-
1
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
Barabási A-L, Oltvai ZN, (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
3
-
-
0035799707
-
Lethality and centrality in protein networks
-
Jeong H, Mason SP, Barabási A-L, Oltvai ZN, (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabási, A.-L.3
Oltvai, Z.N.4
-
4
-
-
53349117774
-
High-quality binary protein interaction map of the yeast interactome network
-
Yu H, Braun P, Yi{dotless}ldi{dotless}ri{dotless}m MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
-
(2008)
Science
, vol.322
, pp. 104-110
-
-
Yu, H.1
Braun, P.2
Yildirim, M.A.3
Lemmens, I.4
Venkatesan, K.5
-
5
-
-
2342648924
-
Integrating high-throughput and computational data elucidates bacterial networks
-
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BØ, (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
-
(2004)
Nature
, vol.429
, pp. 92-96
-
-
Covert, M.W.1
Knight, E.M.2
Reed, J.L.3
Herrgard, M.J.4
Palsson, B.Ø.5
-
6
-
-
33846910173
-
Global reconstruction of the human metabolic network based on genomic and bibliomic data
-
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, et al. (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104: 1777-1782.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 1777-1782
-
-
Duarte, N.C.1
Becker, S.A.2
Jamshidi, N.3
Thiele, I.4
Mo, M.L.5
-
7
-
-
78049255973
-
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
-
Chandrasekaran S, Price ND, (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 107: 17845-17850.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 17845-17850
-
-
Chandrasekaran, S.1
Price, N.D.2
-
8
-
-
11244297914
-
Modular epistasis in yeast metabolism
-
Segrè D, DeLuna A, Church GM, Kishony R, (2004) Modular epistasis in yeast metabolism. Nat Genet 37: 77-83.
-
(2004)
Nat Genet
, vol.37
, pp. 77-83
-
-
Segrè, D.1
DeLuna, A.2
Church, G.M.3
Kishony, R.4
-
9
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
10
-
-
75649111192
-
The genetic landscape of a cell
-
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, et al. (2010) The genetic landscape of a cell. Science 327: 425-431.
-
(2010)
Science
, vol.327
, pp. 425-431
-
-
Costanzo, M.1
Baryshnikova, A.2
Bellay, J.3
Kim, Y.4
Spear, E.D.5
-
11
-
-
50849098825
-
eSGA: E. coli synthetic genetic array analysis
-
Butland G, Babu1 M, Diaz-Mejia JJ, Bohdana F, Phanse S, et al. (2008) eSGA: E. coli synthetic genetic array analysis. Nat Methods 5: 789-795.
-
(2008)
Nat Methods
, vol.5
, pp. 789-795
-
-
Butland, G.1
Babu, M.2
Diaz-Mejia, J.J.3
Bohdana, F.4
Phanse, S.5
-
12
-
-
46949110597
-
Setting the standard in synthetic biology
-
Arkin AP, (2008) Setting the standard in synthetic biology. Nat Biotechnol 26: 771-774.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 771-774
-
-
Arkin, A.P.1
-
13
-
-
0037014269
-
Relationship between measures of fitness and time scale in evolution
-
Rauch EM, Sayama H, Bar-Yam Y, (2002) Relationship between measures of fitness and time scale in evolution. Phys Rev Lett 88: 228101.
-
(2002)
Phys Rev Lett
, vol.88
, pp. 228101
-
-
Rauch, E.M.1
Sayama, H.2
Bar-Yam, Y.3
-
14
-
-
0033832615
-
Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
-
Huynen M, Snel B, Lathe W III, Bork P, (2000) Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res 10: 1204-1210.
-
(2000)
Genome Res
, vol.10
, pp. 1204-1210
-
-
Huynen, M.1
Snel, B.2
Lathe III, W.3
Bork, P.4
-
15
-
-
11144319853
-
Use of logic relationships to decipher protein network organization
-
Bowers PM, Cokus SJ, Eisenberg D, Yeates TO, (2004) Use of logic relationships to decipher protein network organization. Science 306: 2246-2249.
