-
1
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon,S. and Gentleman,R. (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
2
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca,A.L., Draghici,S., Khatri,P., Hassan,S.S.,Mittal,P., Kim,J.S., Kim,C.J., Kusanovic,J.P. and Romero,R. (2009) A novel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
Draghici, S.2
Khatri, P.3
Hassan, S.S.4
Mittal, P.5
Kim, J.S.6
Kim, C.J.7
Kusanovic, J.P.8
Romero, R.9
-
3
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A., 102, 15545-15550.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
-
4
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker,T., Ozier,O., Schwikowski,B. and Siegel,A.F. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
5
-
-
0037059461
-
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
-
Tong,A.H., Drees,B., Nardelli,G., Bader,G.D., Brannetti,B., Castagnoli,L., Evangelista,M., Ferracuti,S., Nelson,B., Paoluzi,S. et al. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science, 295, 321-324.
-
(2002)
Science
, vol.295
, pp. 321-324
-
-
Tong, A.H.1
Drees, B.2
Nardelli, G.3
Bader, G.D.4
Brannetti, B.5
Castagnoli, L.6
Evangelista, M.7
Ferracuti, S.8
Nelson, B.9
Paoluzi, S.10
-
6
-
-
84862703457
-
Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays
-
Braun,P. (2012) Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays. Proteomics, 12, 1499-1518.
-
(2012)
Proteomics
, vol.12
, pp. 1499-1518
-
-
Braun, P.1
-
7
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
-
(2003)
Genome Res.
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
Markiel, A.2
Ozier, O.3
Baliga, N.S.4
Wang, J.T.5
Ramage, D.6
Amin, N.7
Schwikowski, B.8
Ideker, T.9
-
8
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
Ulitsky,I. and Shamir,R. (2007) Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol., 1, 8.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
9
-
-
75249086155
-
NAViGaTOR: Network analysis, visualization and graphing toronto
-
Brown,K.R., Otasek,D., Ali,M., McGuffin,M.J., Xie,W., Devani,B., Toch,I.L. and Jurisica,I. (2009) NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics, 25, 3327-3329.
-
(2009)
Bioinformatics
, vol.25
, pp. 3327-3329
-
-
Brown, K.R.1
Otasek, D.2
Ali, M.3
McGuffin, M.J.4
Xie, W.5
Devani, B.6
Toch, I.L.7
Jurisica, I.8
-
10
-
-
84866348703
-
AtBioNet - An integrated network analysis tool for genomics and biomarker discovery
-
Ding,Y., Chen,M., Liu,Z., Ding,D., Ye,Y., Zhang,M., Kelly,R., Guo,L., Su,Z., Harris,S.C. et al. (2012) atBioNet-an integrated network analysis tool for genomics and biomarker discovery. BMC Genomics, 13, 325.
-
(2012)
BMC Genomics
, vol.13
, pp. 325
-
-
Ding, Y.1
Chen, M.2
Liu, Z.3
Ding, D.4
Ye, Y.5
Zhang, M.6
Kelly, R.7
Guo, L.8
Su, Z.9
Harris, S.C.10
-
11
-
-
84883576667
-
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
-
Hu,Z., Chang,Y.C., Wang,Y., Huang,C.L., Liu,Y., Tian,F., Granger,B. and Delisi,C. (2013) VisANT 4.0: integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res., 41, W225-W231.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Hu, Z.1
Chang, Y.C.2
Wang, Y.3
Huang, C.L.4
Liu, Y.5
Tian, F.6
Granger, B.7
Delisi, C.8
-
12
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini,A., Szklarczyk,D., Frankild,S., Kuhn,M., Simonovic,M., Roth,A., Lin,J., Minguez,P., Bork,P., von Mering,C. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res., 41, D808-D815.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
-
13
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline,M.S., Smoot,M., Cerami,E., Kuchinsky,A., Landys,N., Workman,C., Christmas,R., Avila-Campilo,I., Creech,M., Gross,B. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
Smoot, M.2
Cerami, E.3
Kuchinsky, A.4
Landys, N.5
Workman, C.6
Christmas, R.7
Avila-Campilo, I.8
Creech, M.9
Gross, B.10
-
14
-
-
84880550681
-
Network2Canvas: Network visualization on a canvas with enrichment analysis
-
Tan,C.M., Chen,E.Y., Dannenfelser,R., Clark,N.R. and Ma'ayan,A. (2013) Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics, 29, 1872-1878.
