-
1
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu, T., Miyano, S., and Kuhara, S. (1999). Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacif. Symp. Biocomput. 17-28
-
(1999)
Pacif. Symp. Biocomput
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
2
-
-
77957141016
-
Inferring the conservative causal core of gene regulatory networks
-
Altay, G., and Emmert-Streib, F. (2010a). Inferring the conservative causal core of gene regulatory networks. BMC Syst. Biol. 4:132. doi: 10.1186/1752-0509-4-132
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 132
-
-
Altay, G.1
Emmert-Streib, F.2
-
3
-
-
77954484005
-
Revealing differences in gene network inference algorithms on the network-level by ensemble methods
-
Altay, G., and Emmert-Streib, F. (2010b). Revealing differences in gene network inference algorithms on the network-level by ensemble methods. Bioinformatics 26, 1738-1744. doi: 10.1093/bioinformatics/btq259
-
(2010)
Bioinformatics
, vol.26
, pp. 1738-1744
-
-
Altay, G.1
Emmert-Streib, F.2
-
4
-
-
84921732095
-
tranSMART: an open source and community-driven informatics and data sharing platform for clinical and translational research
-
Athey, B. D., Braxenthaler, M., Haas, M., and Guo, Y. (2013). tranSMART: an open source and community-driven informatics and data sharing platform for clinical and translational research. AMIA Summ. Trans. Sci. Proc. 2013, 6-8
-
(2013)
AMIA Summ. Trans. Sci. Proc
, vol.2013
, pp. 6-8
-
-
Athey, B.D.1
Braxenthaler, M.2
Haas, M.3
Guo, Y.4
-
5
-
-
78650373804
-
Network medicine: a network-based approach to human disease
-
Barabáasi, A.-L., Gulbahce, N., and Loscalzo, J. (2011). Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12, 56-68. doi: 10.1038/nrg2918
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 56-68
-
-
Barabáasi, A.-L.1
Gulbahce, N.2
Loscalzo, J.3
-
6
-
-
16844376909
-
Reverse engineering of regulatory networks in human b cells
-
Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R., and Califano, A. (2005). Reverse engineering of regulatory networks in human b cells. Nat. Genet. 37, 382-390. doi: 10.1038/ng1532
-
(2005)
Nat. Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
7
-
-
82155202989
-
Gene expression and network-based analysis reveals a novel role for hsa-mir-9 and drug control over the p38 network in glioblastoma multiforme progression
-
Ben-Hamo, R., and Efroni, S. (2011). Gene expression and network-based analysis reveals a novel role for hsa-mir-9 and drug control over the p38 network in glioblastoma multiforme progression. Genome Med. 3:77. doi: 10.1186/gm293
-
(2011)
Genome Med
, vol.3
, pp. 77
-
-
Ben-Hamo, R.1
Efroni, S.2
-
8
-
-
0030211964
-
Bagging predictors
-
Breiman, L. (1996). Bagging predictors. Mach. Learn. 24, 123-140. doi: 10.1007/BF00058655
-
(1996)
Mach. Learn
, vol.24
, pp. 123-140
-
-
Breiman, L.1
-
9
-
-
0035478854
-
Random forests
-
Breiman, L. (2001). Random forests. Mach. Learn. 45, 5-32. doi: 10.1023/A:1010933404324
-
(2001)
Mach. Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
10
-
-
18744376914
-
Online predicted human interaction database
-
Brown, K. R., and Jurisica, I. (2005). Online predicted human interaction database. Bioinformatics 21, 2076-2082. doi: 10.1093/bioinformatics/bti273
-
(2005)
Bioinformatics
, vol.21
, pp. 2076-2082
-
-
Brown, K.R.1
Jurisica, I.2
-
11
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker, H. J., Li, H., and Siggia, E. D. (2001). Regulatory element detection using correlation with expression. Nat. Genet. 27, 167-171. doi: 10.1038/84792
-
(2001)
Nat. Genet
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
12
-
-
0033655775
-
Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
-
Butte, A., and Kohane, I. (2000). Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements. Pacif. Symp. Biocomput. 5, 415-426
-
(2000)
Pacif. Symp. Biocomput
, vol.5
