-
1
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
-
(1974)
IEEE Trans Automat Contr
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, 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..
-
3
-
-
77958507116
-
Chaperonin-dependent accelerated substitution rates in prokaryotes
-
Bogumil D, Dagan T. 2010. Chaperonin-dependent accelerated substitution rates in prokaryotes. Genome Biol Evol. 2:602-608.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 602-608
-
-
Bogumil, D.1
Dagan, T.2
-
4
-
-
77951734603
-
A role for codon order in translation dynamics
-
Cannarozzi G, et al. 2010. A role for codon order in translation dynamics. Cell 141:355-367.
-
(2010)
Cell
, vol.141
, pp. 355-367
-
-
Cannarozzi, G.1
-
5
-
-
0030831182
-
Genetic and physical maps of Saccharomyces cerevisiae
-
Cherry JM, et al. 1997. Genetic and physical maps of Saccharomyces cerevisiae. Nature 387:67-73. (Pubitemid 27334668)
-
(1997)
Nature
, vol.387
, pp. 67-73
-
-
Cherry, J.M.1
Ball, C.2
Weng, S.3
Juvik, G.4
Schmidt, R.5
Adler, C.6
Dunn, B.7
Dwight, S.8
Riles, L.9
Mortimer, R.K.10
Botstein, D.11
-
6
-
-
36348993862
-
Functional characterization of the atypical Hsp70 subunit of yeast ribosome-associated complex
-
DOI 10.1074/jbc.M706737200
-
Conz C, et al. 2007. Functional characterization of the atypical Hsp70 subunit of yeast ribosome-associated complex. J Biol Chem. 282:33977-33984. (Pubitemid 350159440)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.47
, pp. 33977-33984
-
-
Conz, C.1
Otto, H.2
Peisker, K.3
Gautschi, M.4
Wolfle, T.5
Mayer, M.P.6
Rospert, S.7
-
7
-
-
79954529507
-
ProtTest 3: Fast selection of best-fit models of protein evolution
-
Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1175.
-
(2011)
Bioinformatics
, vol.27
, pp. 1164-1175
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
8
-
-
0347357617
-
Protein folding and misfolding
-
DOI 10.1038/nature02261
-
Dobson CM. 2003. Protein folding and misfolding. Nature 426:884-890. (Pubitemid 38056880)
-
(2003)
Nature
, vol.426
, Issue.6968
, pp. 884-890
-
-
Dobson, C.M.1
-
9
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
DOI 10.1073/pnas.0504070102
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 102:14338-14343. (Pubitemid 41429699)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.40
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
10
-
-
47549097539
-
Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
-
DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
-
Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
-
(2008)
Cell
, vol.134
, Issue.2
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
11
-
-
0023668329
-
Proteins as molecular chaperones
-
Ellis RJ. 1987. Proteins as molecular chaperones. Nature 328:378-379.
-
(1987)
Nature
, vol.328
, pp. 378-379
-
-
Ellis, R.J.1
-
12
-
-
4143093598
-
A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
-
DOI 10.1093/molbev/msh160
-
Esser C, et al. 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol. 21:1643-1660. (Pubitemid 39096881)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.9
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
Rotte, C.4
Sebastiani, F.5
Gelius-Dietrich, G.6
Henze, K.7
Kretschmann, E.8
Richly, E.9
Leister, D.10
Bryant, D.11
Steel, M.A.12
Lockhart, P.J.13
Penny, D.14
Martin, W.15
-
13
-
-
0037161813
-
GroEL buffers against deleterious mutations
-
Fares MA, Ruiz-Gonzalez MX, Moya A, Elena SF, Barrio E. 2002. GroEL buffers against deleterious mutations. Nature 417:398.
-
(2002)
Nature
, vol.417
, pp. 398
-
-
Fares, M.A.1
Ruiz-Gonzalez, M.X.2
Moya, A.3
Elena, S.F.4
Barrio, E.5
-
14
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
DOI 10.1126/science.1068696
-
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296:750-752. (Pubitemid 34442006)
-
(2002)
Science
, vol.296
, Issue.5568
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
15
-
-
0035957355
-
RAC, a stable ribosome-associated complex in yeast formed by the DnaK-DnaJ homologs Ssz1p and zuotin
-
DOI 10.1073/pnas.071057198
-
Gautschi M, et al. 2001. RAC, a stable ribosome-associated complex in yeast formed by the DnaK-DnaJ homologs Ssz1p and zuotin. Proc Natl Acad Sci U S A. 98:3762-3767. (Pubitemid 32249845)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.7
, pp. 3762-3767
-
-
Gautschi, M.1
Lilie, H.2
Funfschilling, U.3
Mun, A.4
Ross, S.5
Lithgow, T.6
Rucknagel, P.7
Rospert, S.8
-
16
-
-
79551674254
-
Misfolded proteins impose a dosagedependent fitness cost and trigger a cytosolic unfolded protein response in yeast
-
Geiler-Samerotte KA, et al. 2011. Misfolded proteins impose a dosagedependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci U S A. 108:680-685.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 680-685
-
-
Geiler-Samerotte, K.A.1
-
17
-
-
0142215475
-
Global analysis of protein expression in yeast
-
DOI 10.1038/nature02046
-
Ghaemmaghami S, et al. 2003. Global analysis of protein expression in yeast. Nature 425:737-741. (Pubitemid 37314318)
-
(2003)
Nature
, vol.425
, Issue.6959
, 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
-
18
-
-
67650681847
-
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: Implications to protein folding pathways in the cell
-
Gong Y, et al. 2009. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol. 5:275.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 275
-
-
Gong, Y.1
-
19
-
-
0019519371
-
Codon catalog usage is a genome strategy modulated for gene expressivity
-
Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R. 1981. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9:43-74.
