-
1
-
-
0038718854
-
The structure and function of complex networks
-
Newman MEJ. The structure and function of complex networks. SIAM Review 2003, 45:167-256.
-
(2003)
SIAM Review
, vol.45
, pp. 167-256
-
-
Newman, M.E.J.1
-
4
-
-
33748798478
-
Grap-based methods for analysing networks in cell biology
-
10.1093/bib/bbl022, 16880171
-
Aittokallio T, Schwikowski V. Grap-based methods for analysing networks in cell biology. Briefings in Bioinformatics 2006, 7:243-255. 10.1093/bib/bbl022, 16880171.
-
(2006)
Briefings in Bioinformatics
, vol.7
, pp. 243-255
-
-
Aittokallio, T.1
Schwikowski, V.2
-
5
-
-
0742305866
-
Network biology understanding the cell's functional organization
-
10.1038/nrg1272, 14735121
-
Barabási AL, Oltvai ZN. Network biology understanding the cell's functional organization. Nature Reviews Genetics 2004, 5:101-113. 10.1038/nrg1272, 14735121.
-
(2004)
Nature Reviews Genetics
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
7
-
-
33646171940
-
Identifying metabolic enzymes with multiple types of association evidence
-
10.1186/1471-2105-7-177, 1450304, 16571130
-
Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 2006, 7:177. 10.1186/1471-2105-7-177, 1450304, 16571130.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 177
-
-
Kharchenko, P.1
Chen, L.2
Freund, Y.3
Vitkup, D.4
Church, G.M.5
-
8
-
-
0037079050
-
Metabolic network structure determines key aspects of functionality and regulation
-
10.1038/nature01166, 12432396
-
Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420:190-193. 10.1038/nature01166, 12432396.
-
(2002)
Nature
, vol.420
, pp. 190-193
-
-
Stelling, J.1
Klamt, S.2
Bettenbrock, K.3
Schuster, S.4
Gilles, E.D.5
-
9
-
-
14644396645
-
Functional cartography of complex metabolic networks
-
10.1038/nature03288, 2175124, 15729348
-
Guimerà R, Amaral LAN. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900. 10.1038/nature03288, 2175124, 15729348.
-
(2005)
Nature
, vol.433
, pp. 895-900
-
-
Guimerà, R.1
Amaral, L.A.N.2
-
10
-
-
39149119221
-
Predicting synthetic rescues in metabolic networks
-
2267730, 18277384
-
Motter AE, Gulbahce N, Almaas E, Barabási AL. Predicting synthetic rescues in metabolic networks. Molecular Systems Biology 2008, 4:168. 2267730, 18277384.
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 168
-
-
Motter, A.E.1
Gulbahce, N.2
Almaas, E.3
Barabási, A.L.4
-
11
-
-
51649104942
-
Cascading failure and robustness in metabolic networks
-
10.1073/pnas.0803571105, 2533172, 18765805
-
Smart AG, Amaral LAN, Ottino J. Cascading failure and robustness in metabolic networks. Proc Natl Acad Sci USA 2008, 105:13223-13228. 10.1073/pnas.0803571105, 2533172, 18765805.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 13223-13228
-
-
Smart, A.G.1
Amaral, L.A.N.2
Ottino, J.3
-
13
-
-
44349170777
-
A truer measure of our ignorance
-
10.1073/pnas.0802459105, 2383987, 18474865
-
Amaral LAN. A truer measure of our ignorance. Proc Natl Acad Sci USA 2008, 105(19):6795-6796. 10.1073/pnas.0802459105, 2383987, 18474865.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.19
, pp. 6795-6796
-
-
Amaral, L.A.N.1
-
14
-
-
71149116758
-
Systems analysis of cellular networks under uncertainty
-
10.1016/j.febslet.2009.10.074, 19879267
-
Kaltenbacha HM, Dimopoulosa S, Stelling J. Systems analysis of cellular networks under uncertainty. FEBS Letters 2009, 583:3923-3930. 10.1016/j.febslet.2009.10.074, 19879267.
