-
1
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
H Akashi 2003 Translational selection and yeast proteome evolution Genetics 164 1291 1303
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
2
-
-
0037133671
-
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
-
H Akashi T Gojobori 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis Proc Natl Acad Sci USA 99 3695 3700
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 3695-3700
-
-
Akashi, H.1
Gojobori, T.2
-
3
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. the Gene Ontology Consortium
-
M Ashburner CA Ball JA Blake D Botstein H Butler JM Cherry AP Davis K Dolinski SS Dwight JT Eppig MA Harris DP Hill L Issel-Tarver A Kasarskis S Lewis JC Matese JE Richardson M Ringwald GM Rubin G Sherlock 2000 Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nature Genet 25 25 29
-
(2000)
Nature Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
5
-
-
1242317029
-
Intimate evolution of proteins-proteome atomic content correlates with genome base composition
-
P Baudouin-Cornu K Schuerer P Marliere D Thomas 2004 Intimate evolution of proteins-proteome atomic content correlates with genome base composition J Biol Chem 279 5421 5428
-
(2004)
J Biol Chem
, vol.279
, pp. 5421-5428
-
-
Baudouin-Cornu, P.1
Schuerer, K.2
Marliere, P.3
Thomas, D.4
-
7
-
-
10944232800
-
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
-
A Beyer J Hollunder HP Nasheuer T Wilhelm 2004 Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale Mol Cell Proteomics 3 1083 1092
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1083-1092
-
-
Beyer, A.1
Hollunder, J.2
Nasheuer, H.P.3
Wilhelm, T.4
-
8
-
-
0037474301
-
The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur
-
VM Boer JH de Winde JT Pronk MDW Piper 2003 The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur J Biol Chem 278 3265 3274
-
(2003)
J Biol Chem
, vol.278
, pp. 3265-3274
-
-
Boer, V.M.1
De Winde, J.H.2
Pronk, J.T.3
Piper, M.D.W.4
-
9
-
-
34249942028
-
Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes
-
JG Bragg A Wagner 2007 Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes Proc R Soc B 274 1063 1070
-
(2007)
Proc R Soc B
, vol.274
, pp. 1063-1070
-
-
Bragg, J.G.1
Wagner, A.2
-
10
-
-
58149354386
-
Protein material costs: Single atoms can make an evolutionary difference
-
10.1016/j.tig.2008.10.007
-
JG Bragg A Wagner 2009 Protein material costs: single atoms can make an evolutionary difference Trends Genet 10.1016/j.tig.2008.10.007
-
(2009)
Trends Genet
-
-
Bragg, J.G.1
Wagner, A.2
-
11
-
-
34047223024
-
Posttranscriptional expression regulation: What determines translation rates?
-
R Brockmann A Beyer JJ Heinisch T Wilhelm 2007 Posttranscriptional expression regulation: what determines translation rates? PLoS Comput Biol 3 531 539
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 531-539
-
-
Brockmann, R.1
Beyer, A.2
Heinisch, J.J.3
Wilhelm, T.4
-
12
-
-
0032087026
-
Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli
-
CL Craig RS Weber 1998 Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli Mol Biol Evol 15 774 776
-
(1998)
Mol Biol Evol
, vol.15
, pp. 774-776
-
-
Craig, C.L.1
Weber, R.S.2
-
13
-
-
0037745173
-
