-
1
-
-
77649252269
-
Visualization of omics data for systems biology
-
Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. et al. (2010) Visualization of omics data for systems biology. Nat. Methods, 7, S56-S68.
-
(2010)
Nat. Methods
, vol.7
, pp. S56-S68
-
-
Gehlenborg, N.1
O'Donoghue, S.I.2
Baliga, N.S.3
Goesmann, A.4
Hibbs, M.A.5
Kitano, H.6
Kohlbacher, O.7
Neuweger, H.8
Schneider, R.9
Tenenbaum, D.10
-
2
-
-
85128518666
-
-
Chapman & Hall, CRC Mathematical & Computational Biology, Boca Raton, FL
-
Barillot, E., Calzone, L., Hupe, P., Vert, J.-P. and Zinovyev, A. (2012) Computational Systems Biology of Cancer. Chapman & Hall, CRC Mathematical & Computational Biology, Boca Raton, FL.
-
(2012)
Computational Systems Biology of Cancer
-
-
Barillot, E.1
Calzone, L.2
Hupe, P.3
Vert, J.-P.4
Zinovyev, A.5
-
3
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D109-D114
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
4
-
-
84891753483
-
The reactome pathway knowledgebase
-
Croft, D., Mundo, A.F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M.R. et al. (2014) The Reactome pathway knowledgebase. Nucleic Acids Res., 42, D472-D477.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D472-D477
-
-
Croft, D.1
Mundo, A.F.2
Haw, R.3
Milacic, M.4
Weiser, J.5
Wu, G.6
Caudy, M.7
Garapati, P.8
Gillespie, M.9
Kamdar, M.R.10
-
5
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp, P.D., Ouzounis, C.A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V. and López-Bigas, N. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33, 6083-6089.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahrén, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
López-Bigas, N.10
-
6
-
-
27744493624
-
KEGG-based pathway visualization tool for complex omics data
-
Arakawa, K., Kono, N., Yamada, Y., Mori, H. and Tomita, M. (2005) KEGG-based pathway visualization tool for complex omics data. In Silico Biol., 5, 419-423.
-
(2005)
Silico Biol.
, vol.5
, pp. 419-423
-
-
Arakawa, K.1
Kono, N.2
Yamada, Y.3
Mori, H.4
Tomita, M.5
-
7
-
-
54249091564
-
Presenting and exploring biological pathways with Path Visio
-
van Iersel, M.P., Kelder, T., Pico, A.R., Hanspers, K., Coort, S., Conklin, B.R. and Evelo, C. (2008) Presenting and exploring biological pathways with Path Visio. BMC Bioinformatics, 9, 399.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 399
-
-
Van Iersel, M.P.1
Kelder, T.2
Pico, A.R.3
Hanspers, K.4
Coort, S.5
Conklin, B.R.6
Evelo, C.7
-
8
-
-
84880199410
-
Pathview: An R/Bioconductor package for pathway-based data integration and visualization
-
Luo, W. and Brouwer, C. (2013) Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29, 1830-1831.
-
(2013)
Bioinformatics
, vol.29
, pp. 1830-1831
-
-
Luo, W.1
Brouwer, C.2
-
9
-
-
84908659098
-
KEGGscape: A Cytoscape app for pathway data integration
-
Nishida, K., Ono, K., Kanaya, S. and Takahashi, K. (2014) KEGGscape: a Cytoscape app for pathway data integration. F1000 Res, 3, 144.
-
(2014)
F1000 Res
, vol.3
, pp. 144
-
-
Nishida, K.1
Ono, K.2
Kanaya, S.3
Takahashi, K.4
-
10
-
-
84885007150
-
NaviCell: A web-based environment for navigation, curation and maintenance of large molecular interaction maps
-
Kuperstein, I., Cohen, D.P., Pook, S., Viara, E., Calzone, L., Barillot, E. and Zinovyev, A. (2013) NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst. Biol., 7, 100.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 100
-
-
Kuperstein, I.1
Cohen, D.P.2
Pook, S.3
Viara, E.4
Calzone, L.5
Barillot, E.6
Zinovyev, A.7
-
12
-
-
81355123249
-
Software for systems biology: From tools to integrated platforms
-
Ghosh, S., Matsuoka, Y., Asai, Y., Hsin, K.-Y. and Kitano, H. (2011) Software for systems biology: from tools to integrated platforms. Nat. Rev. Genet., 12, 821-832.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 821-832
-
-
Ghosh, S.1
Matsuoka, Y.2
Asai, Y.3
Hsin, K.-Y.4
Kitano, H.5
-
13
-
-
34447626444
-
GeneSpring: Tools for analyzing microarray expression data
-
Chu, L., Scharf, E. and Kondo, T. (2001) GeneSpring: tools for analyzing microarray expression data. Genome Info., 12, 227-229.
-
(2001)
Genome Info.
, vol.12
, pp. 227-229
-
-
Chu, L.1
Scharf, E.2
Kondo, T.3
-
14
-
-
47949099328
-
Cell designer 3.5: A versatile modeling tool for biochemical networks
-
Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N. and Kitano, H. (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc. IEEE, 96, 1254-1265.
-
(2008)
Proc. IEEE
, vol.96
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
15
-
-
68449103579
-
The systems biology graphical notation
-
Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M.I., Wimalaratne, S.M. et al. (2009) The systems biology graphical notation. Nat. Biotechnol., 27, 735-741.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
Demir, E.7
Wegner, K.8
Aladjem, M.I.9
Wimalaratne, S.M.10
-
16
-
-
40749087306
-
BiNoM: A Cytoscape plugin for manipulating and analyzing biological networks
-
Zinovyev, A., Viara, E., Calzone, L. and Barillot, E. (2008) BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics, 24, 876-877.