, pp. 415-426
-
-
Butte, A.1
Kohane, I.2
-
13
-
-
0034710924
-
Discovering functional relationships between rna expression and chemotherapeutic susceptibility using relevance networks
-
Butte, A., Tamayo, P., Slonim, D., Golub, T., and Kohane, I. (2000). Discovering functional relationships between rna expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl. Acad. Sci. U.S.A. 97, 12182-12186. doi: 10.1073/pnas.220392197
-
(2000)
Proc. Natl. Acad. Sci. U.S.A
, vol.97
, pp. 12182-12186
-
-
Butte, A.1
Tamayo, P.2
Slonim, D.3
Golub, T.4
Kohane, I.5
-
14
-
-
80052724921
-
Personalized medicine: progress and promise
-
Chan, I. S., and Ginsburg, G. S. (2011). Personalized medicine: progress and promise. Ann. Rev. Genom. Hum. Genet. 12, 217-244. doi: 10.1146/annurev-genom-082410-101446
-
(2011)
Ann. Rev. Genom. Hum. Genet
, vol.12
, pp. 217-244
-
-
Chan, I.S.1
Ginsburg, G.S.2
-
15
-
-
80053918061
-
Identifying cancer biomarkers by network-constrained support vector machines
-
Chen, L., Xuan, J., Riggins, R. B., Clarke, R., and Wang, Y. (2011). Identifying cancer biomarkers by network-constrained support vector machines. BMC Syst. Biol. 5:161. doi: 10.1186/1752-0509-5-161
-
(2011)
BMC Syst. Biol
, vol.5
, pp. 161
-
-
Chen, L.1
Xuan, J.2
Riggins, R.B.3
Clarke, R.4
Wang, Y.5
-
16
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang, H.-Y., Lee, E., Liu, Y.-T., Lee, D., and Ideker, T. (2007). Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 3, 140. doi: 10.1038/msb4100180
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 140
-
-
Chuang, H.-Y.1
Lee, E.2
Liu, Y.-T.3
Lee, D.4
Ideker, T.5
-
17
-
-
34248165422
-
Comparing large graphs efficiently by margins of feature vectors
-
Dehmer, M., and Emmert-Streib, F. (2007). Comparing large graphs efficiently by margins of feature vectors. Appl. Math. Comput. 188, 1699-1710. doi: 10.1016/j.amc.2006.11.185
-
(2007)
Appl. Math. Comput
, vol.188
, pp. 1699-1710
-
-
Dehmer, M.1
Emmert-Streib, F.2
-
18
-
-
84884974800
-
An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants
-
Dehmer, M., Grabner, M., Mowshowitz, A., and Emmert-Streib, F. (2013c). An efficient heuristic approach to detecting graph isomorphism based on combinations of highly discriminating invariants. Adv. Comput. Math. 39, 311-325. doi: 10.1007/s10444-012-9281-0
-
(2013)
Adv. Comput. Math
, vol.39
, pp. 311-325
-
-
Dehmer, M.1
Grabner, M.2
Mowshowitz, A.3
Emmert-Streib, F.4
-
19
-
-
49849085811
-
A new method of measuring similarity for a special class of directed graphs
-
Dehmer, M., and Mehler, A. (2007). A new method of measuring similarity for a special class of directed graphs. Tatra Mount. Math. Public. 36, 39-59
-
(2007)
Tatra Mount. Math. Public
, vol.36
, pp. 39-59
-
-
Dehmer, M.1
Mehler, A.2
-
20
-
-
84893547080
-
Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers
-
Dehmer, M., Mueller, L., and Emmert-Streib, F. (2013b). Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PLoS ONE 8:e77602. doi: 10.1371/journal.pone.0077602
-
(2013)
PLoS ONE
, vol.8
-
-
Dehmer, M.1
Mueller, L.2
Emmert-Streib, F.3
-
21
-
-
84893547080
-
Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers
-
Dehmer, M., Mueller, L. A. J., and Emmert-Streib, F. (2013a). Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PLoS ONE 8:e77602. doi: 10.1371/journal.pone.0077602
-
(2013)
PLoS ONE
, vol.8
-
-
Dehmer, M.1
Mueller, L.A.J.2
Emmert-Streib, F.3
-
22
-
-
84877302557
-
Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information
-
de Matos Simoes, R., Dehmer, M., and Emmert-Streib, F. (2013a). Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information. BMC Genomics 14:324. doi: 10.1186/1471-2164-14-324
-
(2013)
BMC Genomics
, vol.14
, pp. 324
-
-
de Matos Simoes, R.1
Dehmer, M.2
Emmert-Streib, F.3
-
23
-
-
84892411193
-
B-cell lymphoma gene regulatory networks: biological consistency among inference methods
