 247(1-4):473-481.
a/symmetry

S Cebrat, MR Dudek, P Mackiewicz (1997), "Asymmetry of coding versus non-coding strand in coding sequences of different genomes", Microbial & Comparative Genomics, 2(4):259-268.
[ Medline entry]
a/symmetry

S Cebrat , MR Dudek, A Rogowska (1997), "Asymmetry in nucleotide composition of sense and antisense strands as a parameter for discriminating open reading frames as protein coding sequences", Journal of Applied Genetics, 38(1):1-9.
protein

Irena Cosic ed. (1997), The Resonant Recognition Model of Macromolecular Bioactivity: Theory and Applications (Birkhauser).
Eivind Coward (1997) "Equivalence of two Fourier methods for biological sequences", Journal of Mathematical Biology, 36:64-70.
[ abstract] [ PDF]
NV Dokholyan, SV Buldyrev, S Havlin, HE Stanley (1997), "Distribution of base pair repeats in coding and noncoding DNA sequences", Physical Review Letters, 79(25):5178-5181.
[abstract]
W Ebeling (1997), "Prediction and entropy of nonlinear dynamical systems and symbolic sequences with LRO", Physica D, 109(1-2):42-52.
a/symmetry

MP Francino, H Ochman (1997), "Strand asymmetries in DNA evolution", Trends in Genetics, 13(6), 240-245.
[abstract] [ Medline entry]
GK Frank, VJ Makeev VJ (1997), "G and T nucleotide contents show specie-invariant negative correlation for all three codon positions", Journal of Biomolecular Structure and Dynamics, 14(5):629-39.
sequence

Fraser, C.M., Casjens, S., Huang, W.M., Sutton, G.G., Clayton, R., Lathigra, R., White, O., Ketchum, K.A., Dodson, R., Hickey, E.K., Gwinn, M., Dougherty, B., Tomb, J.-F., Fleischmann, R.D., Richardson, D., Peterson, J., Kerlavage, A.R., Quckenbush, J., Salzberg, S., Hanson, M., van Vugt, R., Palmer, N., Adams, M.D., Gocayne, J., Weidman, J., Utterback, T., Watthey, L., McDonald, L., Artiach, P., Bowman, C., Garland, S., Fujii, C., Cotton, M.D., Horst, K., Roberts, K., Hatch, B., Smith, H.O., and Venter, J.C. (1997), "Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi", Nature, 390:580-586.
binding-energy

N Galtier, JR Lobry (1997), "Relationship between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes", Journal of Molecular Evolution, 44:632-636.
DM Gray (1997), "Deviation of nearest-neighbor properties from data on nucleic acid oligomers. I. Simple sets of independent sequences and the influence of absent nearest neighbors", Biopolymers, 42:783-793.
Hanspeter Herzel, Ivo Große (1997), "Correlations in DNA sequences - the role of protein coding segments", Physical Review E, 55(1):800-810.
[ PDF ]
SK Gupta, TC Ghosh (1997), "Similarities inferred from the studies of long range correlations among mitochondrial DNA sequences", Indian Journal of Biochemistry & Biophysics, 34(3): 259-265. [abstract]
S Karlin, J Mrazek (1997), "Compositional differences within and between eukaryotic genomes", Proceedings of the National Academy of Sciences, 94(19):10227-10232. [ Medline entry ]
S Karlin, J Mrazek, AM Campbell (1997), "Compositional biases of bacterial genomes and evolutionary implications", Journal of Bacteriology, 179(12):3899-3913.

[ abstract]
AR Kerr, JF Peden, PM Sharp (1997) "Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae", Molecular Microbiology, 25(6):1177-1179.
sequence

Klenk, H.-P., Clayton, R.A., Tomb, J.-F., White, O., Nelson, K.E., Ketchum, K.A., Dodson, R.J., Gwinn, M., Hickey, E.K., Peterson, J.D., Richardson, D.L., Kerlavage, A.R., Graham, D.E., Kyrpides, N.C., Fleischmann, R.D., Quackenbush, J., Lee, N.H., Sutton, G.G., Gill, S., Kirkness, E.F., Dougherty, B.A., McKenney, K., Adams, M.D., Loftus, B., Peterson, S., Reich, C.I., McNeil, L.K., Badger, J.H., Glodek, A., Zhou, L., Overbeek, R., Gocayne,J.D., Weidman, J.F., McDonald, L., Utterback,T., Cotton, M.D., Spriggs, T., Artiach, P., Kaine, B.P., Sykes, S.M., Sadow, P.W., D'Andrea, K.P., Bowman, C., Fujii, C., Garland, S.A., Mason, T.M., Olsen, G.J., Fraser, C.M., Smith, H.O., Woese, C.R. and Venter, J.C. (1997), "The complete genome sequence of the hyperthermophilic, sulfate-reducing archeon Archaeoglobus fulgidus", Nature, 390:364-370.
EV Korotkov, MA Korotkova, JS Tulko (1997), "Latent sequence periodicity of some oncogenes and DNA-binding protein gene", Computer Applications in Biosciences, 13(1):37-44.
[ abstract]
EV Korotkov, DA Phoenix (1997), "Latent periodicity of DNA sequences of many genes", Proceedings of Pacific Symposium on Biocomputing, 2:222-231.
[ webpage of PSB'97 ]
sequence

Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, M., Brignell, S.C., Bron, S., Brouillet, S., Bruschi, C.V., Caldwell, B., Capuano, V., Carter, N.M., Choi, S.K., Codani, J.J., Connerton, I.F., A Danchin, et al (1997), "The complete genome sequence of the gram-positive bacterium Bacillus subtilis", Nature, 390:249-256.
GI Kutuzova, GK Frank, V Ju Makeev, NG Esipova, RV Polozov (1997), "Fourier analysis of nucleotide sequences. Periodicity in E. coli promoter sequences" (in Russian), Biofizika, 42(2):354-362.
JG Lawrence, H Ochman (1997), "Amelioration of bacterial genomes: rates of change and exchange", Journal of Molecular Evolution, 44:383-397.
Weijiang Lee, Liaofu Luo (1997), "Periodicity of base correlation in nucleotide sequence", Physical Review E, 56(1):848-851.
[abstract] [ PDF]
W Li (1997), "The study of correlation structures of DNA sequences: a critical review", Computers & Chemistry, 21(4):257-272. [ abstract] [ Medline entry ] [abstract] [ PDF]
W Li (1997), "The complexity of DNA: the measure of compositional heterogeneity in DNA sequences and measures of complexity", Complexity, 3(2):33-37.
[ PDF ]
D Loewenstern, PN Yianilos (1997), "Significantly lower entropy estimates for natural DNA sequences", Proceedings of Data Compression Conference 1997, pp. 151-160
[ abstract]
Liaofu Luo, Fengmin Ji (1997), "The preferential mode analysis of DNA sequence", Journal of Theoretical Biology, 188(3):343-353 (Oct 7)
ES Mamasakhlisov, VF Morozov, MS Shahinian (1997), "The lack of long-range correlations is a necessary condition for a functional biologically active protein", Journal of Physics A, 30(22):7765-7773.
D Pumpernik, D Lukman, B Borstnik (1997), "On the probability of codon-codon mutational replacements", Journal of Chemical Information and Computer Science, 37(6):1033-1036.
A Provata, Y Almirantis (1997), "Scaling Properties of Coding and Non-coding DNA Sequences", Physica A, 247:482-?.
M Ragosta, C Serio, MT Lanfredi, M Macchiato (1997), "Dynamical degrees of freedom of DNA sequences by local and global short-range prediction", Fractals, 5(1):1-10.
M Robinson, C Gautier, D Mouchiroud (1997), "Evolution of isochores in rodents", Molecular Biology and Evolution, 14:823-828.
S Saccone, S Caccio, J Kusuda, L Andreozzi, G Bernardi (1997), "Identification of the gene-richest bands in human chromosomes", Gene, 174(1):85-94. [erratum, 186(1):151]
S Schbath (1997), "An efficient statistic to detect over- and under-represented words in DNA sequences", Journal of Computational Biology, 4(2):189-192.
AO Schmitt, H. Herzel (1997), "Estimating the Entropy of DNA Sequences", Journal of Theoretical Biology, 188(3):369-377 (Oct 7).
GB Singh, JA Kramer, SA Krawetz (1997), "Mathematical model to predict regions of chromatin attachment to the nuclear matrix", Nucleic Acids Research, 25(7):1419-1425.
sequence

Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Safer,H., Patwell,D., Prabhakar,S., McDougall,S., Shimer,G., Goyal,A., Pietrovski,S., Church,G.M., Daniels,C.J., Mao,J.-i., Rice,P., Nolling,J. and Reeve,J.N.(1997), "Complete genome sequence of Methanobacterium thermoautotrophicum DH: functional analysis and comparative genomics", Journal of Bacteriology, 179:7135-7155.
[ abstract]
sequence

JF Tomb, O White, AR Kerlavage, RA Clayton, GG Sutton, RD Fleischmann, KA Ketchum, HP Klenk, S Gill, BA Dougherty, K Nelson, J Quackenbush, L Zhou, EF Kirkness, S Peterson, B Loftus, D Richardson, R Dodson, HG Khalak, A Glodek, K McKenney, LM Fitzegerald, N Lee, MD Adams, EK Hickey, DE Berg, JD Gocayne, TR Utterback, JD Peterson, JM Kelly, MD Cotton, JM Weidman, C Fujii, C Bowman, L Watthey, E Wallin, M Borodovsky, WS Hayes, P Karp, HO Smith, CM Fraser, JC Venter (1997), "The complete genome sequence of the gastric pathogen Helicobacter pylori", Nature, 388:539-547.
[PDF]
GM Viswanathan, SV Buldyrev, S Havlin, HE Stanley (1997), "Quantification of DNA patchiness using long-range correlation measures", Biophysical Journal, 72:866-875 (Feb)
[abstract]
KH Wolfe, DC Shields (1997), "Molecular evidence for an ancient duplication of the entire yeast genome", Nature, 387(6634):708-713.
[ Medline entry]
Tiee-Jian Wu, John P Burke, Daniel B Davison (1997), "A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words", Biometrics, 53:1431-1439.
Chun-Ting Zhang (1997), "A symmetrical theory of DNA sequences and its applications", Journal of Theoretical Biology, 187(3):297-306.
[abstract]