-
1
-
-
65549104397
-
A roadmap of clustering algorithms: Finding a match for a biomedical application
-
Andreopoulos, B., An, A.J., Wang, X.G. and Schroeder, M. (2009) A roadmap of clustering algorithms: finding a match for a biomedical application. Brief Bioinform., 10, 297-314
-
(2009)
Brief Bioinform.
, vol.10
, pp. 297-314
-
-
Andreopoulos, B.1
An, A.J.2
Wang, X.G.3
Schroeder, M.4
-
2
-
-
37549029793
-
The properties of high-dimensional data spaces: Implications for exploring gene and protein expression data
-
Clarke, R., Ressom, H.W., Wang, A.T., Xuan, J.H., Liu, M.C., Gehan, E.A. and Wang, Y. (2008) The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat. Rev. Cancer, 8, 37-49
-
(2008)
Nat. Rev. Cancer
, vol.8
, pp. 37-49
-
-
Clarke, R.1
Ressom, H.W.2
Wang, A.T.3
Xuan, J.H.4
Liu, M.C.5
Gehan, E.A.6
Wang, Y.7
-
3
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, vol.3
-
-
Smyth, G.K.1
-
4
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach, D., Prill, R.J., Schaffter, T., Mattiussi, C., Floreano, D. and Stolovitzky, G. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc. Natl Acad. Sci. USA, 107, 6286-6291
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 6286-6291
-
-
Marbach, D.1
Prill, R.J.2
Schaffter, T.3
Mattiussi, C.4
Floreano, D.5
Stolovitzky, G.6
-
5
-
-
84859149116
-
How to infer gene networks from expression profiles, revisited
-
Penfold, C.A. and Wild, D.L. (2011) How to infer gene networks from expression profiles, revisited. Interface Focus, 1, 857-870
-
(2011)
Interface Focus
, vol.1
, pp. 857-870
-
-
Penfold, C.A.1
Wild, D.L.2
-
6
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S.S., Milo, R., Mangan, S. and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet., 31, 64-68
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
7
-
-
13544269611
-
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
-
DOI 10.1093/nar/gkh1009
-
Ma, H.W., Kumar, B., Ditges, U., Gunzer, F., Buer, J. and Zeng, A.P. (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res., 32, 6643-6649 (Pubitemid 40220376)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.22
, pp. 6643-6649
-
-
Ma, H.-W.1
Kumar, B.2
Ditges, U.3
Gunzer, F.4
Buer, J.5
Zeng, A.-P.6
-
8
-
-
55449126342
-
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death
-
Kohanski, M.A., Dwyer, D.J., Wierzbowski, J., Cottarel, G. and Collins, J.J. (2008) Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell, 135, 679-690
-
(2008)
Cell
, vol.135
, pp. 679-690
-
-
Kohanski, M.A.1
Dwyer, D.J.2
Wierzbowski, J.3
Cottarel, G.4
Collins, J.J.5
-
9
-
-
59649095559
-
Coordinated regulation of virulence during systemic infection of Salmonella enterica Serovar Typhimurium
-
Yoon, H.J., McDermott, J.E., Porwollik, S., McClelland, M. and Heffron, F. (2009) Coordinated regulation of virulence during systemic infection of Salmonella enterica Serovar Typhimurium. PLoS Pathog., 5, e1000306
-
(2009)
PLoS Pathog.
, vol.5
-
-
Yoon, H.J.1
McDermott, J.E.2
Porwollik, S.3
McClelland, M.4
Heffron, F.5
-
10
-
-
37349099750
-
A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
-
DOI 10.1016/j.cell.2007.10.053, PII S009286740701416X
-
Bonneau, R., Facciotti, M.T., Reiss, D.J., Schmid, A.K., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson, M.H., Bare, J.C. et al. (2007) A predictive model for transcriptional control of physiology in a free living cell. Cell, 131, 1354-1365 (Pubitemid 350297417)
-
(2007)
Cell
, vol.131
, Issue.7
, pp. 1354-1365
-
-
Bonneau, R.1
Facciotti, M.T.2
Reiss, D.J.3
Schmid, A.K.4
Pan, M.5
Kaur, A.6
Thorsson, V.7
Shannon, P.8
Johnson, M.H.9
Bare, J.C.10
Longabaugh, W.11
Vuthoori, M.12
Whitehead, K.13
Madar, A.14
Suzuki, L.15
Mori, T.16
Chang, D.-E.17
DiRuggiero, J.18
Johnson, C.H.19
Hood, L.20
Baliga, N.S.21
more..
