-
1
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
DOI 10.1038/75556
-
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
2
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
3
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools, limitations, and open problems
-
DOI 10.1093/bioinformatics/bti565
-
Khatri, P. and Draghici, S. (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics, 21, 3587-3595. (Pubitemid 41264092)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
4
-
-
1542399989
-
FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
-
DOI 10.1093/bioinformatics/btg455
-
Al-Shahrour, F., Diaz-Uriarte, R. and Dopazo, J. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20, 578-580. (Pubitemid 38344339)
-
(2004)
Bioinformatics
, vol.20
, Issue.4
, pp. 578-580
-
-
Al-Shahrour, F.1
Diaz-Uriarte, R.2
Dopazo, J.3
-
5
-
-
0038005018
-
DAVID: Database for annotation, visualization, and integrated discovery
-
Dennis, G. Jr, Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol., 4, 3.
-
(2003)
Genome Biol.
, vol.4
, pp. 3
-
-
Dennis Jr., G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
Lempicki, R.A.7
-
6
-
-
34547571030
-
G: Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments
-
Reimand, J., Kull, M., Peterson, H., Hansen, J. and Vilo, J. (2007) G:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res., 35, W193-W200.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Reimand, J.1
Kull, M.2
Peterson, H.3
Hansen, J.4
Vilo, J.5
-
7
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
-
DOI 10.1093/bioinformatics/bti551
-
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. (Pubitemid 41222459)
-
(2005)
Bioinformatics
, vol.21
, Issue.16
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
8
-
-
77954299992
-
AgriGO: A GO analysis toolkit for the agricultural community
-
Du, Z., Zhou, X., Ling, Y., Zhang, Z. and Su, Z. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res., 38, W64-W70.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Du, Z.1
Zhou, X.2
Ling, Y.3
Zhang, Z.4
Su, Z.5
-
9
-
-
84889418078
-
-
John Wiley & Sons, Hoboken, NJ
-
Chen, L., Wang, R.S. and Zhang, X.S. (2009) Biomolecular Networks: Methods and Applications in Systems Biology. John Wiley & Sons, Hoboken, NJ.
-
(2009)
Biomolecular Networks: Methods and Applications in Systems Biology
-
-
Chen, L.1
Wang, R.S.2
Zhang, X.S.3
-
10
-
-
0036500993
-
Systems biology: A brief overview
-
DOI 10.1126/science.1069492
-
Kitano, H. (2002) Systems biology: a brief overview. Science, 295, 1662-1664. (Pubitemid 34202893)
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1662-1664
-
-
Kitano, H.1
-
11
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
DOI 10.1038/nrg1272
-
Barabasi, A.B. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev., 5, 101-113. (Pubitemid 38160277)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabasi, A.-L.1
Oltvai, Z.N.2
-
13
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
DOI 10.1016/j.cell.2005.08.029, PII S0092867405008664
-
Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S. et al. (2005) Human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968. (Pubitemid 41345212)
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
Goehler, H.6
Stroedicke, M.7
Zenkner, M.8
Schoenherr, A.9
Koeppen, S.10
Timm, J.11
Mintzlaff, S.12
Abraham, C.13
Bock, N.14
Kietzmann, S.15
Goedde, A.16
Toksoz, E.17
Droege, A.18
Krobitsch, S.19
Korn, B.20
Birchmeier, W.21
Lehrach, H.22
Wanker, E.E.23
more..
