-
1
-
-
84875198920
-
Transcriptional regulation and its misregulation in disease
-
Lee, T. I. & Young, R. A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237-51 (2013).
-
(2013)
Cell
, vol.152
, pp. 1237-1251
-
-
Lee, T.I.1
Young, R.A.2
-
2
-
-
84887970699
-
Evolution of crop species: Genetics of domestication and diversification
-
Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14, 840-52 (2013).
-
(2013)
Nat Rev Genet
, vol.14
, pp. 840-852
-
-
Meyer, R.S.1
Purugganan, M.D.2
-
3
-
-
66649113099
-
Manipulation of plant metabolic pathways by transcription factors
-
Iwase, A., Matsui, K. & Ohme-Takagi, M. Manipulation of plant metabolic pathways by transcription factors. Plant Biotechnology 26, 29-38 (2009).
-
(2009)
Plant Biotechnology
, vol.26
, pp. 29-38
-
-
Iwase, A.1
Matsui, K.2
Ohme-Takagi, M.3
-
4
-
-
84892376552
-
Supervised, semi-supervised and unsupervised inference of gene regulatory networks
-
Maetschke, S. R. et al. Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Brief Bioinform 15, 195-211 (2014).
-
(2014)
Brief Bioinform
, vol.15
, pp. 195-211
-
-
Maetschke, S.R.1
-
5
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach, D. et al. Wisdom of crowds for robust gene network inference. Nat Methods 9, 796-804 (2012).
-
(2012)
Nat Methods
, vol.9
, pp. 796-804
-
-
Marbach, D.1
-
6
-
-
77950910419
-
Revealing strengths and weaknesses of methods for gene network inference
-
Marbach, D. et al. Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci USA 107, 6286-91 (2010).
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 6286-6291
-
-
Marbach, D.1
-
7
-
-
77957110013
-
Advantages and limitations of current network inference methods
-
De Smet, R. & Marchal, K. Advantages and limitations of current network inference methods. Nat Rev Microbiol 8, 717-29 (2010).
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 717-729
-
-
De Smet, R.1
Marchal, K.2
-
8
-
-
79953044960
-
Genome-wide transcription factor binding: Beyond direct target regulation
-
MacQuarrie, K. L., Fong, A. P., Morse, R. H. & Tapscott, S. J. Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 27, 141-8 (2011).
-
(2011)
Trends Genet
, vol.27
, pp. 141-148
-
-
MacQuarrie, K.L.1
Fong, A.P.2
Morse, R.H.3
Tapscott, S.J.4
-
9
-
-
84861168271
-
Inferring gene regulatory networks by anova
-
Köffner, R. et al. Inferring gene regulatory networks by anova. Bioinformatics 28, 1376-82 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1376-1382
-
-
Köffner, R.1
-
10
-
-
84883795281
-
Gene regulatory networks in plants: Learning causality from time and perturbation
-
Krouk, G. et al. Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol 14, 123 (2013).
-
(2013)
Genome Biol
, vol.14
, Issue.123
-
-
Krouk, G.1
-
11
-
-
84928996932
-
Measuring the wisdom of the crowds in network-based gene function inference
-
Verleyen, W. et al. Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics 31, 745-52 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 745-752
-
-
Verleyen, W.1
-
12
-
-
84979850686
-
Flynet: A versatile network prioritization server for the drosophila community
-
Shin, J. et al. Flynet: A versatile network prioritization server for the drosophila community. Nucleic Acids Res 43, W91-7 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. W91-W97
-
-
Shin, J.1
-
13
-
-
84941129438
-
Aranet v2: An improved database of co-functional gene networks for the study of arabidopsis thaliana and 27 other nonmodel plant species
-
Lee, T. et al. Aranet v2: An improved database of co-functional gene networks for the study of arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Res 43, D996-1002 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D996-1002
-
-
Lee, T.1
-
14
-
-
84863537088
-
Predictive regulatory models in drosophila melanogaster by integrative inference of transcriptional networks
-
Marbach, D. et al. Predictive regulatory models in drosophila melanogaster by integrative inference of transcriptional networks. Genome Res 22, 1334-49 (2012).
