-
2
-
-
0003410290
-
-
Princeton, N.J., Princeton University Press
-
Hamilton JD, (1994) Time series analysis Princeton, N.J. Princeton University Press 799.
-
(1994)
Time Series Analysis
-
-
Hamilton, J.D.1
-
4
-
-
0000236451
-
Characterizing Long-Range Correlations in DNA Sequences from Wavelet Analysis
-
Arneodo A, Bacry E, Graves PV, Muzy JF, (1995) Characterizing Long-Range Correlations in DNA Sequences from Wavelet Analysis. Physical Review Letters 74: 3293.
-
(1995)
Physical Review Letters
, vol.74
, pp. 3293
-
-
Arneodo, A.1
Bacry, E.2
Graves, P.V.3
Muzy, J.F.4
-
5
-
-
0033637404
-
Finding pathogenicity islands and gene transfer events in genome data
-
Lio P, Vannucci M, (2000) Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics 16: 932-940.
-
(2000)
Bioinformatics
, vol.16
, pp. 932-940
-
-
Lio, P.1
Vannucci, M.2
-
6
-
-
0035847859
-
Long-range correlations in genomic DNA: a signature of the nucleosomal structure
-
Audit B, Thermes C, Vaillant C, d'Aubenton-Carafa Y, Muzy JF, et al.(2001) Long-range correlations in genomic DNA: a signature of the nucleosomal structure. Physical Review Letters 86: 2471-2474.
-
(2001)
Physical Review Letters
, vol.86
, pp. 2471-2474
-
-
Audit, B.1
Thermes, C.2
Vaillant, C.3
d'Aubenton-Carafa, Y.4
Muzy, J.F.5
-
7
-
-
0036290642
-
Wavelet transforms for the characterization and detection of repeating motifs
-
Murray KB, Gorse D, Thornton JM, (2002) Wavelet transforms for the characterization and detection of repeating motifs. Journal of Molecular Biology 316: 341-363.
-
(2002)
Journal of Molecular Biology
, vol.316
, pp. 341-363
-
-
Murray, K.B.1
Gorse, D.2
Thornton, J.M.3
-
8
-
-
10744232769
-
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets
-
Allen TE, Herrgard MJ, Liu M, Qiu Y, Glasner JD, et al.(2003) Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. Journal of bacteriology 185: 6392-6399.
-
(2003)
Journal of Bacteriology
, vol.185
, pp. 6392-6399
-
-
Allen, T.E.1
Herrgard, M.J.2
Liu, M.3
Qiu, Y.4
Glasner, J.D.5
-
9
-
-
0036289102
-
Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes
-
Audit B, Vaillant C, Arneodo A, d'Aubenton-Carafa Y, Thermes C, (2002) Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes. Journal of Molecular Biology 316: 903-918.
-
(2002)
Journal of Molecular Biology
, vol.316
, pp. 903-918
-
-
Audit, B.1
Vaillant, C.2
Arneodo, A.3
d'Aubenton-Carafa, Y.4
Thermes, C.5
-
10
-
-
9144268508
-
Wavelet to predict bacterial ori and ter: a tendency towards a physical balance
-
Song J, Ware A, Liu SL, (2003) Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics 4: 17.
-
(2003)
BMC Genomics
, vol.4
, pp. 17
-
-
Song, J.1
Ware, A.2
Liu, S.L.3
-
11
-
-
19544376315
-
Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation?
-
Nicolay S, Argoul F, Touchon M, d'Aubenton-Carafa Y, Thermes C, et al.(2004) Low frequency rhythms in human DNA sequences: a key to the organization of gene location and orientation? Physical Review Letters 93: 108101.
-
(2004)
Physical Review Letters
, vol.93
, pp. 108101
-
-
Nicolay, S.1
Argoul, F.2
Touchon, M.3
d'Aubenton-Carafa, Y.4
Thermes, C.5
-
12
-
-
33645754507
-
Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization
-
Allen TE, Price ND, Joyce AR, Palsson B, (2006) Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization. PLoS Computational Biology 2: e2.
