-
1
-
-
7444253428
-
Systems biology and new technologies enable predictive and preventative medicine
-
Hood, L., Heath, J. R., Phelps, M. E. & Lin, B. Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640-643 (2004).
-
(2004)
Science
, vol.306
, pp. 640-643
-
-
Hood, L.1
Heath, J.R.2
Phelps, M.E.3
Lin, B.4
-
2
-
-
0035775725
-
A new approach to decoding life: Systems biology
-
Ideker, T., Galitski, T. & Hood, L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372 (2001).
-
(2001)
Annu. Rev. Genomics Hum. Genet.
, vol.2
, pp. 343-372
-
-
Ideker, T.1
Galitski, T.2
Hood, L.3
-
3
-
-
84864797353
-
Editorial: Systems biology and personalized medicine-The future is now
-
Auffray, C. & Hood, L. Editorial: Systems biology and personalized medicine-the future is now. Biotechnol. J. 7, 938-939 (2012).
-
(2012)
Biotechnol. J.
, vol.7
, pp. 938-939
-
-
Auffray, C.1
Hood, L.2
-
4
-
-
84855929701
-
Systems cancer medicine: Towards realization of predictive preventive personalized and participatory (P4) medicine
-
Tian, Q., Price, N. D. & Hood, L. Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J. Intern. Med. 271, 111-121 (2012).
-
(2012)
J. Intern. Med.
, vol.271
, pp. 111-121
-
-
Tian, Q.1
Price, N.D.2
Hood, L.3
-
5
-
-
84873513611
-
Eric Schadt
-
Interview by H. Craig Mak
-
Schadt, E. Eric Schadt. Interview by H. Craig Mak. Nature Biotech. 30, 769-770 (2012).
-
(2012)
Nature Biotech
, vol.30
, pp. 769-770
-
-
Schadt, E.1
-
6
-
-
33644527950
-
The model organism as a system: Integrating 'omics'data sets
-
Joyce, A. R. & Palsson, B. Ø. The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell. Biol. 7, 198-210 (2006).
-
(2006)
Nat. Rev. Mol. Cell. Biol.
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Ø, P.B.2
-
7
-
-
80054033219
-
Semantic Web may be cancer information's next step forward
-
Martin, M. Semantic Web may be cancer information's next step forward. J. Natl. Cancer Inst. 103, 1215-1218 (2011).
-
(2011)
J. Natl. Cancer Inst.
, vol.103
, pp. 1215-1218
-
-
Martin, M.1
-
8
-
-
78651330430
-
COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
-
Forbes, S. A. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945-D950 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Forbes, S.A.1
-
9
-
-
79961062492
-
Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer
-
Cheung, H. W. et al. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc. Natl Acad. Sci. USA 108, 12372-12377 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 12372-12377
-
-
Cheung, H.W.1
-
10
-
-
84855176021
-
Rewriting the mathematics of tumor growth
-
Martin, M. Rewriting the mathematics of tumor growth. J. Natl Cancer Inst. 103, 1564-1565 (2011).
-
(2011)
J. Natl Cancer Inst.
, vol.103
, pp. 1564-1565
-
-
Martin, M.1
-
11
-
-
57549098807
-
The Catalogue of Somatic Mutations in Cancer (COSMIC)
-
Chapter 10, Unit 10.11
-
Forbes, S. A. et al. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet. Chapter 10, Unit 10.11 (2008).
-
(2008)
Curr. Protoc. Hum. Genet.
-
-
Forbes, S.A.1
-
12
-
-
64749094310
-
The cancer genome
-
Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719-724 (2009).
-
(2009)
Nature
, vol.458
, pp. 719-724
-
-
Stratton, M.R.1
Campbell, P.J.2
Futreal, P.A.3
-
13
-
-
77951115122
-
International network of cancer genome projects
-
International Cancer Genome Consortium
-
International Cancer Genome Consortium. International network of cancer genome projects. Nature 464, 993-998 (2010). This is a description and the first results of the ICGC, a worldwide endeavour to characterize a wide range of tumours by next-generation sequencing.
-
(2010)
Nature
, vol.464
, pp. 993-998
-
-
-
14
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
The Cancer Genome Atlas Research Network
-
The Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genet. 45, 1113-1120 (2013).
-
(2013)
Nature Genet
, vol.45
, pp. 1113-1120
-
-
-
15
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
ENCODE Project Consortium
-
ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011). This is a genome-wide encyclopaedia of structural and regulatory elements in the genome.
-
(2011)
PLoS Biol.
, vol.9
-
-
-
16
-
-
84894341726
-
The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors
-
Quigley, D. A. et al. The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors. Mol. Oncol. 8, 273-284 (2013).
-
(2013)
Mol. Oncol.
, vol.8
, pp. 273-284
-
-
Quigley, D.A.1
-
17
-
-
84891925011
-
Master regulators of FGFR2 signalling and breast cancer risk
-
Fletcher, M. N. C. et al. Master regulators of FGFR2 signalling and breast cancer risk. Nature Commun. 4, 2464 (2013).
-
(2013)
Nature Commun.
, vol.4
, pp. 2464
-
-
Fletcher, M.N.C.1
-
18
-
-
79953034492
-
Epigenetics: Unravelling the cancer code
-
Brower, V. Epigenetics: Unravelling the cancer code. Nature 471, S12-13 (2011).
-
(2011)
Nature
, vol.471
-
-
Brower, V.1
-
19
-
-
79952395270
-
Cancer genomics: From discovery science to personalized medicine
-
Chin, L., Andersen, J. N. & Futreal, P. A. Cancer genomics: from discovery science to personalized medicine. Nature Med.17, 297-303 (2011).
-
(2011)
Nature Med.