-
14
-
-
0035319006
-
Computational studies of gene regulatory networks: In numero molecular biology
-
DOI 10.1038/35066056
-
Hasty, J., McMillen, D., Isaacs, F. and Collins, J.J. (2001) Computational studies of gene regulatory networks: in numero molecular biology. Nat. Rev. Genet., 2, 268-279. (Pubitemid 33674775)
-
(2001)
Nature Reviews Genetics
, vol.2
, Issue.4
, pp. 268-279
-
-
Hasty, J.1
McMillen, D.2
Isaacs, F.3
Collins, J.J.4
-
15
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
DOI 10.1126/science.1073374
-
Ravasz, E., Someraz, A.L., Mongru, D.A., Oltvai, Z.N. and Barabasi, A.L. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555. (Pubitemid 34971002)
-
(2002)
Science
, vol.297
, Issue.5586
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.-L.5
-
16
-
-
70349653568
-
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases
-
Wang, J., Zhang, S., Wang, Y., Chen, L. and Zhang, X.S. (2009) Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Comput. Biol., 5, e1000521.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Wang, J.1
Zhang, S.2
Wang, Y.3
Chen, L.4
Zhang, X.S.5
-
17
-
-
77956417789
-
Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
-
Jerby, L., Shlomi, T. and Ruppin, E. (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol., 6, 401.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 401
-
-
Jerby, L.1
Shlomi, T.2
Ruppin, E.3
-
18
-
-
70249108504
-
Genome-wide identification of posttranslational modulators of transcription factor activity in human B cells
-
Wang, K., Saito, M., Bisikirska, B.C., Alvarez, M.J., Lim, W.K., Rajbhandari, P., Shen, Q., Nemenman, I., Basso, K., Margolin, A.A. et al. (2009) Genome-wide identification of posttranslational modulators of transcription factor activity in human B cells. Nat. Biotechnol., 27, 829-837.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 829-837
-
-
Wang, K.1
Saito, M.2
Bisikirska, B.C.3
Alvarez, M.J.4
Lim, W.K.5
Rajbhandari, P.6
Shen, Q.7
Nemenman, I.8
Basso, K.9
Margolin, A.A.10
-
19
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
DOI 10.1038/nature02782
-
Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A. and Gerstein, M.A. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312. (Pubitemid 39265665)
-
(2004)
Nature
, vol.431
, Issue.7006
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
20
-
-
64349094767
-
Tissue specificity and the human protein interaction network
-
Bossi, A. and Lehner, B. (2009) Tissue specificity and the human protein interaction network. Mol. Syst. Biol., 5, 260.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 260
-
-
Bossi, A.1
Lehner, B.2
-
21
-
-
72849142731
-
Edgetic perturbation models of human inherited disorders
-
Zhang, Q., Simonis, N., Li, Q.R., Charloteaux, B., Heuze, F., Klitgord, N., Tam, S., Yu, H., Venkatesan, K., Mou, D. et al. (2009) Edgetic perturbation models of human inherited disorders. Mol. Syst. Biol., 5, 321.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 321
-
-
Zhang, Q.1
Simonis, N.2
Li, Q.R.3
Charloteaux, B.4
Heuze, F.5
Klitgord, N.6
Tam, S.7
Yu, H.8
Venkatesan, K.9
Mou, D.10
-
22
-
-
1342264315
-
A Corepressor/Coactivator Exchange Complex Required for Transcriptional Activation by Nuclear Receptors and Other Regulated Transcription Factors
-
DOI 10.1016/S0092-8674(04)00133-3
-
Perissi, V., Aggarwal, A., Glass, C.K., Rose, D.W. and Rosenfeld, M.G. (2004) A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors. Cell, 116, 511-526. (Pubitemid 38264429)
-
(2004)
Cell
, vol.116
, Issue.4
, pp. 511-526
-
-
Perissi, V.1
Aggarwal, A.2
Glass, C.K.3
Rose, D.W.4
Rosenfeld, M.G.5
-
23
-
-
24644503098
-
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
-
DOI 10.1093/bioinformatics/bti610
-
Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M. and Robles, M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676. (Pubitemid 41264107)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3674-3676
-
-
Conesa, A.1
Gotz, S.2
Garcia-Gomez, J.M.3
Terol, J.4
Talon, M.5
Robles, M.6
-
24
-
-
34248361071
-
GOAnnotator: Linking protein GO annotations to evidence text
-
Couto, F.M., Silva, M.J., Lee, V., Dimmer, E., Camon, E., Apweiler, R., Kirsch, H. and Rebholz-Schuhmann, D. (2006) GOAnnotator: linking protein GO annotations to evidence text. J. Biomed. Discov. Collab., 1, 19.