-
(2006)
PLoS Computational Biology
, vol.2
-
-
Allen, T.E.1
Price, N.D.2
Joyce, A.R.3
Palsson, B.4
-
13
-
-
41149138003
-
From GC skews to wavelets: A gentle guide to the analysis of compositional asymmetries in genomic data
-
Touchon M, Rocha EPC, (2008) From GC skews to wavelets: A gentle guide to the analysis of compositional asymmetries in genomic data. Biochimie 90: 648-659.
-
(2008)
Biochimie
, vol.90
, pp. 648-659
-
-
Touchon, M.1
Rocha, E.P.C.2
-
15
-
-
11344293422
-
Spatial patterns of transcriptional activity in the chromosome of Escherichia coli
-
Jeong KS, Ahn J, Khodursky AB, (2004) Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biology 5: R86.
-
(2004)
Genome Biology
, vol.5
-
-
Jeong, K.S.1
Ahn, J.2
Khodursky, A.B.3
-
16
-
-
70349254460
-
Improved detection of differentially expressed genes through incorporation of gene locations
-
Xiao G, Reilly C, Khodursky AB, (2009) Improved detection of differentially expressed genes through incorporation of gene locations. Biometrics 65: 805-814.
-
(2009)
Biometrics
, vol.65
, pp. 805-814
-
-
Xiao, G.1
Reilly, C.2
Khodursky, A.B.3
-
18
-
-
5144227142
-
Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA
-
Schieg P, Herzel H, (2004) Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA. Journal of Molecular Biology 343: 891-901.
-
(2004)
Journal of Molecular Biology
, vol.343
, pp. 891-901
-
-
Schieg, P.1
Herzel, H.2
-
19
-
-
26444614790
-
Sequence periodicity of Escherichia coli is concentrated in intergenic regions
-
Hosid S, Trifonov EN, Bolshoy A, (2004) Sequence periodicity of Escherichia coli is concentrated in intergenic regions. BMC molecular biology 5: 14.
-
(2004)
BMC Molecular Biology
, vol.5
, pp. 14
-
-
Hosid, S.1
Trifonov, E.N.2
Bolshoy, A.3
-
20
-
-
42749101835
-
Repeats and correlations in human DNA sequences
-
Holste D, Grosse I, Beirer S, Schieg P, Herzel H, (2003) Repeats and correlations in human DNA sequences. Physical review E, Statistical, nonlinear, and soft matter physics 67: 061913.
-
(2003)
Physical Review E, Statistical, Nonlinear, and Soft Matter Physics
, vol.67
, pp. 061913
-
-
Holste, D.1
Grosse, I.2
Beirer, S.3
Schieg, P.4
Herzel, H.5
-
21
-
-
84875385143
-
Genome Assembly/Annotation Projects of The NCBI ftp site
-
Available:. Accessed 2011 June 13
-
Genome Assembly/Annotation Projects of The NCBI ftp site. Available: ftp://ftp.ncbi.nih.gov/genomes/. Accessed 2011 June 13.
-
-
-
-
22
-
-
0023650543
-
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li W-H, (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucl Acids Res 15: 1281-1295.
-
(1987)
Nucl Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.-H.2
-
23
-
-
0030660581
-
A Genomic Perspective on Protein Families
-
Tatusov RL, Koonin EV, Lipman DJ, (1997) A Genomic Perspective on Protein Families. Science 278: 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
24
-
-
33644876685
-
The UCSC Archaeal Genome Browser
-
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM, (2006) The UCSC Archaeal Genome Browser. Nucleic Acids Res 34: D407-410.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Schneider, K.L.1
Pollard, K.S.2
Baertsch, R.3
Pohl, A.4
Lowe, T.M.5
-
26
-
-
84875390174
-
NCBI COGs
-
Available:. Accessed 2011 June 13
-
NCBI COGs. Available: http://www.ncbi.nlm.nih.gov/COG/. Accessed 2011 June 13.
