-
1
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and, Zhao, K., (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
2
-
-
0035206095
-
The Arabidopsis BELL1 and KNOX TALE homeodomain proteins interact through a domain conserved between plants and animals
-
Bellaoui, M., Pidkowich, M.S., Samach, A., Kushalappa, K., Kohalmi, S.E., Modrusan, Z., Crosby, W.L., and, Haughn, G.W., (2001) The Arabidopsis BELL1 and KNOX TALE homeodomain proteins interact through a domain conserved between plants and animals. Plant Cell, 13, 2455-2470.
-
(2001)
Plant Cell
, vol.13
, pp. 2455-2470
-
-
Bellaoui, M.1
Pidkowich, M.S.2
Samach, A.3
Kushalappa, K.4
Kohalmi, S.E.5
Modrusan, Z.6
Crosby, W.L.7
Haughn, G.W.8
-
3
-
-
33747450593
-
KNAT6: an Arabidopsis homeobox gene involved in meristem activity and organ separation
-
Belles-Boix, E., Hamant, O., Witiak, S.M., Morin, H., Traas, J., and, Pautot, V., (2006) KNAT6: an Arabidopsis homeobox gene involved in meristem activity and organ separation. Plant Cell Online, 18, 1900-1907.
-
(2006)
Plant Cell Online
, vol.18
, pp. 1900-1907
-
-
Belles-Boix, E.1
Hamant, O.2
Witiak, S.M.3
Morin, H.4
Traas, J.5
Pautot, V.6
-
4
-
-
78751513159
-
A stele-enriched gene regulatory network in the Arabidopsis root
-
Brady, S.M., Zhang, L., Megraw, M., et al. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7, 459. doi: 10.1038/msb.2010.114
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 459
-
-
Brady, S.M.1
Zhang, L.2
Megraw, M.3
-
5
-
-
0041827272
-
Phyllotactic pattern and stem cell fate are determined by the Arabidopsis homeobox gene BELLRINGER
-
Byrne, M.E., Groover, A.T., Fontana, J.R., and, Martienssen, R.A., (2003) Phyllotactic pattern and stem cell fate are determined by the Arabidopsis homeobox gene BELLRINGER. Development, 130, 3941-3950.
-
(2003)
Development
, vol.130
, pp. 3941-3950
-
-
Byrne, M.E.1
Groover, A.T.2
Fontana, J.R.3
Martienssen, R.A.4
-
6
-
-
0036337173
-
ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis
-
Byrne, M.E., Simorowski, J., and, Martienssen, R.A., (2002) ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis. Development, 129, 1957-1965.
-
(2002)
Development
, vol.129
, pp. 1957-1965
-
-
Byrne, M.E.1
Simorowski, J.2
Martienssen, R.A.3
-
7
-
-
84865712383
-
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
-
Cheng, C., Alexander, R., Min, R., et al. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 22, 1658-1667.
-
(2012)
Genome Res.
, vol.22
, pp. 1658-1667
-
-
Cheng, C.1
Alexander, R.2
Min, R.3
-
8
-
-
71649100687
-
The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth
-
Du, J., Mansfield, S.D., and, Groover, A.T., (2009) The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth. Plant J. 60, 1000-1014.
-
(2009)
Plant J.
, vol.60
, pp. 1000-1014
-
-
Du, J.1
Mansfield, S.D.2
Groover, A.T.3
-
9
-
-
79952215358
-
The Populus class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems
-
Du, J., Miura, E., Robischon, M., Martinez, C., and, Groover, A., (2011) The Populus class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems. PLoS ONE, 6, e17458.
-
(2011)
PLoS ONE
, vol.6
-
-
Du, J.1
Miura, E.2
Robischon, M.3
Martinez, C.4
Groover, A.5
-
10
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENDODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
11
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon, S., and, Gentleman, R., (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
12
-
-
82355191640
-
Enhanced Y1H assays for Arabidopsis
-
Gaudinier, A., Zhang, L., Reece-Hoyes, J.S., et al. (2011) Enhanced Y1H assays for Arabidopsis. Nat. Methods, 8, 1053-1055.