-
(2006)
J. Biomed. Discov. Collab.
, vol.1
, pp. 19
-
-
Couto, F.M.1
Silva, M.J.2
Lee, V.3
Dimmer, E.4
Camon, E.5
Apweiler, R.6
Kirsch, H.7
Rebholz-Schuhmann, D.8
-
25
-
-
11944262819
-
Multiple hypothesis testing
-
Shaffer, J.P. (1995) Multiple hypothesis testing. Ann. Rev. Psych., 46, 561-584.
-
(1995)
Ann. Rev. Psych.
, vol.46
, pp. 561-584
-
-
Shaffer, J.P.1
-
26
-
-
74849132183
-
Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. Proceedings of the 2009
-
Liu, Z.P., Wang, Y., Wen, T., Zhang, Z.S., Xia, W. and Chen, L. (2009) Dynamically dysfunctional protein interactions in the development of Alzheimer's disease. Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics, 4262-4267.
-
(2009)
IEEE International Conference on Systems, Man, and Cybernetics
, pp. 4262-4267
-
-
Liu, Z.P.1
Wang, Y.2
Wen, T.3
Zhang, Z.S.4
Xia, W.5
Chen, L.6
-
27
-
-
77957762129
-
Dynamic interaction networks in a hierarchically organized tissue
-
Kirouac, D.C., Ito, C., Csaszar, E., Roch, A., Yu, M., Sykes, E.A., Bader, G.D. and Zandstra, P.W. (2010) Dynamic interaction networks in a hierarchically organized tissue. Mol. Syst. Biol., 6, 417.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 417
-
-
Kirouac, D.C.1
Ito, C.2
Csaszar, E.3
Roch, A.4
Yu, M.5
Sykes, E.A.6
Bader, G.D.7
Zandstra, P.W.8
-
28
-
-
70350690683
-
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
-
Wang, Y., Zhang, X.S. and Xia, Y. (2009) Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Nucleic Acids Res., 37, 5943-5958.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5943-5958
-
-
Wang, Y.1
Zhang, X.S.2
Xia, Y.3
-
29
-
-
33750705653
-
A century of Alzheimer's disease
-
DOI 10.1126/science.1132814
-
Goedert, M. and Spillantini, M.G. (2006) A century of Alzheimer's disease. Science, 314, 777-781. (Pubitemid 44706636)
-
(2006)
Science
, vol.314
, Issue.5800
, pp. 777-781
-
-
Goedert, M.1
Spillantini, M.G.2
-
30
-
-
1242341923
-
Incipient Alzheimer's disease: Microarray correlation analyses reveal major transcriptional and tumor suppressor responses
-
DOI 10.1073/pnas.0308512100
-
Blalock, E.M., Geddes, J.W., Chen, K.C., Porter, N.M., Markesbery, W.R. and Landfield, P.W. (2004) Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc. Natl Acad. Sci. USA, 101, 2173-2178. (Pubitemid 38229034)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.7
, pp. 2173-2178
-
-
Blalock, E.M.1
Geddes, J.W.2
Chen, K.C.3
Porter, N.M.4
Markesbery, W.R.5
Landfield, P.W.6
-
31
-
-
33846129434
-
Increased level of active GSK-3β in Alzheimer's disease and accumulation in argyrophilic grains and in neurones at different stages of neurofibrillary degeneration
-
DOI 10.1111/j.1365-2990.2006.00795.x
-
Leroy, K., Yilmaz, Z. and Brion, J.P. (2007) Increased level of active GSK-3b in Alzheimer's disease and accumulation in argyrophilic grains and in neurones at different stages of neurofibrillary degeneration. Neuropathol. Appl. Neurobiol., 33, 43-55. (Pubitemid 46090309)
-
(2007)
Neuropathology and Applied Neurobiology
, vol.33
, Issue.1
, pp. 43-55
-
-
Leroy, K.1
Yilmaz, Z.2
Brion, J.-P.3
-
32
-
-
0035066332
-
Alzheimer's disease: Genes, proteins, and therapy
-
Selkoe, D.J. (2001) Alzheimer's disease: genes, proteins, and therapy. Physiol. Rev., 81, 741-766. (Pubitemid 32267077)
-
(2001)
Physiological Reviews
, vol.81
, Issue.2
, pp. 741-766
-
-
Selkoe, D.J.1
-
33
-
-
0036669607
-
Topographic regulation of kinase activity in Alzheimer's disease brains
-
Grant, P. and Pant, H.C. (2002) Topographic regulation of kinase activity in Alzheimer's disease brains. J. Alzheimers Dis., 4, 269-281. (Pubitemid 35257145)
-
(2002)
Journal of Alzheimer's Disease
, vol.4
, Issue.4
, pp. 269-281
-
-
Grant, P.1
Pant, H.C.2
-
34
-
-
75549090213
-
KEGG for representation and analysis of molecular networks involving diseases and drugs
-
Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Kanehisa, M.1
Goto, S.2
Furumichi, M.3
Tanabe, M.4
Hirakawa, M.5
-
35
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30. (Pubitemid 30047706)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
36
-
-
33748706765
-
Global topological features of cancer proteins in the human interactome
-
Jonsson, P.F. and Bates, P.A. (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics, 22, 2291.