-
(2004)
Science
, vol.306
, pp. 2246-2249
-
-
Bowers, P.M.1
Cokus, S.J.2
Eisenberg, D.3
Yeates, T.O.4
-
16
-
-
33846086800
-
STRING 7-recent developments in the integration and prediction of protein interactions
-
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-D362.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
Jensen, L.J.2
Kuhn, M.3
Chaffron, S.4
Doerks, T.5
-
17
-
-
34347374679
-
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: A comprehensive assessment
-
Jothi R, Przytycka TM, Aravind L, (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: A comprehensive assessment. BMC Bioinform 8: 173.
-
(2007)
BMC Bioinform
, vol.8
, pp. 173
-
-
Jothi, R.1
Przytycka, T.M.2
Aravind, L.3
-
18
-
-
48249103069
-
Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function
-
Singh S, Wall DP, (2008) Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. Evol Bioinform Online 4: 217-223.
-
(2008)
Evol Bioinform Online
, vol.4
, pp. 217-223
-
-
Singh, S.1
Wall, D.P.2
-
19
-
-
71549149672
-
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
-
Ruano-Rubio V, Poch O, Thompson JD, (2009) Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. BMC Bioinform 10: 383.
-
(2009)
BMC Bioinform
, vol.10
, pp. 383
-
-
Ruano-Rubio, V.1
Poch, O.2
Thompson, J.D.3
-
20
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
22
-
-
48249158278
-
The implications of human metabolic network topology for disease comorbidity
-
Lee D-S, Park J, Kay KA, Christakis NA, Oltvai ZN, et al. (2008) The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci U S A 105: 9880-9885.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 9880-9885
-
-
Lee, D.-S.1
Park, J.2
Kay, K.A.3
Christakis, N.A.4
Oltvai, Z.N.5
-
23
-
-
64349109427
-
The impact of cellular networks on disease comorbidity
-
Park J, Lee D-S, Christakis NA, Barabási A-L, (2009) The impact of cellular networks on disease comorbidity. Mol Syst Biol 5: 262.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 262
-
-
Park, J.1
Lee, D.-S.2
Christakis, N.A.3
Barabási, A.-L.4
-
24
-
-
77955379943
-
Googling social interactions: Web search engine based social network construction
-
Lee SH, Kim P-J, Ahn Y-Y, Jeong H, (2010) Googling social interactions: Web search engine based social network construction. PLoS ONE 5: e11233.
-
(2010)
PLoS ONE
, vol.5
-
-
Lee, S.H.1
Kim, P.-J.2
Ahn, Y.-Y.3
Jeong, H.4
-
25
-
-
34547844096
-
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: Synthetic versus real data
-
Soranzo N, Bianconi G, Altafini C, (2007) Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: Synthetic versus real data. Bioinformatics 23: 1640-1647.
-
(2007)
Bioinformatics
, vol.23
, pp. 1640-1647
-
-
Soranzo, N.1
Bianconi, G.2
Altafini, C.3
-
26
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
Schäfer J, Strimmer K, (2005) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4: 32.
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
, pp. 32
-
-
Schäfer, J.1
Strimmer, K.2
-
27
-
-
66049143558
-
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins
-
Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7: e1000096.
-
(2009)
PLoS Biol
, vol.7
-
-
Hu, P.1
Janga, S.C.2
Babu, M.3
Díaz-Mejía, J.J.4
Butland, G.5
-
29
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.-D.J.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
-
31
-
-
14544286855
-
The selective cause of an ancient adaptation
-
Zhu G, Golding GB, Dean AM, (2005) The selective cause of an ancient adaptation. Science 307: 1279-1282.
-
(2005)
Science
, vol.307
, pp. 1279-1282
-
-
Zhu, G.1
Golding, G.B.2
Dean, A.M.3
-
32
-
-
0023582671
-
Compensatory regulation in metabolic pathways: Responses to increases and decreases in citrate synthase levels
-
Walsh K, Schena M, Flint AJ, Koshland DE Jr, (1987) Compensatory regulation in metabolic pathways: Responses to increases and decreases in citrate synthase levels. Biochem Soc Symp 54: 183-195.
