-
1
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5:101-13
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
2
-
-
78650373804
-
Network medicine: a network-based approach to human disease
-
Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011;12:56-68
-
(2011)
Nat Rev Genet
, vol.12
, pp. 56-68
-
-
Barabasi, A.L.1
Gulbahce, N.2
Loscalzo, J.3
-
3
-
-
54249155522
-
Network pharmacology: the next paradigm in drug discovery
-
Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008;4:682-90
-
(2008)
Nat Chem Biol
, vol.4
, pp. 682-690
-
-
Hopkins, A.L.1
-
4
-
-
1842580761
-
Functional and topological characterization of protein interaction networks
-
Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics 2004;4:928-42
-
(2004)
Proteomics
, vol.4
, pp. 928-942
-
-
Yook, S.H.1
Oltvai, Z.N.2
Barabasi, A.L.3
-
5
-
-
80052947609
-
Introduction to network analysis in systems biology
-
Ma'ayan A. Introduction to network analysis in systems biology. Sci Signal 2011;4:tr5:22-32
-
(2011)
Sci Signal
, vol.4
, pp. 22-32
-
-
Ma'ayan, A.1
-
7
-
-
84875275699
-
Human diseases through the lens of network biology
-
Furlong LI. Human diseases through the lens of network biology. Trends Genet 2013;29:150-9
-
(2013)
Trends Genet
, vol.29
, pp. 150-159
-
-
Furlong, L.I.1
-
10
-
-
77649182705
-
Unveiling the role of network and systems biology in drug discovery
-
Pujol A, Mosca R, Farres J, et al. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 2010;31:115-23
-
(2010)
Trends Pharmacol Sci
, vol.31
, pp. 115-123
-
-
Pujol, A.1
Mosca, R.2
Farres, J.3
-
11
-
-
84956680067
-
Network-based in silico drug efficacy screening
-
Guney E, Menche J, Vidal M, et al. Network-based in silico drug efficacy screening. Nat Commun 2016;7:10331
-
(2016)
Nat Commun
, vol.7
, pp. 10331
-
-
Guney, E.1
Menche, J.2
Vidal, M.3
-
12
-
-
84865730611
-
A set of measures of centrality based on betweenness
-
Freeman LC. A set of measures of centrality based on betweenness. Sociometry 1977;40:35-41
-
(1977)
Sociometry
, vol.40
, pp. 35-41
-
-
Freeman, L.C.1
-
13
-
-
84970096342
-
Transtivity in structural models of small groups
-
Holland PW, Leinhardt S. Transtivity in structural models of small groups. Small Group Res 1971;2:107-24
-
(1971)
Small Group Res
, vol.2
, pp. 107-124
-
-
Holland, P.W.1
Leinhardt, S.2
-
14
-
-
51249195602
-
Structural parameters of communication networks
-
Shimbel A. Structural parameters of communication networks. Bull Math Biophys 1953;15:501-7
-
(1953)
Bull Math Biophys
, vol.15
, pp. 501-507
-
-
Shimbel, A.1
-
15
-
-
84926504765
-
Cancer: smoother journeys for molecular data
-
Marx V. Cancer: smoother journeys for molecular data. Nat Methods 2015;12:299-302
-
(2015)
Nat Methods
, vol.12
, pp. 299-302
-
-
Marx, V.1
-
16
-
-
33845357608
-
An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
-
Yoon J, Blumer A, Lee K. An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics 2006;22:3106-8
-
(2006)
Bioinformatics
, vol.22
, pp. 3106-3108
-
-
Yoon, J.1
Blumer, A.2
Lee, K.3
-
17
-
-
39049153521
-
Quantitative systems-level determinants of human genes targeted by successful drugs
-
Yao L, Rzhetsky A. Quantitative systems-level determinants of human genes targeted by successful drugs. Genome Res 2008;18:206-13
-
(2008)
Genome Res
, vol.18
, pp. 206-213
-
-
Yao, L.1
Rzhetsky, A.2
-
18
-
-
25144498379
-
A human proteinprotein interaction network: a resource for annotating the proteome
-
Stelzl U, Worm U, Lalowski M, et al. A human proteinprotein interaction network: a resource for annotating the proteome. Cell 2005;122:957-68
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
-
19
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
Maslov S, Sneppen K. Specificity and stability in topology of protein networks. Science 2002;296:910-13
