-
1
-
-
70249134919
-
Molecular networks as sensors and drivers of common human diseases
-
Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009;461:218-23.
-
(2009)
Nature
, vol.461
, pp. 218-223
-
-
Schadt, E.E.1
-
2
-
-
70349526350
-
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
-
Tan CS, Bodenmiller B, Pasculescu A, et al. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal 2009;2:ra39.
-
(2009)
Sci Signal
, vol.2
-
-
Tan, C.S.1
Bodenmiller, B.2
Pasculescu, A.3
-
3
-
-
77956838065
-
Advances in understanding cancer genomes through second-generation sequencing
-
Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010;11:685-96.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 685-696
-
-
Meyerson, M.1
Gabriel, S.2
Getz, G.3
-
4
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
Croft D, O'Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011;39:D691-7.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
-
5
-
-
63649150787
-
A genomic strategy to elucidate modules of oncogenic pathway signaling networks
-
Chang JT, Carvalho C, Mori S, et al. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell 2009;34:104-14.
-
(2009)
Mol Cell
, vol.34
, pp. 104-114
-
-
Chang, J.T.1
Carvalho, C.2
Mori, S.3
-
6
-
-
60749087137
-
PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk
-
Wang CC, Cirit M, Haugh JM. PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk. Mol Syst Biol 2009;5:246.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 246
-
-
Wang, C.C.1
Cirit, M.2
Haugh, J.M.3
-
7
-
-
77950621240
-
Data integration and analysis of biological networks
-
Kim TY, Kim HU, Lee SY. Data integration and analysis of biological networks. Curr Opin Biotechnol 2010;21:78-84.
-
(2010)
Curr Opin Biotechnol
, vol.21
, pp. 78-84
-
-
Kim, T.Y.1
Kim, H.U.2
Lee, S.Y.3
-
8
-
-
74049122828
-
Cancer systems biology: a network modeling perspective
-
Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis 2010;31:2-8.
-
(2010)
Carcinogenesis
, vol.31
, pp. 2-8
-
-
Kreeger, P.K.1
Lauffenburger, D.A.2
-
9
-
-
70450160004
-
Systems-level dynamic analyses of fate change in murine embryonic stem cells
-
Lu R, Markowetz F, Unwin RD, et al. Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 2009;462:358-62.
-
(2009)
Nature
, vol.462
, pp. 358-362
-
-
Lu, R.1
Markowetz, F.2
Unwin, R.D.3
-
10
-
-
0017367852
-
Nucleotide sequence of bacteriophage phi X174 DNA
-
Sanger F, Air GM, Barrell BG, et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977;265:687-95.
-
(1977)
Nature
, vol.265
, pp. 687-695
-
-
Sanger, F.1
Air, G.M.2
Barrell, B.G.3
-
11
-
-
79958247861
-
Omics technologies, data and bioinformatics principles
-
Schneider MV, Orchard S. Omics technologies, data and bioinformatics principles. MethodsMol Biol 2011;719:3-30.
-
(2011)
MethodsMol Biol
, vol.719
, pp. 3-30
-
-
Schneider, M.V.1
Orchard, S.2
-
12
-
-
84872209664
-
Identification of aberrant pathway and network activity from high-throughput data - Workshop Introduction
-
Ochs MF, Karchin R, Ressom H, et al. Identification of aberrant pathway and network activity from high-throughput data - Workshop Introduction. Pac Symp Biocomput 2011; 364-8.
-
(2011)
Pac Symp Biocomput
, pp. 364-368
-
-
Ochs, M.F.1
Karchin, R.2
Ressom, H.3
-
14
-
-
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
-
16
-
-
79551587720
-
Cytoscape 2.8: new features for data integration and network visualization
-
Smoot ME, Ono K, Ruscheinski J, et al. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2010;27:431-2.
-
(2010)
Bioinformatics
, vol.27
, pp. 431-432
-
-
Smoot, M.E.1
Ono, K.2
Ruscheinski, J.3
-
17
-
-
67849122322
-
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
-
Hu Z, Hung JH, Wang Y, et al. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 2009;37:W115-21.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hu, Z.1
Hung, J.H.2
Wang, Y.3
-
18
-
-
0242559054
-
Pathway studio-the analysis and navigation of molecular networks
-
Nikitin A, Egorov S, Daraselia N, et al. Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 2003;19:2155-7.
