-
1
-
-
0032544103
-
Self-identification of protein-coding regions in microbial genomes
-
S. Audic, and J.M. Claverie Self-identification of protein-coding regions in microbial genomes Proc. Natl. Acad. Sci. USA 95 17 1998 10026 10031
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, Issue.17
, pp. 10026-10031
-
-
Audic, S.1
Claverie, J.M.2
-
2
-
-
0034084864
-
On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
-
P. Baldi On the convergence of a clustering algorithm for protein-coding regions in microbial genomes Bioinformatics 16 4 2000 367 371
-
(2000)
Bioinformatics
, vol.16
, Issue.4
, pp. 367-371
-
-
Baldi, P.1
-
3
-
-
0034238085
-
Finding borders between coding and noncoding DNA regions by an entropic segmentation method
-
P. Bernaola-Galvan, I. Grosse, P. Carpena, J.L. Oliver, R. Roman-Roldan, and H.E. Stanley Finding borders between coding and noncoding DNA regions by an entropic segmentation method Phys. Rev. Lett. 85 6 2000 1342 1345
-
(2000)
Phys. Rev. Lett.
, vol.85
, Issue.6
, pp. 1342-1345
-
-
Bernaola-Galvan, P.1
Grosse, I.2
Carpena, P.3
Oliver, J.L.4
Roman-Roldan, R.5
Stanley, H.E.6
-
4
-
-
0037085737
-
Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models
-
P. Nicolas, L. Bize, F. Muri, M. Hoebeke, F. Rodolphe, S.D. Ehrlich, B. Prum, and P. Bessieres Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models Nucleic Acids Res. 30 6 2002 1418 1426
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.6
, pp. 1418-1426
-
-
Nicolas, P.1
Bize, L.2
Muri, F.3
Hoebeke, M.4
Rodolphe, F.5
Ehrlich, S.D.6
Prum, B.7
Bessieres, P.8
-
5
-
-
0000241874
-
GENMARK: Parallel gene recognition for both DNA strands
-
M. Borodovsky, and J. McIninch GENMARK: parallel gene recognition for both DNA strands Comput. Chem. 17 1993 123 133
-
(1993)
Comput. Chem.
, vol.17
, pp. 123-133
-
-
Borodovsky, M.1
McIninch, J.2
-
6
-
-
0032518163
-
Microbial gene identification using interpolated Markov Models
-
S.L. Salzberg, A.L. Delcher, S. Kasif, and O. White Microbial gene identification using interpolated Markov Models Nucleic Acids Res. 26 2 1998 544 548
-
(1998)
Nucleic Acids Res.
, vol.26
, Issue.2
, pp. 544-548
-
-
Salzberg, S.L.1
Delcher, A.L.2
Kasif, S.3
White, O.4
-
7
-
-
0842346757
-
Seven clusters in genomic triplet distributions
-
http://cogprints.ecs.soton.ac.uk/archive/00003077/
-
A. Gorban, A. Zinovyev, T. Popova, Seven clusters in genomic triplet distributions, Silico Biol. 3 (2003), 0039. (E-print: http://arxiv.org/abs/cond- mat/0305681 and http://cogprints.ecs.soton.ac.uk/archive/00003077/)
-
(2003)
Silico Biol.
, vol.3
, pp. 0039
-
-
Gorban, A.1
Zinovyev, A.2
Popova, T.3
-
8
-
-
18844394104
-
-
IHES Preprint, France M/01/34 http://arxiv.org/abs/physics/0108016
-
A.N. Gorban, A.Yu. Zinovyev, T.G. Popova, Statistical approaches to the automated gene identification without teacher, Institut des Hautes Etudes Scientiques. - IHES Preprint, France, 2001, - M/01/34. Available at http://www.ihes.fr web-site. (See also e-print: http://arxiv.org/abs/physics/ 0108016).
-
(2001)
Statistical Approaches to the Automated Gene Identification Without Teacher, Institut des Hautes Etudes Scientiques
-
-
Gorban, A.N.1
Zinovyev, A.Yu.2
Popova, T.G.3
-
11
-
-
0242420364
-
-
Institut des Hautes Etudes Scientiques. - IHES Preprint, France M/01/36
-
A.N. Gorban, A.Yu. Zinovyev, Visualization of data by method of elastic maps and its applications in genomics, economics and sociology, Institut des Hautes Etudes Scientiques. - IHES Preprint, France, 2001, - M/01/36. Available at http://www.ihes.fr web-site
-
(2001)
Visualization of Data by Method of Elastic Maps and Its Applications in Genomics, Economics and Sociology
-
-
Gorban, A.N.1
Zinovyev, A.Yu.2
-
12
-
-
0141682915
-
Application of the method of elastic maps in analysis of genetic texts
-
Portland, Oregon, July 20-24
-
A.N. Gorban, A.Y. Zinovyev, D.C. Wunsch, Application of The Method of Elastic Maps In Analysis of Genetic Texts, in: Proceedings of International Joint Conference on Neural Networks (IJCNN), 2003, Portland, Oregon, July 20-24.