-
(2011)
Nat. Methods
, vol.8
, pp. 1053-1055
-
-
Gaudinier, A.1
Zhang, L.2
Reece-Hoyes, J.S.3
-
13
-
-
84858593012
-
The iPlant collaborative: cyberinfrastructure for plant biology
-
Goff, S.A., Vaughn, M., McKay, S., et al. (2011) The iPlant collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2, doi: 10.3389/fpls.2011.00034.
-
(2011)
Front. Plant Sci.
, vol.2
-
-
Goff, S.A.1
Vaughn, M.2
McKay, S.3
-
14
-
-
33747599143
-
The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium
-
Groover, A.T., Mansfield, S.D., DiFazio, S.P., Dupper, G., Fontana, J.R., Millar, R., and, Wang, Y., (2006) The Populus homeobox gene ARBORKNOX1 reveals overlapping mechanisms regulating the shoot apical meristem and the vascular cambium. Plant Mol. Biol. 61, 917-932.
-
(2006)
Plant Mol. Biol.
, vol.61
, pp. 917-932
-
-
Groover, A.T.1
Mansfield, S.D.2
Difazio, S.P.3
Dupper, G.4
Fontana, J.R.5
Millar, R.6
Wang, Y.7
-
15
-
-
0035807830
-
A transcriptional roadmap to wood formation
-
Hertzberg, M., Aspeborg, H., Schrader, J., et al. (2001) A transcriptional roadmap to wood formation. Proc.Natl Acad. Sci. USA, 98, 14732-14737.
-
(2001)
Proc.Natl Acad. Sci. USA
, vol.98
, pp. 14732-14737
-
-
Hertzberg, M.1
Aspeborg, H.2
Schrader, J.3
-
16
-
-
84912124204
-
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
-
Heyndrickx, K.S., de Velde, J.V., Wang, C., Weigel, D., and, Vandepoele, K., (2014) A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell Online, 26, 3894-3910.
-
(2014)
Plant Cell Online
, vol.26
, pp. 3894-3910
-
-
Heyndrickx, K.S.1
De Velde, J.V.2
Wang, C.3
Weigel, D.4
Vandepoele, K.5
-
17
-
-
0035775725
-
A new approach to decoding life: systems biology
-
Ideker, T., Galitski, T., and, Hood, L., (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372.
-
(2001)
Annu. Rev. Genomics Hum. Genet.
, vol.2
, pp. 343-372
-
-
Ideker, T.1
Galitski, T.2
Hood, L.3
-
18
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M., and, Wold, B., (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
19
-
-
84901742688
-
Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association
-
Karczewski, K.J., Snyder, M., Altman, R.B., and, Tatonetti, N.P., (2014) Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association. PLoS Genet. 10, e1004122.
-
(2014)
PLoS Genet.
, vol.10
-
-
Karczewski, K.J.1
Snyder, M.2
Altman, R.B.3
Tatonetti, N.P.4
-
20
-
-
84865777819
-
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
-
Landt, S.G., Marinov, G.K., Kundaje, A., et al. (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813-1831.
-
(2012)
Genome Res.
, vol.22
, pp. 1813-1831
-
-
Landt, S.G.1
Marinov, G.K.2
Kundaje, A.3
-
21
-
-
79955564639
-
Measuring reproducibility of high-throughput experiments
-
Li, Q., Brown, J.B., Huang, H., and, Bickel, P.J., (2011) Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat., 5, 1752-1779.
-
(2011)
Ann. Appl. Stat.
, vol.5
, pp. 1752-1779
-
-
Li, Q.1
Brown, J.B.2
Huang, H.3
Bickel, P.J.4
-
22
-
-
84919654093
-
Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
-
Liu, L., Missirian, V., Zinkgraf, M., Groover, A., and, Filkov, V., (2014) Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. BMC Genom. 15 (Suppl 5), S3.