-
(2002)
Science
, vol.296
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
22
-
-
0242490780
-
Cytoscape: a software environment for integrated models of biomolecular interaction networks
-
Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498-504
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
-
23
-
-
84897470845
-
NAViGaTOR: large scalable and interactive navigation and analysis of large graphs
-
Djebbari A, Ali M, Otasek D, et al. NAViGaTOR: large scalable and interactive navigation and analysis of large graphs. Internet Math 2011;7:314-47
-
(2011)
Internet Math
, vol.7
, pp. 314-347
-
-
Djebbari, A.1
Ali, M.2
Otasek, D.3
-
24
-
-
85166916238
-
Gephi: an open source software for exploring and manipulating networks
-
San Jose, CA, USA
-
Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks, In 3rd International AAAI Conference on Weblogs and Social Media, San Jose, CA, USA, 2009
-
(2009)
In 3rd International AAAI Conference on Weblogs and Social Media
-
-
Bastian, M.1
Heymann, S.2
Jacomy, M.3
-
25
-
-
84925358621
-
VANESA-a software application for the visualization and analysis of networks in system biology applications
-
Brinkrolf C, Janowski SJ, Kormeier B, et al. VANESA-a software application for the visualization and analysis of networks in system biology applications. J Integr Bioinform 2014;11:239
-
(2014)
J Integr Bioinform
, vol.11
, pp. 239
-
-
Brinkrolf, C.1
Janowski, S.J.2
Kormeier, B.3
-
26
-
-
0002226683
-
Pajek-program for large network analysis
-
Batagelj V, Mrvar A. Pajek-program for large network analysis. Connections 1998;21:47-57
-
(1998)
Connections
, vol.21
, pp. 47-57
-
-
Batagelj, V.1
Mrvar, A.2
-
27
-
-
27744490562
-
SpectralNET-an application for spectral graph analysis and visualization
-
Forman JJ, Clemons PA, Schreiber SL, et al. SpectralNET-an application for spectral graph analysis and visualization. BMC Bioinformatics 2005;6:260
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 260
-
-
Forman, J.J.1
Clemons, P.A.2
Schreiber, S.L.3
-
28
-
-
58149271021
-
Integrated network analysis platform for protein-protein interactions
-
Wu J, Vallenius T, Ovaska K, et al. Integrated network analysis platform for protein-protein interactions. Nat Methods 2009;6:75-7
-
(2009)
Nat Methods
, vol.6
, pp. 75-77
-
-
Wu, J.1
Vallenius, T.2
Ovaska, K.3
-
29
-
-
48449102450
-
Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology
-
Lin CY, Chin CH, Wu HH, et al. Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology. Nucleic Acids Res 2008;36:W438-43
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W438-W443
-
-
Lin, C.Y.1
Chin, C.H.2
Wu, H.H.3
-
30
-
-
48449099258
-
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
-
Reimand J, Tooming L, Peterson H, et al. GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res 2008;36: W452-9
-
(2008)
Nucleic Acids Res
, vol.36
, pp. W452-W459
-
-
Reimand, J.1
Tooming, L.2
Peterson, H.3
-
31
-
-
33751375646
-
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
-
Yip KY, Yu H, Kim PM, et al. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 2006;22: 2968-70
-
(2006)
Bioinformatics
, vol.22
, pp. 2968-2970
-
-
Yip, K.Y.1
Yu, H.2
Kim, P.M.3
-
32
-
-
23144466889
-
VisANT: data-integrating visual framework for biological networks and modules
-
Hu Z, Mellor J, Wu J, et al. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res 2005;33:W352-7
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W352-W357
-
-
Hu, Z.1
Mellor, J.2
Wu, J.3
-
33
-
-
67249148362
-
Exploring network structure, dynamics, and function using networkX
-
Hagberg AA, Schult DA, Swart PJ. Exploring network structure, dynamics, and function using networkX, In Proceedings of 7th Python in Science Conference, 2008:11-15
-
(2008)