, vol.17
, pp. 297-303
-
-
Chin, L.1
Andersen, J.N.2
Futreal, P.A.3
-
20
-
-
84868034841
-
Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
-
Yuan, Y. et al. Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. Sci. Transl. Med. 4, 157ra143-157ra143 (2012).
-
(2012)
Sci. Transl. Med.
, vol.4
, pp. 15743-15743
-
-
Yuan, Y.1
-
21
-
-
84867139157
-
Radiomics: The process and the challenges
-
Kumar, V. et al. Radiomics: the process and the challenges. Magn. Reson. Imaging 30, 1234-1248 (2012).
-
(2012)
Magn. Reson. Imaging
, vol.30
, pp. 1234-1248
-
-
Kumar, V.1
-
22
-
-
54349101605
-
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
-
Kilpinen, S. et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol. 9, R139 (2008).
-
(2008)
Genome Biol.
, vol.9
-
-
Kilpinen, S.1
-
23
-
-
84864455716
-
IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
-
Wong, A. K. et al. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40, W484-W490 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Wong, A.K.1
-
24
-
-
78649334862
-
Independent component analysis: Mining microarray data for fundamental human gene expression modules
-
Engreitz, J. M., Daigle, B. J., Marshall, J. J. & Altman, R. B. Independent component analysis: mining microarray data for fundamental human gene expression modules. J. Biomed. Inform. 43, 932-944 (2010).
-
(2010)
J. Biomed. Inform.
, vol.43
, pp. 932-944
-
-
Engreitz, J.M.1
Daigle, B.J.2
Marshall, J.J.3
Altman, R.B.4
-
25
-
-
82255164258
-
ProfileChaser: Searching microarray repositories based on genome-wide patterns of differential expression
-
Engreitz, J. M. et al. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression. Bioinformatics 27, 3317-3318 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 3317-3318
-
-
Engreitz, J.M.1
-
26
-
-
1642377561
-
ONCOMINE: A cancer microarray database and integrated data-mining platform
-
Rhodes, D. R. et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6, 1-6 (2004).
-
(2004)
Neoplasia
, vol.6
, pp. 1-6
-
-
Rhodes, D.R.1
-
27
-
-
61349128532
-
Rembrandt: Helping personalized medicine become a reality through integrative translational research
-
Madhavan, S. et al. Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol. Cancer Res. 7, 157-167 (2009).
-
(2009)
Mol. Cancer Res.
, vol.7
, pp. 157-167
-
-
Madhavan, S.1
-
28
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
-
(2004)
Genome Biol.
, vol.5
-
-
Gentleman, R.C.1
-
29
-
-
84869054051
-
A travel guide to Cytoscape plugins
-
Saito, R. et al. A travel guide to Cytoscape plugins. Nature Methods 9, 1069-1076 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 1069-1076
-
-
Saito, R.1
-
30
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline, M. S. et al. Integration of biological networks and gene expression data using Cytoscape. Nature Protocol. 2, 2366-2382 (2007).
-
(2007)
Nature Protocol.
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
-
31
-
-
77449141217
-
IntOGen: Integration and data mining of multidimensional oncogenomic data
-
Gundem, G. et al. IntOGen: integration and data mining of multidimensional oncogenomic data. Nature Methods 7, 92-93 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 92-93
-
-
Gundem, G.1
-
33
-
-
84877765675
-
Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer
-
Margolin, A. A. et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci. Transl. Med. 5, 181re1-181re1 (2013).
-
(2013)
Sci. Transl. Med.
, vol.5
, pp. 1811-1811
-
-
Margolin, A.A.1
-
34
-
-
77955868506
-
Computational solutions to large-scale data management and analysis
-
Schadt, E. E., Linderman, M. D., Sorenson, J., Lee, L. & Nolan, G. P. Computational solutions to large-scale data management and analysis. Nature Rev. Genet. 11, 647-657 (2010).
-
(2010)
Nature Rev. Genet.
, vol.11
, pp. 647-657
-
-
Schadt, E.E.1
Linderman, M.D.2
Sorenson, J.3
Lee, L.4
Nolan, G.P.5
-
35
-
-
68949216248
-
Systems genetics analysis of cancer susceptibility: From mouse models to humans
-
Quigley, D. & Balmain, A. Systems genetics analysis of cancer susceptibility: from mouse models to humans. Nature Rev. Genet. 10, 651-657 (2009).
-
(2009)
Nature Rev. Genet.
, vol.10
, pp. 651-657
-
-
Quigley, D.1
Balmain, A.2
-
36
-
-
84885645853
-
Transcriptome and genome sequencing uncovers functional variation in humans
-
Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
-
(2013)
Nature
, vol.501
, pp. 506-511
-
-
Lappalainen, T.1
-
37
-
-
33845191779
-
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
-
Chin, K. et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529-541 (2006).
-
(2006)
Cancer Cell
, vol.10
, pp. 529-541
-
-
Chin, K.1
-
38
-
-
73649112040
-
Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer
-
Lando, M. et al. Gene dosage, expression, and ontology analysis identifies driver genes in the carcinogenesis and chemoradioresistance of cervical cancer. PLoS Genet. 5, e1000719 (2009).
-
(2009)
PLoS Genet.
, vol.5
-
-
Lando, M.1
-
39
-
-
77249119762
-
The landscape of somatic copy-number alteration across human cancers
-
Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899-905 (2010).
-
(2010)
Nature
, vol.463
, pp. 899-905
-
-
Beroukhim, R.1
-
40
-
-
79952122331
-
Integrated analysis of gene expression,CpG island methylation, and gene copy number in breast cancer cells by deep sequencing
-
Sun, Z. et al. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS ONE 6, e17490 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Sun, Z.1
-
41
-
-
78751681684
-
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
-
Ovaska, K. et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med. 2, 65 (2010).
