-
2
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
Network TCGA, (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-8.
-
(2008)
Nature
, vol.455
, pp. 1061-1068
-
-
Network, T.C.G.A.1
-
3
-
-
52149123619
-
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
-
Jones S, Zhang X, Parsons DW, Lin JCH, Leary RJ, et al. (2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (New York, NY) 321: 1801-6.
-
(2008)
Science (New York, NY)
, vol.321
, pp. 1801-1806
-
-
Jones, S.1
Zhang, X.2
Parsons, D.W.3
Lin, J.C.H.4
Leary, R.J.5
-
4
-
-
33845864703
-
Computational prediction of cancer-gene function
-
Hu P, Bader G, Wigle DA, Emili A, (2007) Computational prediction of cancer-gene function. Nature reviews Cancer 7: 23-34.
-
(2007)
Nature Reviews Cancer
, vol.7
, pp. 23-34
-
-
Hu, P.1
Bader, G.2
Wigle, D.A.3
Emili, A.4
-
5
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang HY, Lee E, Liu YT, Lee D, Ideker T, (2007) Network-based classification of breast cancer metastasis. Molecular systems biology 3: 140.
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
6
-
-
33646568805
-
Gene prioritization through genomic data fusion
-
Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, et al. (2006) Gene prioritization through genomic data fusion. Nature biotechnology 24: 537-44.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 537-544
-
-
Aerts, S.1
Lambrechts, D.2
Maity, S.3
Van Loo, P.4
Coessens, B.5
-
7
-
-
67849130563
-
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
-
Chen J, Bardes EE, Aronow BJ, Jegga AG, (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic acids research 37: W305-11.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Chen, J.1
Bardes, E.E.2
Aronow, B.J.3
Jegga, A.G.4
-
8
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, et al. (2010) Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (Oxford, England) 26: i237-45.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
-
-
Vaske, C.J.1
Benz, S.C.2
Sanborn, J.Z.3
Earl, D.4
Szeto, C.5
-
9
-
-
77956664073
-
The BioPAX community standard for pathway data sharing
-
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, et al. (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28: 935-942.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 935-942
-
-
Demir, E.1
Cary, M.P.2
Paley, S.3
Fukuda, K.4
Lemer, C.5
-
10
-
-
84859498694
-
hiPathDB: a human-integrated pathway database with facile visualization
-
Yu N, Seo J, Rho K, Jang Y, Park J, et al. (2012) hiPathDB: a human-integrated pathway database with facile visualization. Nucleic acids research 40: D797-802.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Yu, N.1
Seo, J.2
Rho, K.3
Jang, Y.4
Park, J.5
-
11
-
-
84860691310
-
IPAVS: Integrated Pathway Resources, Analysis and Visualization System
-
Sreenivasaiah PK, Rani S, Cayetano J, Arul N, Kim DH, (2012) IPAVS: Integrated Pathway Resources, Analysis and Visualization System. Nucleic acids research 40: D803-8.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Sreenivasaiah, P.K.1
Rani, S.2
Cayetano, J.3
Arul, N.4
Kim, D.H.5
-
12
-
-
78651332286
-
Pathway Commons, a web resource for biological pathway data
-
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, et al. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 39: D685-90.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
Rodchenkov, I.4
Babur, O.5
-
13
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39: D691-7.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
-
14
-
-
58149186477
-
PID: the Pathway Interaction Database
-
Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: the Pathway Interaction Database. Nucleic acids research 37: D674-9.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Schaefer, C.F.1
Anthony, K.2
Krupa, S.3
Buchoff, J.4
Day, M.5
-
15
-
-
75549090505
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
-
Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic acids research 38: D473-9.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Caspi, R.1
Altman, T.2
Dale, J.M.3
Dreher, K.4
Fulcher, C.A.5
-
16
-
-
75549084894
-
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
-
Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, et al. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic acids research 38: D204-10.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Mi, H.1
Dong, Q.2
Muruganujan, A.3
Gaudet, P.4
Lewis, S.5
-
17
-
-
84857047339
-
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
-
Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, et al. (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic acids research 40: D261-70.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Hornbeck, P.V.1
Kornhauser, J.M.2
Tkachev, S.3
Zhang, B.4
Skrzypek, E.5
-
18
-
-
84862167967
-
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
-
Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, et al. (2012) Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC systems biology 6: 29.
-
(2012)
BMC Systems Biology
, vol.6
, pp. 29
-
-
Kirouac, D.C.1
Saez-Rodriguez, J.2
Swantek, J.3
Burke, J.M.4
Lauffenburger, D.A.5
-
19
-
-
12144262660
-
Data integration: challenges for drug discovery
-
Searls DB, (2005) Data integration: challenges for drug discovery. Nature reviews Drug discovery 4: 45-58.