-
11
-
-
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
-
(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
-
12
-
-
84859322797
-
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function
-
Belcastro, V., Siciliano, V., Gregoretti, F., Mithbaokar, P., Dharmalingam, G., Berlingieri, S., Iorio, F., Oliva, G., Polishchuck, R., Brunetti-Pierri, N. et al. (2012) Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res., 40, D715-D719
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Belcastro, V.1
Siciliano, V.2
Gregoretti, F.3
Mithbaokar, P.4
Dharmalingam, G.5
Berlingieri, S.6
Iorio, F.7
Oliva, G.8
Polishchuck, R.9
Et Al., B.10
-
14
-
-
63849210631
-
Lessons from the DREAM2 challenges
-
Stolovitzky, G., Prill, R.J. and Califano, A. (2009) Lessons from the DREAM2 Challenges. Ann. NY Acad. Sci., 1158, 159-195
-
(2009)
Ann. NY Acad. Sci.
, vol.1158
, pp. 159-195
-
-
Stolovitzky, G.1
Prill, R.J.2
Califano, A.3
-
15
-
-
59649110273
-
Generating realistic in silico gene networks for performance assessment of reverse engineering methods
-
Marbach, D., Schaffter, T., Mattiussi, C. and Floreano, D. (2009) Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J. Comput. Biol., 16, 229-239
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 229-239
-
-
Marbach, D.1
Schaffter, T.2
Mattiussi, C.3
Floreano, D.4
-
16
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
DOI 10.1126/science.1081900
-
Gardner, T.S., di Bernardo, D., Lorenz, D. and Collins, J.J. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301, 102-105 (Pubitemid 36801571)
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
Di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
17
-
-
58149187889
-
FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
-
Pisarev, A., Poustelnikova, E., Samsonova, M. and Reinitz, J. (2009) FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res., 37, D560-D566
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Pisarev, A.1
Poustelnikova, E.2
Samsonova, M.3
Reinitz, J.4
-
18
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
-
Shi, L.M., Reid, L.H., Jones, W.D., Shippy, R., Warrington, J.A., Baker, S.C., Collins, P.J., de Longueville, F., Kawasaki, E.S., Lee, K.Y. et al. (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1151-1161
-
-
Shi, L.M.1
Reid, L.H.2
Jones, W.D.3
Shippy, R.4
Warrington, J.A.5
Baker, S.C.6
Collins, P.J.7
De Longueville, F.8
Kawasaki, E.S.9
Lee, K.Y.10
-
19
-
-
63849195202
-
Inferring gene networks: Dream or nightmare?
-
Scheinine, A., Mentzen, W.I., Fotia, G., Pieroni, E., Maggio, F., Mancosu, G. and Fuente, A.D.L. (2009) Inferring gene networks: dream or nightmare? Ann. NY Acad. Sci., 1158, 287-301
-
(2009)
Ann. NY Acad. Sci.
, vol.1158
, pp. 287-301
-
-
Scheinine, A.1
Mentzen, W.I.2
Fotia, G.3
Pieroni, E.4
Maggio, F.5
Mancosu, G.6
Fuente, A.D.L.7
-
20
-
-
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., Kasif, S., Collins, J.J. and Gardner, T.S. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, 54-66
-
(2007)
PLoS Biol.
, vol.5
, pp. 54-66
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
21
-
-
12344259602
-
Advances to Bayesian network inference for generating causal networks from observational biological data
-
DOI 10.1093/bioinformatics/bth448
-
Yu, J., Smith, V.A., Wang, P.P., Hartemink, A.J. and Jarvis, E.D. (2004) Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics, 20, 3594-3603 (Pubitemid 40136795)
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
Hartemink, A.J.4
Jarvis, E.D.5
-
22
-
-
0036372453
-
Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression
-
Imoto, S., Goto, T. and Miyano, S. (2002) Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. Pac. Symp. Biocomput., 7, 175-186
-
(2002)
Pac. Symp. Biocomput.