-
(2010)
Genome Med.
, vol.2
, pp. 65
-
-
Ovaska, K.1
-
42
-
-
84873859243
-
Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data
-
Aure, M. R. et al. Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data. PLoS ONE 8, e53014 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Aure, M.R.1
-
43
-
-
77954535843
-
Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity
-
Chibon, F. et al. Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity. Nature Med. 16, 781-787 (2010).
-
(2010)
Nature Med.
, vol.16
, pp. 781-787
-
-
Chibon, F.1
-
44
-
-
77953936121
-
An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer
-
Chari, R., Coe, B. P., Vucic, E. A., Lockwood, W. W. & Lam, W. L. An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Syst. Biol. 4, 67 (2010).
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 67
-
-
Chari, R.1
Coe, B.P.2
Vucic, E.A.3
Lockwood, W.W.4
Lam, W.L.5
-
45
-
-
79952606011
-
CNAmet: An R package for integrating copy number, methylation and expression data
-
Louhimo, R. & Hautaniemi, S. CNAmet: an R package for integrating copy number, methylation and expression data. Bioinformatics 27, 887-888 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 887-888
-
-
Louhimo, R.1
Hautaniemi, S.2
-
46
-
-
84863304598
-
-
R Core Team R Foundation for Statistical Computing, Vienna, Austria URL
-
R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org
-
(2013)
R: A Language and Environment for Statistical Computing
-
-
-
47
-
-
77949534211
-
Dynamically weighted clustering with noise set
-
Shen, Y., Sun, W. & Li, K.-C. Dynamically weighted clustering with noise set. Bioinformatics 26, 341-347 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 341-347
-
-
Shen, Y.1
Sun, W.2
Li, K.-C.3
-
48
-
-
84859992638
-
Integrative subtype discovery in glioblastoma using iCluster
-
Shen, R. et al. Integrative subtype discovery in glioblastoma using iCluster. PLoS ONE 7, e35236 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Shen, R.1
-
49
-
-
84861527388
-
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
-
Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346-352 (2012).
-
(2012)
Nature
, vol.486
, pp. 346-352
-
-
Curtis, C.1
-
50
-
-
80055083654
-
Patient-specific data fusion defines prognostic cancer subtypes
-
Yuan, Y., Savage, R. S. & Markowetz, F. Patient-specific data fusion defines prognostic cancer subtypes. PLoS Comput. Biol. 7, e1002227 (2011).
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Yuan, Y.1
Savage, R.S.2
Markowetz, F.3
-
51
-
-
34548565944
-
Predicting survival from microarray data-A comparative study
-
Bøvelstad, H. M. et al. Predicting survival from microarray data-a comparative study. Bioinformatics 23, 2080-2087 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 2080-2087
-
-
Bøvelstad, H.M.1
-
52
-
-
85194972808
-
Regression shrinkage and selection via the Lasso
-
Tibshirani, R. Regression shrinkage and selection via the Lasso. J. R. Statist. Soc. Series B. 58, 267-288 (1996).
-
(1996)
J. R. Statist. Soc. Series B.
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
53
-
-
80052701674
-
A fused lasso latent feature model for analyzing multi-sample aCGH data
-
Nowak, G., Hastie, T., Pollack, J. R. & Tibshirani, R. A fused lasso latent feature model for analyzing multi-sample aCGH data. Biostatistics 12, 776-791 (2011).
-
(2011)
Biostatistics
, vol.12
, pp. 776-791
-
-
Nowak, G.1
Hastie, T.2
Pollack, J.R.3
Tibshirani, R.4
-
54
-
-
80455125871
-
Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles
-
Mankoo, P. K., Shen, R., Schultz, N., Levine, D. A. & Sander, C. Time to recurrence and survival in serous ovarian tumors predicted from integrated genomic profiles. PLoS ONE 6, e24709 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Mankoo, P.K.1
Shen, R.2
Schultz, N.3
Levine, D.A.4
Sander, C.5
-
56
-
-
6944244084
-
A module map showing conditional activity of expression modules in cancer
-
Segal, E., Friedman, N., Koller, D. & Regev, A. A module map showing conditional activity of expression modules in cancer. Nature Genet. 36 1090-1098 (2004). This landmark publication establishes the principles of identification of regulatory modules.
-
(2004)
Nature Genet.
, vol.36
, pp. 1090-1098
-
-
Segal, E.1
Friedman, N.2
Koller, D.3
Regev, A.4
-
57
-
-
84862203775
-
WikiPathways: Building research communities on biological pathways
-
Kelder, T. et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 40, D1301-D1307 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Kelder, T.1
-
58
-
-
45549107329
-
Use and misuse of the gene ontology annotations
-
Rhee, S. Y., Wood, V., Dolinski, K. & Draghici, S. Use and misuse of the gene ontology annotations. Nature Rev. Genet. 9, 509-515 (2008).
-
(2008)
Nature Rev. Genet.
, vol.9
, pp. 509-515
-
-
Rhee, S.Y.1
Wood, V.2
Dolinski, K.3
Draghici, S.4
-
59
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genomewide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genomewide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
60
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: An integrated exact approach
-
Dittrich, M. T., Klau, G. W., Rosenwald, A., Dandekar, T. & Müller, T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24, i223-i231 (2008).
