corr in DNA (1998)

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1998

Guillermo Abramson, Pablo A Alemany, Hilda A Cerdeira (1998), "Noist Levy walk analog of two-dimensional DNA walks for chromosomes of S. cerevisiae", Physical Review E, 58(1):914-918.
[ PDF]
Pankaj Agarwal, Vineet Bafna (1998), "Detecting non-adjoining correlations with signals in DNA", Proceedings of the Second International Conference on Research in Computational Molecular Biology , pp. ?-?.
[abstract]
sequence

Andersson S.G.E., Zomorodipour A., Andersson J.O., Sicheritz-Ponten T., Alsmark U.C.M., Podowski R.M., Naeslund A.K., Eriksson A.S., Winkler H.H., Kurland C.G. (1998), "The genome sequence of Rickettsia prowazekii and the origin of Mitochondria", Nature, 396:133-140.
[PDF]
protein

Roger Abseher and Michael Nilges (1998), "Are there non-trivial dynamic cross-correlations in proteins?" Journal of Molecular Biology, 279:911-920.
[abstract]
Paolo Allegrini, Marco Buiatti, Paolo Grigolini, Bruce J West (1998), "Fractional Brownian motion as a nonstationary process: An alternative for DNA sequences", Physical Review E, 57:4558-4567.
[ abstract] [ PDF ]
Paolo Allegrini, Marco Buiatti, Paolo Grigolini, Bruce J West (1998), "Non-Gaussian statistics of anomalous diffusion: the DNA sequences of prokaryotes", Physical Review E, 58(3):3640-3648.
[ abstract] [ PDF ]
L Allison, T Edgoose, TI Dix (1998), "Compression of strings with approximate repeats", Proceedings of Pacific Symposium on Biocomputing, 3:8-16.
[webpage of PSB'98 ] [ Medline entry]
A Arneodo, Y D'Aubenton-Carafa, B Audit, E Bacry, JF Muzy, C Thermes (1998), "What can we learn with wavelets about DNA sequences?", Physica A, 249(1-4):439-448. [ PDF]
A Arneodo, Y D'Aubenton-Carafa, B Audit, E Bacry, JF Muzy, C Thermes (1998), "Nucleotide composition effects on the long-range correlations in human genes", European Physical Journal B, 1:259-263.
[abstract] [ PDF]
A Barakat, G Matassi, G Bernardi (1998), "Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants", Proceedings of the National Academy of Sciences, 95:10044-10049. [ PDF]
SJ Bell, YC Chow, JYK Ho, DR Forsdyke (1998), "Correlation of chi orientation with transcription indicates a fundamental relationship between recombination and transcription", Gene, 216:285-292. [ Medline entry]
DR Bickel, BJ West (1998), "Multiplicative and fractal processes in DNA evolution", Fractals, 6:211-217.
T Biro, A Czirok, T Vicsek, A Major (1998), "Application of vector space techniques to DNA", Fractals, 6(3):205-210.
Jerome V Braun, Hans-Georg Muller (1998), "Statistical methods for DNA sequence segmentation", Statistical Sciences, 13(2):142-162.
SV Buldyrev, NV Dokholyan, AL Goldberger, S Havlin, CK Peng, HE Stanley, GM Viswanathan (1998), "Analysis of DNA sequences using methods of statistical physics", Physica A, 249(1-4):430-438.
a/symmetry

S Cebrat, MR Dudek, P Mackiewicz (1998), "Sequence asymmetry as a parameter indicating coding sequence in Saccharomyces cerevisiae genome", Theory in Biosciences, 117:78-89.
S Cebrat, MR Dudek (1998), "The effect of DNA phase structure on DNA walk", European Physical Journal B, 3:271-276.
[ abstract]
sequence

The C elegans Sequencing Consortium (1998), "Genome sequence of the Nematode C. elegans: A platform for investigating biology", Science, 282:2012-2018.
VR Chechetkin, VV Lobzin (1998), "Study of correlations in segmented DNA sequences: application to structure coupling between exons and introns", Journal of Theoretical Biology, 190(1):69-83 (Jan 7).
[ abstract]
VR Chechetkin, VV Lobzin (1998), "Nucleosome units and hidden periodicities in DNA sequences", Journal of Biomolecular Structure and Dynamics , 15(5):937-947.
J Christen, JL Torres, J Barrera (1998), "A statistical feature of genetic sequences", Biometrical Journal, 40(7):855-863.
sequence

Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E.III., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream, M-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S. Barrell, B.G. (1998), "Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence", Nature, 393:537-544.
Eivind Coward, Finn Drablos (1998), "Detecting periodic patterns in biological sequences", Bioinformatics, 14(6), 498-507.
[ abstract] [ PDF ]
a/symmetry

Dang KD, Dutt PB, DR Forsdyke (1998), "Chargaff difference analysis of the bithorax complex of Drosophila melanogaster", Biochemistry and Cell Biology, 76(1):129-137 [ Medline entry]
sequence

Deckert, G., Warren, P.V., Gaasterland, T., Young, W.G., Lenox, A.L., Graham, D.E., Overbeek, R., Snead, M.A., Keller, M., Aujay, M., Huber, R., Feldman, R.A., Short, J.M., Olsen, G.J., Swanson, R.V. (1998), "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus", Nature, 392:353-358.
W Ebeling, C Frommel (1998), "Entropy and predictability of information carriers", Biosystems, 46(1-2):47-55.
JT Epplen, W Maueler, EJM Santos (1998), "On GATAGATA and other 'junk' in the barren stretch of genomic desert", Cytogenetics and Cell Genetics, 80(1-4):75-82. [abstract]
D Field, C Wills (1998), "Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and , result from strong mutation pressures and a variety of selective forces", Proceedings of the National Academy of Sciences, 95:1647-1652.
sequence

Fraser,C.M., Norris,S.J., Weinstock,G.M., White,O., Sutton,G.G., Dodson,R., Gwinn,M., Hickey,E.K., Clayton,R., Ketchum,K.A., Sodergren,E., Hardham,J.M., McLeod,M.P., Salzberg,S., Peterson,J., Khalak,H., Richardson,D., Howell,J.K., Chidambaram,M., Utterback,T., McDonald,L., Artiach,P., Bowman,C., Cotton,M.D., Fujii,C., Garland,S., Hatch,B., Horst,K., Roberts,K., Watthey,L., Weidman,J., Smith,H.O. Venter,J.C. (1998), "Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete", Science, 281:375-388.
a/symmetry

James M Freeman, Thomas N Plasterer, Temple F Smith, Scott C Mohr (1998), "Patterns of genome organization in bacteria", Science , 279:1827a (online version only: http://www.sciencemag.org/cgi/content/full/279/5358/1827a) more graphs at http://bmerc-www.bu.edu/genomeplot
a/symmetry

James M Freeman, Thomas N Plasterer, Temple F Smith, Scott C Mohr (1998), response to Grigoriev's technical comments, Science , 281:1923a (online version only: http://www.sciencemag.org/cgi/content/full/281/5385/1923a ). [ PDF ]
a/symmetry

Mitsuru Furusawa, Hirofumi Doi (1998), "Asymmetrical DNA replication promotes evolution: disparity theory of evolution", Genetica, 102-103:333-347.
[abstract]
isochore

Nicolas Galtier, Dominique Mouchiroud (1998), "Isochore evolution in mammals: a human-like ancestral structure", Genetics, 150:1577-1584.
[abstract]
protein

BG Giraud, Alan Lapedes, Lon Chang Liu (1998), "Analysis of correlations between sites in models of protein sequences", Physical Review E, 58(5):6312-6322.
[ PDF]
a/symmetry

Andrei Grigoriev (1998), "Analyzing genomes with cumulative skew diagram", Nucleic Acids Research , 26(10):2286-2290.
[ abstract] [ Medline entry] [ PDF ]
a/symmetry

Andrei Grigoriev (1998), "Genome arithmetic (technical comment), Science , 281:1923a (online version only: http://www.sciencemag.org/cgi/content/full/281/5385/1923a ). [ PDF ]
period:10-11