-
(2003)
Bioinformatics
, vol.19
, pp. 2155-2157
-
-
Nikitin, A.1
Egorov, S.2
Daraselia, N.3
-
19
-
-
59449094654
-
Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array
-
Andre F, Job B, Dessen P, et al. Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res 2009; 15:441-51.
-
(2009)
Clin Cancer Res
, vol.15
, pp. 441-451
-
-
Andre, F.1
Job, B.2
Dessen, P.3
-
20
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
Vaske CJ, Benz SC, Sanborn JZ, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010;26:i237-45.
-
(2010)
Bioinformatics
, vol.26
-
-
Vaske, C.J.1
Benz, S.C.2
Sanborn, J.Z.3
-
21
-
-
70349518562
-
Positive selection of tyrosine loss in metazoan evolution
-
Tan CS, Pasculescu A, Lim WA, et al. Positive selection of tyrosine loss in metazoan evolution. Science 2009;325: 1686-8.
-
(2009)
Science
, vol.325
, pp. 1686-1688
-
-
Tan, C.S.1
Pasculescu, A.2
Lim, W.A.3
-
22
-
-
77349120489
-
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer
-
Chari R, Thu KL, Wilson IM, et al. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev 2011;29:73-93.
-
(2011)
Cancer Metastasis Rev
, vol.29
, pp. 73-93
-
-
Chari, R.1
Thu, K.L.2
Wilson, I.M.3
-
23
-
-
79958292800
-
Profiling epigenetic alterations in disease
-
Martin-Subero JI, Esteller M. Profiling epigenetic alterations in disease. Adv ExpMed Biol 2011;711:162-77.
-
(2011)
Adv ExpMed Biol
, vol.711
, pp. 162-177
-
-
Martin-Subero, J.I.1
Esteller, M.2
-
24
-
-
78951482208
-
Deconstructing the molecular portraits of breast cancer
-
Prat A, Perou CM. Deconstructing the molecular portraits of breast cancer. Mol Oncol 2011;5:5-23.
-
(2011)
Mol Oncol
, vol.5
, pp. 5-23
-
-
Prat, A.1
Perou, C.M.2
-
25
-
-
79957458567
-
Cell-free nucleic acids as biomarkers in cancer patients
-
Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011; 11:426-37.
-
(2011)
Nat Rev Cancer
, vol.11
, pp. 426-437
-
-
Schwarzenbach, H.1
Hoon, D.S.2
Pantel, K.3
-
26
-
-
78751570979
-
RNA sequencing: advances, challenges and opportunities
-
Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011;12: 87-98.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 87-98
-
-
Ozsolak, F.1
Milos, P.M.2
-
27
-
-
70350452746
-
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
-
Huang SS, Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal 2009;2:ra40.
-
(2009)
Sci Signal
, vol.2
-
-
Huang, S.S.1
Fraenkel, E.2
-
28
-
-
70049105859
-
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data
-
Samaga R, Saez-Rodriguez J, Alexopoulos LG, et al. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol 2009;5: e1000438.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Samaga, R.1
Saez-Rodriguez, J.2
Alexopoulos, L.G.3
-
29
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
-
Jerby L, Shlomi T, Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010;6:401.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 401
-
-
Jerby, L.1
Shlomi, T.2
Ruppin, E.3
-
30
-
-
60149091657
-
Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression
-
Sreekumar A, Poisson LM, Rajendiran TM, et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 2009;457:910-14.
-
(2009)
Nature
, vol.457
, pp. 910-914
-
-
Sreekumar, A.1
Poisson, L.M.2
Rajendiran, T.M.3
-
31
-
-
0036898577
-
Microarray data normalization and transformation
-
Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002;32(Suppl):496-501.
-
(2002)
Nat Genet
, vol.32
, Issue.SUPPL.
, pp. 496-501
-
-
Quackenbush, J.1
-
32
-
-
58349085083
-
Receiver-operating characteristic curve analysis in diagnostic, prognostic and predictive biomarker research
-
Soreide K. Receiver-operating characteristic curve analysis in diagnostic, prognostic and predictive biomarker research. JClin Pathol 2009;62:1-5.