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Müller, T.5
-
61
-
-
77349088313
-
Detecting disease associated modules and prioritizing active genes based on high throughput data
-
Qiu, Y.-Q., Zhang, S., Zhang, X.-S. & Chen, L. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics 11, 26 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 26
-
-
Qiu, Y.-Q.1
Zhang, S.2
Zhang, X.-S.3
Chen, L.4
-
62
-
-
34548583420
-
Edge-based scoring and searching method for identifying condition-responsive proteinprotein interaction sub-network
-
Guo, Z. et al. Edge-based scoring and searching method for identifying condition-responsive proteinprotein interaction sub-network. Bioinformatics 23, 2121-2128 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 2121-2128
-
-
Guo, Z.1
-
63
-
-
84866873258
-
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression
-
Chuang, H.-Y. et al. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood 120, 2639-2649 (2012).
-
(2012)
Blood
, vol.120
, pp. 2639-2649
-
-
Chuang, H.-Y.1
-
64
-
-
0037263812
-
MAPPFinder: Using Gene Ontology and GenMAPP to create a global geneexpression profile from microarray data
-
Doniger, S. W. et al. MAPPFinder: using Gene Ontology and GenMAPP to create a global geneexpression profile from microarray data. Genome Biol. 4, R7 (2003).
-
(2003)
Genome Biol.
, vol.4
-
-
Doniger, S.W.1
-
65
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca, A. L. et al. A novel signaling pathway impact analysis. Bioinformatics 25, 75-82 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
-
66
-
-
37849022459
-
Identification of key processes underlying cancer phenotypes using biologic pathway analysis
-
Efroni, S., Schaefer, C. F. & Buetow, K. H. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS ONE 2, e425 (2007).
-
(2007)
PLoS ONE
, vol.2
-
-
Efroni, S.1
Schaefer, C.F.2
Buetow, K.H.3
-
67
-
-
84876261160
-
Pathway-based personalized analysis of cancer
-
Drier, Y., Sheffer, M. & Domany, E. Pathway-based personalized analysis of cancer. Proc. Natl Acad. Sci. USA 110, 6388-6393 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 6388-6393
-
-
Drier, Y.1
Sheffer, M.2
Domany, E.3
-
68
-
-
75849134576
-
Detailing regulatory networks through large scale data integration
-
Huttenhower, C. et al. Detailing regulatory networks through large scale data integration. Bioinformatics 25, 3267-3274 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 3267-3274
-
-
Huttenhower, C.1
-
69
-
-
66449120271
-
Exploring the human genome with functional maps
-
Huttenhower, C. et al. Exploring the human genome with functional maps. Genome Res. 19, 1093-1106 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1093-1106
-
-
Huttenhower, C.1
-
70
-
-
79953684044
-
Exploratory analysis of multiple omics datasets using the adjusted RV coefficient
-
Article 14
-
Mayer, C.-D., Lorent, J. & Horgan, G. W. Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Stat. Appl. Genet. Mol. Biol. 10, Article 14 (2011).
-
(2011)
Stat. Appl. Genet. Mol. Biol.
, vol.10
-
-
Mayer, C.-D.1
Lorent, J.2
Horgan, G.W.3
-
71
-
-
63649143888
-
Genetic architecture of mouse skin inflammation and tumour susceptibility
-
Quigley, D. A. et al. Genetic architecture of mouse skin inflammation and tumour susceptibility. Nature 458, 505-508 (2009).
-
(2009)
Nature
, vol.458
, pp. 505-508
-
-
Quigley, D.A.1
-
72
-
-
70350694448
-
IntegrOmics: An R package to unravel relationships between two omics datasets
-
Lê Cao, K.-A., González, I. & Déjean, S. integrOmics: an R package to unravel relationships between two omics datasets. Bioinformatics 25, 2855-2856 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2855-2856
-
-
Lê Cao, K.-A.1
González, I.2
Déjean, S.3
-
73
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
74
-
-
78149438375
-
Multivariate dependence and genetic networks inference
-
Margolin, A. A., Wang, K., Califano, A. & Nemenman, I. Multivariate dependence and genetic networks inference. IET Syst. Biol. 4, 428-440 (2010).
-
(2010)
IET Syst. Biol.
, vol.4
, pp. 428-440
-
-
Margolin, A.A.1
Wang, K.2
Califano, A.3
Nemenman, I.4
-
75
-
-
36248989626
-
Theory and limitations of genetic network inference from microarray data
-
Margolin, A. A. & Califano, A. Theory and limitations of genetic network inference from microarray data. Ann. NY Acad. Sci. 1115, 51-72 (2007).
-
(2007)
Ann. NY Acad. Sci.
, vol.1115
, pp. 51-72
-
-
Margolin, A.A.1
Califano, A.2
-
77
-
-
84864402194
-
Leveraging models of cell regulation and GWAS data in integrative network-based association studies
-
Califano, A., Butte, A. J., Friend, S., Ideker, T. & Schadt, E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genet. 44, 841-847 (2012).
-
(2012)
Nature Genet.
, vol.44
, pp. 841-847
-
-
Califano, A.1
Butte, A.J.2
Friend, S.3
Ideker, T.4
Schadt, E.5
-
78
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A. F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl. 1), S233-240 (2002).
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
79
-
-
13244253770
-
Graphbased iterative Group Analysis enhances microarray interpretation
-
Breitling, R., Amtmann, A. & Herzyk, P. Graphbased iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics 5, 100 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 100
-
-
Breitling, R.1
Amtmann, A.2
Herzyk, P.3
-
81
-
-
79951528449
-
Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data
-
Stingo, F. C. & Vannucci, M. Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data. Bioinformatics 27, 495-501 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 495-501
-
-
Stingo, F.C.1
Vannucci, M.2
-
82
-
-
77954376945
-
GOing Bayesian: Model-based gene set analysis of genomescale data
-
Bauer, S., Gagneur, J. & Robinson, P. N. GOing Bayesian: model-based gene set analysis of genomescale data. Nucleic Acids Res. 38, 3523-3532 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 3523-3532
-
-
Bauer, S.1
Gagneur, J.2
Robinson, P.N.3
-
83
-
-
84857757127
-
A modelbased analysis to infer the functional content of a gene list
-
Newton, M. A., He, Q. & Kendziorski, C. A modelbased analysis to infer the functional content of a gene list. Stat. Appl. Genet. Mol. Biol. 11, http://dx.doi. org/10.2202/1544-6115.1716 (2012).