H Herzel, O Weiss, EN Trifonov (1998), "Sequence periodicity in complete genomes of Archaea suggests positive supercoiling"", Journal of Biomolecular Structure and Dynamics , 16:341-345.
[ abstract] [ Medline entry]
H Herzel, EN Trifonov, O Weiss, I Große (1998), "Interpreting correlations in biosequences", Physica A, 249, 449-459.
[ PDF]
D Holste, H Herzel, I Große (1998), "Bayes estimators of generalized entropies", Journal of Physics A, 31:2551-2566.
[ abstract]
K Jabbari, G Bernardi (1998), "CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families", Gene, 224(1-2):123-127.
R Jauregui, F O'Reilly, F Bolivar, E Merino (1998), "Relationship between codon usage and sequence-dependent curvature of genomes", Microbial & Comparative Genomics, 3(4):243-253.
[ Medline entry]
repeats

J Jurka (1998), "Repeats in genomic DNA: mining and meaning", Current Opinion in Structural Biology, 8(3):333-337.
repeats

J Jurka, P Klonowski, EN Trifonov (1998), "Mammalian retroposons integrate at kinkable DNA sites", Journal of Biomolecular Structure and Dynamics , 15(4):717-721.
repeats

VV Kapitonov, GP Holmquist, J Jurka (1998), "L1 repeat is a basic unit of heterochromatin satellites in cetaceans", Molecular Biology and Evolution, 15(5):611-612.
Samuel Karlin (1998), "Global dinucleotide signatures and analysis of genomic heterogeneity", Current Opinion in Microbiology, 1(5):598-610. [ Medline entry ]
Samuel Karlin, AM Campbell, J Mrazek (1998), "Comparative DNA analysis across diverse genomes", Annual Review of Genetics, 32:185-225. [ Medline entry]
sequence

Kawarabayasi,Y., Sawada,M., Horikawa,H., Haikawa,Y., Hino,Y., Yamamoto,S., Sekine,M., Baba,S., Kosugi,H., Hosoyama,A., Nagai,Y., Sakai,M., Ogura,K., Otsuka,R., Nakazawa,H., Takamiya,M., Ohfuku,Y., Funahashi,T., Tanaka,T., Kudoh,Y., Yamazaki,J., Kushida,N., Oguchi,A., Aoki,K., Yoshizawa,T., Nakamura,Y., Robb,F.T., Horikoshi,K., Masuchi,Y., Shizuya,H. and Kikuchi,H. (1998), "Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3", DNA Research, 5:147-155.
protein

RH Lathrop, M Casale, DJ Tobias, JL Marsh, LM Thompson (1998), "Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington's disease", Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pp. 105-114.
[webpage of ISMB'98] [webpage of ISMB'98 proceedings] [ Medline entry]
JG Lawrence, H Ochman (1998), "Molecular archaeology of the Escherichia coli genome", Proceedings of the National Academy of Sciences, 95:9413-9417.
P Lio, S Ruffo (1998), "Searching for genomic constraints", Nuovo Cimento Della Societa Italiana di Fisica D, 20(1):113-127.
W Li, G Stolovitzky, P Bernaola-Galvan, JL Oliver (1998), "Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes", Genome Research , 8(9):916-928.
[ abstract] [ PDF ]
DM Loewenstern, HM Berman, H Hirsh (1998), "Maximum A posteriori classification of DNA structure from sequence information", Proceedings of Pacific Symposium on Biocomputing, 3:669-680.
[webpage of PSB'98 ] [ Medline entry ]
Xin Lu, Zhirong Sun, Huimin Chen, Yanda Li (1998), "Characterizing self-similarity in bacteria DNA sequences", Physical Review E, 58(3):3578-3584.
[ abstract] [ PDF ]
Liaofu Luo, Weijiang Lee, Lijun Jia, Fengmin Ji, Lu Tsai (1998), "Statistical correlation of nucleotides in a DNA sequence", Physical Review E, 58(1):861-871.
[ PDF]
a/symmetry

Michael J McLean, Kenneth H Wolfe, Kevin M Devine (1998), "Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes", Journal of Molecular Evolution, 47:691-696.
[ abstract] [ Medline entry] [ PDF]
a/symmetry

Jan Mrazek, Samuel Karlin (1998), "Strand compositional asymmetry in bacterial and large viral genomes", Proceedings of the National Academy of Sciences, 95:3720-3725. [abstract] [ Medline entry ] [ PDF ]
F Muri, D Chauveau, D Cellier (1998), "Convergence assessment in latent variable models: DNA applications", in Discretization and MCMC convergence assessment, eds. CP Robert (Springer-Verlag), pp.127-146.
bending