In Proceedings of 7th Python in Science Conference
, pp. 11-15
-
-
Hagberg, A.A.1
Schult, D.A.2
Swart, P.J.3
-
34
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi G, Nepusz T. The igraph software package for complex network research. InterJ Complex Syst 2006:1695
-
(2006)
InterJ Complex Syst
, pp. 1695
-
-
Csardi, G.1
Nepusz, T.2
-
35
-
-
78650544547
-
QuACN: an R package for analyzing complex biological networks quantitatively
-
Mueller LA, Kugler KG, Dander A, et al. QuACN: an R package for analyzing complex biological networks quantitatively. Bioinformatics 2011;27:140-1
-
(2011)
Bioinformatics
, vol.27
, pp. 140-141
-
-
Mueller, L.A.1
Kugler, K.G.2
Dander, A.3
-
36
-
-
84861779036
-
Topological analysis and interactive visualization of biological networks and protein structures
-
Doncheva NT, Assenov Y, Domingues FS, et al. Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc 2012;7:670-85
-
(2012)
Nat Protoc
, vol.7
, pp. 670-685
-
-
Doncheva, N.T.1
Assenov, Y.2
Domingues, F.S.3
-
37
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, et al. Hierarchical organization of modularity in metabolic networks. Science 2002;297:1551-5
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
-
38
-
-
0037197886
-
The identification of functional modules from the genomic association of genes
-
Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 2002;99:5890-5
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5890-5895
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
40
-
-
84862663073
-
Predicting candidate genes based on combined network topological features: a case study in coronary artery disease
-
Zhang L, Li X, Tai J, et al. Predicting candidate genes based on combined network topological features: a case study in coronary artery disease. PLoS One 2012;7:e39542
-
(2012)
PLoS One
, vol.7
-
-
Zhang, L.1
Li, X.2
Tai, J.3
-
41
-
-
84875963165
-
Drug target prediction and repositioning using an integrated network-based approach
-
Emig D, Ivliev A, Pustovalova O, et al. Drug target prediction and repositioning using an integrated network-based approach. PLoS One 2013;8:e60618
-
(2013)
PLoS One
, vol.8
-
-
Emig, D.1
Ivliev, A.2
Pustovalova, O.3
-
42
-
-
84862249788
-
Prioritizing disease candidate genes by a gene interconnectedness-based approach
-
Hsu CL, Huang YH, Hsu CT, et al. Prioritizing disease candidate genes by a gene interconnectedness-based approach. BMC Genomics 2011;12(Suppl 3):S25
-
(2011)
BMC Genomics
, vol.12
, pp. S25
-
-
Hsu, C.L.1
Huang, Y.H.2
Hsu, C.T.3
-
43
-
-
84878889476
-
A vertex similaritybased framework to discover and rank orphan diseaserelated genes
-
Zhu C, Kushwaha A, Berman K, et al. A vertex similaritybased framework to discover and rank orphan diseaserelated genes. BMC Syst Biol 2012;6 (Suppl 3):S8
-
(2012)
BMC Syst Biol
, vol.6
, pp. S8
-
-
Zhu, C.1
Kushwaha, A.2
Berman, K.3
-
44
-
-
84864070819
-
A network-based feature selection approach to identify metabolic signatures in disease
-
Netzer M, Kugler KG, Muller LA, et al. A network-based feature selection approach to identify metabolic signatures in disease. J Theor Biol 2012;310:216-22
-
(2012)
J Theor Biol
, vol.310
, pp. 216-222
-
-
Netzer, M.1
Kugler, K.G.2
Muller, L.A.3
-
45
-
-
77953433317
-
Centrality analysis methods for biological networks and their application to gene regulatory networks
-
Dirk Koschützki FS. Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul Syst Bio 2008;2:193-201
-
(2008)
Gene Regul Syst Bio
, vol.2
, pp. 193-201
-
-
Dirk Koschützki, F.S.1
-
46
-
-
84888014252
-
Connecting the dots: applications of network medicine in pharmacology and disease
-
Jacunski A, Tatonetti NP. Connecting the dots: applications of network medicine in pharmacology and disease. Clin Pharmacol Ther 2013;94:659-69
-
(2013)
Clin Pharmacol Ther