-
(2012)
Stat. Appl. Genet. Mol. Biol.
, vol.11
-
-
Newton, M.A.1
He, Q.2
Kendziorski, C.3
-
84
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genet. 34, 166-176 (2003).
-
(2003)
Nature Genet.
, vol.34
, pp. 166-176
-
-
Segal, E.1
-
85
-
-
20044388557
-
From signatures to models: Understanding cancer using microarrays
-
Segal, E., Friedman, N., Kaminski, N., Regev, A. & Koller, D. From signatures to models: understanding cancer using microarrays. Nature Genet. 37 S38-S45 (2005).
-
(2005)
Nature Genet.
, vol.37
-
-
Segal, E.1
Friedman, N.2
Kaminski, N.3
Regev, A.4
Koller, D.5
-
86
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 26, i237-i245 (2010).
-
(2010)
Bioinformatics
, vol.26
-
-
Vaske, C.J.1
-
87
-
-
84857417363
-
Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling
-
Kristensen, V. N. et al. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc. Natl Acad. Sci. USA 109, 2802-2807 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 2802-2807
-
-
Kristensen, V.N.1
-
88
-
-
45549094777
-
Indirect genomic effects on survival from gene expression data
-
Ferkingstad, E., Frigessi, A. & Lyng, H. Indirect genomic effects on survival from gene expression data. Genome Biol. 9, R58 (2008).
-
(2008)
Genome Biol.
, vol.9
-
-
Ferkingstad, E.1
Frigessi, A.2
Lyng, H.3
-
89
-
-
3242875300
-
Combining microarrays and biological knowledge for estimating gene networks via bayesian networks
-
Imoto, S. et al. Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J. Bioinform. Comput. Biol. 2, 77-98 (2004).
-
(2004)
J. Bioinform. Comput. Biol.
, vol.2
, pp. 77-98
-
-
Imoto, S.1
-
90
-
-
83455198480
-
Bayesian detection of expression quantitative trait loci hot spots
-
Bottolo, L. et al. Bayesian detection of expression quantitative trait loci hot spots. Genetics 189, 1449-1459 (2011).
-
(2011)
Genetics
, vol.189
, pp. 1449-1459
-
-
Bottolo, L.1
-
91
-
-
78649976005
-
An integrated approach to uncover drivers of cancer
-
Akavia, U. D. et al. An integrated approach to uncover drivers of cancer. Cell 143, 1005-1017 (2010).
-
(2010)
Cell
, vol.143
, pp. 1005-1017
-
-
Akavia, U.D.1
-
92
-
-
36248988538
-
Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses
-
Birtwistle, M. R. et al. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol. Syst. Biol. 3, 144 (2007).
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 144
-
-
Birtwistle, M.R.1
-
93
-
-
84861550476
-
The life history of 21 breast cancers
-
Nik-Zainal, S. A. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
-
(2012)
Cell
, vol.149
, pp. 994-1007
-
-
Nik-Zainal, S.A.1
-
94
-
-
84862526929
-
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
-
Shah, S. P. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486, 395-399 (2012).
-
(2012)
Nature
, vol.486
, pp. 395-399
-
-
Shah, S.P.1
-
95
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
Cancer, Genome Atlas Research Network
-
Cancer, Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
-
(2008)
Nature
, vol.455
, pp. 1061-1068
-
-
-
96
-
-
84884997982
-
Emerging landscape of oncogenic signatures across human cancers
-
Ciriello, G. et al. Emerging landscape of oncogenic signatures across human cancers. Nature Genet. 45, 1127-1133 (2013).
-
(2013)
Nature Genet.
, vol.45
, pp. 1127-1133
-
-
Ciriello, G.1
-
97
-
-
84885008220
-
Pan-cancer patterns of somatic copy number alteration
-
Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nature Genet. 45, 1134-1140 (2013).
-
(2013)
Nature Genet.
, vol.45
, pp. 1134-1140
-
-
Zack, T.I.1
-
98
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Cancer Genome Atlas Research Network
-
Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genet. 45, 1113-1120 (2013).
-
(2013)
Nature Genet.
, vol.45
, pp. 1113-1120
-
-
-
99
-
-
42749100809
-
Fast algorithm for detecting community structure in networks
-
Newman, M. E. J. Fast algorithm for detecting community structure in networks. Phys. Rev. E Stat. Nonlin Soft Matter Phys. 69, 066133 (2004).
-
(2004)
Phys. Rev. e Stat. Nonlin Soft Matter Phys.
, vol.69
, pp. 066133
-
-
Newman, M.E.J.1
-
100
-
-
84859218110
-
Comparative analysis of algorithms for integration of copy number and expression data
-
Louhimo, R., Lepikhova, T., Monni, O. & Hautaniemi, S. Comparative analysis of algorithms for integration of copy number and expression data. Nature Methods 9, 351-355 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 351-355
-
-
Louhimo, R.1
Lepikhova, T.2
Monni, O.3
Hautaniemi, S.4
-
101
-
-
79956281142
-
Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer
-
Solvang, H. K., Lingjærde, O. C., Frigessi, A., Børresen-Dale, A.-L. & Kristensen, V. N. Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in breast cancer. BMC Bioinformatics 12, 197 (2011).