-
(2005)
Nature Reviews Drug Discovery
, vol.4
, pp. 45-58
-
-
Searls, D.B.1
-
20
-
-
12344296457
-
A reductionist's systems biology: opinion
-
Sorger PK, (2005) A reductionist's systems biology: opinion. Current opinion in cell biology 17: 9-11.
-
(2005)
Current Opinion in Cell Biology
, vol.17
, pp. 9-11
-
-
Sorger, P.K.1
-
21
-
-
77956795975
-
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets
-
Kelder T, Conklin BR, Evelo CT, Pico AR, (2010) Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS biology 8: 5.
-
(2010)
PLoS Biology
, vol.8
, pp. 5
-
-
Kelder, T.1
Conklin, B.R.2
Evelo, C.T.3
Pico, A.R.4
-
22
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nature protocols 2: 2366-82.
-
(2007)
Nature Protocols
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
-
23
-
-
83355177254
-
BioPAX support in CellDesigner
-
Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, et al. (2011) BioPAX support in CellDesigner. Bioinformatics (Oxford, England) 27: 3437-8.
-
(2011)
Bioinformatics (Oxford, England)
, vol.27
, pp. 3437-3438
-
-
Mi, H.1
Muruganujan, A.2
Demir, E.3
Matsuoka, Y.4
Funahashi, A.5
-
24
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, et al. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC systems biology 4: 92.
-
(2010)
BMC Systems Biology
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
-
25
-
-
77957226956
-
Discovering modulators of gene expression
-
Babur O, Demir E, Gönen M, Sander C, Dogrusoz U, (2010) Discovering modulators of gene expression. Nucleic Acids Res 38: 5648-5656.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5648-5656
-
-
Babur, O.1
Demir, E.2
Gönen, M.3
Sander, C.4
Dogrusoz, U.5
-
26
-
-
71549124335
-
Algorithms for effective querying of compound graph-based pathway databases
-
Dogrusoz U, Cetintas A, Demir E, Babur O, (2009) Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinformatics 10: 376.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 376
-
-
Dogrusoz, U.1
Cetintas, A.2
Demir, E.3
Babur, O.4
-
27
-
-
35348976204
-
Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions
-
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, et al. (2007) Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol 5: 44.
-
(2007)
BMC Biol
, vol.5
, pp. 44
-
-
Kerrien, S.1
Orchard, S.2
Montecchi-Palazzi, L.3
Aranda, B.4
Quinn, A.F.5
-
28
-
-
84865123095
-
Software support for SBGN maps: SBGN-ML and LibSBGN
-
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, et al. (2012) Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28: 2016-21.
-
(2012)
Bioinformatics
, vol.28
, pp. 2016-2021
-
-
van Iersel, M.P.1
Villéger, A.C.2
Czauderna, T.3
Boyd, S.E.4
Bergmann, F.T.5
-
29
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102: 15545-50.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
-
30
-
-
84866002291
-
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data
-
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, et al. (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer discovery 2: 401-4.
-
(2012)
Cancer Discovery
, vol.2
, pp. 401-404
-
-
Cerami, E.1
Gao, J.2
Dogrusoz, U.3
Gross, B.E.4
Sumer, S.O.5
-
31
-
-
65549162694
-
Insights into the organization of biochemical regulatory networks using graph theory analyses
-
Ma'ayan A, (2009) Insights into the organization of biochemical regulatory networks using graph theory analyses. The Journal of biological chemistry 284: 5451-5.
-
(2009)
The Journal of Biological Chemistry
, vol.284
, pp. 5451-5455
-
-
Ma'ayan, A.1
-
32
-
-
33751435209
-
cPath: open source software for collecting, storing, and querying biological pathways
-
Cerami EG, Bader GD, Gross BE, Sander C, (2006) cPath: open source software for collecting, storing, and querying biological pathways. BMC bioinformatics 7: 497.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 497
-
-
Cerami, E.G.1
Bader, G.D.2
Gross, B.E.3
Sander, C.4
-
33
-
-
84856535081
-
Mutual exclusivity analysis identifies oncogenic network modules
-
Ciriello G, Cerami E, Sander C, Schultz N, (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome research 22: 398-406.
-
(2012)
Genome Research
, vol.22
, pp. 398-406
-
-
Ciriello, G.1
Cerami, E.2
Sander, C.3
Schultz, N.4
-
34
-
-
77949499064
-
ChiBE: interactive visualization and manipulation of BioPAX pathway models
-
Babur O, Dogrusoz U, Demir E, Sander C, (2010) ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics (Oxford, England) 26: 429-31.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
, pp. 429-431
-
-
Babur, O.1
Dogrusoz, U.2
Demir, E.3
Sander, C.4
-
35
-
-
77956549590
-
Editing, validating and translating of SBGN maps
-
Czauderna T, Klukas C, Schreiber F, (2010) Editing, validating and translating of SBGN maps. Bioinformatics (Oxford, England) 26: 2340-1.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
, pp. 2340-2341
-
-
Czauderna, T.1
Klukas, C.2
Schreiber, F.3
|