, vol.94
, pp. 659-669
-
-
Jacunski, A.1
Tatonetti, N.P.2
-
47
-
-
27744469130
-
High-betweenness proteins in the yeast protein interaction network
-
Joy MP, Brock A, Ingber DE, et al. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005;2005:96-103
-
(2005)
J Biomed Biotechnol
, vol.2005
, pp. 96-103
-
-
Joy, M.P.1
Brock, A.2
Ingber, D.E.3
-
48
-
-
34247622363
-
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
-
Yu H, Kim PM, Sprecher E, et al. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007;3:e59
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Yu, H.1
Kim, P.M.2
Sprecher, E.3
-
49
-
-
84888011244
-
Network-based approaches in drug discovery and early development
-
Harrold JM, Ramanathan M, Mager DE. Network-based approaches in drug discovery and early development. Clin Pharmacol Ther 2013;94:651-8
-
(2013)
Clin Pharmacol Ther
, vol.94
, pp. 651-658
-
-
Harrold, J.M.1
Ramanathan, M.2
Mager, D.E.3
-
51
-
-
84873815205
-
Equal opportunity for lowdegree network nodes: a PageRank-based method for protein target identification in metabolic graphs
-
Banky D, Ivan G, Grolmusz V. Equal opportunity for lowdegree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PLoS One 2013;8:e54204
-
(2013)
PLoS One
, vol.8
-
-
Banky, D.1
Ivan, G.2
Grolmusz, V.3
-
52
-
-
84863677563
-
Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes
-
Winter C, Kristiansen G, Kersting S, et al. Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PLoS Comput Biol 2012;8:e1002511
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Winter, C.1
Kristiansen, G.2
Kersting, S.3
-
53
-
-
55349094009
-
Mining protein networks for synthetic genetic interactions
-
Paladugu SR, Zhao S, Ray A, et al. Mining protein networks for synthetic genetic interactions. BMC Bioinformatics 2008;9:426
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 426
-
-
Paladugu, S.R.1
Zhao, S.2
Ray, A.3
-
54
-
-
77955106017
-
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
-
You ZH, Yin Z, Han K, et al. A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. BMC Bioinformatics 2010;11:343
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 343
-
-
You, Z.H.1
Yin, Z.2
Han, K.3
-
55
-
-
84855378129
-
NEW: network-enabled wisdom in biology, medicine and healthcare
-
Schadt EE, Björkegren JL. NEW: network-enabled wisdom in biology, medicine and healthcare. Sci Transl Med 2012;4:115rv111
-
(2012)
Sci Transl Med
, vol.4
-
-
Schadt, E.E.1
Björkegren, J.L.2
-
56
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 2005;4:Article17
-
(2005)
Stat Appl Genet Mol Biol
, vol.4
-
-
Zhang, B.1
Horvath, S.2
-
58
-
-
84915798929
-
Identification of important nodes in directed biological networks: a betwork motif approach
-
Pei Wang JL, Yu X. Identification of important nodes in directed biological networks: a betwork motif approach. PLoS One 2014;9:e106132
-
(2014)
PLoS One
, vol.9
-
-
Pei Wang, J.L.1
Yu, X.2
-
59
-
-
34447512704
-
Understanding network concepts in modules
-
Dong J, Horvath S. Understanding network concepts in modules. BMC Syst Biol 2007;1:24
-
(2007)
BMC Syst Biol
, vol.1
, pp. 24
-
-
Dong, J.1
Horvath, S.2
-
60
-
-
77954385460
-
Complex network measures of brain connectivity: uses and interpretations
-
Rubinov M, Sporns O. Complex network measures of brain connectivity: uses and interpretations. Neuroimage 2010;52:1059-69
-
(2010)
Neuroimage
, vol.52
, pp. 1059-1069
-
-
Rubinov, M.1
Sporns, O.2
-
61
-
-
79960325408
-
Networks for systems biology: conceptual connection of data and function
-
Emmert-Streib F, Dehmer M. Networks for systems biology: conceptual connection of data and function. IET Syst Biol 2011;5:185-207
-
(2011)
IET Syst Biol
, vol.5
, pp. 185-207
-
-
Emmert-Streib, F.1
Dehmer, M.2
-
63
-
-
39649124450
-
What is a complex graph?