-
(2012)
Genome Res
, vol.22
, pp. 1334-1349
-
-
Marbach, D.1
-
15
-
-
84897374792
-
Towards revealing the functions of all genes in plants
-
Rhee, S. Y. & Mutwil, M. Towards revealing the functions of all genes in plants. Trends Plant Sci 19, 212-21 (2014).
-
(2014)
Trends Plant Sci
, vol.19
, pp. 212-221
-
-
Rhee, S.Y.1
Mutwil, M.2
-
18
-
-
84887360598
-
A principled deep random field model for image segmentation
-
IEEE
-
Kohli, P. et al. A principled deep random field model for image segmentation. In CVPR 1971-1978 (IEEE, 2013).
-
(2013)
CVPR
, pp. 1971-1978
-
-
Kohli, P.1
-
19
-
-
84946406582
-
Brane cut: Biologically-related a priori network enhancement with graph cuts for gene regulatory network inference
-
Pirayre, A. et al. Brane cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference. BMC Bioinformatics 16, 369 (2015).
-
(2015)
BMC Bioinformatics
, vol.16
, Issue.369
-
-
Pirayre, A.1
-
20
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu, V. A. et al. Inferring regulatory networks from expression data using tree-based methods. PLoS One 5 (2010).
-
(2010)
PLoS One
, vol.5
-
-
Huynh-Thu, V.A.1
-
21
-
-
84936881609
-
An arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors
-
Jin, J. et al. An arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Mol Biol Evol 32, 1767-73 (2015).
-
(2015)
Mol Biol Evol
, vol.32
, pp. 1767-1773
-
-
Jin, J.1
-
22
-
-
84876544295
-
Suba3: A database for integrating experimentation and prediction to define the subcellular location of proteins in arabidopsis
-
Tanz, S. K. et al. Suba3: A database for integrating experimentation and prediction to define the subcellular location of proteins in arabidopsis. Nucleic Acids Res 41, D1185-91 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D1185-D1191
-
-
Tanz, S.K.1
-
23
-
-
27244443126
-
Metacyc and aracyc. Metabolic pathway databases for plant research
-
Zhang, P. et al. Metacyc and aracyc. metabolic pathway databases for plant research. Plant Physiol 138, 27-37 (2005).
-
(2005)
Plant Physiol
, vol.138
, pp. 27-37
-
-
Zhang, P.1
-
24
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith, J. J. et al. Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5, e8 (2007).
-
(2007)
PLoS Biol
, vol.5
, pp. e8
-
-
Faith, J.J.1
-
25
-
-
15944364151
-
An empirical bayes approach to inferring large-scale gene association networks
-
Schäfer, J. & Strimmer, K.An empirical bayes approach to inferring large-scale gene association networks. Bioinformatics 21, 754-64 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
26
-
-
84943375424
-
Gene networks in plant biology: Approaches in reconstruction and analysis
-
Li, Y., Pearl, S. A. & Jackson, S. A. Gene networks in plant biology: Approaches in reconstruction and analysis. Trends Plant Sci 20, 664-75 (2015).
-
(2015)
Trends Plant Sci
, vol.20
, pp. 664-675
-
-
Li, Y.1
Pearl, S.A.2
Jackson, S.A.3
-
27
-
-
84931051773
-
Integrative random forest for gene regulatory network inference
-
Petralia, F. et al. Integrative random forest for gene regulatory network inference. Bioinformatics 31, i197-205 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. i197-205
-
-
Petralia, F.1
-
28
-
-
0742305866
-
Network biology: Understanding the cells functional organization
-
Barabási, A.-L. & Oltvai, Z. N. Network biology: understanding the cells functional organization. Nat Rev Genet 5, 101-13 (2004).