-
(2009)
JClin Pathol
, vol.62
, pp. 1-5
-
-
Soreide, K.1
-
33
-
-
59849125136
-
Dynamic modularity in protein interaction networks predicts breast cancer outcome
-
Taylor IW, Linding R, Warde-Farley D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 2009;27:199-204.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 199-204
-
-
Taylor, I.W.1
Linding, R.2
Warde-Farley, D.3
-
34
-
-
71549130141
-
Detection of treatmentinduced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data
-
Ochs MF, Rink L, Tarn C, et al. Detection of treatmentinduced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data. Cancer Res 2009; 69:9125-32.
-
(2009)
Cancer Res
, vol.69
, pp. 9125-9132
-
-
Ochs, M.F.1
Rink, L.2
Tarn, C.3
-
35
-
-
77955258637
-
Identification and validation of the pathways and functions regulated by the orphan nuclear receptor, ROR alpha1, in skeletal muscle
-
Raichur S, Fitzsimmons RL, Myers SA, et al. Identification and validation of the pathways and functions regulated by the orphan nuclear receptor, ROR alpha1, in skeletal muscle. Nucleic Acids Res 2010;38:4296-312.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 4296-4312
-
-
Raichur, S.1
Fitzsimmons, R.L.2
Myers, S.A.3
-
36
-
-
78650562728
-
dmGWAS: dense module searching for genome-wide association studies in protein- protein interaction networks
-
Jia P, Zheng S, Long J, et al. dmGWAS: dense module searching for genome-wide association studies in protein- protein interaction networks. Bioinformatics 2010;27: 95-102.
-
(2010)
Bioinformatics
, vol.27
, pp. 95-102
-
-
Jia, P.1
Zheng, S.2
Long, J.3
-
37
-
-
77952310528
-
A human functional protein interaction network and its application to cancer data analysis
-
Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010;11:R53.
-
(2010)
Genome Biol
, vol.11
-
-
Wu, G.1
Feng, X.2
Stein, L.3
-
38
-
-
77449127150
-
Sources of bias in specimens for research about molecular markers for cancer
-
Ransohoff DF, Gourlay ML. Sources of bias in specimens for research about molecular markers for cancer. J Clin Oncol 2010;28:698-704.
-
(2010)
J Clin Oncol
, vol.28
, pp. 698-704
-
-
Ransohoff, D.F.1
Gourlay, M.L.2
-
39
-
-
70349939382
-
Biomarkers predicting clinical outcome of epidermal growth factor receptor-targeted therapy in metastatic colorectal cancer
-
Siena S, Sartore-Bianchi A, Di Nicolantonio F, et al. Biomarkers predicting clinical outcome of epidermal growth factor receptor-targeted therapy in metastatic colorectal cancer. JNatl Cancer Inst 2009;101:1308-24.
-
(2009)
J Natl Cancer Inst
, vol.101
, pp. 1308-1324
-
-
Siena, S.1
Sartore-Bianchi, A.2
Di Nicolantonio, F.3
-
40
-
-
77953007415
-
Prediction of epigenetically regulated genes in breast cancer cell lines
-
Loss LA, Sadanandam A, Durinck S, et al. Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinformatics 2010;11:305.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 305
-
-
Loss, L.A.1
Sadanandam, A.2
Durinck, S.3
-
41
-
-
63549098588
-
Identification of differential gene pathways with principal component analysis
-
Ma S, Kosorok MR. Identification of differential gene pathways with principal component analysis. Bioinformatics 2009; 25:882-9.
-
(2009)
Bioinformatics
, vol.25
, pp. 882-889
-
-
Ma, S.1
Kosorok, M.R.2
-
42
-
-
77952822943
-
Pathway discovery in metabolic networks by subgraph extraction
-
Faust K, Dupont P, Callut J, et al. Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics 2010;26:1211-18.
-
(2010)
Bioinformatics
, vol.26
, pp. 1211-1218
-
-
Faust, K.1
Dupont, P.2
Callut, J.3
-
43
-
-
79959454002
-
Physical Module Networks: an integrative approach for reconstructing transcription regulation
-
Novershtern N, Regev A, Friedman N. Physical Module Networks: an integrative approach for reconstructing transcription regulation. Bioinformatics 2011;27:i177-85.