, vol.7
, pp. 175-186
-
-
Imoto, S.1
Goto, T.2
Miyano, S.3
-
23
-
-
3042738945
-
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data
-
DOI 10.1016/j.biosystems.2004.03.004, PII S0303264704000383
-
Kim, S., Imoto, S. and Miyano, S. (2004) Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems, 75, 57-65 (Pubitemid 38887551)
-
(2004)
BioSystems
, vol.75
, Issue.1-3
, pp. 57-65
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
24
-
-
33746616957
-
Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles
-
Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, S.D., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S. et al. (2006) Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pac. Symp. Biocomput., 559-571
-
(2006)
Pac. Symp. Biocomput.
, pp. 559-571
-
-
Imoto, S.1
Tamada, Y.2
Araki, H.3
Yasuda, K.4
Print, C.G.5
Charnock-Jones, S.D.6
Sanders, D.7
Savoie, C.J.8
Tashiro, K.9
Kuhara, S.10
-
25
-
-
33746602343
-
Reconstructing gene regulatory networks: From random to scale-free connectivity
-
DOI 10.1049/ip-syb:20050092
-
Wildenhain, J. and Crampin, E.J. (2006) Reconstructing gene regulatory networks: from random to scale-free connectivity. Syst. Biol., 153, 247-256 (Pubitemid 44151484)
-
(2006)
IEE Proceedings: Systems Biology
, vol.153
, Issue.4
, pp. 247-256
-
-
Wildenhain, J.1
Crampin, E.J.2
-
26
-
-
33947732288
-
Reconstructing biochemical pathways from time course data
-
DOI 10.1002/pmic.200600428
-
Srividhya, J., Crampin, E.J., McSharry, P.E. and Schnell, S. (2007) Reconstructing biochemical pathways from time course data. Proteomics, 7, 828-838 (Pubitemid 46506730)
-
(2007)
Proteomics
, vol.7
, Issue.6
, pp. 828-838
-
-
Srividhya, J.1
Crampin, E.J.2
McSharry, P.E.3
Schnell, S.4
-
27
-
-
44849118743
-
Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
-
DOI 10.1101/gr.073601.107
-
Della Gatta, G., Bansal, M., Ambesi-Impiombato, A., Antonini, D., Missero, C. and di Bernardo, D. (2008) Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome Res., 18, 939-948 (Pubitemid 351793066)
-
(2008)
Genome Research
, vol.18
, Issue.6
, pp. 939-948
-
-
Gatta, G.D.1
Bansal, M.2
Ambesi-Impiombato, A.3
Antonini, D.4
Missero, C.5
Di Bernardo, D.6
-
28
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
DOI 10.1093/bioinformatics/btl391
-
Werhli, A.V., 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 (Pubitemid 44560759)
-
(2006)
Bioinformatics
, vol.22
, Issue.20
, pp. 2523-2531
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
29
-
-
34547844096
-
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: Synthetic versus real data
-
DOI 10.1093/bioinformatics/btm163
-
Soranzo, N., Bianconi, G. and Altafini, C. (2007) Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data. Bioinformatics, 23, 1640-1647 (Pubitemid 47244454)
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 1640-1647
-
-
Soranzo, N.1
Bianconi, G.2
Altafini, C.3
-
30
-
-
34548388925
-
Inference of gene networks from temporal gene expression profiles
-
DOI 10.1049/iet-syb:20060079
-
Bansal, M. and di Bernardo, D. (2007) Inference of gene networks from temporal gene expression profiles. IET Syst. Biol., 1, 306-312 (Pubitemid 47354629)
-
(2007)
IET Systems Biology
, vol.1
, Issue.5
, pp. 306-312
-
-
Bansal, M.1
Di Bernardo, D.2
-
31
-
-
63849145908
-
NIRest: A tool for gene network and mode of action inference
-
Lauria, M., Iorio, F. and Bernardo, D.D. (2009) NIRest: a tool for gene network and mode of action inference. Ann. NY Acad. Sci., 1158, 257-264
-
(2009)
Ann. NY Acad. Sci.
