-
1
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
Dekel E, Alon U, (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
2
-
-
33646568438
-
Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research
-
Kitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 12: 291-299.
-
(2005)
DNA Res
, vol.12
, pp. 291-299
-
-
Kitagawa, M.1
Ara, T.2
Arifuzzaman, M.3
Ioka-Nakamichi, T.4
Inamoto, E.5
-
3
-
-
0033772459
-
Expressing genes in different Escherichia coli compartments
-
Cornelis P, (2000) Expressing genes in different Escherichia coli compartments. Curr Opin Biotechnology 11: 450-454.
-
(2000)
Curr Opin Biotechnology
, vol.11
, pp. 450-454
-
-
Cornelis, P.1
-
4
-
-
45149111660
-
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
-
Feist AM, Palsson BO, (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnology 26: 659-667.
-
(2008)
Nat Biotechnology
, vol.26
, pp. 659-667
-
-
Feist, A.M.1
Palsson, B.O.2
-
5
-
-
78149460454
-
Genetic engineering of Escherichia coli for biofuel production
-
Liu T, Khosla C, (2010) Genetic engineering of Escherichia coli for biofuel production. Annu Rev Genet 44: 53-69.
-
(2010)
Annu Rev Genet
, vol.44
, pp. 53-69
-
-
Liu, T.1
Khosla, C.2
-
6
-
-
0035195086
-
Biodegradation of aromatic compounds by Escherichia coli
-
Diaz E, Ferrandez A, Prieto MA, Garcia JL, (2001) Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 65: 523-69.
-
(2001)
Microbiol Mol Biol Rev
, vol.65
, pp. 523-569
-
-
Diaz, E.1
Ferrandez, A.2
Prieto, M.A.3
Garcia, J.L.4
-
7
-
-
36749083463
-
Ohno's dilemma: evolution of new genes under continuous selection
-
Bergthorsson U, Andersson DI, Roth JR, (2007) Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A 104: 17004-17009.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 17004-17009
-
-
Bergthorsson, U.1
Andersson, D.I.2
Roth, J.R.3
-
8
-
-
79952166228
-
Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli
-
Soo VW, Hanson-Manful P, Patrick WM, (2011) Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proceedings of the National Academy of Sciences 108: 1484-1489.
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 1484-1489
-
-
Soo, V.W.1
Hanson-Manful, P.2
Patrick, W.M.3
-
9
-
-
31544482407
-
Mapping pathways and phenotypes by systematic gene overexpression
-
Sopko R, Huang D, Preston N, Chua G, Papp B, et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Molecular Cell 21: 319-330.
-
(2006)
Molecular Cell
, vol.21
, pp. 319-330
-
-
Sopko, R.1
Huang, D.2
Preston, N.3
Chua, G.4
Papp, B.5
-
10
-
-
67649635978
-
Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity
-
Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B, (2009) Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138: 198-208.
-
(2009)
Cell
, vol.138
, pp. 198-208
-
-
Vavouri, T.1
Semple, J.I.2
Garcia-Verdugo, R.3
Lehner, B.4
-
11
-
-
0032749078
-
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
-
Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293: 321-331.
-
(1999)
Journal of Molecular Biology
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
12
-
-
33847081239
-
Role of intrinsic disorder in transient interactions of hub proteins
-
Singh GP, Ganapathi M, Dash D, (2006) Role of intrinsic disorder in transient interactions of hub proteins. Proteins: Structure, Function, and Bioinformatics 66: 761-765.
-
(2006)
Proteins: Structure, Function, and Bioinformatics
, vol.66
, pp. 761-765
-
-
Singh, G.P.1
Ganapathi, M.2
Dash, D.3
-
13
-
-
34447558571
-
Intrinsic disorder in yeast transcriptional regulatory network
-
Singh GP, Dash D, (2007) Intrinsic disorder in yeast transcriptional regulatory network. Proteins: Structure, Function, and Bioinformatics 68: 602-605.
-
(2007)
Proteins: Structure, Function, and Bioinformatics
, vol.68
, pp. 602-605
-
-
Singh, G.P.1
Dash, D.2
-
14
-
-
84873345436
-
Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method
-
Makanae K, Kintaka R, Makino T, Kitano H, Moriya H, (2013) Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. Genome Research 23: 300-311.