-
(2003)
Proceedings of International Joint Conference on Neural Networks (IJCNN)
-
-
Gorban, A.N.1
Zinovyev, A.Y.2
Wunsch, D.C.3
-
13
-
-
0037431063
-
Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method
-
H.Y. Ou, F.B. Guo, and C.T. Zhang Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method FEBS Lett. 540 1-3 2003 188 194
-
(2003)
FEBS Lett.
, vol.540
, Issue.1-3
, pp. 188-194
-
-
Ou, H.Y.1
Guo, F.B.2
Zhang, C.T.3
-
14
-
-
0027669090
-
A new approach to the investigations of statistical properties of genetic texts
-
A.N. Gorban, E.M. Mirkes, T.G. Popova, and M.G. Sadovsky A new approach to the investigations of statistical properties of genetic texts Biofizika 38 5 1993 762 767
-
(1993)
Biofizika
, vol.38
, Issue.5
, pp. 762-767
-
-
Gorban, A.N.1
Mirkes, E.M.2
Popova, T.G.3
Sadovsky, M.G.4
-
15
-
-
0000111518
-
Maximum entropy method in analysis of genetic text and measurement of its information content
-
N.N. Bugaenko, A.N. Gorban, and M.G. Sadovskii Maximum entropy method in analysis of genetic text and measurement of its information content Open Systems and Inform. Dyn. 5 1998 265 278
-
(1998)
Open Systems and Inform. Dyn.
, vol.5
, pp. 265-278
-
-
Bugaenko, N.N.1
Gorban, A.N.2
Sadovskii, M.G.3
-
16
-
-
0002813049
-
Classification of symbol sequences over their frequency dictionaries: Towards the connection between structure and natural taxonomy
-
A.N. Gorban, T.G. Popova, and M.G. Sadovsky Classification of symbol sequences over their frequency dictionaries: towards the connection between structure and natural taxonomy Open System Inform. Dyn. 7 2000 1 17
-
(2000)
Open System Inform. Dyn.
, vol.7
, pp. 1-17
-
-
Gorban, A.N.1
Popova, T.G.2
Sadovsky, M.G.3
-
17
-
-
0032173634
-
Global dinucleotide signatures and analysis of genomic heterogeneity
-
S. Karlin Global dinucleotide signatures and analysis of genomic heterogeneity Curr. Opinion Microbiol. 1 5 1998 598 610
-
(1998)
Curr. Opinion Microbiol.
, vol.1
, Issue.5
, pp. 598-610
-
-
Karlin, S.1
-
18
-
-
2942542784
-
Gene prediction using the self-organizing map: Automatic generation of multiple gene models
-
S. Mahony, J.O. McInerney, T.J. Smith, A. Golden, Gene prediction using the self-organizing map: automatic generation of multiple gene models, BMC Bioinform. (2004) 5(1):23. Online: http://www.biomedcentral.com/1471-2105/5/23
-
(2004)
BMC Bioinform.
, vol.5
, Issue.1
, pp. 23
-
-
Mahony, S.1
McInerney, J.O.2
Smith, T.J.3
Golden, A.4
-
19
-
-
0035875343
-
GeneMarkS: A self-training method for prediction of gene starts in microbial genomes Implications for finding sequence motifs in regulatory regions
-
J. Besemer, A. Lomsadze, and M. Borodovsky GeneMarkS: a self-training method for prediction of gene starts in microbial genomes Implications for finding sequence motifs in regulatory regions Nucleic Acids Res 29 12 2001 2607 2618
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.12
, pp. 2607-2618
-
-
Besemer, J.1
Lomsadze, A.2
Borodovsky, M.3
-
20
-
-
0036796369
-
Current methods of gene prediction, their strengths and weaknesses
-
C. Mathe, M.F. Sagot, T. Schiex, and P. Rouze Current methods of gene prediction, their strengths and weaknesses Nucleic Acids Res. 30 19 2002 4103 4117
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.19
, pp. 4103-4117
-
-
Mathe, C.1
Sagot, M.F.2
Schiex, T.3
Rouze, P.4
-
21
-
-
0028956546
-
Properties of a general model of DNA evolution under no-strand-bias conditions
-
J.R. Lobry Properties of a general model of DNA evolution under no-strand-bias conditions J. Mol. Evol. 40 3 1995 326 330
-
(1995)
