-
1
-
-
0035445792
-
A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae
-
Grigoriev,A. (2001) A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res., 29, 3513-3519.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3513-3519
-
-
Grigoriev, A.1
-
2
-
-
0036141992
-
Relating whole-genome expression data with protein-protein interactions
-
Jansen,R., Greenbaum,D. and Gerstein,M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res., 12, 37-46.
-
(2002)
Genome Res.
, vol.12
, pp. 37-46
-
-
Jansen, R.1
Greenbaum, D.2
Gerstein, M.3
-
3
-
-
0036601233
-
Functional transcriptomes: Comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts
-
Bono,H. and Okazaki,Y. (2002) Functional transcriptomes: Comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts. Curr. Opin. Struct. Biol., 12, 355-361.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 355-361
-
-
Bono, H.1
Okazaki, Y.2
-
4
-
-
0036279153
-
Protein interaction verification and functional annotation by integrated analysis of genome-scale data
-
Kemmeren,P., van Berkum,N.L., Vilo,J., Bijma,T., Donders,R., Brazma,A. and Holstege,F.C. (2002) Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell, 9, 1133-1143.
-
(2002)
Mol. Cell
, vol.9
, pp. 1133-1143
-
-
Kemmeren, P.1
van Berkum, N.L.2
Vilo, J.3
Bijma, T.4
Donders, R.5
Brazma, A.6
Holstege, F.C.7
-
5
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
6
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek,R, Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
7
-
-
0036533931
-
Identifying functional links between genes using conserved chromosomal proximity
-
Yanai,I., Mellor,J.C. and DeLisi,C. (2002) Identifying functional links between genes using conserved chromosomal proximity. Trends Genet. 18, 176-179.
-
(2002)
Trends Genet.
, vol.18
, pp. 176-179
-
-
Yanai, I.1
Mellor, J.C.2
DeLisi, C.3
-
8
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-753.
-
(1999)
Science
, vol.285
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ng, H.L.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
9
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
11
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285-4288.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
12
-
-
0030805979
-
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12
-
Link,A.J., Robison,K. and Church,G.M. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis, 18, 1259-1313.
-
(1997)
Electrophoresis
, vol.18
, pp. 1259-1313
-
-
Link, A.J.1
Robison, K.2
Church, G.M.3
-
13
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami,S., Huh,W.K., Bower,K., Howson,R.W., Belle,A., Dephoure,N., O'Shea,E.K. and Weissman,J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
14
-
-
0034888743
-
Characterizations of highly expressed genes of four fast-growing bacteria
-
Karlin,S., Mrazek,J., Campbell,A. and Kaiser,D. (2001) Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol., 183, 5025-5040.
-
(2001)
J. Bacteriol.
, vol.183
, pp. 5025-5040
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.3
Kaiser, D.4
-
15
-
-
0348013051
-
Hierarchy of sequence-dependent features associated with prokaryotic translation
-
Lithwick,G. and Margalit,H. (2003) Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res., 13, 2665-2673.
-
(2003)
Genome Res.
, vol.13
, pp. 2665-2673
-
-
Lithwick, G.1
Margalit, H.2
-
16
-
-
0942287071
-
Comparing expression level-dependent features in codon usage with protein abundance: An analysis of 'predictive proteomics'
-
McHardy,A.C., Puhler,A., Kalinowski,J. and Meyer,F. (2004) Comparing expression level-dependent features in codon usage with protein abundance: An analysis of 'predictive proteomics'. Proteomics, 4, 46-58.
-
(2004)
Proteomics
, vol.4
, pp. 46-58
-
-
McHardy, A.C.1
Puhler, A.2
Kalinowski, J.3
Meyer, F.4
-
17
-
-
0023650543
-
The codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp,P.M. and Li,W.H. (1987) The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
18
-
-
0035150079
-
Synonymous codon usage in bacteria
-
Ermolaeva,M.D. (2001) Synonymous codon usage in bacteria. Curr. Issues Mol. Biol., 3, 91-97.
-
(2001)
Curr. Issues Mol. Biol.
, vol.3
, pp. 91-97
-
-
Ermolaeva, M.D.1
-
19
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
-
Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol., 151 389-409.
-
(1981)
J. Mol. Biol.
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
20
-
-
0019949369
-
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
-
Ikemura,T. (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol., 158, 573-597.