-
-
-
-
27
-
-
0029985398
-
Asymmetric substitution patterns in the two DNA strands of bacteria
-
Lobry JR, (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 660-665
-
-
Lobry, J.R.1
-
28
-
-
0000992937
-
Patterns of genome organization in bacteria
-
Freeman JM, Plasterer TN, Smith TF, Mohr SC, (1998) Patterns of genome organization in bacteria. Science 279: 1827.
-
(1998)
Science
, vol.279
, pp. 1827
-
-
Freeman, J.M.1
Plasterer, T.N.2
Smith, T.F.3
Mohr, S.C.4
-
29
-
-
0032524384
-
Analyzing genomes with cumulative skew diagrams
-
Grigoriev A, (1998) Analyzing genomes with cumulative skew diagrams. Nucl Acids Res 26: 2286-2290.
-
(1998)
Nucl Acids Res
, vol.26
, pp. 2286-2290
-
-
Grigoriev, A.1
-
30
-
-
0032417093
-
Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
-
McLean MJ, Wolfe KH, Devine KM, (1998) Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. Journal of Molecular Evolution 47: 691-696.
-
(1998)
Journal of Molecular Evolution
, vol.47
, pp. 691-696
-
-
McLean, M.J.1
Wolfe, K.H.2
Devine, K.M.3
-
31
-
-
0033935187
-
The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes
-
Tillier ERM, Collins RA, (2000) The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes. Journal of Molecular Evolution 50: 249-257.
-
(2000)
Journal of Molecular Evolution
, vol.50
, pp. 249-257
-
-
Tillier, E.R.M.1
Collins, R.A.2
-
32
-
-
3142679507
-
The replication-related organization of bacterial genomes
-
Rocha EPC, (2004) The replication-related organization of bacterial genomes. Microbiology 150: 1609-1627.
-
(2004)
Microbiology
, vol.150
, pp. 1609-1627
-
-
Rocha, E.P.C.1
-
33
-
-
3142748120
-
Where does bacterial replication start? Rules for predicting the oriC region
-
Mackiewicz P, Zakrzewska-Czerwinska J, Zawilak A, Dudek MR, Cebrat S, (2004) Where does bacterial replication start? Rules for predicting the oriC region. Nucl Acids Res 32: 3781-3791.
-
(2004)
Nucl Acids Res
, vol.32
, pp. 3781-3791
-
-
Mackiewicz, P.1
Zakrzewska-Czerwinska, J.2
Zawilak, A.3
Dudek, M.R.4
Cebrat, S.5
-
34
-
-
33644853927
-
Origin of replication in circular prokaryotic chromosomes
-
Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW, (2006) Origin of replication in circular prokaryotic chromosomes. Environmental Microbiology 8: 353-361.
-
(2006)
Environmental Microbiology
, vol.8
, pp. 353-361
-
-
Worning, P.1
Jensen, L.J.2
Hallin, P.F.3
Staerfeldt, H.H.4
Ussery, D.W.5
-
35
-
-
34547912489
-
DoriC: a database of oriC regions in bacterial genomes
-
Gao F, Zhang CT, (2007) DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23: 1866-1867.
-
(2007)
Bioinformatics
, vol.23
, pp. 1866-1867
-
-
Gao, F.1
Zhang, C.T.2
-
36
-
-
49949118733
-
Identification of replication origins in prokaryotic genomes
-
Sernova NV, Gelfand MS, (2008) Identification of replication origins in prokaryotic genomes. Brief Bioinform 9: 376-391.
-
(2008)
Brief Bioinform
, vol.9
, pp. 376-391
-
-
Sernova, N.V.1
Gelfand, M.S.2
-
37
-
-
35348993681
-
Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes
-
Chen C, Chen CW, (2007) Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes. BMC Genomics 8: 286.
