-
1
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi, A., Oltvai, Z.: 'Network biology: understanding the cell's functional organization', Nat. Rev. Genet., 2004, 5, pp. 101-113
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabasi, A.1
Oltvai, Z.2
-
2
-
-
84889418078
-
Biomolecular networks: methods and applications in systems biology
-
(John Wiley & Sons, New York, 2009)
-
Chen, L., Wang, R.S., Zhang, X.S.: 'Biomolecular networks: methods and applications in systems biology' (John Wiley & Sons, New York, 2009)
-
-
-
Chen, L.1
Wang, R.S.2
Zhang, X.S.3
-
3
-
-
54049146919
-
Network evaluation from the consistency of the graph structure with the measured data
-
Saito, S., Aburatani, S., Horimoto, K.: 'Network evaluation from the consistency of the graph structure with the measured data', BMC Syst. Biol., 2008, 2, pp. 84
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 84
-
-
Saito, S.1
Aburatani, S.2
Horimoto, K.3
-
4
-
-
33750016109
-
Inferring gene regulatory networks from multiple microarray datasets
-
Wang, Y., Joshi, T., Zhang, X.S., Xu, D., Chen, L.: 'Inferring gene regulatory networks from multiple microarray datasets', Bioinformatics, 2006, 22, pp. 2413-2420
-
(2006)
Bioinformatics
, vol.22
, pp. 2413-2420
-
-
Wang, Y.1
Joshi, T.2
Zhang, X.S.3
Xu, D.4
Chen, L.5
-
5
-
-
84855160951
-
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
-
Zhang, X., Zhao, X., He, K., et al.: 'Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information', Bioinformatics, 2012, 28, pp. 98-104
-
(2012)
Bioinformatics
, vol.28
, pp. 98-104
-
-
Zhang, X.1
Zhao, X.2
He, K.3
-
6
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach, D., Prill, R.J., Schaffter, T., Mattiussi, C., Floreano, D., Stolovitzky, G.: 'Revealing strengths and weaknesses of methods for gene network inference'. Proc. Natl. Acad. Sci., 2010, vol. 107, pp. 6286-6291
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, pp. 6286-6291
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
Mattiussi, C.4
Floreano, D.5
Stolovitzky, G.6
-
7
-
-
0242574985
-
Reconciling gene expression data with known genome-scale regulatory network structures?
-
Herrgard, M.J., Covert, M.W., Palsson, B.O.: 'Reconciling gene expression data with known genome-scale regulatory network structures', Genome Res., 2003, 13, pp. 2423-2434
-
(2003)
Genome Res.
, vol.13
, pp. 2423-2434
-
-
Herrgard, M.J.1
Covert, M.W.2
Palsson, B.O.3
-
8
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa, M., Araki, M., Goto, S., et al.: 'KEGG for linking genomes to life and the environment', Nucleic Acids Res., 2008, 36, pp. D480-D484
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Kanehisa, M.1
Araki, M.2
Goto, S.3
-
9
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response.
-
Tusher, V.G., Tibshirani, R., Chu, G.: 'Significance analysis of microarrays applied to the ionizing radiation response'. Proc. Natl. Acad. Sci., 2001, vol. 98, pp. 5116-5621
-
(2001)
Proc. Natl. Acad. Sci
, vol.98
, pp. 5116-5621
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
10
-
-
14644430468
-
Calculating the statistical significance of changes in pathway activity from gene expression data
-
Rahnenfuhrer, J., Domingues, F.S., Maydt, J., Lengauer, T.: 'Calculating the statistical significance of changes in pathway activity from gene expression data', Stat. Appl. Genet. Mol. Biol., 2004, 3, p. 16
-
(2004)
Stat. Appl. Genet. Mol. Biol
, vol.3
, pp. 16
-
-
Rahnenfuhrer, J.1
Domingues, F.S.2
Maydt, J.3
Lengauer, T.4
-
11
-
-
14844332708
-
Pathway information for systems biology
-
Cary, M.P., Bader, G.D., Sander, C.: 'Pathway information for systems biology', FEBS Lett., 2005, 579, pp. 1815-1820
-
(2005)
FEBS Lett.