-
(1982)
J. Mol. Biol.
, vol.158
, pp. 573-597
-
-
Ikemura, T.1
-
21
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura,T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol., 2, 13-34.
-
(1985)
Mol. Biol. Evol.
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
22
-
-
0030564828
-
Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
-
Dong,H., Nilsson,L. and Kurland,C.G. (1996) Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol., 260, 649-663.
-
(1996)
J. Mol. Biol.
, vol.260
, pp. 649-663
-
-
Dong, H.1
Nilsson, L.2
Kurland, C.G.3
-
23
-
-
0032882170
-
Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
-
Kanaya,S., Yamada,Y., Kudo,Y. and Ikemura,T. (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene, 238, 143-155.
-
(1999)
Gene
, vol.238
, pp. 143-155
-
-
Kanaya, S.1
Yamada, Y.2
Kudo, Y.3
Ikemura, T.4
-
24
-
-
0034821884
-
Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis
-
Kanaya,S., Yamada,Y., Kinouchi,M., Kudo,Y. and Ikemura,T. (2001) Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol. Evol., 53, 290-298.
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 290-298
-
-
Kanaya, S.1
Yamada, Y.2
Kinouchi, M.3
Kudo, Y.4
Ikemura, T.5
-
25
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright,F. (1990) The 'effective number of codons' used in a gene. Gene, 87, 23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
26
-
-
2942695714
-
Coevolution of gene expression among interacting proteins
-
Fraser,H.B., Hirsh,A.E., Wall,D.P. and Eisen,M.B. (2004) Coevolution of gene expression among interacting proteins. Proc. Natl Acad. Sci. USA 101, 9033-9038.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 9033-9038
-
-
Fraser, H.B.1
Hirsh, A.E.2
Wall, D.P.3
Eisen, M.B.4
-
27
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
28
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
29
-
-
0034086295
-
Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
-
Lafay,B., Atherton,J.C. and Sharp,P.M. (2000) Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology, 146, 851-860.
-
(2000)
Microbiology
, vol.146
, pp. 851-860
-
-
Lafay, B.1
Atherton, J.C.2
Sharp, P.M.3
-
30
-
-
0037109119
-
Use and misuse of correspondence analysis in codon usage studies
-
Perriere,G. and Thioulouse,J. (2002) Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res., 30, 4548-4555.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4548-4555
-
-
Perriere, G.1
Thioulouse, J.2
-
31
-
-
0036088133
-
DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
-
Xenarios,I., Salwinski,L., Duan,X.J., Higney,P., Kim,S.M. and Eisenberg,D. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 303-305
-
-
Xenarios, I.1
Salwinski, L.2
Duan, X.J.3
Higney, P.4
Kim, S.M.5
Eisenberg, D.6
-
32
-
-
6944256505
-
The E. coli EcoCyc Database: No longer just a metabolic pathway database
-
Karp,P.D., Arnaud,M., Collado-Vides,J., Ingraham,J., Paulsen,I.T. and Saier,M.H. (2004) The E. coli EcoCyc Database: No longer just a metabolic pathway database. ASM News, 70, 25-30.
-
(2004)
ASM News
, vol.70
, pp. 25-30
-
-
Karp, P.D.1
Arnaud, M.2
Collado-Vides, J.3
Ingraham, J.4
Paulsen, I.T.5
Saier, M.H.6
-
33
-
-
0038460047
-
AraCyc: A biochemical pathway database for Arabidopsis
-
Mueller,L.A., Zhang,P. and Rhee,S.Y. (2003) AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiol., 132, 453-460.
-
(2003)
Plant Physiol.
, vol.132
, pp. 453-460
-
-
Mueller, L.A.1
Zhang, P.2
Rhee, S.Y.3
-
34
-
-
11244328060
-
The Pathway Tools software
-
Karp,P.D., Paley,S. and Romero,P. (2002) The Pathway Tools software. Bioinformatics, 18(Suppl. 1), S225-S232.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Karp, P.D.1
Paley, S.2
Romero, P.3
-
35
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka,R. and Gentleman,R. (1996) R: A language for data analysis and graphics. J. Comput. Graph. Statist., 5, 299-314.
-
(1996)
J. Comput. Graph. Statist.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
36
-
-
0029873217
-
Histidine biosynthetic pathway and genes: Structure, regulation, and evolution
-
Alifano,P., Fani,R, Lio,P., Lazcano,A., Bazzicalupo,M., Carlomagno,M.S. and Bruni,C.B. (1996) Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiol. Rev., 60, 44-69.