-
(2008)
Bioinformatics
, vol.24
, pp. 876-877
-
-
Zinovyev, A.1
Viara, E.2
Calzone, L.3
Barillot, E.4
-
17
-
-
84874398455
-
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
-
Bonnet, E., Calzone, L., Rovera, D., Stoll, G., Barillot, E. and Zinovyev, A. (2013) BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst. Biol., 7, 18.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 18
-
-
Bonnet, E.1
Calzone, L.2
Rovera, D.3
Stoll, G.4
Barillot, E.5
Zinovyev, A.6
-
18
-
-
84976826673
-
Voronoi diagrams: A survey of a fundamental geometric data structure
-
Aurenhammer, F. (1991) Voronoi diagrams: a survey of a fundamental geometric data structure. ACM Comput. Surv., 23, 345-405.
-
(1991)
ACM Comput. Surv.
, vol.23
, pp. 345-405
-
-
Aurenhammer, F.1
-
19
-
-
84861547140
-
AlzPathway: A comprehensive map of signaling pathways of Alzheimer's disease
-
Mizuno, S., Iijima, R., Ogishima, S., Kikuchi, M., Matsuoka, Y., Ghosh, S., Miyamoto, T., Miyashita, A., Kuwano, R. and Tanaka, H. (2012) AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. BMC Syst. Biol., 6, 52.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 52
-
-
Mizuno, S.1
Iijima, R.2
Ogishima, S.3
Kikuchi, M.4
Matsuoka, Y.5
Ghosh, S.6
Miyamoto, T.7
Miyashita, A.8
Kuwano, R.9
Tanaka, H.10
-
20
-
-
84906987763
-
Altered expression of diabetes-related genes in Alzheimer's disease brains: The Hisayama study
-
Hokama, M., Oka, S., Leon, J., Ninomiya, T., Honda, H., Sasaki, K., Iwaki, T., Ohara, T., Sasaki, T., LaFerla, F.M. et al. (2014) Altered expression of diabetes-related genes in Alzheimer's disease brains: the Hisayama study. Cereb. Cortex, 24, 2476-2488.
-
(2014)
Cereb. Cortex
, vol.24
, pp. 2476-2488
-
-
Hokama, M.1
Oka, S.2
Leon, J.3
Ninomiya, T.4
Honda, H.5
Sasaki, K.6
Iwaki, T.7
Ohara, T.8
Sasaki, T.9
LaFerla, F.M.10
-
21
-
-
79959838081
-
Integrated genomic analyses of ovarian carcinoma
-
The-Cancer-Genome-Atlas-Research-Network. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 609-615.
-
(2011)
Nature
, vol.474
, pp. 609-615
-
-
-
22
-
-
84935094294
-
The shortest path is not the one you know: Application of biological network resources in precision oncology research
-
Kuperstein, I., Grieco, L., Cohen, D., Thieffry, D., Zinovyev, A. and Barillot, E. (2015) The shortest path is not the one you know: application of biological network resources in precision oncology research. Mutagenesis, 30, 191-204.
-
(2015)
Mutagenesis
, vol.30
, pp. 191-204
-
-
Kuperstein, I.1
Grieco, L.2
Cohen, D.3
Thieffry, D.4
Zinovyev, A.5
Barillot, E.6
-
23
-
-
84886036480
-
Systems biology of Ewing sarcoma: A network model of EWS-FLI1 effect on proliferation and apoptosis
-
Stoll, G., Surdez, D., Tirode, F., Laud, K., Barillot, E., Zinovyev, A. and Delattre, O. (2013) Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. Nucleic Acids Res., 41, 8853-8871.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 8853-8871
-
-
Stoll, G.1
Surdez, D.2
Tirode, F.3
Laud, K.4
Barillot, E.5
Zinovyev, A.6
Delattre, O.7
-
24
-
-
84859169877
-
The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity
-
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A.A., Kim, S., Wilson, C.J., Lehár, J., Kryukov, G.V., Sonkin, D. et al. (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature, 483, 603-607.
-
(2012)
Nature
, vol.483
, pp. 603-607
-
-
Barretina, J.1
Caponigro, G.2
Stransky, N.3
Venkatesan, K.4
Margolin, A.A.5
Kim, S.6
Wilson, C.J.7
Lehár, J.8
Kryukov, G.V.9
Sonkin, D.10
-
25
-
-
40749120501
-
A comprehensive modular map of molecular interactions in RB/E2F pathway
-
Calzone, L., Gelay, A., Zinovyev, A., Radvanyi, F. and Barillot, E. (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol. Syst. Biol., 4, 173.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 173
-
-
Calzone, L.1
Gelay, A.2
Zinovyev, A.3
Radvanyi, F.4
Barillot, E.5
-
26
-
-
39949084468
-
IPath: Interactive exploration of biochemical pathways and networks
-
Letunic, I., Yamada, T., Kanehisa, M. and Bork, P. (2008) iPath: interactive exploration of biochemical pathways and networks. Trends Biochem. Sci., 33, 101-103.
-
(2008)
Trends Biochem. Sci.
, vol.33
, pp. 101-103
-
-
Letunic, I.1
Yamada, T.2
Kanehisa, M.3
Bork, P.4
-
27
-
-
0036326896
-
PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways
-
Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R. and Ozturk, M. (2002) PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics, 18, 996-1003.
-
(2002)
Bioinformatics
, vol.18
, pp. 996-1003
-
-
Demir, E.1
Babur, O.2
Dogrusoz, U.3
Gursoy, A.4
Nisanci, G.5
Cetin-Atalay, R.6
Ozturk, M.7
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