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 197
-
-
Solvang, H.K.1
Lingjærde, O.C.2
Frigessi, A.3
Børresen-Dale, A.-L.4
Kristensen, V.N.5
-
102
-
-
84863115693
-
Subtype and pathway specific responses to anticancer compounds in breast cancer
-
Heiser, L. M. et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc. Natl Acad. Sci. USA 109, 2724-2729 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 2724-2729
-
-
Heiser, L.M.1
-
103
-
-
84866368324
-
Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCa invasive signaling axis
-
Hoshino, D. et al. Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCa invasive signaling axis. Sci. Signal. 5, ra66 (2012).
-
(2012)
Sci. Signal.
, vol.5
-
-
Hoshino, D.1
-
104
-
-
81355151361
-
DNA-PK mediates AKT activation and apoptosis inhibition in clinically acquired platinum resistance
-
Stronach, E. A. et al. DNA-PK mediates AKT activation and apoptosis inhibition in clinically acquired platinum resistance. Neoplasia 13, 1069-1080 (2011).
-
(2011)
Neoplasia
, vol.13
, pp. 1069-1080
-
-
Stronach, E.A.1
-
105
-
-
69949162760
-
Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma
-
Mok, T. S. et al. Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. N. Engl. J. Med. 361, 947-957 (2009).
-
(2009)
N. Engl. J. Med.
, vol.361
, pp. 947-957
-
-
Mok, T.S.1
-
106
-
-
22044445517
-
Erlotinib in previously treated non-small-cell lung cancer
-
Shepherd, F. A. et al. Erlotinib in previously treated non-small-cell lung cancer. N. Engl. J. Med. 353, 123-132 (2005).
-
(2005)
N. Engl. J. Med.
, vol.353
, pp. 123-132
-
-
Shepherd, F.A.1
-
107
-
-
26844503270
-
Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer
-
Piccart-Gebhart, M. J. et al. Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N. Engl. J. Med. 353, 1659-1672 (2005).
-
(2005)
N. Engl. J. Med.
, vol.353
, pp. 1659-1672
-
-
Piccart-Gebhart, M.J.1
-
108
-
-
26844536978
-
Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer
-
Romond, E. H. et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N. Engl. J. Med. 353, 1673-1684 (2005).
-
(2005)
N. Engl. J. Med.
, vol.353
, pp. 1673-1684
-
-
Romond, E.H.1
-
109
-
-
79959795786
-
Improved survival with vemurafenib in melanoma with BRAF V600E mutation
-
Chapman, P. B. et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N. Engl. J. Med. 364, 2507-2516 (2011).
-
(2011)
N. Engl. J. Med.
, vol.364
, pp. 2507-2516
-
-
Chapman, P.B.1
-
110
-
-
36148941301
-
Cetuximab for the treatment of colorectal cancer
-
Jonker, D. J. et al. Cetuximab for the treatment of colorectal cancer. N. Engl. J. Med. 357, 2040-2048 (2007).
-
(2007)
N. Engl. J. Med.
, vol.357
, pp. 2040-2048
-
-
Jonker, D.J.1
-
111
-
-
54949085398
-
K-ras mutations and benefit from cetuximab in advanced colorectal cancer
-
Karapetis, C. S. et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N. Engl. J. Med. 359, 1757-1765 (2008).
-
(2008)
N. Engl. J. Med.
, vol.359
, pp. 1757-1765
-
-
Karapetis, C.S.1
-
112
-
-
77956274693
-
Identification of optimal drug combinations targeting cellular networks: Integrating phospho-proteomics and computational network analysis
-
Iadevaia, S., Lu, Y., Morales, F. C., Mills, G. B. & Ram, P. T. Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. Cancer Res. 70, 6704-6714 (2010).
-
(2010)
Cancer Res.
, vol.70
, pp. 6704-6714
-
-
Iadevaia, S.1
Lu, Y.2
Morales, F.C.3
Mills, G.B.4
Ram, P.T.5
-
113
-
-
0037137519
-
A gene-expression signature as a predictor of survival in breast cancer
-
van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999-2009 (2002).
-
(2002)
N. Engl. J. Med.
, vol.347
, pp. 1999-2009
-
-
Van De Vijver, M.J.1
-
114
-
-
19944422061
-
A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer
-
Paik, S. et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N. Engl. J. Med. 351, 2817-2826 (2004).
-
(2004)
N. Engl. J. Med.
, vol.351
, pp. 2817-2826
-
-
Paik, S.1
-
115
-
-
77955491294
-
Predicting protein structures with a multiplayer online game
-
Cooper, S. et al. Predicting protein structures with a multiplayer online game. Nature 466, 756-760 (2010).
-
(2010)
Nature
, vol.466
, pp. 756-760
-
-
Cooper, S.1
-
116
-
-
84874663959
-
A large-scale evaluation of computational protein function prediction
-
Radivojac, P. et al. A large-scale evaluation of computational protein function prediction. Nature Methods 10, 221-227 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 221-227
-
-
Radivojac, P.1
-
118
-
-
84877737214
-
Development of a prognostic model for breast cancer survival in an open challenge environment
-
Cheng, W.-Y., Ou Yang, T.-H. & Anastassiou, D. Development of a prognostic model for breast cancer survival in an open challenge environment. Sci. Transl. Med. 5, 181ra50-181ra50 (2013).
-
(2013)
Sci. Transl. Med.
, vol.5
, pp. 18150-18150
-
-
Cheng, W.-Y.1
Ou Yang, T.-H.2
Anastassiou, D.3
-
119
-
-
0034680102
-
Molecular portraits of human breast tumours
-
Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747-752 (2000).
-
(2000)
Nature
, vol.406
, pp. 747-752
-
-
Perou, C.M.1
-
120
-
-
0035845511
-
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
-
Sørlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869-10874 (2001).