-
(2013)
Genome Research
, vol.23
, pp. 300-311
-
-
Makanae, K.1
Kintaka, R.2
Makino, T.3
Kitano, H.4
Moriya, H.5
-
15
-
-
34848823739
-
Consequences of membrane protein overexpression in Escherichia coli
-
Wagner S, Baars L, Ytterberg AJ, Klussmeier A, Wagner CS, et al. (2007) Consequences of membrane protein overexpression in Escherichia coli. Molecular & Cellular Proteomics 6: 1527-1550.
-
(2007)
Molecular & Cellular Proteomics
, vol.6
, pp. 1527-1550
-
-
Wagner, S.1
Baars, L.2
Ytterberg, A.J.3
Klussmeier, A.4
Wagner, C.S.5
-
16
-
-
0035478854
-
Random forests
-
Breiman L, (2001) Random forests. Machine learning 45: 5-32.
-
(2001)
Machine Learning
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
17
-
-
33749267302
-
Analysis of high throughput protein expression in Escherichia coli
-
Benita Y, Wise MJ, Lok MC, Humphery-Smith I, Oosting RS, (2006) Analysis of high throughput protein expression in Escherichia coli. Molecular & Cellular Proteomics 5: 1567-1580.
-
(2006)
Molecular & Cellular Proteomics
, vol.5
, pp. 1567-1580
-
-
Benita, Y.1
Wise, M.J.2
Lok, M.C.3
Humphery-Smith, I.4
Oosting, R.S.5
-
18
-
-
13244265563
-
Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression
-
Dyson MR, Shadbolt SP, Vincent KJ, Perera RL, McCafferty J, (2004) Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression. BMC Biotechnology 4: 32.
-
(2004)
BMC Biotechnology
, vol.4
, pp. 32
-
-
Dyson, M.R.1
Shadbolt, S.P.2
Vincent, K.J.3
Perera, R.L.4
McCafferty, J.5
-
19
-
-
9144261138
-
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis
-
Goh CS, Lan N, Douglas SM, Wu B, Echols N, et al. (2004) Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. Journal of Molecular Biology 336: 115-130.
-
(2004)
Journal of Molecular Biology
, vol.336
, pp. 115-130
-
-
Goh, C.S.1
Lan, N.2
Douglas, S.M.3
Wu, B.4
Echols, N.5
-
20
-
-
79960086045
-
Statistical analysis of features associated with protein expression/solubility in an in vivo Escherichia coli expression system and a wheat germ cell-free expression system
-
Hirose S, Kawamura Y, Yokota K, Kuroita T, Natsume T, et al. (2011) Statistical analysis of features associated with protein expression/solubility in an in vivo Escherichia coli expression system and a wheat germ cell-free expression system. Journal of Biochemistry 150: 73-81.
-
(2011)
Journal of Biochemistry
, vol.150
, pp. 73-81
-
-
Hirose, S.1
Kawamura, Y.2
Yokota, K.3
Kuroita, T.4
Natsume, T.5
-
21
-
-
32144443802
-
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli
-
Idicula-Thomas S, Kulkarni AJ, Kulkarni BD, Jayaraman VK, Balaji PV, (2006) A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli. Bioinformatics 22: 278-284.
-
(2006)
Bioinformatics
, vol.22
, pp. 278-284
-
-
Idicula-Thomas, S.1
Kulkarni, A.J.2
Kulkarni, B.D.3
Jayaraman, V.K.4
Balaji, P.V.5
-
22
-
-
25444461690
-
How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli
-
Koschorreck M, Fischer M, Barth S, Pleiss J, (2005) How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli. BMC Genomics 6: 49.
-
(2005)
BMC Genomics
, vol.6
, pp. 49
-
-
Koschorreck, M.1
Fischer, M.2
Barth, S.3
Pleiss, J.4
-
23
-
-
77951633563
-
Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression
-
Kurotani A, Takagi T, Toyama M, Shirouzu M, Yokoyama S, et al. (2010) Comprehensive bioinformatics analysis of cell-free protein synthesis: identification of multiple protein properties that correlate with successful expression. The FASEB Journal 24: 1095-1104.
-
(2010)
The FASEB Journal
, vol.24
, pp. 1095-1104
-
-
Kurotani, A.1
Takagi, T.2
Toyama, M.3
Shirouzu, M.4
Yokoyama, S.5
-
24
-
-
7444250757
-
High-throughput expression of C. elegans proteins
-
Luan CH, Qiu S, Finley JB, Carson M, Gray RJ, et al. (2004) High-throughput expression of C. elegans proteins. Genome Research 14: 2102-2110.