-
de Matos Simoes, R., Dehmer, M., and Emmert-Streib, F. (2013b). B-cell lymphoma gene regulatory networks: biological consistency among inference methods. Front. Genet. 4:281. doi: 10.3389/fgene.2013.00281
-
(2013)
Front. Genet
, vol.4
, pp. 281
-
-
de Matos Simoes, R.1
Dehmer, M.2
Emmert-Streib, F.3
-
24
-
-
84859125037
-
Bagging statistical network inference from large-scale gene expression data
-
de Matos Simoes, R., and Emmert-Streib, F. (2012). Bagging statistical network inference from large-scale gene expression data. PLoS ONE 7:e33624. doi: 10.1371/journal.pone.0033624
-
(2012)
PLoS ONE
, vol.7
-
-
de Matos Simoes, R.1
Emmert-Streib, F.2
-
25
-
-
77954479475
-
Local network-based measures to assess the inferability of different regulatory networks
-
Emmert-Streib, F., and Altay, G. (2010). Local network-based measures to assess the inferability of different regulatory networks. IET Syst. Biol. 4, 277-288. doi: 10.1049/iet-syb.2010.0028
-
(2010)
IET Syst. Biol
, vol.4
, pp. 277-288
-
-
Emmert-Streib, F.1
Altay, G.2
-
26
-
-
84897675326
-
The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks
-
Emmert-Streib, F., de Matos Simoes, R., Mullan, P., Haibe-Kains, B., and Dehmer, M. (2014). The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks. Front. Genet. 5:15. doi: 10.3389/fgene.2014.00015
-
(2014)
Front. Genet
, vol.5
, pp. 15
-
-
Emmert-Streib, F.1
de Matos Simoes, R.2
Mullan, P.3
Haibe-Kains, B.4
Dehmer, M.5
-
27
-
-
79958145357
-
Network biology: a direct approach to study biological function
-
Emmert-Streib, F., and Glazko, G. (2011). Network biology: a direct approach to study biological function. Wiley Interdiscip. Rev. Syst. Biol. Med. 3, 379-391. doi: 10.1002/wsbm.134
-
(2011)
Wiley Interdiscip. Rev. Syst. Biol. Med
, vol.3
, pp. 379-391
-
-
Emmert-Streib, F.1
Glazko, G.2
-
28
-
-
84859112389
-
Statistical inference and reverse engineering of gene regulatory networks from observational expression data
-
Emmert-Streib, F., Glazko, G., Altay, G., and de Matos Simoes, R. (2012). Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front. Genet. 3:8. doi: 10.3389/fgene.2012.00008
-
(2012)
Front. Genet
, vol.3
, pp. 8
-
-
Emmert-Streib, F.1
Glazko, G.2
Altay, G.3
de Matos Simoes, R.4
-
29
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., et al. (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5:e8. doi: 10.1371/journal.pbio.0050008
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
-
30
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman, N. (2004). Inferring cellular networks using probabilistic graphical models. Science 303, 799-805. doi: 10.1126/science.1094068
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
31
-
-
54949105871
-
Analyzing gene perturbation screens with nested effects models in R and bioconductor
-
Frohlich, H., Beissbarth, T., Tresch, A., Kostka, D., Jacob, J., Spang, R., et al. (2008). Analyzing gene perturbation screens with nested effects models in R and bioconductor. Bioinformatics 24, 2549-2550. doi: 10.1093/bioinformatics/btn446
-
(2008)
Bioinformatics
, vol.24
, pp. 2549-2550
-
-
Frohlich, H.1
Beissbarth, T.2
Tresch, A.3
Kostka, D.4
Jacob, J.5
Spang, R.6
-
32
-
-
84876566428
-
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
-
Fortney, K., Xie, W., Kotlyar, M., Griesman, J., Kotseruba, Y., and Jurisica, I. (2013). NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. Nucleic Acids Res. 41, D720-D727. doi: 10.1093/nar/gks1106
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D720-D727
-
-
Fortney, K.1
Xie, W.2
Kotlyar, M.3
Griesman, J.4
Kotseruba, Y.5
Jurisica, I.6
-
33
-
-
84861647487
-
Network medicine in drug design: implications for neuroinflammation
-
Ghosh, S., and Basu, A. (2012). Network medicine in drug design: implications for neuroinflammation. Drug Discov. Today 17, 600-607. doi: 10.1016/j.drudis.2012.01.018
-