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 10869-10874
-
-
Sørlie, T.1
-
121
-
-
0037478605
-
Repeated observation of breast tumor subtypes in independent gene expression data sets
-
Sørlie, T. et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA 100, 8418-8423 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 8418-8423
-
-
Sørlie, T.1
-
122
-
-
77955603605
-
Genomic architecture characterizes tumor progression paths and fate in breast cancer patients
-
Russnes, H. G. et al. Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci. Transl. Med. 2, 38ra47-38ra47 (2010).
-
(2010)
Sci. Transl. Med.
, vol.2
, pp. 3847-3847
-
-
Russnes, H.G.1
-
123
-
-
33947529520
-
Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers
-
Chin, S.-F. et al. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene 26, 1959-1970 (2007).
-
(2007)
Oncogene
, vol.26
, pp. 1959-1970
-
-
Chin, S.-F.1
-
124
-
-
84861576201
-
The landscape of cancer genes and mutational processes in breast cancer
-
Stephens, P. J. et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 486, 400-404 (2012).
-
(2012)
Nature
, vol.486
, pp. 400-404
-
-
Stephens, P.J.1
-
125
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas Research Network
-
Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
126
-
-
34547555607
-
Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer
-
Naume, B. et al. Presence of bone marrow micrometastasis is associated with different recurrence risk within molecular subtypes of breast cancer. Mol. Oncol. 1, 160-171 (2007).
-
(2007)
Mol. Oncol.
, vol.1
, pp. 160-171
-
-
Naume, B.1
-
127
-
-
45349092558
-
Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients
-
Nordgard, S. H. et al. Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients. Genes Chromosomes Cancer 47, 680-696 (2008).
-
(2008)
Genes Chromosomes Cancer
, vol.47
, pp. 680-696
-
-
Nordgard, S.H.1
-
128
-
-
78951491753
-
Methylation profiling with a panel of cancer related genes: Association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer
-
Rønneberg, J. A. et al. Methylation profiling with a panel of cancer related genes: association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol. Oncol. 5, 61-76 (2011).
-
(2011)
Mol. Oncol.
, vol.5
, pp. 61-76
-
-
Rønneberg, J.A.1
-
129
-
-
79952049614
-
MiRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors
-
Enerly, E. et al. miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS ONE 6, e16915 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Enerly, E.1
-
130
-
-
84869083240
-
Potential tumorigenic programs associated with TP53 mutation status reveal role of VEGF pathway
-
Joshi, H., Bhanot, G., Børresen-Dale, A.-L. & Kristensen, V. N. Potential tumorigenic programs associated with TP53 mutation status reveal role of VEGF pathway. Br. J. Cancer 107, 1722-1728 (2012).
-
(2012)
Br. J. Cancer
, vol.107
, pp. 1722-1728
-
-
Joshi, H.1
Bhanot, G.2
Børresen-Dale, A.-L.3
Kristensen, V.N.4
-
131
-
-
72949119310
-
Complex landscapes of somatic rearrangement in human breast cancer genomes
-
Stephens, P. J. et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462, 1005-1010 (2009).
-
(2009)
Nature
, vol.462
, pp. 1005-1010
-
-
Stephens, P.J.1
-
132
-
-
83455237886
-
Batch effect correction for genome-wide methylation data with Illumina Infinium platform
-
Sun, Z. et al. Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med. Genom. 4, 84 (2011).
-
(2011)
BMC Med. Genom.
, vol.4
, pp. 84
-
-
Sun, Z.1
-
133
-
-
0041965980
-
Cluster ensembles-A knowledge reuse framework for combining partitionings
-
Strehl, A. & Ghosh, J. Cluster ensembles-a knowledge reuse framework for combining partitionings. Journal of Machine Learning 3, 583-617 (2002).
-
(2002)
Journal of Machine Learning
, vol.3
, pp. 583-617
-
-
Strehl, A.1
Ghosh, J.2
-
134
-
-
0038724494
-
Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data
-
Monti, S., Tamayo, P., Mesirov, J. & Golub, T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learn. 52, 91-118 (2003).
-
(2003)
Machine Learn.
, vol.52
, pp. 91-118
-
-
Monti, S.1
Tamayo, P.2
Mesirov, J.3
Golub, T.4
-
135
-
-
79953756460
-
Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy
-
Collisson, E. A. et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nature Med. 17, 500-503 (2011).
-
(2011)
Nature Med.
, vol.17
, pp. 500-503
-
-
Collisson, E.A.1
-
136
-
-
84859762521
-
Consensus clustering in complex networks
-
Lancichinetti, A. & Fortunato, S. Consensus clustering in complex networks. Sci. Rep. 2, 336 (2012).
-
(2012)
Sci. Rep.
, vol.2
, pp. 336
-
-
Lancichinetti, A.1
Fortunato, S.2
-
137
-
-
74049111290
-
CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome
-
Lee, M. & Kim, Y. CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome. BMC Bioinformatics 10, 424 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 424
-
-
Lee, M.1
Kim, Y.2
-
138
-
-
70449331456
-
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
-
Shen, R., Olshen, A. B. & Ladanyi, M. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906-2912 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2906-2912
-
-
Shen, R.1
Olshen, A.B.2
Ladanyi, M.3
-
139
-
-
84876240418
-
PLRS: A flexible tool for the joint analysis of DNA copy number and mRNA expression data
-
Leday, G. G. R. & van de Wiel, M. A. PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data. Bioinformatics 29, 1081-1082 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 1081-1082
-
-
Leday, G.G.R.1
Van De Wiel, M.A.2
-
140
-
-
73149109513
-
Harnessing gene expression to identify the genetic basis of drug resistance
-
Chen, B.-J. et al. Harnessing gene expression to identify the genetic basis of drug resistance. Mol. Syst. Biol. 5, 310 (2009).