-
Kim J, Wilhelm T. What is a complex graph? Physica A 2008;387:2637-52
-
(2008)
Physica A
, vol.387
, pp. 2637-2652
-
-
Kim, J.1
Wilhelm, T.2
-
64
-
-
80053904998
-
A network-based approach to classify the three domains of life
-
Mueller LA, Kugler KG, Netzer M, et al. A network-based approach to classify the three domains of life. Biol Direct 2011;6:53
-
(2011)
Biol Direct
, vol.6
, pp. 53
-
-
Mueller, L.A.1
Kugler, K.G.2
Netzer, M.3
-
65
-
-
77958091914
-
A history of graph entropy measures
-
Dehmer M, Mowshowitz A. A history of graph entropy measures. Inf Sci 2011;181:57-78
-
(2011)
Inf Sci
, vol.181
, pp. 57-78
-
-
Dehmer, M.1
Mowshowitz, A.2
-
66
-
-
84857678752
-
Information indices with high discriminative power for graphs
-
Dehmer M, Grabner M, Varmuza K. Information indices with high discriminative power for graphs. PLoS One 2012;7:e31214
-
(2012)
PLoS One
, vol.7
-
-
Dehmer, M.1
Grabner, M.2
Varmuza, K.3
-
67
-
-
84857799805
-
Uniquely discriminating molecular structures using novel eigenvalue-based descriptors
-
Dehmer M. Uniquely discriminating molecular structures using novel eigenvalue-based descriptors. MATCH Commun Math Comput Chem 2012;67:147-72
-
(2012)
MATCH Commun Math Comput Chem
, vol.67
, pp. 147-172
-
-
Dehmer, M.1
-
68
-
-
79551609075
-
When the web meets the cell: using personalized PageRank for analyzing protein interaction networks
-
Ivan G, Grolmusz V. When the web meets the cell: using personalized PageRank for analyzing protein interaction networks. Bioinformatics 2011;27:405-7
-
(2011)
Bioinformatics
, vol.27
, pp. 405-407
-
-
Ivan, G.1
Grolmusz, V.2
-
69
-
-
33847254923
-
Generalizations of the clustering coefficient to weighted complex networks
-
Saramäki J, Kivelä M, Onnela JP, et al. Generalizations of the clustering coefficient to weighted complex networks. Phys Rev E 2007;75:027105
-
(2007)
Phys Rev E
, vol.75
-
-
Saramäki, J.1
Kivelä, M.2
Onnela, J.P.3
-
70
-
-
33747816816
-
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
-
Li ZR, Lin HH, Han LY, et al. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 2006;34:W32-7
-
(2006)
Nucleic Acids Res
, vol.34
, pp. W32-W37
-
-
Li, Z.R.1
Lin, H.H.2
Han, L.Y.3
-
71
-
-
79959928391
-
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
-
Rao HB, Zhu F, Yang GB, et al. Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 2011;39:W385-90
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W385-W390
-
-
Rao, H.B.1
Zhu, F.2
Yang, G.B.3
-
72
-
-
78651332286
-
Pathway commons, a web resource for biological pathway data
-
Cerami EG, Gross BE, Demir E, et al. Pathway commons, a web resource for biological pathway data. Nucleic Acids Res 2011;39:D685-90
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D685-D690
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
-
73
-
-
77349091815
-
NetPath: a public resource of curated signal transduction pathways
-
Kandasamy K, Mohan SS, Raju R, et al. NetPath: a public resource of curated signal transduction pathways. Genome Biol 2010;11:R3
-
(2010)
Genome Biol
, vol.11
, pp. R3
-
-
Kandasamy, K.1
Mohan, S.S.2
Raju, R.3
-
75
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998;393:440-2
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
76
-
-
13944252976
-
A measure of betweenness centrality based on random walks
-
Newman MEJ. A measure of betweenness centrality based on random walks. Soc Networks 2003;27:39-54
-
(2003)
Soc Networks
, vol.27
, pp. 39-54
-
-
Newman, M.E.J.1
-
77
-
-
34147120474
-
A note on two problems in connexion with graphs
-
Dijkstra EW. A note on two problems in connexion with graphs. Numer Math 1959;1:269-71
-
(1959)
Numer Math
, vol.1
, pp. 269-271
-
-
Dijkstra, E.W.1
-
78
-
-
0035648637
-
A faster algorithm for betweenness centrality
-
Brandes U. A faster algorithm for betweenness centrality. J Math Sociol 2001;25:163-77