-
(2006)
Bioinformatics
, vol.22
, pp. 2291
-
-
Jonsson, P.F.1
Bates, P.A.2
-
37
-
-
0028329172
-
Apoptosis: Its significance in cancer and cancer therapy
-
Kerr, J.F., Winterford, C.M. and Harmon, B.V. (1994) Apoptosis. its significance in cancer and cancer therapy. Cancer, 73, 2013-2026. (Pubitemid 24107952)
-
(1994)
Cancer
, vol.73
, Issue.8
, pp. 2013-2026
-
-
Kerr, J.F.R.1
Winterford, C.M.2
Harmon, B.V.3
-
38
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
DOI 10.1038/nature02555
-
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. (Pubitemid 38915230)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 88-93
-
-
Han, J.-D.J.1
Berlin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
39
-
-
78649923026
-
Protein's "part-time job" reveals new facet of signaling pathway
-
Inman, M. (2010) Protein's "part-time job" reveals new facet of signaling pathway. PLoS Biol., 8, e1001001.
-
(2010)
PLoS Biol.
, vol.8
-
-
Inman, M.1
-
40
-
-
34848827433
-
Comparing classical pathways and modern networks: towards the development of an edge ontology
-
DOI 10.1016/j.tibs.2007.06.003, PII S0968000407001466
-
Lu, L.J., Sboner, A., Huang, Y.J., Lu, H.X., Gianoulis, T.A., Yip, K.Y., Kim, P.M., Montelione, G.T. and Gerstein, M.B. (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem. Sci., 32, 320-331. (Pubitemid 47021418)
-
(2007)
Trends in Biochemical Sciences
, vol.32
, Issue.7
, pp. 320-331
-
-
Lu, L.J.1
Sboner, A.2
Huang, Y.J.3
Lu, H.X.4
Gianoulis, T.A.5
Yip, K.Y.6
Kim, P.M.7
Montelione, G.T.8
Gerstein, M.B.9
-
42
-
-
33847103869
-
Measuring semantic similarity between Gene Ontology terms
-
DOI 10.1016/j.datak.2006.05.003, PII S0169023X06000875, Business Process Management Where business processes and web services meet
-
Couto, F.M., Silva, M.J. and Coutinho, P.M. (2007) Measuring semantic similarity between Gene Ontology terms. Data & knowledge engineering, 61, 137-152. (Pubitemid 46282157)
-
(2007)
Data and Knowledge Engineering
, vol.61
, Issue.1
, pp. 137-152
-
-
Couto, F.M.1
Silva, M.J.2
Coutinho, P.M.3
-
43
-
-
33947252154
-
Network-based prediction of protein function Mol
-
Sharan, R., Ulitsky, I. and Shamir, R. (2007) Network-based prediction of protein function Mol. Syst. Biol., 3, 88.
-
(2007)
Syst. Biol.
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
44
-
-
0025894713
-
p53 mutations in human cancers
-
Hollstein, M., Sidransky, D., Vogelstein, B. and Harris, C.C. (1991) p53 mutations in human cancers. Science, 253, 49-53. (Pubitemid 21917115)
-
(1991)
Science
, vol.253
, Issue.5015
, pp. 49-53
-
-
Hollsteln, M.1
Sidransky, D.2
Vogelstein, B.3
Harris, C.C.4
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