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 310
-
-
Chen, B.-J.1
-
141
-
-
84861490192
-
Sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes
-
Yuan, Y., Curtis, C., Caldas, C. & Markowetz, F. A. Sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes. IEEE/ACM Trans. Comput. Biol. Bioinform. 9, 947-954 (2012).
-
(2012)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.9
, pp. 947-954
-
-
Yuan, Y.1
Curtis, C.2
Caldas, C.3
Markowetz, F.A.4
-
142
-
-
75149195336
-
The transcriptional network for mesenchymal transformation of brain tumours
-
Carro, M. S. et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature 463, 318-325 (2010).
-
(2010)
Nature
, vol.463
, pp. 318-325
-
-
Carro, M.S.1
-
143
-
-
76649134465
-
Stromal genes discriminate preinvasive from invasive disease, predict outcome, and highlight inflammatory pathways in digestive cancers
-
Saadi, A. et al. Stromal genes discriminate preinvasive from invasive disease, predict outcome, and highlight inflammatory pathways in digestive cancers. Proc. Natl Acad. Sci. USA 107, 2177-2182 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 2177-2182
-
-
Saadi, A.1
-
144
-
-
3142712894
-
Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation
-
Hamatani, T. et al. Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc. Natl Acad. Sci. USA 101, 10326-10331 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 10326-10331
-
-
Hamatani, T.1
-
145
-
-
34548400259
-
A systems biology approach for pathway level analysis
-
Draghici, S. et al. A systems biology approach for pathway level analysis. Genome Res. 17, 1537-1545 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 1537-1545
-
-
Draghici, S.1
-
146
-
-
84867125364
-
Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
-
Engström, P. G. et al. Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival. Genome Med. 4, 76 (2012).
-
(2012)
Genome Med.
, vol.4
, pp. 76
-
-
Engström, P.G.1
-
147
-
-
33747868144
-
KOBAS server: A web-based platform for automated annotation and pathway identification
-
Wu, J., Mao, X., Cai, T., Luo, J. & Wei, L. KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res. 34, W720-W724 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Wu, J.1
Mao, X.2
Cai, T.3
Luo, J.4
Wei, L.5
-
148
-
-
79959986975
-
KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases
-
Xie, C. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316-W322 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Xie, C.1
-
149
-
-
71049148804
-
SubpathwayMiner: A software package for flexible identification of pathways
-
Li, C. et al. SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res. 37, e131-e131 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Li, C.1
-
150
-
-
84878802380
-
Comprehensive analysis of microRNAs in breast cancer
-
Chang, H.-T. et al. Comprehensive analysis of microRNAs in breast cancer. BMCGenomics 13, S18 (2012).
-
(2012)
BMCGenomics
, vol.13
-
-
Chang, H.-T.1
-
151
-
-
84873686922
-
Oncodrive-CIS: A method to reveal likely driver genes based on the impact of their copy number changes on expression
-
Tamborero, D., Lopez-Bigas, N. & Gonzalez-Perez, A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS ONE 8, e55489 (2013).
-
(2013)
PLoS ONE
, vol.8
-
-
Tamborero, D.1
Lopez-Bigas, N.2
Gonzalez-Perez, A.3
-
152
-
-
78649489546
-
ExprEssence-revealing the essence of differential experimental data in the context of an interaction/regulation net-work
-
Warsow, G. et al. ExprEssence-revealing the essence of differential experimental data in the context of an interaction/regulation net-work. BMC Syst. Biol. 4, 164 (2010).
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 164
-
-
Warsow, G.1
-
153
-
-
78651236629
-
A scalable approach for discovering conserved active subnetworks across species
-
Deshpande, R., Sharma, S., Verfaillie, C. M., Hu, W.-S. & Myers, C. L. A scalable approach for discovering conserved active subnetworks across species. PLoS Comput. Biol. 6, e1001028 (2010).
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Deshpande, R.1
Sharma, S.2
Verfaillie, C.M.3
Hu, W.-S.4
Myers, C.L.5
-
154
-
-
67849116896
-
PathExpress update: The enzyme neighbourhood method of associating gene-expression data with metabolic pathways
-
Goffard, N., Frickey, T. & Weiller, G. PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. Nucleic Acids Res. 37, W335-W339 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Goffard, N.1
Frickey, T.2
Weiller, G.3
-
155
-
-
84875288826
-
AMBIENT: Active Modules for Bipartite Networks-using high-throughput transcriptomic data to dissect metabolic response
-
Bryant, W. A., Sternberg, M. J. E. & Pinney, J. W. AMBIENT: Active Modules for Bipartite Networks-using high-throughput transcriptomic data to dissect metabolic response. BMC Syst. Biol. 7, 26 (2013).
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 26
-
-
Bryant, W.A.1
Sternberg, M.J.E.2
Pinney, J.W.3
-
156
-
-
84870796415
-
Bayesian correlated clustering to integrate multiple datasets
-
Kirk, P., Griffin, J. E., Savage, R. S., Ghahramani, Z. & Wild, D. L. Bayesian correlated clustering to integrate multiple datasets. Bioinformatics 28, 3290-3297 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 3290-3297
-
-
Kirk, P.1
Griffin, J.E.2
Savage, R.S.3
Ghahramani, Z.4
Wild, D.L.5
-
157
-
-
84898828598
-
Whole-genome integrative analysis reveals expression signatures predicting transformation in follicular lymphoma
-
Brodtkorb, M. et al. Whole-genome integrative analysis reveals expression signatures predicting transformation in follicular lymphoma. Blood, 123, 1051-1054 (2014).
-
(2014)
Blood
, vol.123
, pp. 1051-1054
-
-
Brodtkorb, M.1
|