-
1
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25
-
-
Ashburner, M.1
-
2
-
-
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
-
3
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi, A.L. and Albert, R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
4
-
-
84859169877
-
The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity
-
Barretina, J. 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
-
5
-
-
85166916238
-
Gephi: An open source software for exploring and manipulating networks
-
AAAI Press, Menlo Park, CA
-
Bastian, M. et al. (2009) Gephi: an open source software for exploring and manipulating networks. In: International AAAI conference on weblogs and social media. Vol. 2, AAAI Press, Menlo Park, CA.
-
(2009)
International AAAI Conference on Weblogs and Social Media
, vol.2
-
-
Bastian, M.1
-
6
-
-
0002226683
-
Pajek-program for large network analysis
-
Batagelj, V. and Mrvar, A. (1998) Pajek-program for large network analysis. Connections, 21, 47-57.
-
(1998)
Connections
, vol.21
, pp. 47-57
-
-
Batagelj, V.1
Mrvar, A.2
-
7
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein, B.E. et al. (2010) The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol., 28, 1045-1048.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
-
8
-
-
80855141795
-
D3: Data-driven documents
-
Bostock, M. et al. (2011) D3: Data-driven documents. IEEE Trans. Vis. Comput. Graph., 17, 2301-2309.
-
(2011)
IEEE Trans. Vis. Comput. Graph.
, vol.17
, pp. 2301-2309
-
-
Bostock, M.1
-
9
-
-
0037264280
-
Osprey: A network visualization system
-
Breitkreutz, B.J. et al. (2003) Osprey: a network visualization system. Genome Biol., 4, R22.
-
(2003)
Genome Biol.
, vol.4
-
-
Breitkreutz, B.J.1
-
10
-
-
48249143990
-
ChemmineR: A compound mining framework for R
-
Cao, Y. et al. (2008) ChemmineR: a compound mining framework for R. Bioinformatics, 24, 1733-1734.
-
(2008)
Bioinformatics
, vol.24
, pp. 1733-1734
-
-
Cao, Y.1
-
11
-
-
84855171722
-
Expression2Kinases: Mrna profiling linked to multiple upstream regulatory layers
-
Chen, E.Y. et al. (2012) Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics, 28, 105-111.
-
(2012)
Bioinformatics
, vol.28
, pp. 105-111
-
-
Chen, E.Y.1
-
12
-
-
21744444920
-
Reciprocal transcriptional regulation of pou5f1 and sox2 via the oct4/Sox2 complex in embryonic stem cells
-
Chew, J.L. et al. (2005) Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol. Cell. Biol., 25, 6031-6046.
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 6031-6046
-
-
Chew, J.L.1
-
13
-
-
84866325965
-
Sets2Networks: Network inference from repeated observations of sets
-
Clark, N.R. et al. (2012) Sets2Networks: network inference from repeated observations of sets. BMC Syst. Biol., 6, 89.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 89
-
-
Clark, N.R.1
-
14
-
-
0000153536
-
Distance to nearest neighbor as a measure of spatial relationships in populations
-
Clark, P.J. and Evans, F.C. (1954) Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology, 35, 445-453.
-
(1954)
Ecology
, vol.35
, pp. 445-453
-
-
Clark, P.J.1
Evans, F.C.2
-
15
-
-
75549084555
-
GeneSigDB a curated database of gene expression signatures
-
Culhane, A.C. et al. (2010) GeneSigDB a curated database of gene expression signatures. Nucleic Acids Res., 38, D716-D725.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Culhane, A.C.1
-
16
-
-
32144455205
-
PATIKAweb: A Web interface for analyzing biological pathways through advanced querying and visualization
-
DOI 10.1093/bioinformatics/bti776
-
Dogrusoz, U. et al. (2006) PATIKAweb: a web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics, 22, 374-375. (Pubitemid 43205392)
-
(2006)
Bioinformatics
, vol.22
, Issue.3
, pp. 374-375
-
-
Dogrusoz, U.1
Erson, E.Z.2
Giral, E.3
Demir, E.4
Babur, O.5
Cetintas, A.6
Colak, R.7
-
17
-
-
84880542781
-
Meta-signatures identify two major subtypes of breast cancer
-
Duan, Q. et al. (2013) Meta-signatures identify two major subtypes of breast cancer. CPT Pharmacometrics Syst. Pharmacol., 2, e35.
-
(2013)
CPT Pharmacometrics Syst. Pharmacol.