WK Olson, AA Gorin, XJ Lu, LM Hock, VB Zhurkin (1998), "DNA sequence-dependent deformability deduced from protein-DNA crystal complex", Proceedings of the National Academy of Sciences,95(19):11163-11168.
CM Pasquier, VI Promponas, NJ Varvayannis, SJ Hamodrakas (1998), "A Web server to locate periodicities in a sequence", Bioinformatics, 14(8):749-750.
DR Powell, DL Dowe, L Allison, TI Dix (1998), "Discovering simple DNA sequences by compression", Proceedings of Pacific Symposium on Biocomputing, 3:597-608.
[webpage of PSB'98 ] [ Medline entry]
EP Rocha, A Viari, A Danchin (1998), "Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparison", Nucleic Acids Research, 26(12):2971-2980.
protein

S Rackovsky (1998), " 'Hidden' sequence periodicities and protein architecture", Proceedings of the National Academy of Sciences,95:8580-8584.
Ramon Roman-Roldan, Pedro Bernaola-Galvan, Jose L Oliver (1998), "Sequence compositional complexity of DNA through an entropic segmentation method", Physical Review Letters, 80(4):1344-1347 (Feb 8).
[ abstract] [ PDF ]
A Roy, C Raychaudhury, A Nandy (1998), "Novel techniques of graphical representation and analysis of DNA sequences - A review", Journal of Biosciences, 23(1):55-71.
[PDF]
a/symmetry

S Salzberg, A Salzberg, A Kerlavage, JF Tomb (1998), "Skewed oligomers and origins of replication", Gene, 217(1-2):57-67. [ PDF ]
binding-energy

John SantaLucia Jr. (1998), "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics", Proceedings of the National Academy of Sciences, 95(4):1460-1465.
C Seoighe, KH Wolfe (1998), "Extent of genomic rearrangement after genome duplication in yeast", Proceedings of the National Academy of Sciences, 95(8):4447-4452 . [ abstract] [ Medline entry]
Yu Shi, Ido Kanter, David Kessler (1998), "Distribution of triplets in genetic sequences", Physica A, 252:48-60.
Lucy Skrabanek, Kenneth H Wolfe(1998), "Eukaryote genome duplication - where's the evidence?", Current Opinion in Genetics & Development, 8:694-700.
[ abstract] [ Medline entry]
HE Stanley, LAN Amaral, JS Andrade, SV Buldyrev, S Havlin, HA Makse, CK Peng, B Suki, G Viswanathan (1998), "Scale-invariant correlations in the biological and social science", Philosophical Magazine B, 77(5):1373-1388.
sequence

Stephens,R.S., Kalman,S., Lammel,C.J., Fan,J., Marathe,R., Aravind,L., Mitchell,W.P., Olinger,L., Tatusov,R.L., Zhao,Q., Koonin,E.V. and Davis,R.W. (1998), "Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis", Science, 282:754-759.
period:10-11

EN Trifonov (1998), "3-, 10.5-, 200- and 400-base periodicities in genome sequences", Physica A, 249(1-4):511-516.
[ PDF ]
protein

Olaf Weiss, Hanspeter Herzel (1998), "Measuring correlations in protein sequences", Z. Phys. Chem., 204:183-197.
protein

Olaf Weiss, Hanspeter Herzel (1998), "Correlations in protein sequences and property codes", Journal of Theoretical Biology, 190:341-353.
[ abstract] [ Medline entry ]
GM Viswanathan, SV Buldyrev, S Havlin, HE Stanley (1998), "Long-range correlation measures for quantifying patchiness: Deviations from uniform power-law scaling in genomic DNA", Physica A, 249(1-4):581-586.
A Wagner (1998), "The fate of duplicated genes: loss or new function?", Bioessays, 20(10):785-788. [ Medline entry]
GF Zebende, PMC de Oliveira, Thadeu JP Penna (1998), "Long-range correlations in computer diskettes," Physical Review E, 57(3):3311-3314.
[ abstract] [ PDF ]