-
1
-
-
0035367064
-
Whole-genome expression analysis: Challenges beyond clustering
-
Altman, R.B. and Raychaudhuri, S. (2001) Whole-genome expression analysis: challenges beyond clustering. Curr. Opin. Struct. Biol., 11, 340-347.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 340-347
-
-
Altman, R.B.1
Raychaudhuri, S.2
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
-
(2000)
The Gene Ontology Consortium. Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
3
-
-
84878239479
-
Transcriptome profiling of mice testes following low dose irradiation
-
Belling, K. et al. (2013) Transcriptome profiling of mice testes following low dose irradiation. Reprod. Biol. Endocrinol., 11, 50.
-
(2013)
Reprod. Biol. Endocrinol.
, vol.11
, pp. 50
-
-
Belling, K.1
-
4
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol., 57, 289-300.
-
(1995)
J. R. Stat. Soc. B Methodol.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
0028931857
-
Multiple significance tests: The bonferroni method
-
Bland, J.M. and Altman, D.G. (1995) Multiple significance tests: the bonferroni method. BMJ, 310, 170.
-
(1995)
BMJ
, vol.310
, pp. 170
-
-
Bland, J.M.1
Altman, D.G.2
-
6
-
-
79955626693
-
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation
-
Breeze, E. et al. (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell, 23, 873-894.
-
(2011)
Plant Cell
, vol.23
, pp. 873-894
-
-
Breeze, E.1
-
7
-
-
84879967750
-
MEME-LaB: Motif analysis in clusters
-
Brown, P. et al. (2013) MEME-LaB: motif analysis in clusters. Bioinformatics, 29, 1696-1697.
-
(2013)
Bioinformatics
, vol.29
, pp. 1696-1697
-
-
Brown, P.1
-
8
-
-
84856598466
-
The role of WRKY transcription factors in plant abiotic stresses
-
Chen, L. et al. (2012) The role of WRKY transcription factors in plant abiotic stresses. Biochim. Biophys. Acta, 1819, 120-128.
-
(2012)
Biochim. Biophys. Acta
, vol.1819
, pp. 120-128
-
-
Chen, L.1
-
9
-
-
0033119581
-
The TCP domain: A motif found in proteins regulating plant growth and development
-
Cubas, P. et al. (1999) The TCP domain: a motif found in proteins regulating plant growth and development. Plant J., 18, 215-222.
-
(1999)
Plant J.
, vol.18
, pp. 215-222
-
-
Cubas, P.1
-
10
-
-
0029803731
-
Characterization of a zinc-dependent transcriptional activator from Arabidopsis
-
de Pater, S. et al. (1996) Characterization of a zinc-dependent transcriptional activator from Arabidopsis. Nucleic Acids Res., 24, 4624-4631.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 4624-4631
-
-
De Pater, S.1
-
12
-
-
34547219390
-
Networks of WRKY transcription factors in defense signaling
-
Eulgem, T. and Somssich, I.E. (2007) Networks of WRKY transcription factors in defense signaling. Curr. Opin. Plant Biol., 10, 366-371.
-
(2007)
Curr. Opin. Plant Biol.
, vol.10
, pp. 366-371
-
-
Eulgem, T.1
Somssich, I.E.2
-
13
-
-
0034192491
-
The WRKY superfamily of plant transcription factors
-
Eulgem, T. et al. (2000) The WRKY superfamily of plant transcription factors. Trends Plant Sci., 5, 199-206.
-
(2000)
Trends Plant Sci.
, vol.5
, pp. 199-206
-
-
Eulgem, T.1
-
14
-
-
28044449342
-
Bayesian coclustering of Anopheles gene expression time series: Study of immune defense response to multiple experimental challenges
-
Heard, N.A. et al. (2005) Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges. Proc. Natl. Acad. Sci. USA, 102, 16939-16944.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 16939-16944
-
-
Heard, N.A.1
-
15
-
-
84879213336
-
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves
-
Hickman, R. et al. (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. Plant J., 75, 26-39.
-
(2013)
Plant J.
, vol.75
, pp. 26-39
-
-
Hickman, R.1
-
16
-
-
0032918558
-
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
-
Higo, K. et al. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res., 27, 297-300.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 297-300
-
-
Higo, K.1
-
17
-
-
34247200577
-
The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
-
Kilian, J. et al. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J., 50, 347-363.
-
(2007)
Plant J.
, vol.50
, pp. 347-363
-
-
Kilian, J.1
-
18
-
-
84896484065
-
Inference of dynamic networks using time-course data
-
doi:10.1093/bib/bbt028
-
Kim, Y. et al. (2013) Inference of dynamic networks using time-course data. Brief. Bioinform., doi:10.1093/bib/bbt028.
-
(2013)
Brief. Bioinform.
-
-
Kim, Y.1
-
19
-
-
84872549196
-
MultiFacTV: Finding modules from higher-order gene expression profiles with time dimension
-
Li, X. et al. (2012) MultiFacTV: finding modules from higher-order gene expression profiles with time dimension. In: IEEE International Conference on Bioinformatics and Biomedicine. pp. 1-6.