, vol.2
-
-
Duan, Q.1
-
18
-
-
28444449880
-
Graphviz open source graph drawing tools
-
Springer, Berlin Heidelberg
-
Ellson, J. et al. (2002) Graphviz open source graph drawing tools. In: Graph Drawing. Springer, Berlin Heidelberg, pp. 594-597.
-
(2002)
Graph Drawing
, pp. 594-597
-
-
Ellson, J.1
-
19
-
-
2942609149
-
VisANT: An online visualization and analysis tool for biological interaction data
-
Hu, Z. et al. (2004) VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics, 5, 17.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 17
-
-
Hu, Z.1
-
21
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
DOI 10.1073/pnas.061034498
-
Ito, T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574. (Pubitemid 32295017)
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.8
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
Sakaki, Y.6
-
22
-
-
33746773659
-
Dissecting self-renewal in stem cells with RNA interference
-
DOI 10.1038/nature04915, PII NATURE04915
-
Ivanova, N. et al. (2006) Dissecting self-renewal in stem cells with RNA interference. Nature, 442, 533-538. (Pubitemid 44167907)
-
(2006)
Nature
, vol.442
, Issue.7102
, pp. 533-538
-
-
Ivanova, N.1
Dobrin, R.2
Lu, R.3
Kotenko, I.4
Levorse, J.5
DeCoste, C.6
Schafer, X.7
Lun, Y.8
Lemischka, I.R.9
-
23
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong, H. et al. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
-
24
-
-
0038962938
-
-
Institut de Recherche Mathematique avancee, Universite Louis Pasteur et CNRS (URA 01)
-
Kassel, C. and Turaev, V. (1995) Chord diagram invariants of tangles and graphs. Institut de Recherche Mathematique avancee, Universite Louis Pasteur et CNRS (URA 01).
-
(1995)
Chord Diagram Invariants of Tangles and Graphs
-
-
Kassel, C.1
Turaev, V.2
-
25
-
-
70349687407
-
Direct reprogramming of human neural stem cells by OCT4
-
Kim, J.B. et al. (2009) Direct reprogramming of human neural stem cells by OCT4. Nature, 461, 649-653.
-
(2009)
Nature
, vol.461
, pp. 649-653
-
-
Kim, J.B.1
-
26
-
-
76149120425
-
A side effect resource to capture phenotypic effects of drugs
-
Kuhn, M. et al. (2010) A side effect resource to capture phenotypic effects of drugs. Mol. Syst. Biol., 6, 343.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 343
-
-
Kuhn, M.1
-
27
-
-
61449203001
-
KEA: Kinase enrichment analysis
-
Lachmann, A. and Ma'ayan, A. (2009) KEA: kinase enrichment analysis. Bioinformatics, 25, 684-686.
-
(2009)
Bioinformatics
, vol.25
, pp. 684-686
-
-
Lachmann, A.1
Ma'ayan, A.2
-
28
-
-
77957243164
-
ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
-
Lachmann, A. et al. (2010) ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics, 26, 2438-2444.
-
(2010)
Bioinformatics
, vol.26
, pp. 2438-2444
-
-
Lachmann, A.1
-
29
-
-
33749335282
-
The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease
-
DOI 10.1126/science.1132939
-
Lamb, J. et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science, 313, 1929-1935. (Pubitemid 44497995)
-
(2006)
Science
, vol.313
, Issue.5795
, pp. 1929-1935
-
-
Lamb, J.1
Crawford, E.D.2
Peck, D.3
Modell, J.W.4
Blat, I.C.5
Wrobel, M.J.6
Lerner, J.7
Brunet, J.-P.8
Subramanian, A.9
Ross, K.N.10
Reich, M.11
Hieronymus, H.12
Wei, G.13
Armstrong, S.A.14
Haggarty, S.J.15
Clemons, P.A.16
Wei, R.17
Carr, S.A.18
Lander, E.S.19
Golub, T.R.20
more..