-
(2011)
Bioinformatics
, vol.27
-
-
Novershtern, N.1
Regev, A.2
Friedman, N.3
-
44
-
-
79251567361
-
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
-
Krumsiek J, Suhre K, Illig T, et al. Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMCSyst Biol 2011;5:21.
-
(2011)
BMCSyst Biol
, vol.5
, pp. 21
-
-
Krumsiek, J.1
Suhre, K.2
Illig, T.3
-
45
-
-
64649098960
-
Integrated analysis of breast cancer cell lines reveals unique signaling pathways
-
Heiser LM, Wang NJ, Talcott CL, et al. Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol 2009;10:R31.
-
(2009)
Genome Biol
, vol.10
-
-
Heiser, L.M.1
Wang, N.J.2
Talcott, C.L.3
-
46
-
-
65349179556
-
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/ insulin-induced signaling
-
Aldridge BB, Saez-Rodriguez J, Muhlich JL, et al. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/ insulin-induced signaling. PLoS Comput Biol 2009;5: e1000340.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Aldridge, B.B.1
Saez-Rodriguez, J.2
Muhlich, J.L.3
-
47
-
-
82255185653
-
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data
-
Chien CH, Sun YM, Chang WC, et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res 2011; 39(21):9345-56.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.21
, pp. 9345-9356
-
-
Chien, C.H.1
Sun, Y.M.2
Chang, W.C.3
-
48
-
-
77954195270
-
Path Text: a text mining integrator for biological pathway visualizations
-
Kemper B, Matsuzaki T, Matsuoka Y, et al. Path Text: a text mining integrator for biological pathway visualizations. Bioinformatics 2010;26:i374-81.
-
(2010)
Bioinformatics
, vol.26
-
-
Kemper, B.1
Matsuzaki, T.2
Matsuoka, Y.3
-
49
-
-
77958590561
-
Ontology-based meta-analysis of global collections of high-throughput public data
-
pii: e13066
-
Kupershmidt I, Su QJ, Grewal A, et al. Ontology-based meta-analysis of global collections of high-throughput public data. PLoS One 2010. 5(9). pii: e13066.
-
(2010)
PLoS One
, vol.5
, Issue.9
-
-
Kupershmidt, I.1
Su, Q.J.2
Grewal, A.3
-
50
-
-
70349882120
-
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
-
Amit I, Garber M, Chevrier N, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009;326:257-63.
-
(2009)
Science
, vol.326
, pp. 257-263
-
-
Amit, I.1
Garber, M.2
Chevrier, N.3
-
51
-
-
61349180117
-
Gene regulatory network inference: data integration in dynamic models-a review
-
Hecker M, Lambeck S, Toepfer S, et al. Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 2009;96:86-103.
-
(2009)
Biosystems
, vol.96
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Toepfer, S.3
-
52
-
-
58149154663
-
Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism
-
Trinh CT, Wlaschin A, Srienc F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 2009;81:813-26.
-
(2009)
Appl Microbiol Biotechnol
, vol.81
, pp. 813-826
-
-
Trinh, C.T.1
Wlaschin, A.2
Srienc, F.3
-
53
-
-
79959896639
-
Building protein-protein interaction networks with proteomics and informatics tools
-
Sardiu ME, Washburn MP. Building protein-protein interaction networks with proteomics and informatics tools. J Biol Chem 2011;286:23645-51.
-
(2011)
J Biol Chem
, vol.286
, pp. 23645-23651
-
-
Sardiu, M.E.1
Washburn, M.P.2
-
54
-
-
61349114190
-
Bridging highthroughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
-
Yeger-Lotem E, Riva L, Su LJ, et al. Bridging highthroughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet 2009;41: 316-23.
-
(2009)
Nat Genet
, vol.41
, pp. 316-323
-
-
Yeger-Lotem, E.1
Riva, L.2
Su, L.J.3
-
55
-
-
70350701855
-
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
-
Keller A, Backes C, Gerasch A, et al. A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. Bioinformatics 2009;25: 2787-94.
-
(2009)
Bioinformatics
, vol.25
, pp. 2787-2794
-
-
Keller, A.1
Backes, C.2
Gerasch, A.3
-
56
-
-
77953839617
-
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
-
Xu TR, Vyshemirsky V, Gormand A, et al. Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Sci Signal 2010;3: ra20.