-
(2013)
Bioinformatics
, vol.29
, pp. 1872-1878
-
-
Tan, C.M.1
Chen, E.Y.2
Dannenfelser, R.3
Clark, N.R.4
Ma'ayan, A.5
-
15
-
-
84900376656
-
INVEX - A web-based tool for integrative visualization of expression data
-
Xia,J., Lyle,N.H., Mayer,M.L., Pena,O.M. and Hancock,R.E.W. (2013) INVEX-a web-based tool for integrative visualization of expression data. Bioinformatics, 29, 3232-3234.
-
(2013)
Bioinformatics
, vol.29
, pp. 3232-3234
-
-
Xia, J.1
Lyle, N.H.2
Mayer, M.L.3
Pena, O.M.4
Hancock, R.E.W.5
-
16
-
-
84873284657
-
Scribl: An HTML5 Canvas-based graphics library for visualizing genomic data over the web
-
Miller,C.A., Anthony,J.,Meyer,M.M. and Marth,G. (2013) Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics, 29, 381-383.
-
(2013)
Bioinformatics
, vol.29
, pp. 381-383
-
-
Miller, C.A.1
Anthony, J.2
Meyer, M.M.3
Marth, G.4
-
17
-
-
84891817932
-
NeXO Web: The NeXO ontology database and visualization platform
-
Dutkowski,J., Ono,K., Kramer,M., Yu,M., Pratt,D., Demchak,B. and Ideker,T. (2014) NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res., 42, D1269-D1274.
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Dutkowski, J.1
Ono, K.2
Kramer, M.3
Yu, M.4
Pratt, D.5
Demchak, B.6
Ideker, T.7
-
18
-
-
33644872577
-
Limma: Linear models for microarray data
-
Gentleman,R.C., Carey,V.J., Dudoit,S., Irizarry,R. and Huber,W., (eds.). Springer, New York
-
Smyth,G.K. (2005) Limma: linear models for microarray data. In: Gentleman,R.C., Carey,V.J., Dudoit,S., Irizarry,R. and Huber,W., (eds.). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, New York, pp. 397 -420.
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
19
-
-
84876581893
-
InnateDB: Systems biology of innate immunity and beyond-recent updates and continuing curation
-
Breuer,K., Foroushani,A.K., Laird,M.R., Chen,C., Sribnaia,A., Lo,R., Winsor,G.L., Hancock,R.E.W., Brinkman,F.S. and Lynn,D.J. (2013) InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res., 41, D1228-D1233.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Breuer, K.1
Foroushani, A.K.2
Laird, M.R.3
Chen, C.4
Sribnaia, A.5
Lo, R.6
Winsor, G.L.7
Hancock, R.E.W.8
Brinkman, F.S.9
Lynn, D.J.10
-
20
-
-
84859208501
-
Protein interaction data curation: The International Molecular Exchange (IMEx) consortium
-
Orchard,S., Kerrien,S., Abbani,S., Aranda,B., Bhate,J., Bidwell,S., Bridge,A., Briganti,L., Brinkman,F.S., Cesareni,G. et al. (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods, 9, 345-350.
-
(2012)
Nat. Methods
, vol.9
, pp. 345-350
-
-
Orchard, S.1
Kerrien, S.2
Abbani, S.3
Aranda, B.4
Bhate, J.5
Bidwell, S.6
Bridge, A.7
Briganti, L.8
Brinkman, F.S.9
Cesareni, G.10
-
21
-
-
84891799734
-
The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
-
Orchard,S., Ammari,M., Aranda,B., Breuza,L., Briganti,L., Broackes-Carter,F., Campbell,N.H., Chavali,G., Chen,C., Del-Toro,N. et al. (2014) The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.