J. Mol. Evol.
, vol.40
, Issue.3
, pp. 326-330
-
-
Lobry, J.R.1
-
22
-
-
0029985398
-
Asymmetric substitution patterns in the two DNA strands of bacteria
-
J.R. Lobry Asymmetric substitution patterns in the two DNA strands of bacteria Mol. Biol. Evol. 13 5 1996 660 665
-
(1996)
Mol. Biol. Evol.
, vol.13
, Issue.5
, pp. 660-665
-
-
Lobry, J.R.1
-
23
-
-
0032584101
-
Strand compositional asymmetry in bacterial and large viral genomes
-
J. Mrazek, and S. Karlin Strand compositional asymmetry in bacterial and large viral genomes Proc. Natl. Acad. Sci. USA 95 1998 3720 3725
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 3720-3725
-
-
Mrazek, J.1
Karlin, S.2
-
24
-
-
0012534043
-
DNA asymmetry and the replicational mutational pressure
-
M. Kowalczuk, P. Mackiewicz, D. Mackiewicz, A. Nowicka, M. Dudkiewicz, M.R. Dudek, and S. Cebrat DNA asymmetry and the replicational mutational pressure J. Appl. Genet. 42 4 2001 553 577
-
(2001)
J. Appl. Genet.
, vol.42
, Issue.4
, pp. 553-577
-
-
Kowalczuk, M.1
MacKiewicz, P.2
MacKiewicz, D.3
Nowicka, A.4
Dudkiewicz, M.5
Dudek, M.R.6
Cebrat, S.7
-
25
-
-
0037179524
-
Asymmetric directional mutation pressures in bacteria
-
J.R. Lobry, and N. Sueoka Asymmetric directional mutation pressures in bacteria Genome Biol. 3 10 2002 RESEARCH0058
-
(2002)
Genome Biol.
, vol.3
, Issue.10
-
-
Lobry, J.R.1
Sueoka, N.2
-
26
-
-
0032860238
-
Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms
-
A.C. Frank, and J.R. Lobry Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms Gene 238 1 1999 65 77
-
(1999)
Gene
, vol.238
, Issue.1
, pp. 65-77
-
-
Frank, A.C.1
Lobry, J.R.2
-
27
-
-
0033053160
-
Two Aspects of DNA base composition: G + C content and translation-coupled deviation from intra-strand rule of A= T and G = C
-
N. Sueoka Two Aspects of DNA base composition: G + C content and translation-coupled deviation from intra-strand rule of A = T and G = C J. Mol. Evol. 49 1999 49 62
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 49-62
-
-
Sueoka, N.1
-
30
-
-
0026059039
-
Analysis of distribution of bases in the coding sequences by a diagrammatic technique
-
C.T. Zhang, and R. Zhang Analysis of distribution of bases in the coding sequences by a diagrammatic technique Nucleic Acids Res. 19 1991 6313 6317
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 6313-6317
-
-
Zhang, C.T.1
Zhang, R.2
-
31
-
-
0028237028
-
A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences
-
C.T. Zhang, and K.C. Chou A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences J. Mol. Biol. 238 1994 1 8
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 1-8
-
-
Zhang, C.T.1
Chou, K.C.2
-
32
-
-
0023194889
-
Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences
-
E.N. Trifonov Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences J. Mol. Biol. 194 1987 643 652
-
(1987)
J. Mol. Biol.
, vol.194
, pp. 643-652
-
-
Trifonov, E.N.1
-
33
-
-
0038480747
-
Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria
-
J.R. Lobry, and D. Chessel Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria J. Appl. Genet. 44 2 2003 235 261
-
(2003)
J. Appl. Genet.
, vol.44
, Issue.2
, pp. 235-261
-
-
Lobry, J.R.1
Chessel, D.2
-
34
-
-
0031593216
-
Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species
-
J. Lobry Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species Gene 205 1-2 1997 309 316
-
(1997)
Gene
, vol.205
, Issue.1-2
, pp. 309-316
-
-
Lobry, J.1
-
35
-
-
13444269018
-
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
-
X.F. Wan, D. Xu, A. Kleinhofs, and J. Zhou Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes BMC Evol. Biol. 4 1 2004 19
-
(2004)
BMC Evol. Biol.