Assimilatory sulfur metabolism in marine microorganisms: Sulfur metabolism, growth, and protein synthesis of Pseudomonas halodurans and Alteromonas luteo-violaceus during sulfate limitation
-
RL Cuhel CD Taylor HW Jannasch 1981 Assimilatory sulfur metabolism in marine microorganisms: Sulfur metabolism, growth, and protein synthesis of Pseudomonas halodurans and Alteromonas luteo-violaceus during sulfate limitation Arch Microbiol 130 1 7
-
(1981)
Arch Microbiol
, vol.130
, pp. 1-7
-
-
Cuhel, R.L.1
Taylor, C.D.2
Jannasch, H.W.3
-
14
-
-
33748761394
-
Signatures of ecological resource availability in the animal and plant proteomes
-
JJ Elser WF Fagan S Subramanian S Kumar 2006 Signatures of ecological resource availability in the animal and plant proteomes Mol Biol Evol 23 1946 1951
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1946-1951
-
-
Elser, J.J.1
Fagan, W.F.2
Subramanian, S.3
Kumar, S.4
-
15
-
-
18344387669
-
Sulfur sparing in the yeast proteome in response to sulfur demand
-
M Fauchon G Lagniel JC Aude L Lombardia P Soularue C Petat G Marguerie A Sentenac M Werner J Labarre 2002 Sulfur sparing in the yeast proteome in response to sulfur demand Mol Cell 9 713 723
-
(2002)
Mol Cell
, vol.9
, pp. 713-723
-
-
Fauchon, M.1
Lagniel, G.2
Aude, J.C.3
Lombardia, L.4
Soularue, P.5
Petat, C.6
Marguerie, G.7
Sentenac, A.8
Werner, M.9
Labarre, J.10
-
17
-
-
0142215475
-
Global analysis of protein expression in yeast
-
S Ghaemmaghami W Huh K Bower RW Howson A Belle N Dephoure EK O'Shea JS Weissman 2003 Global analysis of protein expression in yeast Nature 425 737 741
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
18
-
-
0035999672
-
Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
-
D Greenbaum R Jansen M Gerstein 2002 Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts Bioinformatics 18 585 596
-
(2002)
Bioinformatics
, vol.18
, pp. 585-596
-
-
Greenbaum, D.1
Jansen, R.2
Gerstein, M.3
-
22
-
-
9144264843
-
GeneDB: A resource for prokaryotic and eukaryotic organisms
-
C Hertz-Fowler CS Peacock V Wood M Aslett A Kerhornou P Mooney A Tivey M Berriman N Hall K Rutherford J Parkhill AC Ivens MA Rajandream B Barrell 2004 GeneDB: a resource for prokaryotic and eukaryotic organisms Nucleic Acids Res 32 D339 D343
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Hertz-Fowler, C.1
Peacock, C.S.2
Wood, V.3
Aslett, M.4
Kerhornou, A.5
Mooney, P.6
Tivey, A.7
Berriman, M.8
Hall, N.9
Rutherford, K.10
Parkhill, J.11
Ivens, A.C.12
Rajandream, M.A.13
Barrell, B.14
-
23
-
-
38549123363
-
Gene Ontology annotations at SGD: New data sources and annotation methods
-
EL Hong R Balakrishnan Q Dong KR Christie J Park G Binkley MC Costanzo SS Dwight SR Engel DG Fisk JE Hirschman BC Hitz CJ Krieger MS Livstone SR Miyasato RS Nash R Oughtred MS Skrzypek S Weng ED Wong KK Zhu K Dolinski D Botstein JM Cherry 2008 Gene Ontology annotations at SGD: new data sources and annotation methods Nucleic Acids Res 36 D577 D581
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Hong, E.L.1
Balakrishnan, R.2
Dong, Q.3
Christie, K.R.4
Park, J.5
Binkley, G.6
Costanzo, M.C.7
Dwight, S.S.8
Engel, S.R.9
Fisk, D.G.10
Hirschman, J.E.11
Hitz, B.C.12
Krieger, C.J.13
Livstone, M.S.14
Miyasato, S.R.15
Nash, R.S.16
Oughtred, R.17
Skrzypek, M.S.18
Weng, S.19
Wong, E.D.20
Zhu, K.K.21
Dolinski, K.22
Botstein, D.23
Cherry, J.M.24
more..