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabási, A.-L.1
Oltvai, Z.N.2
-
29
-
-
84862906124
-
Identification of putative cancer genes through data integration and comparative genomics between plants and humans
-
Quimbaya, M. et al. Identification of putative cancer genes through data integration and comparative genomics between plants and humans. Cell Mol Life Sci 69, 2041-55 (2012).
-
(2012)
Cell Mol Life Sci
, vol.69
, pp. 2041-2055
-
-
Quimbaya, M.1
-
30
-
-
82755161225
-
Auxin-dependent cell cycle reactivation through transcriptional regulation of arabidopsis e2fa by lateral organ boundary proteins
-
Berckmans, B. et al. Auxin-dependent cell cycle reactivation through transcriptional regulation of arabidopsis e2fa by lateral organ boundary proteins. Plant Cell 23, 3671-83 (2011).
-
(2011)
Plant Cell
, vol.23
, pp. 3671-3683
-
-
Berckmans, B.1
-
31
-
-
80055012555
-
The jaz proteins: A crucial interface in the jasmonate signaling cascade
-
Pauwels, L. & Goossens, A. The jaz proteins: A crucial interface in the jasmonate signaling cascade. Plant Cell 23, 3089-100 (2011).
-
(2011)
Plant Cell
, vol.23
, pp. 3089-3100
-
-
Pauwels, L.1
Goossens, A.2
-
32
-
-
77449150365
-
The e2fd/del2 factor is a component of a regulatory network controlling cell proliferation and development in arabidopsis
-
Sozzani, R. et al. The e2fd/del2 factor is a component of a regulatory network controlling cell proliferation and development in arabidopsis. Plant Mol Biol 72, 381-395 (2010).
-
(2010)
Plant Mol Biol
, vol.72
, pp. 381-395
-
-
Sozzani, R.1
-
33
-
-
34547870179
-
Genome-wide analysis of the core DNA replication machinery in the higher plants arabidopsis and rice
-
Shultz, R. W. et al. Genome-wide analysis of the core dna replication machinery in the higher plants arabidopsis and rice. Plant Physiol 144, 1697-714 (2007).
-
(2007)
Plant Physiol
, vol.144
, pp. 1697-1714
-
-
Shultz, R.W.1
-
34
-
-
33645818783
-
Cell type-specific role of the retinoblastoma/e2f pathway during arabidopsis leaf development
-
Desvoyes, B. et al. Cell type-specific role of the retinoblastoma/e2f pathway during arabidopsis leaf development. Plant Physiol 140, 67-80 (2006).
-
(2006)
Plant Physiol
, vol.140
, pp. 67-80
-
-
Desvoyes, B.1
-
35
-
-
76749139516
-
The mcm-binding protein etg1 AIDS sister chromatid cohesion required for postreplicative homologous recombination repair
-
Takahashi, N. et al. The mcm-binding protein etg1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genet 6, e1000817 (2010).
-
(2010)
PLoS Genet
, vol.6
, pp. e1000817
-
-
Takahashi, N.1
-
36
-
-
84897624321
-
A generic tool for transcription factor target gene discovery in arabidopsis cell suspension cultures based on tandem chromatin affinity purification
-
Verkest, A. et al. A generic tool for transcription factor target gene discovery in arabidopsis cell suspension cultures based on tandem chromatin affinity purification. Plant Physiol 164, 1122-33 (2014).
-
(2014)
Plant Physiol
, vol.164
, pp. 1122-1133
-
-
Verkest, A.1
-
37
-
-
84936970580
-
Regulation of jasmonate-mediated stamen development and seed production by a bhlh-myb complex in arabidopsis
-
Qi, T. et al. Regulation of jasmonate-mediated stamen development and seed production by a bhlh-myb complex in arabidopsis. Plant Cell 27, 1620-33 (2015).
-
(2015)
Plant Cell
, vol.27
, pp. 1620-1633
-
-
Qi, T.1
-
38
-
-
84878268346
-
Myc2: The master in action
-
Kazan, K. & Manners, J. M. Myc2: The master in action. Mol Plant 6, 686-703 (2013).