, vol.1158
, pp. 257-264
-
-
Lauria, M.1
Iorio, F.2
Bernardo, D.D.3
-
32
-
-
54949116240
-
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia
-
Cosgrove, E.J., Zhou, Y., Gardner, T.S. and Kolaczyk, E.D. (2008) Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. Bioinformatics, 24, 2482-2490
-
(2008)
Bioinformatics
, vol.24
, pp. 2482-2490
-
-
Cosgrove, E.J.1
Zhou, Y.2
Gardner, T.S.3
Kolaczyk, E.D.4
-
33
-
-
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. and Califano, A. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
34
-
-
3242891560
-
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
-
Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S. and Miyano, S. (2003) Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics, 19(Suppl. 2), 227-236
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
, pp. 227-236
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
35
-
-
33847008688
-
A network biology approach to prostate cancer
-
Ergun, A., Lawrence, C.A., Kohanski, M.A., Brennan, T.A. and Collins, J.J. (2007) A network biology approach to prostate cancer. Mol. Syst. Biol., 3, 6
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 6
-
-
Ergun, A.1
Lawrence, C.A.2
Kohanski, M.A.3
Brennan, T.A.4
Collins, J.J.5
-
36
-
-
61949220761
-
Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks
-
Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D. et al. (2009) Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pac. Symp. Biocomput., 14, 251-263
-
(2009)
Pac. Symp. Biocomput.
, vol.14
, pp. 251-263
-
-
Tamada, Y.1
Araki, H.2
Imoto, S.3
Nagasaki, M.4
Doi, A.5
Nakanishi, Y.6
Tomiyasu, Y.7
Yasuda, K.8
Dunmore, B.9
Sanders, D.10
-
37
-
-
33646884801
-
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes
-
DOI 10.1086/504300
-
Franke, L., van Bakel, H., Fokkens, L., de Jong, E.D., Egmont-Petersen, M. and Wijmenga, C. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet., 78, 1011-1025 (Pubitemid 43787692)
-
(2006)
American Journal of Human Genetics
, vol.78
, Issue.6
, pp. 1011-1025
-
-
Franke, L.1
Van Bakel, H.2
Fokkens, L.3
De Jong, E.D.4
Egmont-Petersen, M.5
Wijmenga, C.6
-
38
-
-
33646361583
-
GenePattern 2.0
-
Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P. and Mesirov, J.P. (2006) GenePattern 2.0. Nat. Genet., 38, 500-501
-
(2006)
Nat. Genet.
, vol.38
, pp. 500-501
-
-
Reich, M.1
Liefeld, T.2
Gould, J.3
Lerner, J.4
Tamayo, P.5
Mesirov, J.P.6
-
39
-
-
33646038227
-
Taverna: Lessons in creating a workflow environment for the life sciences
-
DOI 10.1002/cpe.993
-
Oinn, T., Greenwood, M., Addis, M., Alpdemir, M.N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D. et al. (2006) Taverna: lessons in creating a workflow environment for the life sciences. Concurr. Comput. Pract. Exp., 18, 1067-1100 (Pubitemid 44258498)
-
(2006)
Concurrency Computation Practice and Experience
, vol.18
, Issue.10
, pp. 1067-1100
-
-
Oinn, T.1
Greenwood, M.2
Addis, M.3
Alpdemir, M.N.4
Ferris, J.5
Glover, K.6
Goble, C.7
Goderis, A.8
Hull, D.9
Marvin, D.10
Li, P.11
Lord, P.12
Pocock, M.R.13
Senger, M.14
Stevens, R.15
Wipat, A.16
Wroe, C.17
-
40
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86
-
(2010)
Genome Biol.