, vol.579
, pp. 1815-1820
-
-
Cary, M.P.1
Bader, G.D.2
Sander, C.3
-
12
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V.K., et al.: 'Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles'. Proc. Natl. Acad. Sci., 2005, vol. 102, pp. 15545-15550
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
-
13
-
-
35348890683
-
On testing the significance of sets of genes
-
Efron, B., Tibshirani, R.: 'On testing the significance of sets of genes', Ann. Appl. Stat., 2007, 1, pp. 107-129
-
(2007)
Ann. Appl. Stat.
, vol.1
, pp. 107-129
-
-
Efron, B.1
Tibshirani, R.2
-
14
-
-
26444608611
-
Discovering statistically significant pathways in expression profiling studies
-
Tian, L., Greenberg, S.A., Kong, S.W., Altschuler, J., Kohane, I.S., Park, P.J.: 'Discovering statistically significant pathways in expression profiling studies'. Proc. Natl. Acad. Sci., 2005, vol. 102, pp. 13544-13549
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 13544-13549
-
-
Tian, L.1
Greenberg, S.A.2
Kong, S.W.3
Altschuler, J.4
Kohane, I.S.5
Park, P.J.6
-
15
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca, A.L., Draghici, S., Khatri, P., et al.: 'A novel signaling pathway impact analysis', Bioinformatics, 2009, 25, pp. 75-82
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
Draghici, S.2
Khatri, P.3
-
16
-
-
34548400259
-
A systems biology approach for pathway level analysis
-
Draghici, S., Khatri, P., Tarca, A.L., et al.: 'A systems biology approach for pathway level analysis', Genome Res., 2007, 17, pp. 1537-1545
-
(2007)
Genome Res.
, vol.17
, pp. 1537-1545
-
-
Draghici, S.1
Khatri, P.2
Tarca, A.L.3
-
17
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman, N., Linial, M., Nachman, I., Péer, D.: 'Using Bayesian networks to analyze expression data', J. Comput. Biol., 2000, 7, pp. 601-620
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Péer, D.4
-
18
-
-
44349093750
-
Uncovering signal transduction networks from high-throughput data by integer linear programming
-
Zhao, X.M., Wang, R.S., Chen, L., Aihara, K.: 'Uncovering signal transduction networks from high-throughput data by integer linear programming', Nucleic Acids Res., 2008, 36, p. e48
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Zhao, X.M.1
Wang, R.S.2
Chen, L.3
Aihara, K.4
-
19
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A., Gerstein, M.: 'Genomic analysis of regulatory network dynamics reveals large topological changes', Nature, 2004, 431, pp. 308-312
-
(2004)
Nature
, vol.431
, 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
-
-
79959265839
-
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression
-
Zhou, H., Saito, S., Piao, G., et al.: 'Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression', BMC Syst. Biol., 2011, 5, (Suppl 1), pp. S16
-
(2011)
BMC Syst. Biol.
, vol.5
, Issue.SUPPL. 1
-
-
Zhou, H.1
Saito, S.2
Piao, G.3
-
21
-
-
36249019789
-
Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference
-
Stolovitzky, G., Monroe, D., Califano, A.: 'Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference', Ann. N. Y. Acad. Sci., 2007, 1115, pp. 11-22
-
(2007)
Ann. N. Y. Acad. Sci.
, vol.1115
, pp. 11-22
-
-
Stolovitzky, G.1
Monroe, D.2
Califano, A.3
-
22
-
-
33846064113
-
NCBI GEO: mining tens of millions of expression profiles-database and tools update
-
Barrett, T., Troup, D.B., Wilhite, S.E., et al.: 'NCBI GEO: mining tens of millions of expression profiles-database and tools update', Nucleic Acids Res., 2007, 35, pp. D760-D765
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
-
23
-
-
79959351684
-
Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action
-
Sukumaran, S., Jusko, W.J., Dubois, D.C., Almon, R.R.: 'Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action', J. Appl. Physiol., 2011, 110, pp. 1732-1747
-
(2011)