-
(2012)
IEEE International Conference on Bioinformatics and Biomedicine
, pp. 1-6
-
-
Li, X.1
-
20
-
-
76849109141
-
Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm
-
Madeira, S.C. et al. (2010) Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 153-165.
-
(2010)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.7
, pp. 153-165
-
-
Madeira, S.C.1
-
21
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere, S. et al. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21, 3448-3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
-
22
-
-
44149121700
-
Extracting expression modules from perturbational gene expression compendia
-
Maere, S. et al. (2008) Extracting expression modules from perturbational gene expression compendia. BMC Syst. Biol., 2, 33.
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 33
-
-
Maere, S.1
-
23
-
-
73449098946
-
TCP genes: A family snapshot ten years later
-
Mart?n-Trillo, M. and Cubas, P. (2010) TCP genes: a family snapshot ten years later. Trends Plant Sci., 15, 31-39.
-
(2010)
Trends Plant Sci.
, vol.15
, pp. 31-39
-
-
Martn-Trillo, M.1
Cubas, P.2
-
24
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys, V. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Matys, V.1
-
25
-
-
66349129690
-
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
-
Meng, J. et al. (2009) Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules. Bioinformatics, 25, 1521-1527.
-
(2009)
Bioinformatics
, vol.25
, pp. 1521-1527
-
-
Meng, J.1
-
26
-
-
2342501846
-
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
-
Redman, J.C. et al. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J., 38, 545-561.
-
(2004)
Plant J.
, vol.38
, pp. 545-561
-
-
Redman, J.C.1
-
27
-
-
33746067911
-
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
-
Reiss, D.J. et al. (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics, 7, 280.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 280
-
-
Reiss, D.J.1
-
28
-
-
80051746279
-
Hormone crosstalk in plant disease and defense: More than just jasmonate-salicylate antagonism
-
Robert-Seilaniantz, A. et al. (2011) Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu. Rev. Phytopathol., 49, 317-343.
-
(2011)
Annu. Rev. Phytopathol.
, vol.49
, pp. 317-343
-
-
Robert-Seilaniantz, A.1
-
29
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G.G. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
-
(2007)
Nat. Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.G.1
-
30
-
-
69849104854
-
R/BHC: Fast Bayesian hierarchical clustering for microarray data
-
Savage, R.S. et al. (2009) R/BHC: fast Bayesian hierarchical clustering for microarray data. BMC Bioinformatics, 10, 242.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 242
-
-
Savage, R.S.1
-
31
-
-
37249069096
-
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
-
Sclep, G. et al. (2007) CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinformatics, 8, 400.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 400
-
-
Sclep, G.1
-
32
-
-
77950803115
-
A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series
-
Stegle, O. et al. (2010) A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. J. Comput. Biol., 17, 355-367.
-
(2010)
J. Comput. Biol.
, vol.17
, pp. 355-367
-
-
Stegle, O.1
-
33
-
-
35748941236
-
EDISA: Extracting biclusters from multiple time-series of gene expression profiles
-
Supper, J. et al. (2007) EDISA: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics, 8, 334.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 334
-
-
Supper, J.1
-
34
-
-
0042930859
-
Genomic effects of IFN-beta in multiple sclerosis patients
-
Weinstock-Guttman, B. et al. (2003) Genomic effects of IFN-beta in multiple sclerosis patients. J. Immunol., 171, 2694-2702.
-
(2003)
J. Immunol.
, vol.171
, pp. 2694-2702
-
-
Weinstock-Guttman, B.1
-
35
-
-
33745647013
-
Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation machinery
-
Welchen, E. and Gonzalez, D.H. (2006) Overrepresentation of elements recognized by TCP-domain transcription factors in the upstream regions of nuclear genes encoding components of the mitochondrial oxidative phosphorylation machinery. Plant Physiol., 141, 540-545.
-
(2006)
Plant Physiol.
, vol.141
, pp. 540-545
-
-
Welchen, E.1
Gonzalez, D.H.2
-
36
-
-
84868288164
-
Arabidopsis defense against Botrytis cinerea: Chronology and regulation deciphered by high-resolution temporal transcriptomic analysis
-
Windram, O. et al. (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell, 24, 3530-3557.
-
(2012)
Plant Cell
, vol.24
, pp. 3530-3557
-
-
Windram, O.1
-
37
-
-
4844229238
-
From co-expression to co-regulation: How many microarray experiments do we need?
-
Yeung, K.Y. et al. (2004) From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol., 5, R48.
-
(2004)
Genome Biol.
, vol.5
-
-
Yeung, K.Y.1
-
38
-
-
84868708561
-
A unified adaptive co-identification framework for high-d expression data
-
In: Shibuya, T., Kashima, H., Sese, J. and Ahmad, S. (eds), Springer, Berlin, Heidelberg
-
Zhang, S. et al. (2012) A unified adaptive co-identification framework for high-d expression data. In: Shibuya, T., Kashima, H., Sese, J. and Ahmad, S. (eds) Lecture Notes in Computer Science. Vol. 7632, Springer, Berlin, Heidelberg, pp. 59-70.
-
(2012)
Lecture Notes in Computer Science
, vol.7632
, pp. 59-70
-
-
Zhang, S.1
|