-
(2009)
FEBS Letters
, vol.583
, pp. 3923-3930
-
-
Kaltenbacha, H.M.1
Dimopoulosa, S.2
Stelling, J.3
-
15
-
-
0037161731
-
Comparative assessment of large-scale data sets of protein-protein interactions
-
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
-
(2002)
Nature
, vol.417
, pp. 399-403
-
-
von Mering, C.1
Krause, R.2
Snel, B.3
Cornell, M.4
Oliver, S.G.5
Fields, S.6
Bork, P.7
-
16
-
-
0036493195
-
Interaction generality, a measurement to assess the reliability of a protein-protein interaction
-
10.1093/nar/30.5.1163, 101243, 11861907
-
Saito R, Suzuki H, Hayashizaki Y. Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Research 2002, 30:1163-1168. 10.1093/nar/30.5.1163, 101243, 11861907.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1163-1168
-
-
Saito, R.1
Suzuki, H.2
Hayashizaki, Y.3
-
17
-
-
0037447257
-
Assessing experimentally derived interactions in a small world
-
10.1073/pnas.0735871100, 404686, 12676999
-
Goldberg DS, Roth FP. Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA 2003, 100(8):4372-4376. 10.1073/pnas.0735871100, 404686, 12676999.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.8
, pp. 4372-4376
-
-
Goldberg, D.S.1
Roth, F.P.2
-
18
-
-
27144533653
-
Reconstructing the metabolic network of a bacterium from its genome
-
10.1016/j.tim.2005.09.001, 16169729
-
Francke C, Siezen RJ, Teusink B. Reconstructing the metabolic network of a bacterium from its genome. TRENDS in Microbiology 2005, 13:550-558. 10.1016/j.tim.2005.09.001, 16169729.
-
(2005)
TRENDS in Microbiology
, vol.13
, pp. 550-558
-
-
Francke, C.1
Siezen, R.J.2
Teusink, B.3
-
19
-
-
73149122136
-
Applications of genome-scale metabolic reconstructions
-
2795471, 19888215
-
Oberhardt MA, Palsson BO, Papin JA. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology 2009, 5:320. 2795471, 19888215.
-
(2009)
Molecular Systems Biology
, vol.5
, pp. 320
-
-
Oberhardt, M.A.1
Palsson, B.O.2
Papin, J.A.3
-
20
-
-
70849102021
-
Impact of Genome Reduction on Bacterial Metabolism and Its Regulation
-
10.1126/science.1177263, 19965476
-
Yus E, et al. Impact of Genome Reduction on Bacterial Metabolism and Its Regulation. Science 2009, 326:1263-1268. 10.1126/science.1177263, 19965476.
-
(2009)
Science
, vol.326
, pp. 1263-1268
-
-
Yus, E.1
-
21
-
-
75149129569
-
A protocol for generating a high-quality genome-scale metabolic reconstruction
-
Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols 2010, 5:93-121.
-
(2010)
Nature Protocols
, vol.5
, pp. 93-121
-
-
Thiele, I.1
Palsson, B.O.2
-
22
-
-
0035823264
-
The small world inside large metabolic networks
-
Wagner A, Fell D. The small world inside large metabolic networks. Proc R Soc Lond B 2001, 268:1803-1810.
-
(2001)
Proc R Soc Lond B
, vol.268
, pp. 1803-1810
-
-
Wagner, A.1
Fell, D.2
-
23
-
-
0037199968
-
Hierarchical Organization of Modularity in Metabolic Networks
-
10.1126/science.1073374, 12202830
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297:1551-1555. 10.1126/science.1073374, 12202830.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabási, A.L.5
-
24
-
-
0035420732
-
Random graphs with arbitrary degree distributions and their applications
-
Newman MEJ, Strogatz SH, Watts DJ. Random graphs with arbitrary degree distributions and their applications. Phys Rev E 2001, 64:026118.
-
(2001)
Phys Rev E
, vol.64
, pp. 026118
-
-
Newman, M.E.J.1
Strogatz, S.H.2
Watts, D.J.3
-
25
-
-
0942300164
-
Network bipartivity
-
Holme P, Liljeros F, Edling CR, Kim BJ. Network bipartivity. Phys Rev E 2003, 68:056107.