-
(1981)
Nucleic Acids Res
, vol.9
, pp. 43-74
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Jacobzone, M.4
Mercier, R.5
-
20
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704. (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
21
-
-
0028960169
-
Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells
-
Gupta RS. 1995. Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol Microbiol. 15:1-11.
-
(1995)
Mol Microbiol
, vol.15
, pp. 1-11
-
-
Gupta, R.S.1
-
22
-
-
66849143696
-
Converging concepts of protein folding in vitro and in vivo
-
Hartl FU, Hayer-Hartl M. 2009. Converging concepts of protein folding in vitro and in vivo. Nat Struct Mol Biol. 16:574-581.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 574-581
-
-
Hartl, F.U.1
Hayer-Hartl, M.2
-
23
-
-
68649123756
-
The GroEL/GroES cis cavity as a passive anti-aggregation device
-
Horwich AL, Apetri AC, Fenton WA. 2009. The GroEL/GroES cis cavity as a passive anti-aggregation device. FEBS Lett. 583:2654-2662.
-
(2009)
FEBS Lett
, vol.583
, pp. 2654-2662
-
-
Horwich, A.L.1
Apetri, A.C.2
Fenton, W.A.3
-
24
-
-
0142184341
-
Global analysis of protein localization in budding yeast
-
Huh WK, et al. 2003. Global analysis of protein localization in budding yeast. Nature 425:686-691.
-
(2003)
Nature
, vol.425
, pp. 686-691
-
-
Huh, W.K.1
-
25
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
DOI 10.1006/jmbi.1999.3091
-
Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 292:195-202. (Pubitemid 29435759)
-
(1999)
Journal of Molecular Biology
, vol.292
, Issue.2
, pp. 195-202
-
-
Jones, D.T.1
-
26
-
-
77954947810
-
The HSP70 chaperone machinery: J proteins as drivers of functional specificity
-
Kampinga HH, Craig EA. 2010. The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nat Rev Mol Cell Biol. 11:579-592.
-
(2010)
Nat Rev Mol Cell Biol
, vol.11
, pp. 579-592
-
-
Kampinga, H.H.1
Craig, E.A.2
-
27
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
DOI 10.1093/nar/gki198
-
Katoh K, Kuma KI, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518. (Pubitemid 40360980)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.-I.2
Toh, H.3
Miyata, T.4
-
28
-
-
22744447508
-
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli
-
DOI 10.1016/j.cell.2005.05.028, PII S0092867405005441
-
Kerner MJ, et al. 2005. Proteome-wide analysis of chaperonindependent protein folding in Escherichia coli. Cell 122:209-220. (Pubitemid 41032985)
-
(2005)
Cell
, vol.122
, Issue.2
, pp. 209-220
-
-
Kerner, M.J.1
Naylor, D.J.2
Ishihama, Y.3
Maier, T.4
Chang, H.-C.5
Stines, A.P.6
Georgopoulos, C.7
Frishman, D.8
Hayer-Hartl, M.9
Mann, M.10
Hartl, F.U.11
-
29
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
DOI 10.1101/gr.1589103
-
Krylov DM, Wolf YI, Rogozin IB, Koonin EV. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13:2229-2235. (Pubitemid 37265987)
-
(2003)
Genome Research
, vol.13
, Issue.10
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
30
-
-
33749468596
-
Finding community structure in networks using the eigenvectors of matrices
-
Newman MEJ. 2006. Finding community structure in networks using the eigenvectors of matrices. Phys Rev E. 74:036104.