, vol.4
, Issue.1
, pp. 19
-
-
Wan, X.F.1
Xu, D.2
Kleinhofs, A.3
Zhou, J.4
-
36
-
-
0023991945
-
Directional mutation pressure and neutral molecular evolution
-
N. Sueoka Directional mutation pressure and neutral molecular evolution Proc. Natl. Acad. Sci. USA 85 8 1988 2653 2657
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, Issue.8
, pp. 2653-2657
-
-
Sueoka, N.1
-
37
-
-
0028922156
-
Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
-
N. Sueoka Intrastrand parity rules of DNA base composition and usage biases of synonymous codons J. Mol. Evol. 40 3 1995 318 325
-
(1995)
J. Mol. Evol.
, vol.40
, Issue.3
, pp. 318-325
-
-
Sueoka, N.1
-
38
-
-
3643052747
-
On the genetic basis of variation and heterogeneity of DNA base composition
-
N. Sueoka On the genetic basis of variation and heterogeneity of DNA base composition Proc. Natl. Acad. Sci. USA 48 1962 582 592
-
(1962)
Proc. Natl. Acad. Sci. USA
, vol.48
, pp. 582-592
-
-
Sueoka, N.1
-
39
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
M. Bulmer The selection-mutation-drift theory of synonymous codon usage Genetics 129 3 1991 897 907
-
(1991)
Genetics
, vol.129
, Issue.3
, pp. 897-907
-
-
Bulmer, M.1
-
40
-
-
1542618322
-
Codon usage between genomes is constrained by genome-wide mutational processes
-
S.L. Chen, W. Lee, A.K. Hottes, L. Shapiro, and H.H. McAdams Codon usage between genomes is constrained by genome-wide mutational processes Proc. Natl. Acad. Sci. USA 101 10 2004 3480 3485
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.10
, pp. 3480-3485
-
-
Chen, S.L.1
Lee, W.2
Hottes, A.K.3
Shapiro, L.4
McAdams, H.H.5
-
41
-
-
4043056141
-
Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code
-
M. Archetti Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code J. Mol. Evol. 59 2 2004 258 266
-
(2004)
J. Mol. Evol.
, vol.59
, Issue.2
, pp. 258-266
-
-
Archetti, M.1
-
42
-
-
0027715731
-
Codon usage: Mutational bias translational selection or both?
-
P.M. Sharp, M. Stenico, J.F. Peden, and A.T. Lloyd Codon usage: mutational bias translational selection or both? Biochem. Soc. Trans. 21 4 1993 835 841
-
(1993)
Biochem. Soc. Trans.
, vol.21
, Issue.4
, pp. 835-841
-
-
Sharp, P.M.1
Stenico, M.2
Peden, J.F.3
Lloyd, A.T.4
-
43
-
-
18844388812
-
Cluster structures in genomic word frequency distributions
-
Cluster structures in genomic word frequency distributions. Web-site with supplementary materials. http://www.ihes.fr/ ∼ zinovyev/7clusters/index.htm
-
Web-site with Supplementary Materials
-
-
-
45
-
-
0037401310
-
Coding DNA sequences: Statistical distributions
-
A. Som, S. Sahoo, and J. Chakrabarti Coding DNA sequences: statistical distributions Math. Biosci. 183 1 2003 49 61
-
(2003)
Math. Biosci.
, vol.183
, Issue.1
, pp. 49-61
-
-
Som, A.1
Sahoo, S.2
Chakrabarti, J.3
-
46
-
-
0036796799
-
Synonymous codon usage is subject to selection in thermophilic bacteria
-
D.J. Lynn, A.C. Gregory, G.A.C. Singer, and D.A. Hickey Synonymous codon usage is subject to selection in thermophilic bacteria Nucleic Acids Res. 30 19 2002 4272 4277
-
(2002)
Nucleic Acids Res.
, vol.30
, Issue.19
, pp. 4272-4277
-
-
Lynn, D.J.1
Gregory, A.C.2
Singer, G.A.C.3
Hickey, D.A.4
-
47
-
-
0242391986
-
Codon Adaptation Index as a measure of dominating codon bias
-
A. Carbone, A. Zinovyev, and F. Kepes Codon Adaptation Index as a measure of dominating codon bias Bioinformatics 19 13 2003 2005 2015
-
(2003)
Bioinformatics
, vol.19
, Issue.13
, pp. 2005-2015
-
-
Carbone, A.1
Zinovyev, A.2
Kepes, F.3
|