-
(1996)
Microbiol. Rev.
, vol.60
, pp. 44-69
-
-
Alifano, P.1
Fani, R.2
Lio, P.3
Lazcano, A.4
Bazzicalupo, M.5
Carlomagno, M.S.6
Bruni, C.B.7
-
37
-
-
0031720281
-
Codon usages in different gene classes of the Escherichia coli genome
-
Karlin,S., Mrazek,J. and Campbell,A.M. (1998) Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29, 1341-1355.
-
(1998)
Mol. Microbiol.
, vol.29
, pp. 1341-1355
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.M.3
-
38
-
-
0035461311
-
ATP synthase - A marvellous rotary engine of the cell
-
Yoshida,M., Muneyuki,E. and Hisabori,T. (2001) ATP synthase - a marvellous rotary engine of the cell. Nature Rev. Mol. Cell. Biol. 2, 669-677.
-
(2001)
Nature Rev. Mol. Cell. Biol.
, vol.2
, pp. 669-677
-
-
Yoshida, M.1
Muneyuki, E.2
Hisabori, T.3
-
39
-
-
0031008228
-
The ATP synthase - A splendid molecular machine
-
Boyer,P.D. (1997) The ATP synthase - a splendid molecular machine. Annu. Rev. Biochem., 66, 717-749.
-
(1997)
Annu. Rev. Biochem.
, vol.66
, pp. 717-749
-
-
Boyer, P.D.1
-
40
-
-
0000545299
-
Evidence for nuclear control of the expression of the atpA and atpB chloroplast genes in Chlamydomonas
-
Drapier,D., Girard-Bascou,J. and Wollman,F.A. (1992) Evidence for nuclear control of the expression of the atpA and atpB chloroplast genes in Chlamydomonas. Plant Cell, 4, 283-295.
-
(1992)
Plant Cell
, vol.4
, pp. 283-295
-
-
Drapier, D.1
Girard-Bascou, J.2
Wollman, F.A.3
-
41
-
-
0029938306
-
Codon usage and base composition in Rickettsia prowazekii
-
Andersson,S.G. and Sharp,P.M. (1996) Codon usage and base composition in Rickettsia prowazekii. J. Mol. Evol., 42, 525-536.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 525-536
-
-
Andersson, S.G.1
Sharp, P.M.2
-
42
-
-
0037328264
-
Proteome analysis of the plant pathogen Xylella fastidiosa reveals major cellular and extracellular proteins and a peculiar codon bias distribution
-
Smolka,M.B., Martins,D., Winck,F.V., Santoro,C.E., Castellari,R.R., Ferrari,F., Brum,I.J., Galembeck,E., Della Coletta Filho,H., Machado,M.A. et al. (2003) Proteome analysis of the plant pathogen Xylella fastidiosa reveals major cellular and extracellular proteins and a peculiar codon bias distribution. Proteomics, 3 224-237.
-
(2003)
Proteomics
, vol.3
, pp. 224-237
-
-
Smolka, M.B.1
Martins, D.2
Winck, F.V.3
Santoro, C.E.4
Castellari, R.R.5
Ferrari, F.6
Brum, I.J.7
Galembeck, E.8
Della Coletta Filho, H.9
Machado, M.A.10
-
43
-
-
0036286279
-
Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
-
Meidanis,J., Braga,M.D. and Verjovski-Almeida,S. (2002) Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa. Microbiol. Mol. Biol. Rev., 66, 272-299.
-
(2002)
Microbiol. Mol. Biol. Rev.
, vol.66
, pp. 272-299
-
-
Meidanis, J.1
Braga, M.D.2
Verjovski-Almeida, S.3
-
44
-
-
2942576138
-
Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
-
Iyer,L.M., Koonin,E.V. and Aravind,L. (2004) Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene, 335, 73-88.
-
(2004)
Gene
, vol.335
, pp. 73-88
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
45
-
-
0030808646
-
Tethering of the large subunits of Escherichia coli RNA polymerase
-
Severinov,K., Mooney,R., Darst,S.A. and Landick,R. (1997) Tethering of the large subunits of Escherichia coli RNA polymerase. J. Biol. Chem., 272, 24137-24140.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 24137-24140
-
-
Severinov, K.1
Mooney, R.2
Darst, S.A.3
Landick, R.4
|