-
(2006)
Phys Rev e
, vol.74
, pp. 036104
-
-
Newman, M.E.J.1
-
31
-
-
0034978556
-
Highly expressed genes in yeast evolve slowly
-
Pál C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931. (Pubitemid 32552328)
-
(2001)
Genetics
, vol.158
, Issue.2
, pp. 927-931
-
-
Pal, C.1
Papp, B.2
Hurst, L.D.3
-
32
-
-
33646182934
-
An integrated view of protein evolution
-
Pál C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
-
(2006)
Nat Rev Genet
, vol.7
, pp. 337-348
-
-
Pál, C.1
Papp, B.2
Lercher, M.J.3
-
33
-
-
0037030713
-
Hsp90 as a capacitor of phenotypic variation
-
Queitsch C, Sangster TA, Lindquist S. 2002. Hsp90 as a capacitor of phenotypic variation. Nature 417:618-623.
-
(2002)
Nature
, vol.417
, pp. 618-623
-
-
Queitsch, C.1
Sangster, T.A.2
Lindquist, S.3
-
34
-
-
0027496477
-
Identification and functional analysis of chaperonin 10, the groES homolog from yeast mitochondria
-
DOI 10.1073/pnas.90.23.10967
-
Rospert S, et al. 1993. Identification and functional analysis of chaperonin 10, the groES homolog from yeast mitochondria. Proc Natl Acad Sci U S A. 90:10967-10971. (Pubitemid 23354349)
-
(1993)
Proceedings of the National Academy of Sciences of the United States of America
, vol.90
, Issue.23
, pp. 10967-10971
-
-
Rospert, S.1
Glick, B.S.2
Jeno, P.3
Schatz, G.4
Todd, M.J.5
Lorimer, G.H.6
Viitanen, P.V.7
-
35
-
-
0037379626
-
Between genotype and phenotype: Protein chaperones and evolvability
-
Rutherford SL. 2003. Between genotype and phenotype: protein chaperones and evolvability. Nat Rev Genet. 4:264-274.
-
(2003)
Nat Rev Genet
, vol.4
, pp. 264-274
-
-
Rutherford, S.L.1
-
36
-
-
0023650543
-
The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH. 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
-
37
-
-
54349091742
-
Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions
-
Shorter J, Lindquist S. 2008. Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions. EMBO J. 27:2712-2724.
-
(2008)
EMBO J
, vol.27
, pp. 2712-2724
-
-
Shorter, J.1
Lindquist, S.2
-
38
-
-
33644873184
-
Biogrid: A general repository for interaction datasets
-
Stark C, et al. 2006. Biogrid: a general repository for interaction datasets. Nucleic Acids Res. 34:535-539.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 535-539
-
-
Stark, C.1
-
39
-
-
78651324347
-
The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk D, et al. 2011. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39:561-568.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 561-568
-
-
Szklarczyk, D.1
-
40
-
-
66649132872
-
Chaperonin overexpression promotes genetic variation and enzyme evolution
-
Tokuriki N, Tawfik DS. 2009. Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459:668-673.
-
(2009)
Nature
, vol.459
, pp. 668-673
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
41
-
-
77951715627
-
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
-
Tuller T, et al. 2010. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141:344-354.
-
(2010)
Cell
, vol.141
, pp. 344-354
-
-
Tuller, T.1
-
42
-
-
0037009130
-
Molecular chaperones as essential mediators of mitochondrial biogenesis
-
Voos W, Röttgers K. 2003. Molecular chaperones as essential mediators of mitochondrial biogenesis. Biochim Biophys Acta. 1592:51-62.
-
(2003)
Biochim Biophys Acta
, vol.1592
, pp. 51-62
-
-
Voos, W.1
Röttgers, K.2
-
43
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
DOI 10.1038/nature06107, PII NATURE06107
-
Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449:54-61. (Pubitemid 47373776)
-
(2007)
Nature
, vol.449
, Issue.7158
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
44
-
-
76149095944
-
GroEL dependency affects codon usage - Support for a critical role of misfolding in gene evolution
-
Warnecke T, Hurst LD. 2010. GroEL dependency affects codon usage - support for a critical role of misfolding in gene evolution. Mol Syst Biol. 6:340.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 340
-
-
Warnecke, T.1
Hurst, L.D.2
-
45
-
-
77958577844
-
Impact of translational errorinduced and error-free misfolding on the rate of protein evolution
-
Yang JR, Zhuang SM, Zhang J. 2010. Impact of translational errorinduced and error-free misfolding on the rate of protein evolution. Mol Syst Biol. 6:421.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 421
-
-
Yang, J.R.1
Zhuang, S.M.2
Zhang, J.3
-
46
-
-
5044239107
-
Pathways of chaperone-mediated protein folding in the cytosol
-
DOI 10.1038/nrm1492
-
Young JC, Agashe VR, Siegers K, Hartl FU. 2004. Pathways of chaperone-mediated protein folding in the cytosol. Nat Rev Mol Cell Biol. 5:781-791. (Pubitemid 39336272)
-
(2004)
Nature Reviews Molecular Cell Biology
, vol.5
, Issue.10
, pp. 781-791
-
-
Young, J.C.1
Agashe, V.R.2
Siegers, K.3
Hartl, F.U.4
|