-
(2014)
Nucleic Acids Res.
, vol.42
-
-
Orchard, S.1
Ammari, M.2
Aranda, B.3
Breuza, L.4
Briganti, L.5
Broackes-Carter, F.6
Campbell, N.H.7
Chavali, G.8
Chen, C.9
Del-Toro, N.10
-
22
-
-
84860918589
-
MINT, the molecular interaction database: 2012 update
-
Licata,L., Briganti,L., Peluso,D., Perfetto,L., Iannuccelli,M., Galeota,E., Sacco,F., Palma,A., Nardozza,A.P., Santonico,E. et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res., 40, D857-D861.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Licata, L.1
Briganti, L.2
Peluso, D.3
Perfetto, L.4
Iannuccelli, M.5
Galeota, E.6
Sacco, F.7
Palma, A.8
Nardozza, A.P.9
Santonico, E.10
-
23
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski,L., Miller,C.S., Smith,A.J., Pettit,F.K., Bowie,J.U. and Eisenberg,D. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
24
-
-
79955667824
-
The biomolecular interaction network database in PSI-MI 2.5
-
Isserlin,R., El-Badrawi,R.A. and Bader,G.D. (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford), 2011, baq037.
-
(2011)
Database (Oxford)
, vol.2011
-
-
Isserlin, R.1
El-Badrawi, R.A.2
Bader, G.D.3
-
25
-
-
84874947727
-
The BioGRID interaction database: 2013 update
-
Chatr-Aryamontri,A., Breitkreutz,B.J., Heinicke,S., Boucher,L., Winter,A., Stark,C., Nixon,J., Ramage,L., Kolas,N., O'Donnell,L. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-823.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.J.2
Heinicke, S.3
Boucher, L.4
Winter, A.5
Stark, C.6
Nixon, J.7
Ramage, L.8
Kolas, N.9
O'donnell, L.10
-
26
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han,J.D., Bertin,N., Hao,T., Goldberg,D.S., Berriz,G.F., Zhang,L.V., Dupuy,D., Walhout,A.J., Cusick,M.E., Roth,F.P. 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.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.8
Cusick, M.E.9
Roth, F.P.10
-
27
-
-
33646530046
-
Computing communities in large networks using random walks
-
Pons,P. and Latapy,M. (2005) Computing communities in large networks using random walks. Lect. Notes Comput. Sci., 3733, 284-293.
-
(2005)
Lect. Notes Comput. Sci.
, vol.3733
, pp. 284-293
-
-
Pons, P.1
Latapy, M.2
-
28
-
-
84885338039
-
Using random walks to identify cancer-associated modules in expression data
-
Petrochilos,D., Shojaie,A., Gennari,J. and Abernethy,N. (2013) Using random walks to identify cancer-associated modules in expression data. BioData Min., 6, 17.
-
(2013)
BioData Min.
, vol.6
, pp. 17
-
-
Petrochilos, D.1
Shojaie, A.2
Gennari, J.3
Abernethy, N.4
-
29
-
-
84904811413
-
-
California, San Jose
-
Bastian,M., Heymann,S. and Jacomy,M. (2009) In: International AAAI Conference on Weblogs and Social Media, California, San Jose.
-
(2009)
International AAAI Conference on Weblogs and Social Media
-
-
Bastian, M.1
Heymann, S.2
Jacomy, M.3
-
31
-
-
84869054051
-
A travel guide to Cytoscape plugins
-
Saito,R., Smoot,M.E., Ono,K., Ruscheinski,J., Wang,P.L., Lotia,S., Pico,A.R., Bader,G.D. and Ideker,T. (2012) A travel guide to Cytoscape plugins. Nat. Methods, 9, 1069-1076.