J. Appl. Physiol.
, vol.110
, pp. 1732-1747
-
-
Sukumaran, S.1
Jusko, W.J.2
Dubois, D.C.3
Almon, R.R.4
-
24
-
-
77958067872
-
Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology
-
Sukumaran, S., Xue, B., Jusko, W.J., DuBois, D.C., Almon, R.R.: 'Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology', Physiol. Genomics, 2010, 42A, pp. 141-152
-
(2010)
Physiol. Genomics
, vol.42 A
, pp. 141-152
-
-
Sukumaran, S.1
Xue, B.2
Jusko, W.J.3
DuBois, D.C.4
Almon, R.R.5
-
25
-
-
0036191190
-
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
-
Toh, H., Horimoto, K.: 'Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling', Bioinformatics, 2002, 18, pp. 287-297
-
(2002)
Bioinformatics
, vol.18
, pp. 287-297
-
-
Toh, H.1
Horimoto, K.2
-
26
-
-
13844253637
-
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
-
Beal, M.J., Falciani, F., Ghahramani, Z., Rangel, C., Wild, D.L.: 'A Bayesian approach to reconstructing genetic regulatory networks with hidden factors', Bioinformatics, 2005, 21, pp. 349-356
-
(2005)
Bioinformatics
, vol.21
, pp. 349-356
-
-
Beal, M.J.1
Falciani, F.2
Ghahramani, Z.3
Rangel, C.4
Wild, D.L.5
-
27
-
-
12744261506
-
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
-
Zou, M., Conzen, S.D.: 'A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data', Bioinformatics, 2005, 21, pp. 71-79
-
(2005)
Bioinformatics
, vol.21
, pp. 71-79
-
-
Zou, M.1
Conzen, S.D.2
-
28
-
-
69249154268
-
A network biology study on circadian rhythm by integrating various Omics data
-
Wang, Y., Zhang, X.S., Chen, L.: 'A network biology study on circadian rhythm by integrating various Omics data', OMICS, 2009, 13, pp. 313-324
-
(2009)
OMICS
, vol.13
, pp. 313-324
-
-
Wang, Y.1
Zhang, X.S.2
Chen, L.3
-
29
-
-
77956850355
-
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains
-
Liu, Z.P., Wang, Y., Zhang, X.S., Chen, L.: 'Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains', BMC Syst. Biol., 2010, 4, (Suppl 2), p. S11
-
(2010)
BMC Syst. Biol.
, vol.4
, Issue.SUPPL. 2
-
-
Liu, Z.P.1
Wang, Y.2
Zhang, X.S.3
Chen, L.4
-
30
-
-
84863128658
-
Identifying disease genes and module biomarkers with differential interactions
-
Liu, X., Liu, Z.P., Zhao, X., Chen, L.: 'Identifying disease genes and module biomarkers with differential interactions', J. Am. Med. Inform. Assoc., 2012, 19, pp. 241-248
-
(2012)
J. Am. Med. Inform. Assoc.
, vol.19
, pp. 241-248
-
-
Liu, X.1
Liu, Z.P.2
Zhao, X.3
Chen, L.4
-
31
-
-
84859741480
-
Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers
-
Chen, L., Liu, R., Liu, Z.P., Li, M., Aihara, K.: 'Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers', Sci. Rep., 2012, 2, p. 342
-
(2012)
Sci. Rep.
, vol.2
, pp. 342
-
-
Chen, L.1
Liu, R.2
Liu, Z.P.3
Li, M.4
Aihara, K.5
-
32
-
-
84861893428
-
Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma
-
He, D., Liu, Z.P., Honda, M., Kaneko, S., Chen, L.: 'Coexpression network analysis in chronic hepatitis B and C hepatic lesion reveals distinct patterns of disease progression to hepatocellular carcinoma', J. Mol. Cell. Biol., 2012, 4, pp. 140-152
-
(2012)
J. Mol. Cell. Biol.
, vol.4
, pp. 140-152
-
-
He, D.1
Liu, Z.P.2
Honda, M.3
Kaneko, S.4
Chen, L.5
|