-
(2013)
Mol Plant
, vol.6
, pp. 686-703
-
-
Kazan, K.1
Manners, J.M.2
-
39
-
-
84922568257
-
Mutation of the arabidopsis calmodulin-like protein cml37 deregulates the jasmonate pathway and enhances susceptibility to herbivory
-
Scholz, S. S. et al. Mutation of the arabidopsis calmodulin-like protein cml37 deregulates the jasmonate pathway and enhances susceptibility to herbivory. Mol Plant 7, 1712-26 (2014).
-
(2014)
Mol Plant
, vol.7
, pp. 1712-1726
-
-
Scholz, S.S.1
-
40
-
-
84937802374
-
Multilayered organization of jasmonate signalling in the regulation of root growth
-
Gasperini, D. et al. Multilayered organization of jasmonate signalling in the regulation of root growth. PLoS Genet 11, e1005300 (2015).
-
(2015)
PLoS Genet
, vol.11
, pp. e1005300
-
-
Gasperini, D.1
-
41
-
-
84923238603
-
B-gata transcription factors-insights into their structure, regulation, and role in plant development
-
Behringer, C. & Schwechheimer, C. B-gata transcription factors-insights into their structure, regulation, and role in plant development. Front Plant Sci 6, 90 (2015).
-
(2015)
Front Plant Sci
, vol.6
, Issue.90
-
-
Behringer, C.1
Schwechheimer, C.2
-
42
-
-
84899714436
-
Molecular control of cell specification and cell differentiation during procambial development
-
Furuta, K. M. et al. Molecular control of cell specification and cell differentiation during procambial development. Annu Rev Plant Biol 65, 607-38 (2014).
-
(2014)
Annu Rev Plant Biol
, vol.65
, pp. 607-638
-
-
Furuta, K.M.1
-
43
-
-
34548531622
-
Modification of cell proliferation patterns alters leaf vein architecture in arabidopsis thaliana
-
Kang, J. et al. Modification of cell proliferation patterns alters leaf vein architecture in arabidopsis thaliana. Planta 226, 1207-18 (2007).
-
(2007)
Planta
, vol.226
, pp. 1207-1218
-
-
Kang, J.1
-
44
-
-
84927172064
-
Arabidopsis vim proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with met1
-
Kim, J. et al. Arabidopsis vim proteins regulate epigenetic silencing by modulating dna methylation and histone modification in cooperation with met1. Mol Plant 7, 1470-85 (2014).
-
(2014)
Mol Plant
, vol.7
, pp. 1470-1485
-
-
Kim, J.1
-
45
-
-
34250169781
-
Pxy, a receptor-like kinase essential for maintaining polarity during plant vascular-Tissue development
-
Fisher, K. & Turner, S. Pxy, a receptor-like kinase essential for maintaining polarity during plant vascular-Tissue development. Curr Biol 17, 1061-6 (2007).
-
(2007)
Curr Biol
, vol.17
, pp. 1061-1066
-
-
Fisher, K.1
Turner, S.2
-
46
-
-
0034681156
-
Plant organ size control: Aintegumenta regulates growth and cell numbers during organogenesis
-
Mizukami, Y. & Fischer, R. L. Plant organ size control: Aintegumenta regulates growth and cell numbers during organogenesis. Proc Natl Acad Sci USA 97, 942-7 (2000).
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 942-947
-
-
Mizukami, Y.1
Fischer, R.L.2
-
47
-
-
80054838468
-
Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in arabidopsis thaliana
-
Wynn, A. N. et al. Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in arabidopsis thaliana. PLoS One 6, e26231 (2011).
-
(2011)
PLoS One
, vol.6
, pp. e26231
-
-
Wynn, A.N.1
-
48
-
-
84901002654
-
Novel functional roles for perianthia and seuss during floral organ identity specification, floral meristem termination, and gynoecial development
-
Wynn, A. N. et al. Novel functional roles for perianthia and seuss during floral organ identity specification, floral meristem termination, and gynoecial development. Front Plant Sci 5, 130 (2014).