-
(2001)
J Math Sociol
, vol.25
, pp. 163-177
-
-
Brandes, U.1
-
81
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
Ma HW, Zeng AP. The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003;19:1423-30
-
(2003)
Bioinformatics
, vol.19
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
82
-
-
84877983676
-
Node-weighted interacting network measures improve the representation of real-world complex systems
-
Wiedermann M, Donges JF, Heitzig J, et al. Node-weighted interacting network measures improve the representation of real-world complex systems. EPL 2013;102:28007
-
(2013)
EPL
, vol.102
, pp. 28007
-
-
Wiedermann, M.1
Donges, J.F.2
Heitzig, J.3
-
83
-
-
84946069451
-
UniProt: a hub for protein information
-
UniProt C. UniProt: a hub for protein information. Nucleic Acids Res 2015;43:D204-12
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D204-D212
-
-
UniProt, C.1
-
84
-
-
84946735654
-
Gene Ontology Consortium: going forward
-
Gene Ontology C. Gene Ontology Consortium: going forward. Nucleic Acids Res 2015;43:D1049-56
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D1049-D1056
-
-
Gene Ontology, C.1
-
85
-
-
64049086247
-
Topological and organizational properties of the products of house-keeping and tissuespecific genes in protein-protein interaction networks
-
Lin WH, Liu WC, Hwang MJ. Topological and organizational properties of the products of house-keeping and tissuespecific genes in protein-protein interaction networks. BMC Syst Biol 2009;3:32
-
(2009)
BMC Syst Biol
, vol.3
, pp. 32
-
-
Lin, W.H.1
Liu, W.C.2
Hwang, M.J.3
-
86
-
-
85039150228
-
Computational methods to identify metabolic sub-networks based on metabolomic profiles
-
Frainay C, Jourdan F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Brief Bioinform 2016;pii: bbv115
-
(2016)
Brief Bioinform
-
-
Frainay, C.1
Jourdan, F.2
-
87
-
-
84879911126
-
Simple topological properties predict functional misannotations in a metabolic network
-
Liberal R, Pinney JW. Simple topological properties predict functional misannotations in a metabolic network. Bioinformatics 2013;29:i154-61
-
(2013)
Bioinformatics
, vol.29
, pp. i154-i161
-
-
Liberal, R.1
Pinney, J.W.2
-
88
-
-
70350482286
-
Evolution of biomolecular networks: lessons from metabolic and protein interactions
-
Yamada T, Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 2009;10:791-803
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 791-803
-
-
Yamada, T.1
Bork, P.2
-
89
-
-
55749096609
-
Phylogenetic distances are encoded in networks of interacting pathways
-
Mazurie A, Bonchev D, Schwikowski B, et al. Phylogenetic distances are encoded in networks of interacting pathways. Bioinformatics 2008;24:2579-85
-
(2008)
Bioinformatics
, vol.24
, pp. 2579-2585
-
-
Mazurie, A.1
Bonchev, D.2
Schwikowski, B.3
-
90
-
-
0035931072
-
A compendium of gene expression in normal human tissues
-
Hsiao LL, Dangond F, Yoshida T, et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001;7:97-104
-
(2001)
Physiol Genomics
, vol.7
, pp. 97-104
-
-
Hsiao, L.L.1
Dangond, F.2
Yoshida, T.3
-
91
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
Peri S, Navarro JD, Amanchy R, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003;13:2363-71
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
-
92
-
-
33645211903
-
The effect of oxygen on biochemical networks and the evolution of complex life
-
Raymond J, Segre D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 2006;311:1764-7
-
(2006)
Science
, vol.311
, pp. 1764-1767
-
-
Raymond, J.1
Segre, D.2
-
93
-
-
0015980083
-
On earlier states of the biochemical system
-
Ycas M. On earlier states of the biochemical system. J Theor Biol 1974;44:145-60
-
(1974)
J Theor Biol
, vol.44
, pp. 145-160
-
-
Ycas, M.1
-
94
-
-
39749195677
-
Impacts of yeast metabolic network structure on enzyme evolution