-
(2003)
Phys Rev E
, vol.68
, pp. 056107
-
-
Holme, P.1
Liljeros, F.2
Edling, C.R.3
Kim, B.J.4
-
26
-
-
40849116812
-
Self-similarity of complex networks and hidden metric spaces
-
Serrano MA, Krioukov D, Boguñá M. Self-similarity of complex networks and hidden metric spaces. Phys Rev Lett 2008, 100:078701.
-
(2008)
Phys Rev Lett
, vol.100
, pp. 078701
-
-
Serrano, M.A.1
Krioukov, D.2
Boguñá, M.3
-
27
-
-
43049151837
-
Hierarchical structure and the prediction of missing links in networks
-
10.1038/nature06830, 18451861
-
Clauset A, Moore C, Newman M. Hierarchical structure and the prediction of missing links in networks. Nature 2008, 453:98-101. 10.1038/nature06830, 18451861.
-
(2008)
Nature
, vol.453
, pp. 98-101
-
-
Clauset, A.1
Moore, C.2
Newman, M.3
-
28
-
-
76049100050
-
Missing and spurious interactions and the reconstruction of complex networks
-
10.1073/pnas.0908366106, 2799723, 20018705
-
Guimerà R, Sales-Pardo9 M. Missing and spurious interactions and the reconstruction of complex networks. Proc Natl Acad Sci USA 2009, 106:22073-22078. 10.1073/pnas.0908366106, 2799723, 20018705.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 22073-22078
-
-
Guimerà, R.1
Sales-Pardo9, M.2
-
29
-
-
0037316239
-
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
-
10.1093/bioinformatics/19.2.270, 12538249
-
Ma H, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277. 10.1093/bioinformatics/19.2.270, 12538249.
-
(2003)
Bioinformatics
, vol.19
, pp. 270-277
-
-
Ma, H.1
Zeng, A.P.2
-
30
-
-
48249155053
-
Exhaustive identification of steady state cycles in large stoichiometric networks
-
10.1186/1752-0509-2-61, 2478680, 18616835
-
Wright J, Wagner A. Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Systems Biology 2008, 2:61. 10.1186/1752-0509-2-61, 2478680, 18616835.
-
(2008)
BMC Systems Biology
, vol.2
, pp. 61
-
-
Wright, J.1
Wagner, A.2
-
31
-
-
0034609791
-
The large-scale organization of metabolic networks
-
10.1038/35036627, 11034217
-
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabási, A.L.5
-
32
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
1911197, 17593909
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 2007, 3:121. 1911197, 17593909.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
33
-
-
77951612556
-
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
-
10.1186/1471-2105-11-213, 2874806, 20426874
-
Schellenberger J, Park JO, Conrad TC, Palsson BO. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010, 11:213. 10.1186/1471-2105-11-213, 2874806, 20426874.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 213
-
-
Schellenberger, J.1
Park, J.O.2
Conrad, T.C.3
Palsson, B.O.4
-
34
-
-
84901180915
-
The BiGG database
-
The BiGG database. , http://bigg.ucsd.edu/
-
-
-
-
35
-
-
33646023117
-
An introduction to ROC analysis
-
Fawcett T. An introduction to ROC analysis. Pattern Recognition Letters 2006, 27:861-874.
-
(2006)
Pattern Recognition Letters
, vol.27
, pp. 861-874
-
-
Fawcett, T.1
-
36
-
-
0037133227
-
Random graph models of social networks
-
128577, 11875211
-
Newman MEJ, Watts DJ, Strogatz SH. Random graph models of social networks. Proc Natl Acad Sci USA 2002, 99(suppl 1):2566-2572. 128577, 11875211.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.SUPPL. 1
, pp. 2566-2572
-
-
Newman, M.E.J.1
Watts, D.J.2
Strogatz, S.H.3
-
38
-
-
0001964443
-
Structural equivalence of individuals in social networks
-
Lorrain F, White HC. Structural equivalence of individuals in social networks. J Math Sociol 1971, 1:49-80.
-
(1971)
J Math Sociol
, vol.1
, pp. 49-80
-
-
Lorrain, F.1
White, H.C.2
-
39
-
-
0020083498
-
The meaning and use of the area under a receiver characteristic (ROC) curve
-
Hanley JA, McNeil BJ. The meaning and use of the area under a receiver characteristic (ROC) curve. Radiology 1982, 143:29-36.
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.A.1
McNeil, B.J.2
|