-
(2010)
Sci Signal
, vol.3
-
-
Xu, T.R.1
Vyshemirsky, V.2
Gormand, A.3
-
58
-
-
80053436505
-
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
-
Li Z, Li P, Krishnan A, et al. Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis. Bioinformatics 2011;27:2686-91.
-
(2011)
Bioinformatics
, vol.27
, pp. 2686-2691
-
-
Li, Z.1
Li, P.2
Krishnan, A.3
-
59
-
-
0345824737
-
Network component analysis: reconstruction of regulatory signals in biological systems
-
Liao JC, Boscolo R, Yang YL, et al. Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 2003;100: 15522-7.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.C.1
Boscolo, R.2
Yang, Y.L.3
-
60
-
-
80054757930
-
Construction of Gene Regulatory Networks using biclustering and Bayesian networks
-
Alakwaa FM, Solouma NH, Kadah YM. Construction of Gene Regulatory Networks using biclustering and Bayesian networks. Theor Biol Med Model 2011;8:39.
-
(2011)
Theor Biol Med Model
, vol.8
, pp. 39
-
-
Alakwaa, F.M.1
Solouma, N.H.2
Kadah, Y.M.3
-
61
-
-
33846047770
-
IntAct-open source resource for molecular interaction data
-
Kerrien S, Alam-Faruque Y, Aranda B, et al. IntAct-open source resource for molecular interaction data. Nucleic Acids Res 2007;35:D561-5.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kerrien, S.1
Alam-Faruque, Y.2
Aranda, B.3
-
62
-
-
84862844337
-
Topological analysis of metabolic networks based on petri net theory
-
Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on petri net theory. Stud Health Technol Inform 2003;162:17-37.
-
(2003)
Stud Health Technol Inform
, vol.162
, pp. 17-37
-
-
Zevedei-Oancea, I.1
Schuster, S.2
-
63
-
-
79951528622
-
Exploring metabolic pathways in genome-scale networks via generating flux modes
-
Rezola A, de Figueiredo LF, Brock M, et al. Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics 2010;27:534-40.
-
(2010)
Bioinformatics
, vol.27
, pp. 534-540
-
-
Rezola, A.1
de Figueiredo, L.F.2
Brock, M.3
-
64
-
-
66349136048
-
A stochastic model for the evolution of metabolic networks with neighbor dependence
-
Mithani A, Preston GM, Hein J. A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics 2009;25:1528-35.
-
(2009)
Bioinformatics
, vol.25
, pp. 1528-1535
-
-
Mithani, A.1
Preston, G.M.2
Hein, J.3
-
65
-
-
77954197778
-
Integrating quantitative proteomics and metabolomics with a genomescale metabolic network model
-
Yizhak K, Benyamini T, Liebermeister W, et al. Integrating quantitative proteomics and metabolomics with a genomescale metabolic network model. Bioinformatics 2010;26: i255-60.
-
(2010)
Bioinformatics
, vol.26
-
-
Yizhak, K.1
Benyamini, T.2
Liebermeister, W.3
-
66
-
-
79959406807
-
Identification of metabolic network models from incomplete highthroughput datasets
-
Berthoumieux S, Brilli M, de Jong H, et al. Identification of metabolic network models from incomplete highthroughput datasets. Bioinformatics 2011;27:i186-95.
-
(2011)
Bioinformatics
, vol.27
-
-
Berthoumieux, S.1
Brilli, M.2
de Jong, H.3
-
67
-
-
67849116896
-
PathExpress update: the enzyme neighbourhood method of associating geneexpression data with metabolic pathways
-
Goffard N, Frickey T, Weiller G. PathExpress update: the enzyme neighbourhood method of associating geneexpression data with metabolic pathways. Nucleic Acids Res 2009;37:W335-9.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Goffard, N.1
Frickey, T.2
Weiller, G.3
-
69
-
-
79959415714
-
Generative probabilistic models for protein-protein interaction networks-the biclique perspective
-
Schweiger R, Linial M, Linial N. Generative probabilistic models for protein-protein interaction networks-the biclique perspective. Bioinformatics 2011;27:i142-8.
-
(2011)
Bioinformatics
, vol.27
-
-
Schweiger, R.1
Linial, M.2
Linial, N.3
-
70
-
-
78651423600
-
A hybrid approach to extract protein-protein interactions
-
Bui QC, Katrenko S, Sloot PM. A hybrid approach to extract protein-protein interactions. Bioinformatics 2011;27: 259-65.