-
25
-
-
0016656665
-
The fate of ribosomes in Escherichia coli cells starved for a carbon source
-
R Kaplan D Apirion 1975 The fate of ribosomes in Escherichia coli cells starved for a carbon source J Biol Chem 250 1854 1863
-
(1975)
J Biol Chem
, vol.250
, pp. 1854-1863
-
-
Kaplan, R.1
Apirion, D.2
-
26
-
-
33745459776
-
Proteome analysis of yeast response to various nutrient limitations
-
Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MMA, Pronk JT, Slijper M, Heck AJR (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2:2006.0026
-
(2006)
Mol Syst Biol
, vol.2
-
-
Kolkman, A.1
Daran-Lapujade, P.2
Fullaondo, A.3
Olsthoorn, M.M.A.4
Pronk, J.T.5
Slijper, M.6
Heck, A.J.R.7
-
27
-
-
43049138051
-
Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease
-
C Kraft A Deplazes M Sohrmann M Peter 2008 Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease Nat Cell Biol 10 602 610
-
(2008)
Nat Cell Biol
, vol.10
, pp. 602-610
-
-
Kraft, C.1
Deplazes, A.2
Sohrmann, M.3
Peter, M.4
-
28
-
-
3242731195
-
A model for random sampling and estimation of relative protein abundance in shotgun proteomics
-
HB Liu RG Sadygov JR Yates 2004 A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 76 4193 4201
-
(2004)
Anal Chem
, vol.76
, pp. 4193-4201
-
-
Liu, H.B.1
Sadygov, R.G.2
Yates, J.R.3
-
29
-
-
0028088517
-
Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
-
JR Lobry C Gautier 1994 Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes Nucleic Acids Res 22 3174 3180
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3174-3180
-
-
Lobry, J.R.1
Gautier, C.2
-
30
-
-
50249155987
-
Association between the availability of environmental resources and the atomic composition of organismal proteomes: Evidence from Prochlorococcus strains living at different depths
-
J Lv N Li D-K Niu 2008 Association between the availability of environmental resources and the atomic composition of organismal proteomes: evidence from Prochlorococcus strains living at different depths Biochem Biophys Res Commun 375 241 246
-
(2008)
Biochem Biophys Res Commun
, vol.375
, pp. 241-246
-
-
Lv, J.1
Li, N.2
Niu, D.-K.3
-
31
-
-
0024975803
-
Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins
-
D Mazel P Marliere 1989 Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins Nature 341 245 248
-
(1989)
Nature
, vol.341
, pp. 245-248
-
-
Mazel, D.1
Marliere, P.2
-
33
-
-
28444475607
-
Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations
-
L Nie G Wu W Zhang 2006 Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations Biochem Biophys Res Commun 339 603 610
-
(2006)
Biochem Biophys Res Commun
, vol.339
, pp. 603-610
-
-
Nie, L.1
Wu, G.2
Zhang, W.3
-
34
-
-
0014028234
-
Purification and properties of a sulfate-binding protein from Salmonella typhimurium
-
AB Pardee 1966 Purification and properties of a sulfate-binding protein from Salmonella typhimurium J Biol Chem 241 5886 5892
-
(1966)
J Biol Chem
, vol.241
, pp. 5886-5892
-
-
Pardee, A.B.1
-
35
-
-
33847081243
-
Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
-
MW Schmidt A Houseman AR Ivanov DA Wolf 2007 Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe Mol Syst Biol 3 79
-
(2007)
Mol Syst Biol
, vol.3
, pp. 79
-
-
Schmidt, M.W.1
Houseman, A.2
Ivanov, A.R.3
Wolf, D.A.4
-
36
-
-
34248157233
-
Selection on synthesis cost affects interprotein amino acid usage in all three domains of life
-
J Swire 2007 Selection on synthesis cost affects interprotein amino acid usage in all three domains of life J Mol Evol 64 558 571
-
(2007)
J Mol Evol
, vol.64
, pp. 558-571
-
-
Swire, J.1
-
37
-
-
38549097071
-
The Universal Protein Resource (UniProt)
-
The UniProt Consortium
-
The UniProt Consortium 2008 The Universal Protein Resource (UniProt) Nucleic Acids Res 36 D190 D195
-
(2008)
Nucleic Acids Res
, vol.36
-
-
-
38
-
-
19544389317
-
Energy constraints on the evolution of gene expression
-
A Wagner 2005 Energy constraints on the evolution of gene expression Mol Biol Evol 22 1365 1374
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1365-1374
-
-
Wagner, A.1
-
39
-
-
33947409158
-
SPIDer: Saccharomyces protein-protein interaction database
-
XM Wu L Zhu J Guo C Fu HJ Zhou D Dong ZB Li DY Zhang K Lin 2006 SPIDer: Saccharomyces protein-protein interaction database BMC Bioinformatics 7 S16
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 16
-
-
Wu, X.M.1
Zhu, L.2
Guo, J.3
Fu, C.4
Zhou, H.J.5
Dong, D.6
Li, Z.B.7
Zhang, D.Y.8
Lin, K.9
|