(2012)
Drug Discov. Today
, vol.17
, pp. 600-607
-
-
Ghosh, S.1
Basu, A.2
-
34
-
-
84866931187
-
Tissue-specific functional networks for prioritizing phenotype and disease genes
-
Guan, Y., Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. A., et al. (2012). Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput. Biol. 8:e1002694. doi: 10.1371/journal.pcbi.1002694
-
(2012)
PLoS Comput. Biol
, vol.8
-
-
Guan, Y.1
Gorenshteyn, D.2
Burmeister, M.3
Wong, A.K.4
Schimenti, J.C.5
Handel, M.A.6
-
35
-
-
84862197985
-
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
-
Haibe-Kains, B., Olsen, C., Djebbari, A., Bontempi, G., Correll, M., Bouton, C., et al. (2012). Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res. 40, D866-D875. doi: 10.1093/nar/gkr1050
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D866-D875
-
-
Haibe-Kains, B.1
Olsen, C.2
Djebbari, A.3
Bontempi, G.4
Correll, M.5
Bouton, C.6
-
36
-
-
79952284127
-
Hallmarks of cancer: the next generation
-
Hanahan, D., and Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. Cell 144, 646-674. doi: 10.1016/j.cell.2011.02.013
-
(2011)
Cell
, vol.144
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.A.2
-
37
-
-
61349180117
-
Gene regulatory network inference: data integration in dynamic models-A review
-
Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., and Guthke, R. (2009). Gene regulatory network inference: data integration in dynamic models-A review. Biosystems 96, 86-103. doi: 10.1016/j.biosystems.2008.12.004
-
(2009)
Biosystems
, vol.96
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Toepfer, S.3
van Someren, E.4
Guthke, R.5
-
38
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., and Geurts, P. (2010). Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5:e12776. doi: 10.1371/journal.pone.0012776
-
(2010)
PLoS ONE
, vol.5
-
-
Huynh-Thu, V.A.1
Irrthum, A.2
Wehenkel, L.3
Geurts, P.4
-
39
-
-
84856094560
-
Differential network biology
-
Ideker, T., and Krogan, N. J. (2012). Differential network biology. Mol. Syst. Biol. 8, 565. doi: 10.1038/msb.2011.99
-
(2012)
Mol. Syst. Biol
, vol.8
, pp. 565
-
-
Ideker, T.1
Krogan, N.J.2
-
40
-
-
85032068327
-
Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks
-
Islam, M., Hoque, M., Banik, R., Roy, S., Sumi, S., Hassan, F. M., et al. (2013). Comparative analysis of differential network modularity in tissue specific normal and cancer protein interaction networks. J. Clin. Bioinform. 3:19. doi: 10.1186/2043-9113-3-19
-
(2013)
J. Clin. Bioinform
, vol.3
, pp. 19
-
-
Islam, M.1
Hoque, M.2
Banik, R.3
Roy, S.4
Sumi, S.5
Hassan, F.M.6
-
41
-
-
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. doi: 10.1093/nar/28.1.27
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
42
-
-
33749335282
-
The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease
-
Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., et al. (2006). The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313, 1929-1935. doi: 10.1126/science.1132939
-
(2006)
Science
, vol.313
, 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
-
43
-
-
67449095889
-
Computational methods for discovering gene networks from expression data
-
Lee, W. P., and Tzou, W. S. (2009). Computational methods for discovering gene networks from expression data. Brief. Bioinform. 10, 408-423. doi: 10.1093/bib/bbp028
-
(2009)
Brief. Bioinform
, vol.10
, pp. 408-423
-
-
Lee, W.P.1
Tzou, W.S.2
-
44
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang, S., Fuhrman, S., and Somogyi, R. (1998). Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. 1998, 18-29
-
(1998)
Pac. Symp. Biocomput
, vol.1998
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
45
-
-
58149349958
-
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
-
Luo, W., Hankenson, K., and Woolf, P. (2008). Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics 9:467. doi: 10.1186/1471-2105-9-467