-
(2011)
Bioinformatics
, vol.27
, pp. 259-265
-
-
Bui, Q.C.1
Katrenko, S.2
Sloot, P.M.3
-
71
-
-
33644527950
-
The model organism as a system: integrating 'omics' data sets
-
Joyce AR, Palsson BO. The model organism as a system: integrating 'omics' data sets. Nat RevMol Cell Biol 2006;7: 198-210.
-
(2006)
Nat RevMol Cell Biol
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Palsson, B.O.2
-
72
-
-
81055140498
-
Fusion methodologies for biomedical data
-
Tsiliki G, Kossida S. Fusion methodologies for biomedical data. J Proteomics 2011;74:2774-85.
-
(2011)
J Proteomics
, vol.74
, pp. 2774-2785
-
-
Tsiliki, G.1
Kossida, S.2
-
73
-
-
80053526511
-
Adeno-associated viral vectors for correction of inborn errors of metabolism: progressing towards clinical application
-
Jacobs F, Wang L. Adeno-associated viral vectors for correction of inborn errors of metabolism: progressing towards clinical application. Curr PharmDes 2011;17:2500-15.
-
(2011)
Curr PharmDes
, vol.17
, pp. 2500-2515
-
-
Jacobs, F.1
Wang, L.2
-
74
-
-
79955757477
-
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery
-
Johannes M, Frohlich H, Sultmann H, et al. pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. Bioinformatics 2011;27:1442-3.
-
(2011)
Bioinformatics
, vol.27
, pp. 1442-1443
-
-
Johannes, M.1
Frohlich, H.2
Sultmann, H.3
-
75
-
-
80155156908
-
Kernel-based data fusion improves the drug-protein interaction prediction
-
Wang YC, Zhang CH, Deng NY, et al. Kernel-based data fusion improves the drug-protein interaction prediction. Comput Biol Chem 2011;35:353-62.
-
(2011)
Comput Biol Chem
, vol.35
, pp. 353-362
-
-
Wang, Y.C.1
Zhang, C.H.2
Deng, N.Y.3
-
76
-
-
68749099453
-
Pathway databases and tools for their exploitation: benefits, current limitations and challenges
-
Bauer-Mehren A, Furlong LI, Sanz F. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 2009;5:290.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 290
-
-
Bauer-Mehren, A.1
Furlong, L.I.2
Sanz, F.3
-
77
-
-
79959873016
-
Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival
-
Masica DL, Karchin R. Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res 2011;71: 4550-61.
-
(2011)
Cancer Res
, vol.71
, pp. 4550-4561
-
-
Masica, D.L.1
Karchin, R.2
-
78
-
-
79959381299
-
Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease
-
Hart GW, Slawson C, Ramirez-Correa G, et al. Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease. Annu Rev Biochem 2011;80:825-58.
-
(2011)
Annu Rev Biochem
, vol.80
, pp. 825-858
-
-
Hart, G.W.1
Slawson, C.2
Ramirez-Correa, G.3
-
79
-
-
77951651658
-
Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis
-
Wang Z, Udeshi ND, Slawson C, et al. Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci Signal 2010;3:ra2.
-
(2010)
Sci Signal
, vol.3
-
-
Wang, Z.1
Udeshi, N.D.2
Slawson, C.3
-
80
-
-
71949118375
-
Identifying differentially expressed pathways via a mixed integer linear programming model
-
Qiu YQ, Zhang S, Zhang XS, et al. Identifying differentially expressed pathways via a mixed integer linear programming model. IETSyst Biol 2009;3:475-86.
-
(2009)
IETSyst Biol
, vol.3
, pp. 475-486
-
-
Qiu, Y.Q.1
Zhang, S.2
Zhang, X.S.3
-
81
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang HY, Lee E, Liu YT, et al. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007;3:140.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
-
82
-
-
79955736449
-
Computational integration of homolog and pathway gene module expression reveals general stemness signatures
-
Koeva M, Forsberg EC, Stuart JM. Computational integration of homolog and pathway gene module expression reveals general stemness signatures. PLoS One 2011;6: e18968.