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
41
-
-
77954519381
-
GeWorkbench: An open source platform for integrative genomics
-
Floratos, A., Smith, K., Ji, Z., Watkinson, J. and Califano, A. (2010) geWorkbench: an open source platform for integrative genomics. Bioinformatics, 26, 1779-1780
-
(2010)
Bioinformatics
, Issue.26
, pp. 1779-1780
-
-
Floratos, A.1
Smith, K.2
Ji, Z.3
Watkinson, J.4
Califano, A.5
-
42
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
DOI 10.1093/bioinformatics/19.2.185
-
Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193 (Pubitemid 36181903)
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
43
-
-
2342646842
-
LSimpute: Accurate estimation of missing values in microarray data with least squares methods
-
Bo, T.H., Dysvik, J. and Jonassen, I. (2004) LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res., 32, e34
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bo, T.H.1
Dysvik, J.2
Jonassen, I.3
-
44
-
-
46049087782
-
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
-
DOI 10.1093/bib/bbn016, Special Issue: Critical Technologies for Bioinformatics
-
Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform., 9, 326-332 (Pubitemid 351894493)
-
(2008)
Briefings in Bioinformatics
, vol.9
, Issue.4
, pp. 326-332
-
-
Wingender, E.1
-
45
-
-
33644876958
-
TRANSFAC(R) and its module TRANSCompel(R): Transcriptional gene regulation in eukaryotes
-
Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
46
-
-
0035958877
-
Activation of NF-kappa B via the i kappa B kinase complex is both essential and sufficient for proinflammatory gene expression in primary endothelial cells
-
Denk, A., Goebeler, M., Schmid, S., Berberich, I., Ritz, O., Lindemann, D., Ludwig, S. and Wirth, T. (2001) Activation of NF-kappa B via the I kappa B kinase complex is both essential and sufficient for proinflammatory gene expression in primary endothelial cells. J. Biol. Chem., 276, 28451-28458
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 28451-28458
-
-
Denk, A.1
Goebeler, M.2
Schmid, S.3
Berberich, I.4
Ritz, O.5
Lindemann, D.6
Ludwig, S.7
Wirth, T.8
-
47
-
-
79251566745
-
Novel cross-talk within the IKK family controls innate immunity
-
Clark, K., Peggie, M., Plater, L., Sorcek, R.J., Young, E.R.R., Madwed, J.B., Hough, J., McIver, E.G. and Cohen, P. (2011) Novel cross-talk within the IKK family controls innate immunity. Biochem. J., 434, 93-104
-
(2011)
Biochem. J.
, vol.434
, pp. 93-104
-
-
Clark, K.1
Peggie, M.2
Plater, L.3
Sorcek, R.J.4
Young, E.R.R.5
Madwed, J.B.6
Hough, J.7
McIver, E.G.8
Cohen, P.9
-
48
-
-
13244267007
-
Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data
-
Daub, C.O., Steuer, R., Selbig, J. and Kloska, S. (2004) Estimating mutual information using B-spline functions-an improved similarity measure for analysing gene expression data. BMC Bioinform., 5
-
(2004)
BMC Bioinform.
, vol.5
-
-
Daub, C.O.1
Steuer, R.2
Selbig, J.3
Kloska, S.4
-
49
-
-
77249109446
-
Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction
-
Hansen, M., Everett, L., Singh, L. and Hannenhalli, S. (2010) Mimosa: mixture model of co-expression to detect modulators of regulatory interaction. Algorithms Mol. Biol., 5
-
(2010)
Algorithms Mol. Biol.