-
30
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
DOI 10.1126/science.1099511
-
Lee, I. et al. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555-1558. (Pubitemid 39564951)
-
(2004)
Science
, vol.306
, Issue.5701
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
31
-
-
79958135926
-
Molecular signatures database (MSigDB) 3.0
-
Liberzon, A. et al. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
-
(2011)
Bioinformatics
, vol.27
, pp. 1739-1740
-
-
Liberzon, A.1
-
32
-
-
23644437498
-
Formation of regulatory patterns during signal propagation in a mammalian cellular network
-
DOI 10.1126/science.1108876
-
Ma'ayan, A. et al. (2005) Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science, 309, 1078-1083. (Pubitemid 41134466)
-
(2005)
Science
, vol.309
, Issue.5737
, pp. 1078-1083
-
-
Ma'ayan, A.1
Jenkins, S.L.2
Neves, S.3
Hasseldine, A.4
Grace, E.5
Dubin-Thaler, B.6
Eungdamrong, N.J.7
Weng, G.8
Ram, P.T.9
Rice, J.J.10
Kershenbaum, A.11
Stolovitzky, G.A.12
Blitzer, R.D.13
Iyengar, R.14
-
33
-
-
34250777249
-
Network analysis of FDA approved drugs and their targets
-
DOI 10.1002/msj.20002
-
Ma'ayan, A. et al. (2007) Network analysis of FDA approved drugs and their targets. Mt. Sinai J. Med., 74, 27-32. (Pubitemid 46957753)
-
(2007)
Mount Sinai Journal of Medicine
, vol.74
, Issue.1
, pp. 27-32
-
-
Ma'ayan, A.1
Jenkins, S.L.2
Goldfarb, J.3
Iyengar, R.4
-
34
-
-
70349445264
-
Systems biology of stem cell fate and cellular reprogramming
-
MacArthur, B.D. et al. (2009) Systems biology of stem cell fate and cellular reprogramming. Nat. Rev. Mol. Cell Biol., 10, 672-681.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 672-681
-
-
MacArthur, B.D.1
-
35
-
-
75249097584
-
GATE: Software for the analysis and visualization of high-dimensional time series expression data
-
MacArthur, B.D. et al. (2010) GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinformatics, 26, 143-144.
-
(2010)
Bioinformatics
, vol.26
, pp. 143-144
-
-
MacArthur, B.D.1
-
36
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
-
DOI 10.1093/bioinformatics/bti551
-
Maere, S. et al. (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
-
37
-
-
78649775562
-
Enrichment map: A network-based method for gene-set enrichment visualization and interpretation
-
Merico, D. et al. (2010) Enrichment Map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One, 5, e13984.
-
(2010)
PLoS One
, vol.5
-
-
Merico, D.1
-
38
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
DOI 10.1126/science.298.5594.824
-
Milo, R. et al. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824-827. (Pubitemid 35231534)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
39
-
-
0032919364
-
KEGG: Kyoto encyclopedia of genes and genomes
-
DOI 10.1093/nar/27.1.29
-
Ogata, H. et al. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34. (Pubitemid 29209394)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
40
-
-
84861859517
-
ENCODE whole-genome data in the UCSC genome browser: Update 2012
-
Rosenbloom, K.R. et al. (2012) ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res., 40, D912-D917.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Rosenbloom, K.R.1
-
41
-
-
84876543942
-
Regulon DB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Salgado, H. et al. (2013) Regulon DB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Salgado, H.1
-
42
-
-
0242490780
-
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
-
DOI 10.1101/gr.1239303
-
Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504. (Pubitemid 37428274)
-
(2003)
Genome Research
, vol.13
, Issue.11
, 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
-
43
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
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
-
-
Sherman, B.T.1
Lempicki, R.A.2
-
45
-
-
84982024645
-
Studies in statistical ecology: I. Spatial pattern
-
Skellam, J. (1952) Studies in statistical ecology: I. Spatial Pattern. Biometrika, 346-362.
-
(1952)
Biometrika
, pp. 346-362
-
-
Skellam, J.1
-
46
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
DOI 10.1073/pnas.0506580102
-
Subramanian, A. et al. (2005) Gene-set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550. (Pubitemid 41528093)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.43
, 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
Mesirov, J.P.11
-
47
-
-
84856805878
-
A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports
-
Tatonetti, N.P. et al. (2012) A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. J. Am. Med. Inform. Assoc., 19, 79-85.
-
(2012)
J. Am. Med. Inform. Assoc.
, vol.19
, pp. 79-85
-
-
Tatonetti, N.P.1
-
48
-
-
0032482432
-
The small world problem, collective dynamics of small-world networks
-
Watts, D. and Strogatz, S. (1998) The small world problem, collective dynamics of small-world networks. Nature, 393, 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.1
Strogatz, S.2
-
49
-
-
84861248544
-
Yfiles - Visualization and automatic layout of graphs
-
Springer, Berlin Heidelberg
-
Wiese, R., Eiglsperger, M. and Kaufmann, M. (2004) yfiles - visualization and automatic layout of graphs. In: Graph Drawing Software. Springer, Berlin Heidelberg, pp. 173-191.
-
(2004)
Graph Drawing Software
, pp. 173-191
-
-
Wiese, R.1
Eiglsperger, M.2
Kaufmann, M.3
-
50
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
Wishart, D.S. et al. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 34, D668-D672.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Wishart, D.S.1
|