-
(2014)
Front Plant Sci
, vol.5
, Issue.130
-
-
Wynn, A.N.1
-
49
-
-
68249140337
-
Aintegumenta and aintegumenta-like6 act redundantly to regulate arabidopsis floral growth and patterning
-
Krizek, B. Aintegumenta and aintegumenta-like6 act redundantly to regulate arabidopsis floral growth and patterning. Plant Physiol 150, 1916-29 (2009).
-
(2009)
Plant Physiol
, vol.150
, pp. 1916-1929
-
-
Krizek, B.1
-
50
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
Alon, U. Network motifs: Theory and experimental approaches. Nat Rev Genet 8, 450-61 (2007).
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
51
-
-
84939604164
-
Cmonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism
-
Reiss, D. J. et al. cmonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res 43, e87 (2015).
-
(2015)
Nucleic Acids Res
, vol.43
, pp. e87
-
-
Reiss, D.J.1
-
52
-
-
84887283985
-
Integrated module and gene-specific regulatory inference implicates upstream signaling networks
-
Roy, S. et al. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PLoS Comput Biol 9, e1003252 (2013).
-
(2013)
PLoS Comput Biol
, vol.9
, pp. e1003252
-
-
Roy, S.1
-
53
-
-
84907307297
-
Inference of transcriptional networks in arabidopsis through conserved noncoding sequence analysis
-
Van de Velde, J. et al. Inference of transcriptional networks in arabidopsis through conserved noncoding sequence analysis. Plant Cell 26, 2729-45 (2014).
-
(2014)
Plant Cell
, vol.26
, pp. 2729-2745
-
-
Van De Velde, J.1
-
54
-
-
84976884426
-
Jaspar 2016: A major expansion and update of the open-Access database of transcription factor binding profiles
-
Mathelier, A. et al. Jaspar 2016: A major expansion and update of the open-Access database of transcription factor binding profiles. Nucleic Acids Res 44, D110-5 (2016).
-
(2016)
Nucleic Acids Res
, vol.44
, pp. D110-D115
-
-
Mathelier, A.1
-
55
-
-
84893861206
-
DNA-binding specificities of plant transcription factors and their potential to define target genes
-
Franco-Zorrilla, J. M. et al. Dna-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci USA 111, 2367-72 (2014).
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 2367-2372
-
-
Franco-Zorrilla, J.M.1
-
56
-
-
84907413210
-
Determination and inference of eukaryotic transcription factor sequence specificity
-
Weirauch, M. T. et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158, 1431-43 (2014).
-
(2014)
Cell
, vol.158
, pp. 1431-1443
-
-
Weirauch, M.T.1
-
57
-
-
16244362244
-
A gene expression map of arabidopsis thaliana development
-
Schmid, M. et al. A gene expression map of arabidopsis thaliana development. Nat Genet 37, 501-6 (2005).
-
(2005)
Nat Genet
, vol.37
, pp. 501-506
-
-
Schmid, M.1
-
58
-
-
84865249952
-
Transcription factors: From enhancer binding to developmental control
-
Spitz, F. & Furlong, E. E. M. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13, 613-26 (2012).
-
(2012)
Nat Rev Genet
, vol.13
, pp. 613-626
-
-
Spitz, F.1
Furlong, E.E.M.2
-
59
-
-
84911584312
-
Shortest connection networks and some generalizations
-
Prim, R. Shortest connection networks and some generalizations. Bell System Technical Journal (1957).
-
(1957)
Bell System Technical Journal
-
-
Prim, R.1
-
63
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S. Jr., C. D. G. & Vecchi, M. P. Optimization by simulated annealing. Science 220, 671-680 (1983).
-
(1983)
Science
, vol.220
, pp. 671-680
-
-
Kirkpatrick, S.1
Vecchi, M.P.2
|