-
(2012)
Nat. Methods
, vol.9
, pp. 1069-1076
-
-
Saito, R.1
Smoot, M.E.2
Ono, K.3
Ruscheinski, J.4
Wang, P.L.5
Lotia, S.6
Pico, A.R.7
Bader, G.D.8
Ideker, T.9
-
32
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere,S., Heymans,K. and Kuiper,M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
33
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader,G.D. and Hogue,C.W. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4, 2.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 2
-
-
Bader, G.D.1
Hogue, C.W.2
-
34
-
-
34249751614
-
Cerebral: A Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
-
Barsky,A., Gardy,J.L., Hancock,R.E.W. and Munzner,T. (2007) Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics, 23, 1040-1042.
-
(2007)
Bioinformatics
, vol.23
, pp. 1040-1042
-
-
Barsky, A.1
Gardy, J.L.2
Hancock, R.E.W.3
Munzner, T.4
-
35
-
-
48449099258
-
GraphWeb: Mining heterogeneous biological networks for gene modules with functional significance
-
Reimand,J., Tooming,L., Peterson,H., Adler,P. and Vilo,J. (2008) GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Res., 36, W452-W459.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Reimand, J.1
Tooming, L.2
Peterson, H.3
Adler, P.4
Vilo, J.5
-
36
-
-
48449094106
-
NeAT: A toolbox for the analysis of biological networks, clusters, classes and pathways
-
Brohee,S., Faust,K., Lima-Mendez,G., Sand,O., Janky,R., Vanderstocken,G., Deville,Y. and van Helden,J. (2008) NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res., 36, W444-W451.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Brohee, S.1
Faust, K.2
Lima-Mendez, G.3
Sand, O.4
Janky, R.5
Vanderstocken, G.6
Deville, Y.7
Van Helden, J.8
-
37
-
-
84872735966
-
Rescue of dysfunctional autophagy attenuates hyperinflammatory responses from cystic fibrosis cells
-
Mayer,M.L., Blohmke,C.J., Falsafi,R., Fjell,C.D., Madera,L., Turvey,S.E. and Hancock,R.E.W. (2013) Rescue of dysfunctional autophagy attenuates hyperinflammatory responses from cystic fibrosis cells. J. Immunol., 190, 1227-1238.
-
(2013)
J. Immunol.
, vol.190
, pp. 1227-1238
-
-
Mayer, M.L.1
Blohmke, C.J.2
Falsafi, R.3
Fjell, C.D.4
Madera, L.5
Turvey, S.E.6
Hancock, R.E.W.7
-
38
-
-
84864479791
-
MetaboAnalyst 2.0 - A comprehensive server for metabolomic data analysis
-
Xia,J., Mandal,R., Sinelnikov,I.V., Broadhurst,D. and Wishart,D.S. (2012) MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis. Nucleic Acids Res., 40, W127-W133.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Xia, J.1
Mandal, R.2
Sinelnikov, I.V.3
Broadhurst, D.4
Wishart, D.S.5
-
39
-
-
48449100027
-
GEPAS, a web-based tool for microarray data analysis and interpretation
-
Tarraga,J., Medina,I., Carbonell,J., Huerta-Cepas,J., Minguez,P., Alloza,E., Al-Shahrour,F., Vegas-Azcarate,S., Goetz,S., Escobar,P. et al. (2008) GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res., 36, W308-W314.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Tarraga, J.1
Medina, I.2
Carbonell, J.3
Huerta-Cepas, J.4
Minguez, P.5
Alloza, E.6
Al-Shahrour, F.7
Vegas-Azcarate, S.8
Goetz, S.9
Escobar, P.10
-
40
-
-
84861414639
-
Comprehensive literature review and statistical considerations for microarray meta-analysis
-
Tseng,G.C., Ghosh,D. and Feingold,E. (2012) Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res., 40, 3785-3799.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3785-3799
-
-
Tseng, G.C.1
Ghosh, D.2
Feingold, E.3
-
41
-
-
84883580836
-
INMEX - A web-based tool for integrative meta-analysis of expression data
-
Xia,J., Fjell,C.D., Mayer,M.L., Pena,O.M., Wishart,D.S. and Hancock,R.E.W. (2013) INMEX - a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res., 41, W63-W70.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Xia, J.1
Fjell, C.D.2
Mayer, M.L.3
Pena, O.M.4
Wishart, D.S.5
Hancock, R.E.W.6
|