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 467
-
-
Luo, W.1
Hankenson, K.2
Woolf, P.3
-
46
-
-
84860280305
-
Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets
-
Madhamshettiwar, P., Maetschke, S., Davis, M., Reverter, A., and Ragan, M. (2012). Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Med. 4:41. doi: 10.1186/gm340
-
(2012)
Genome Med
, vol.4
, pp. 41
-
-
Madhamshettiwar, P.1
Maetschke, S.2
Davis, M.3
Reverter, A.4
Ragan, M.5
-
47
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach, D., Costello, J. C., KUffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., et al. (2012). Wisdom of crowds for robust gene network inference. Nat. Methods 9, 796-804. doi: 10.1038/nmeth.2016
-
(2012)
Nat. Methods
, vol.9
, pp. 796-804
-
-
Marbach, D.1
Costello, J.C.2
Kuffner, R.3
Vega, N.M.4
Prill, R.J.5
Camacho, D.M.6
-
48
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Dalla Favera, R., et al. (2006). ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl. 1):S7. doi: 10.1186/1471-2105-7-S1-S7
-
(2006)
BMC Bioinformatics
, vol.7
, pp. S7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
-
49
-
-
38449088751
-
Inferring cellular networks D a review
-
Markowetz, F., and Spang, R. (2007). Inferring cellular networks D a review. BMC Bioinformatics 8(Suppl. 6):S5. doi: 10.1186/1471-2105-8-S6-S5
-
(2007)
BMC Bioinformatics
, vol.8
, pp. S5
-
-
Markowetz, F.1
Spang, R.2
-
50
-
-
59949086432
-
minet: a R/Bioconductor package for inferring large transcriptional networks using mutual information
-
Meyer, P., Lafitte, F., and Bontempi, G. (2008). minet: a R/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics 9:461. doi: 10.1186/1471-2105-9-461
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 461
-
-
Meyer, P.1
Lafitte, F.2
Bontempi, G.3
-
51
-
-
78650490181
-
Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in pseudomonas
-
Mithani, A., Hein, J., and Preston, G. M. (2011). Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in pseudomonas. Mol. Biol. Evol. 28, 483-499. doi: 10.1093/molbev/msq213
-
(2011)
Mol. Biol. Evol
, vol.28
, pp. 483-499
-
-
Mithani, A.1
Hein, J.2
Preston, G.M.3
-
52
-
-
47549107689
-
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
-
Mostafavi, S., Ray, D., Warde-Farley, D., Grouios, C., and Morris, Q. (2008). GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 9(Suppl. 1)S4. doi: 10.1186/gb-2008-9-s1-s4
-
(2008)
Genome Biol
, vol.9
, pp. S4
-
-
Mostafavi, S.1
Ray, D.2
Warde-Farley, D.3
Grouios, C.4
Morris, Q.5
-
53
-
-
84902160817
-
Inference and validation of predictive gene networks from biomedical literature and gene expression data
-
Olsen, C., Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., et al. (2014). Inference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics 103, 329-336. doi: 10.1016/j.ygeno.2014.03.004
-
(2014)
Genomics
, vol.103
, pp. 329-336
-
-
Olsen, C.1
Fleming, K.2
Prendergast, N.3
Rubio, R.4
Emmert-Streib, F.5
Bontempi, G.6
-
54
-
-
84857402984
-
A novel framework for the comparative analysis of biological networks
-
Pache, R. A., and Aloy, P. (2012). A novel framework for the comparative analysis of biological networks. PLoS ONE 7:e31220. doi: 10.1371/journal.pone.0031220
-
(2012)
PLoS ONE
, vol.7
-
-
Pache, R.A.1
Aloy, P.2
-
55
-
-
33846672214
-
Biological network comparison using graphlet degree distribution
-
Przulj, N. (2007). Biological network comparison using graphlet degree distribution. Bioinformatics 23, e177-e183. doi: 10.1093/bioinformatics/btl301
-
(2007)
Bioinformatics
, vol.23
, pp. e177-e183
-
-
Przulj, N.1
-
56
-
-
84864285545
-
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins
-
Rozenblatt-Rosen, O., Deo, R. C., Padi, M., Adelmant, G., Calderwood, M. A., Rolland, T., et al. (2012). Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 487, 491-495. doi: 10.1038/nature11288