, pp. 5
-
-
Hansen, M.1
Everett, L.2
Singh, L.3
Hannenhalli, S.4
-
50
-
-
3042514191
-
Coexpresion analysis of human genes across many microarray data sets
-
DOI 10.1101/gr.1910904
-
Lee, H.K., Hsu, A.K., Sajdak, J., Qin, J. and Pavlidis, P. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res., 14, 1085-1094 (Pubitemid 38811545)
-
(2004)
Genome Research
, vol.14
, Issue.6
, pp. 1085-1094
-
-
Lee, H.K.1
Hsu, A.K.2
Sajdak, J.3
Qin, J.4
Pavlidis, P.5
-
51
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
DOI 10.1038/nature02555
-
Han, J.D.J., Bertin, N., Hao, T., Goldberg, D.S., Berriz, G.F., Zhang, L.V., Dupuy, D., Walhout, A.J.M., Cusick, M.E., Roth, F.P. et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93 (Pubitemid 38915230)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 88-93
-
-
Han, J.-D.J.1
Berlin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
52
-
-
0036500609
-
A genomic regulatory network for development
-
DOI 10.1126/science.1069883
-
Davidson, E.H., Rast, J.P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C.H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C. et al. (2002) A genomic regulatory network for development. Science, 295, 1669-1678 (Pubitemid 34202895)
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.-H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
Otim, O.11
Brown, C.T.12
Livi, C.B.13
Lee, P.Y.14
Revilla, R.15
Rust, A.G.16
Pan, Z.J.17
Schilstra, M.J.18
Clarke, P.J.C.19
Arnone, M.I.20
Rowen, L.21
Cameron, R.A.22
McClay, D.R.23
Hood, L.24
Bolouri, H.25
more..
-
53
-
-
0030591733
-
Haematopoiesis-master regulator unmasked
-
Green, T. (1996) Haematopoiesis-master regulator unmasked. Nature, 383, 575-577
-
(1996)
Nature
, vol.383
, pp. 575-577
-
-
Green, T.1
-
54
-
-
52249100151
-
Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8 desmin and enolase 1 as the central elements
-
Jiang, W., Li, X., Rao, S.Q., Wang, L.H., Du, L., Li, C.X., Wu, C., Wang, H.Z., Wang, Y.D. and Yang, B.F. (2008) Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Syst. Biol., 2, 72
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 72
-
-
Jiang, W.1
Li, X.2
Rao, S.Q.3
Wang, L.H.4
Du, L.5
Li, C.X.6
Wu, C.7
Wang, H.Z.8
Wang, Y.D.9
Yang, B.F.10
-
55
-
-
34547140875
-
The human disease network
-
DOI 10.1073/pnas.0701361104
-
Goh, K.I., Cusick, M.E., Valle, D., Childs, B., Vidal, M. and Barabasi, A.L. (2007) The human disease network. Proc. Natl Acad. Sci. USA, 104, 8685-8690 (Pubitemid 47175372)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.21
, pp. 8685-8690
-
-
Goh, K.-I.1
Cusick, M.E.2
Valle, D.3
Childs, B.4
Vidal, M.5
Barabasi, A.-L.6
-
56
-
-
77952691738
-
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
-
Yan, K.-K., Fang, G., Bhardwaj, N., Alexander, R.P. and Gerstein, M. (2010) Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proc, Natl Acad. Sci USA, 107, 9186-9191
-
(2010)
Proc, Natl Acad. Sci USA
, Issue.107
, pp. 9186-9191
-
-
Yan, K.-K.1
Fang, G.2
Bhardwaj, N.3
Alexander, R.P.4
Gerstein, M.5
-
57
-
-
33750457370
-
Post-translational modifications regulating the activity and function of the nuclear factor kappa B pathway
-
DOI 10.1038/sj.onc.1209937, PII 1209937
-
Perkins, N.D. (2006) Post-translational modifications regulating the activity and function of the nuclear factor kappa B pathway. Oncogene, 25, 6717-6730 (Pubitemid 44657848)
-
(2006)
Oncogene
, vol.25
, Issue.51
, pp. 6717-6730
-
-
Perkins, N.D.1
-
58
-
-
11844269840
-
Phosphorylation of NF-κB and IκB proteins: Implications in cancer and inflammation
-
DOI 10.1016/j.tibs.2004.11.009, PII S0968000404002993
-