-
(2011)
PLoS One
, vol.6
-
-
Koeva, M.1
Forsberg, E.C.2
Stuart, J.M.3
-
83
-
-
65649108558
-
A gene expression signature associated with "K-Ras addiction" reveals regulators of EMT and tumor cell survival
-
Singh A, Greninger P, Rhodes D, et al. A gene expression signature associated with "K-Ras addiction" reveals regulators of EMT and tumor cell survival. Cancer Cell 2009;15: 489-500.
-
(2009)
Cancer Cell
, vol.15
, pp. 489-500
-
-
Singh, A.1
Greninger, P.2
Rhodes, D.3
-
84
-
-
77951083686
-
A pathway-based classification of human breast cancer
-
Gatza ML, Lucas JE, Barry WT, et al. A pathway-based classification of human breast cancer. Proc Natl Acad Sci USA 2010;107:6994-9.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 6994-6999
-
-
Gatza, M.L.1
Lucas, J.E.2
Barry, W.T.3
-
85
-
-
77949446630
-
Automated network analysis identifies core pathways in glioblastoma
-
Cerami E, Demir E, Schultz N, et al. Automated network analysis identifies core pathways in glioblastoma. PLoS One 2010;5:e8918.
-
(2010)
PLoS One
, vol.5
-
-
Cerami, E.1
Demir, E.2
Schultz, N.3
-
86
-
-
77952745604
-
Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures
-
Chen J, Sam L, Huang Y, et al. Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. J Biomed Inform 2010;43:385-96.
-
(2010)
J Biomed Inform
, vol.43
, pp. 385-396
-
-
Chen, J.1
Sam, L.2
Huang, Y.3
-
87
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han JD, Bertin N, Hao T, et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004;430:88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.D.1
Bertin, N.2
Hao, T.3
-
89
-
-
78651318867
-
Sarcosine in prostate cancer tissue is not a differential metabolite for prostate cancer aggressiveness and biochemical progression
-
Jentzmik F, Stephan C, Lein M, et al. Sarcosine in prostate cancer tissue is not a differential metabolite for prostate cancer aggressiveness and biochemical progression. J Urol 2011;185:706-11.
-
(2011)
J Urol
, vol.185
, pp. 706-711
-
-
Jentzmik, F.1
Stephan, C.2
Lein, M.3
-
90
-
-
77952880168
-
Sarcosine in urine after digital rectal examination fails as a marker in prostate cancer detection and identification of aggressive tumours
-
Re: Florian Jentzmik, Carsten Stephan, Kurt Miller, et al.
-
Colleselli D, Stenzl A, Schwentner C. Re: Florian Jentzmik, Carsten Stephan, Kurt Miller, et al. Sarcosine in urine after digital rectal examination fails as a marker in prostate cancer detection and identification of aggressive tumours. Eur Urol 2010;58:12-18. Eur Urol 58:e51.
-
(2010)
Eur Urol
, vol.58
, pp. 12-18
-
-
Colleselli, D.1
Stenzl, A.2
Schwentner, C.3
-
91
-
-
84975860562
-
Biomolecular network motif counting and discovery by color coding
-
Alon N, Dao P, Hajirasouliha I, et al. Biomolecular network motif counting and discovery by color coding. Bioinformatics 2008;24:i241-9.
-
(2008)
Bioinformatics
, vol.24
-
-
Alon, N.1
Dao, P.2
Hajirasouliha, I.3
-
92
-
-
70449091786
-
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
-
Barbie DA, Tamayo P, Boehm JS, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature 2009;462:108-12.
-
(2009)
Nature
, vol.462
, pp. 108-112
-
-
Barbie, D.A.1
Tamayo, P.2
Boehm, J.S.3
-
93
-
-
66149091940
-
A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene
-
Luo J, Emanuele MJ, Li D, et al. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 2009;137:835-48.
-
(2009)
Cell
, vol.137
, pp. 835-848
-
-
Luo, J.1
Emanuele, M.J.2
Li, D.3
-
94
-
-
65849111219
-
Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells
-
Scholl C, Frohling S, Dunn IF, et al. Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 2009;137: 821-34.
-
(2009)
Cell
, vol.137
, pp. 821-834
-
-
Scholl, C.1
Frohling, S.2
Dunn, I.F.3
|