-
(2012)
Nature
, vol.487
, pp. 491-495
-
-
Rozenblatt-Rosen, O.1
Deo, R.C.2
Padi, M.3
Adelmant, G.4
Calderwood, M.A.5
Rolland, T.6
-
57
-
-
70249134919
-
Molecular networks as sensors and drivers of common human diseases
-
Schadt, E. (2009). Molecular networks as sensors and drivers of common human diseases. Nature 461, 218-223. doi: 10.1038/nature08454
-
(2009)
Nature
, vol.461
, pp. 218-223
-
-
Schadt, E.1
-
58
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan, R., and Ideker, T. (2006). Modeling cellular machinery through biological network comparison. Nat. Biotechnol. 24, 427-433. doi: 10.1038/nbt1196
-
(2006)
Nat. Biotechnol
, vol.24
, pp. 427-433
-
-
Sharan, R.1
Ideker, T.2
-
59
-
-
72249103485
-
A physical and regulatory map of Host-Influenza interactions reveals pathways in H1N1 infection
-
Shapira, S. D., Gat-Viks, I., Shum, B. O. V., Dricot, A., Grace, M. M. D., Wu, L., et al. (2009). A physical and regulatory map of Host-Influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255-1267. doi: 10.1016/j.cell.2009.12.018
-
(2009)
Cell
, vol.139
, pp. 1255-1267
-
-
Shapira, S.D.1
Gat-Viks, I.2
Shum, B.O.V.3
Dricot, A.4
Grace, M.M.D.5
Wu, L.6
-
60
-
-
84895923109
-
Recent advances in modeling languages for pathway maps and computable biological networks
-
Slater, T. (2014). Recent advances in modeling languages for pathway maps and computable biological networks. Drug Disco. Today 19, 193-198. doi: 10.1016/j.drudis.2013.12.011
-
(2014)
Drug Disco. Today
, vol.19
, pp. 193-198
-
-
Slater, T.1
-
61
-
-
84860478431
-
A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer
-
Staiger, C., Cadot, S., Kooter, R., Dittrich, M., Müller, T., Klau, G. W., et al. (2012). A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PLoS ONE 7:e34796. doi: 10.1371/journal.pone.0034796
-
(2012)
PLoS ONE
, vol.7
-
-
Staiger, C.1
Cadot, S.2
Kooter, R.3
Dittrich, M.4
Müller, T.5
Klau, G.W.6
-
62
-
-
63849210631
-
Lessons from the DREAM 2 challenges
-
Stolovitzky, G., Prill, R., and Califano, A. (2009). Lessons from the DREAM 2 challenges. Ann. N.Y. Acad. Sci. 1158, 159-195. doi: 10.1111/j.1749-6632.2009.04497.x
-
(2009)
Ann. N.Y. Acad. Sci
, vol.1158
, pp. 159-195
-
-
Stolovitzky, G.1
Prill, R.2
Califano, A.3
-
63
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
Werhli, A., Grzegorczyk, M., and Husmeier, D. (2006). Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 22, 2523-2531. doi: 10.1093/bioinformatics/btl391
-
(2006)
Bioinformatics
, vol.22
, pp. 2523-2531
-
-
Werhli, A.1
Grzegorczyk, M.2
Husmeier, D.3
-
64
-
-
22044448669
-
Sparse graphical gaussian modeling of the isoprenoid gene network in arabidopsis thaliana
-
Wille, A., Zimmermann, P., Vranova, E., Furholz, A., Laule, O., Bleuler, S., et al. (2004). Sparse graphical gaussian modeling of the isoprenoid gene network in arabidopsis thaliana. Genome Biol. 5:R92. doi: 10.1186/gb-2004-5-11-r92
-
(2004)
Genome Biol
, vol.5
, pp. R92
-
-
Wille, A.1
Zimmermann, P.2
Vranova, E.3
Furholz, A.4
Laule, O.5
Bleuler, S.6
-
65
-
-
84876806691
-
Dynamic regulatory network controlling th17 cell differentiation
-
Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., et al. (2013). Dynamic regulatory network controlling th17 cell differentiation. Nature 496, 461-468. doi: 10.1038/nature11981
-
(2013)
Nature
, vol.496
, pp. 461-468
-
-
Yosef, N.1
Shalek, A.K.2
Gaublomme, J.T.3
Jin, H.4
Lee, Y.5
Awasthi, A.6
-
67
-
-
84855160951
-
Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information
-
Zhang, X., Zhao, X.-M., He, K., Lu, L., Cao, Y., Liu, J., et al. (2011). Inferring gene regulatory networks from gene expression data by PC-algorithm based on conditional mutual information. Bioinformatics 28, 98-104. doi: 10.1093/bioinformatics/btr626
-
(2011)
Bioinformatics
, vol.28
, pp. 98-104
-
-
Zhang, X.1
Zhao, X.-M.2
He, K.3
Lu, L.4
Cao, Y.5
Liu, J.6
|