-
(1987)
Biochem Soc Symp
, vol.54
, pp. 183-195
-
-
Walsh, K.1
Schena, M.2
Flint, A.J.3
Koshland Jr., D.E.4
-
33
-
-
79551670374
-
Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation
-
Ha S-J, Galazka JM, Kim SR, Choi J-H, Yang X, et al. (2011) Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci U S A 108: 504-509.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 504-509
-
-
Ha, S.-J.1
Galazka, J.M.2
Kim, S.R.3
Choi, J.-H.4
Yang, X.5
-
34
-
-
64749094343
-
Functional expression of a bacterial xylose isomerase in Saccharomyces cerevisiae
-
Brat D, Boles E, Wiedemann B, (2009) Functional expression of a bacterial xylose isomerase in Saccharomyces cerevisiae. Appl Environ Microbiol 75: 2304-2311.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 2304-2311
-
-
Brat, D.1
Boles, E.2
Wiedemann, B.3
-
35
-
-
0038489504
-
Role for the cyanobacterial HtpG in protection from oxidative stress
-
Hossain MM, Nakamoto H, (2003) Role for the cyanobacterial HtpG in protection from oxidative stress. Curr Microbiol 46: 70-76.
-
(2003)
Curr Microbiol
, vol.46
, pp. 70-76
-
-
Hossain, M.M.1
Nakamoto, H.2
-
36
-
-
0142074781
-
Genome-wide transcriptional profiling of the response of Staphylococcus aureus to cell-wall-active antibiotics reveals a cell-wall-stress stimulon
-
Utaida S, Dunman PM, Macapagal D, Murphy E, Projan SJ, et al. (2003) Genome-wide transcriptional profiling of the response of Staphylococcus aureus to cell-wall-active antibiotics reveals a cell-wall-stress stimulon. Microbiology 149: 2719-2732.
-
(2003)
Microbiology
, vol.149
, pp. 2719-2732
-
-
Utaida, S.1
Dunman, P.M.2
Macapagal, D.3
Murphy, E.4
Projan, S.J.5
-
37
-
-
0035074011
-
Responses of Gram-negative bacteria to certain environmental stressors
-
Ramos JL, Gallegos M-T, Marqués S, Ramos-González M-I, Espinosa-Urge M, et al. (2001) Responses of Gram-negative bacteria to certain environmental stressors. Curr Opin Microbiol 4: 166-171.
-
(2001)
Curr Opin Microbiol
, vol.4
, pp. 166-171
-
-
Ramos, J.L.1
Gallegos, M.-T.2
Marqués, S.3
Ramos-González, M.-I.4
Espinosa-Urge, M.5
-
38
-
-
0036047508
-
Regulation of inducible peroxide stress responses
-
Mongkolsuk S, Helmann JD, (2002) Regulation of inducible peroxide stress responses. Mol Microbiol 45: 9-15.
-
(2002)
Mol Microbiol
, vol.45
, pp. 9-15
-
-
Mongkolsuk, S.1
Helmann, J.D.2
-
39
-
-
52949115612
-
Microbiology: Metagenomics
-
Hugenholtz P, Tyson GW, (2008) Microbiology: Metagenomics. Nature 455: 481-483.
-
(2008)
Nature
, vol.455
, pp. 481-483
-
-
Hugenholtz, P.1
Tyson, G.W.2
-
40
-
-
75549083619
-
The integrated microbial genomes system: An expanding comparative analysis resource
-
Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, et al. (2010) The integrated microbial genomes system: An expanding comparative analysis resource. Nucleic Acids Res 38: D382-D390.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Markowitz, V.M.1
Chen, I.-M.A.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
-
41
-
-
32844465575
-
Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea
-
Frigaard N-U, Martinez A, Mincer TJ, DeLong EF, (2006) Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439: 847-850.
-
(2006)
Nature
, vol.439
, pp. 847-850
-
-
Frigaard, N.-U.1
Martinez, A.2
Mincer, T.J.3
DeLong, E.F.4
-
42
-
-
34547676311
-
Optimization based automated curation of metabolic reconstructions
-
Kumar VS, Dasika MS, Maranas CD, (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8: 212.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 212
-
-
Kumar, V.S.1
Dasika, M.S.2
Maranas, C.D.3
-
43
-
-
0041841552
-
Improved estimation of the covariance matrix of stock returns with an application to portfolio selection
-
Ledoit O, Wolf M, (2003) Improved estimation of the covariance matrix of stock returns with an application to portfolio selection. J Empir Finance 10: 603-621.
-
(2003)
J Empir Finance
, vol.10
, pp. 603-621
-
-
Ledoit, O.1
Wolf, M.2
|