-
(2004)
Genome Research
, vol.14
, pp. 2102-2110
-
-
Luan, C.H.1
Qiu, S.2
Finley, J.B.3
Carson, M.4
Gray, R.J.5
-
25
-
-
63149130741
-
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins
-
Niwa T, Ying BW, Saito K, Jin W, Takada S, et al. (2009) Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proceedings of the National Academy of Sciences 106: 4201-4206.
-
(2009)
Proceedings of the National Academy of Sciences
, vol.106
, pp. 4201-4206
-
-
Niwa, T.1
Ying, B.W.2
Saito, K.3
Jin, W.4
Takada, S.5
-
26
-
-
35748966976
-
Protein solubility: sequence based prediction and experimental verification
-
Smialowski P, Martin-Galiano AJ, Mikolajka A, Girschick T, Holak TA, et al. (2007) Protein solubility: sequence based prediction and experimental verification. Bioinformatics 23: 2536-2542.
-
(2007)
Bioinformatics
, vol.23
, pp. 2536-2542
-
-
Smialowski, P.1
Martin-Galiano, A.J.2
Mikolajka, A.3
Girschick, T.4
Holak, T.A.5
-
27
-
-
14744278850
-
Predicting the solubility of recombinant proteins in Escherichia coli
-
Wilkinson DL, Harrison RG, (1991) Predicting the solubility of recombinant proteins in Escherichia coli. Nature Biotechnology 9: 443-448.
-
(1991)
Nature Biotechnology
, vol.9
, pp. 443-448
-
-
Wilkinson, D.L.1
Harrison, R.G.2
-
29
-
-
34548174652
-
Supercharging proteins can impart unusual resilience
-
Lawrence MS, Phillips KJ, Liu DR, (2007) Supercharging proteins can impart unusual resilience. J Am Chem Soc 129: 10110-10112.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 10110-10112
-
-
Lawrence, M.S.1
Phillips, K.J.2
Liu, D.R.3
-
30
-
-
77951974784
-
A systematic survey of in vivo obligate chaperonin-dependent substrates
-
Fujiwara K, Ishihama Y, Nakahigashi K, Soga T, Taguchi H, (2010) A systematic survey of in vivo obligate chaperonin-dependent substrates. EMBO J 29: 1552-1564.
-
(2010)
EMBO J
, vol.29
, pp. 1552-1564
-
-
Fujiwara, K.1
Ishihama, Y.2
Nakahigashi, K.3
Soga, T.4
Taguchi, H.5
-
31
-
-
22744447508
-
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli
-
Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122: 209-220.
-
(2005)
Cell
, vol.122
, pp. 209-220
-
-
Kerner, M.J.1
Naylor, D.J.2
Ishihama, Y.3
Maier, T.4
Chang, H.C.5
-
32
-
-
84857411069
-
Designing antimicrobial peptides: form follows function
-
Fjell CD, Hiss JA, Hancock REW, Schneider G, (2011) Designing antimicrobial peptides: form follows function. Nature Reviews Drug Discovery 11: 37-51.
-
(2011)
Nature Reviews Drug Discovery
, vol.11
, pp. 37-51
-
-
Fjell, C.D.1
Hiss, J.A.2
Hancock, R.E.W.3
Schneider, G.4
-
33
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp B, Pal C, Hurst LD, (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pal, C.2
Hurst, L.D.3
-
34
-
-
1642538313
-
From butyribacterium to E. coli: an essay on unity in biochemistry
-
Friedmann HC, (2004) From butyribacterium to E. coli: an essay on unity in biochemistry. Perspectives in Biology and Medicine 47: 47-66.
-
(2004)
Perspectives in Biology and Medicine
, vol.47
, pp. 47-66
-
-
Friedmann, H.C.1
-
35
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh A, Larsson B, Von Heijne G, Sonnhammer ELL, (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology 305: 567-580.
-
(2001)
Journal of Molecular Biology
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
Von Heijne, G.3
Sonnhammer, E.L.L.4
-
36
-
-
13444262374
-
EcoCyc: a comprehensive database resource for Escherichia coli
-
Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, et al. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research 33: D334-D337.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
-
37
-
-
33847096395
-
Bias in random forest variable importance measures: Illustrations, sources and a solution
-
Strobl C, Boulesteix AL, Zeileis A, Hothorn T, (2007) Bias in random forest variable importance measures: Illustrations, sources and a solution. BMC Bioinformatics 8: 25.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 25
-
-
Strobl, C.1
Boulesteix, A.L.2
Zeileis, A.3
Hothorn, T.4
|