-
(2007)
BMC Genomics
, vol.8
, pp. 286
-
-
Chen, C.1
Chen, C.W.2
-
38
-
-
78650270761
-
DNA motifs that sculpt the bacterial chromosome
-
Touzain F, Petit MA, Schbath S, Karoui ME, (2011) DNA motifs that sculpt the bacterial chromosome. Nat Rev Microbiol 9: 15-26.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 15-26
-
-
Touzain, F.1
Petit, M.A.2
Schbath, S.3
Karoui, M.E.4
-
41
-
-
51749088608
-
BioJava: an open-source framework for bioinformatics
-
Holland RC, Down TA, Pocock M, Prlic A, Huen D, et al.(2008) BioJava: an open-source framework for bioinformatics. Bioinformatics 24: 2096-2097.
-
(2008)
Bioinformatics
, vol.24
, pp. 2096-2097
-
-
Holland, R.C.1
Down, T.A.2
Pocock, M.3
Prlic, A.4
Huen, D.5
-
43
-
-
0345237922
-
IslandPath: aiding detection of genomic islands in prokaryotes
-
Hsiao W, Wan I, Jones SJ, Brinkman FS, (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19: 418-420.
-
(2003)
Bioinformatics
, vol.19
, pp. 418-420
-
-
Hsiao, W.1
Wan, I.2
Jones, S.J.3
Brinkman, F.S.4
-
44
-
-
33745828696
-
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
-
Waack S, Keller O, Asper R, Brodag T, Damm C, et al.(2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7: 142.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 142
-
-
Waack, S.1
Keller, O.2
Asper, R.3
Brodag, T.4
Damm, C.5
-
45
-
-
84875390909
-
SVG, Scalale Vector Graphics
-
Available:. Accessed 2011 June 13
-
SVG, Scalale Vector Graphics. Available: http://www.w3.org/TR/SVG/. Accessed 2011 June 13.
-
-
-
-
46
-
-
0003740085
-
DOM, Document Object Model
-
Available:. Accessed 2011 June 13
-
DOM, Document Object Model. Available: http://www.w3.org/DOM/. Accessed 2011 June 13.
-
-
-
-
47
-
-
79961135005
-
R: A language and environment for statistical computing
-
R Development Core Team, Available:. Accessed 2011 June 13, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
-
R Development Core Team(2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. Available: http://www.R-project.org. Accessed 2011 June 13.
-
(2011)
-
-
-
48
-
-
84887173584
-
Rserve: Binary R server
-
Available:. Accessed 2011 June 13
-
Urbanek S, (2010) Rserve: Binary R server. Available: http://CRAN.R-project.org/package=Rserve. Accessed 2011 June 13.
-
(2010)
-
-
Urbanek, S.1
-
49
-
-
0033785280
-
Wavelet analysis of covariance with application to atmospheric time series
-
Whitcher B, Guttorp P, Percival D, (2000) Wavelet analysis of covariance with application to atmospheric time series. Journal of Geophysical Research 105: 941-962.
-
(2000)
Journal of Geophysical Research
, vol.105
, pp. 941-962
-
-
Whitcher, B.1
Guttorp, P.2
Percival, D.3
-
50
-
-
84875400817
-
waveslim: Basic wavelet routines for one-, two- and three-dimensional signal processing
-
Available:. Accessed 2011 June 13
-
Whitcher B, (2009) waveslim: Basic wavelet routines for one-, two- and three-dimensional signal processing. Available: http://CRAN.R-project.org/package=waveslim. Accessed 2011 June 13.
-
(2009)
-
-
Whitcher, B.1
-
52
-
-
2642555649
-
Signal analysis of behavioral and molecular cycles
-
Levine JD, Funes P, Dowse HB, Hall JC, (2002) Signal analysis of behavioral and molecular cycles. BMC Neurosci 3: 1.
-
(2002)
BMC Neurosci
, vol.3
, pp. 1
-
-
Levine, J.D.1
Funes, P.2
Dowse, H.B.3
Hall, J.C.4
|