-
Lu C, Zhang Z, Leach L, et al. Impacts of yeast metabolic network structure on enzyme evolution. Genome Biol 2007;8:407
-
(2007)
Genome Biol
, vol.8
, pp. 407
-
-
Lu, C.1
Zhang, Z.2
Leach, L.3
-
95
-
-
34447502516
-
A network perspective on the evolution of metabolism by gene duplication
-
Diaz-Mejia JJ, Perez-Rueda E, Segovia L. A network perspective on the evolution of metabolism by gene duplication. Genome Biol 2007;8:R26
-
(2007)
Genome Biol
, vol.8
, pp. R26
-
-
Diaz-Mejia, J.J.1
Perez-Rueda, E.2
Segovia, L.3
-
96
-
-
33646754515
-
Therapeutic targets: progress of their exploration and investigation of their characteristics
-
Zheng CJ, Han LY, Yap CW, et al. Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol Rev 2006;58:259-79
-
(2006)
Pharmacol Rev
, vol.58
, pp. 259-279
-
-
Zheng, C.J.1
Han, L.Y.2
Yap, C.W.3
-
98
-
-
27144530248
-
Towards a proteomescale map of the human protein-protein interaction network
-
Rual JF, Venkatesan K, Hao T, et al. Towards a proteomescale map of the human protein-protein interaction network. Nature 2005;437:1173-8
-
(2005)
Nature
, vol.437
, pp. 1173-1178
-
-
Rual, J.F.1
Venkatesan, K.2
Hao, T.3
-
99
-
-
0020083498
-
The meaning and use of the area under a receiver operating characteristic (ROC) curve
-
Hanley J, McNeil B. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982;143:29-36
-
(1982)
Radiology
, vol.143
, pp. 29-36
-
-
Hanley, J.1
McNeil, B.2
-
100
-
-
84922591049
-
Efficient behavior of small-world networks
-
Latora V, Marchiori M. Efficient behavior of small-world networks. Phys Rev Lett 2001;87:198701
-
(2001)
Phys Rev Lett
, vol.87
-
-
Latora, V.1
Marchiori, M.2
-
101
-
-
0013987194
-
The centrality index of a graph
-
Sabidussi G. The centrality index of a graph. Psychometrika 1966;31:581-603
-
(1966)
Psychometrika
, vol.31
, pp. 581-603
-
-
Sabidussi, G.1
-
102
-
-
85055760867
-
Clustering and hierarchy in interpersonal relations: testing two graph theoretical models on 742 sociomatrices
-
Davis JA. Clustering and hierarchy in interpersonal relations: testing two graph theoretical models on 742 sociomatrices. Am Sociol Rev 1970;35:843-51
-
(1970)
Am Sociol Rev
, vol.35
, pp. 843-851
-
-
Davis, J.A.1
-
103
-
-
84865705620
-
Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors
-
Zhang J, Jia J, Zhu F, et al. Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors. Mol Biosyst 2012;8:2645-56
-
(2012)
Mol Biosyst
, vol.8
, pp. 2645-2656
-
-
Zhang, J.1
Jia, J.2
Zhu, F.3
-
104
-
-
84891760956
-
Data, information, knowledge and principle: back to metabolism in KEGG
-
Kanehisa M, Goto S, Sato Y, et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014;42:D199-205
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
-
106
-
-
58149200933
-
Update of KDBI: kinetic data of bio-molecular interaction database
-
Kumar P, Han BC, Shi Z, et al. Update of KDBI: kinetic data of bio-molecular interaction database. Nucleic Acids Res 2009;37:D636-41
-
(2009)
Nucleic Acids Res
, vol.37
, pp. D636-D641
-
-
Kumar, P.1
Han, B.C.2
Shi, Z.3
-
107
-
-
84941051170
-
STRING v10: protein-protein interaction networks, integrated over the tree of life
-
Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015;43:D447-52
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D447-D452
-
-
Szklarczyk, D.1
Franceschini, A.2
Wyder, S.3
-
108
-
-
84891799734
-
The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
-
Orchard S, Ammari M, Aranda B, et al. The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 2014;42: D358-63
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D358-D363
-
-
Orchard, S.1
Ammari, M.2
Aranda, B.3
-
109
-
-
3042786293
-
A gene network for navigating the literature
-
Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004;36:664
-
(2004)
Nat Genet
, vol.36
, pp. 664
-
-
Hoffmann, R.1
Valencia, A.2
|