Viatour, P., Merville, M.P., Bours, V. and Chariot, A. (2005) Phosphorylation of NF-kappa B and I kappa B proteins: implications in cancer and inflammation. Trends Biochem. Sci., 30, 43-52 (Pubitemid 40093740)
-
(2005)
Trends in Biochemical Sciences
, vol.30
, Issue.1
, pp. 43-52
-
-
Viatour, P.1
Merville, M.-P.2
Bours, V.3
Chariot, A.4
-
59
-
-
33750475959
-
Cross-talk between nuclear receptors and nuclear factor kB
-
De Bosscher, K., Vanden Berghe, W. and Haegeman, G. (2006) Cross-talk between nuclear receptors and nuclear factor kB. Oncogene, 25, 6868-6886
-
(2006)
Oncogene
, vol.25
, pp. 6868-6886
-
-
De Bosscher, K.1
Vanden Berghe, W.2
Haegeman, G.3
-
60
-
-
21744444276
-
Nucleolar sequestration of RelA (p65) regulates NF-κB-driven transcription and apoptosis
-
DOI 10.1128/MCB.25.14.5985-6004.2005
-
Stark, L.A. and Dunlop, M.G. (2005) Nucleolar sequestration of RelA (p65) regulates NF-kappa B-driven transcription and apoptosis. Mol. Cell. Biol., 25, 5985-6004 (Pubitemid 40946553)
-
(2005)
Molecular and Cellular Biology
, vol.25
, Issue.14
, pp. 5985-6004
-
-
Stark, L.A.1
Dunlop, M.G.2
-
61
-
-
0038771214
-
Modulation of NF-κB activity by exchange of dimers
-
DOI 10.1016/S1097-2765(03)00227-2
-
Saccani, S., Pantano, S. and Natoli, G. (2003) Modulation of NF-kappa B activity by exchange of dimers. Mol. Cell., 11, 1563-1574 (Pubitemid 36776542)
-
(2003)
Molecular Cell
, vol.11
, Issue.6
, pp. 1563-1574
-
-
Saccani, S.1
Pantano, S.2
Natoli, G.3
-
62
-
-
79952108539
-
Regulating the regulators: Modulators of transcription factor activity
-
Ladunga, I. (ed.) Binding Humana Press, NY
-
Ladunga, I., Everett, L., Hansen, M. and Hannenhalli, S. (2010) Regulating the regulators: modulators of transcription factor activity. In: Ladunga, I. (ed.), Computational Biology of Transcription Factor Binding, Vol Humana Press, NY, pp. 297-312
-
(2010)
Computational Biology of Transcription Factor
, pp. 297-312
-
-
Ladunga, I.1
Everett, L.2
Hansen, M.3
Hannenhalli, S.4
-
63
-
-
58149200951
-
PTM-Switchboard - A database of posttranslational modifications of transcription factors, the mediating enzymes and target genes
-
Everett, L., Vo, A. and Hannenhalli, S. (2009) PTM-Switchboard-a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res., 37, D66-D71
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Everett, L.1
Vo, A.2
Hannenhalli, S.3
-
64
-
-
0038281453
-
Observing and interpreting correlations in metabolomic networks
-
DOI 10.1093/bioinformatics/btg120
-
Steuer, R., Kurths, J., Fiehn, O. and Weckwerth, W. (2003) Observing and interpreting correlations in metabolomic networks. Bioinformatics, 19, 1019-1026 (Pubitemid 36675824)
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1019-1026
-
-
Steuer, R.1
Kurths, J.2
Fiehn, O.3
Weckwerth, W.4
-
65
-
-
79952856971
-
Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Trans
-
Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, S. and Miyano, S. (2010) Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Trans. Comput. Biol. Bioinform, 8, 683-697
-
(2010)
Comput. Biol. Bioinform
, Issue.8
, pp. 683-697
-
-
Tamada, Y.1
Imoto, S.2
Araki, H.3
Nagasaki, M.4
Print, C.5
Charnock-Jones, S.6
Miyano, S.7
-
66
-
-
78651472654
-
Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation
-
Thorrez, L., Laudadio, I., Van Deun, K., Quintens, R., Hendrickx, N., Granvik, M., Lemaire, K., Schraenen, A., Van Lommel, L., Lehnert, S. et al. (2010) Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation. Genome Res., 21, 95-105.
-
(2010)
Genome Res.
, vol.21
, pp. 95-95
-
-
Thorrez, L.1
Laudadio, I.2
Van Deun, K.3
Quintens, R.4
Hendrickx, N.5
Granvik, M.6
Lemaire, K.7
Schraenen, A.8
Van Lommel, L.9
Lehnert, S.10
|