-
(2014)
BMC Genom.
, vol.15
, pp. S3
-
-
Liu, L.1
Missirian, V.2
Zinkgraf, M.3
Groover, A.4
Filkov, V.5
-
23
-
-
84919665128
-
The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function
-
Liu, L., Zinkgraf, M., Patzold, E., Beers, E., Filkov, V., and, Groover, A., (2015) The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. New Phytol., 205, 1469-8137.
-
(2015)
New Phytol.
, vol.205
, pp. 1469-8137
-
-
Liu, L.1
Zinkgraf, M.2
Patzold, E.3
Beers, E.4
Filkov, V.5
Groover, A.6
-
24
-
-
55849151275
-
Systems approaches to identifying gene regulatory networks in plants
-
Long, T., Brady, S., and, Benfey, P., (2008) Systems approaches to identifying gene regulatory networks in plants. Annu. Rev. Cell Dev. Biol. 24, 81-103.
-
(2008)
Annu. Rev. Cell Dev. Biol.
, vol.24
, pp. 81-103
-
-
Long, T.1
Brady, S.2
Benfey, P.3
-
25
-
-
70450265540
-
A comprehensive classification and evolutionary analysis of plant Homeobox genes
-
Mukherjee, K., Brocchieri, L., and, Bürglin, T.R., (2009) A comprehensive classification and evolutionary analysis of plant Homeobox genes. Mol. Biol. Evol. 26, 2775-2794.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 2775-2794
-
-
Mukherjee, K.1
Brocchieri, L.2
Bürglin, T.R.3
-
26
-
-
48549086906
-
Interaction of KNAT6 and KNAT2 with BREVIPEDICELLUS and PENNYWISE in Arabidopsis inflorescences
-
Ragni, L., Belles-Boix, E., Günl, M., and, Pautot, V., (2008) Interaction of KNAT6 and KNAT2 with BREVIPEDICELLUS and PENNYWISE in Arabidopsis inflorescences. Plant Cell, 20, 888-900.
-
(2008)
Plant Cell
, vol.20
, pp. 888-900
-
-
Ragni, L.1
Belles-Boix, E.2
Günl, M.3
Pautot, V.4
-
27
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson, G., Hirst, M., Bainbridge, M., 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.1
Hirst, M.2
Bainbridge, M.3
-
28
-
-
79952290449
-
The Populus Class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems
-
Robischon, M., Du, J., Miura, E., and, Groover, A., (2011) The Populus Class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems. Plant Physiol. 155, 1214-1225.
-
(2011)
Plant Physiol.
, vol.155
, pp. 1214-1225
-
-
Robischon, M.1
Du, J.2
Miura, E.3
Groover, A.4
-
29
-
-
4544352472
-
A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity
-
Schrader, J., Nilsson, J., Mellerowicz, E., Berglund, A., Nilsson, P., Hertzberg, M., and, Sandberg, G., (2004) A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity. Plant Cell, 16, 2278-2292.
-
(2004)
Plant Cell
, vol.16
, pp. 2278-2292
-
-
Schrader, J.1
Nilsson, J.2
Mellerowicz, E.3
Berglund, A.4
Nilsson, P.5
Hertzberg, M.6
Sandberg, G.7
-
30
-
-
65549102151
-
The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome
-
Sjodin, A., Street, N.R., Sandberg, G., Gustafsson, P., and, Jansson, S., (2009) The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome. New Phytol. 182, 1013-1025.
-
(2009)
New Phytol.
, vol.182
, pp. 1013-1025
-
-
Sjodin, A.1
Street, N.R.2
Sandberg, G.3
Gustafsson, P.4
Jansson, S.5
-
31
-
-
0042922504
-
The interaction of two homeobox genes, BREVIPEDICELLUS and PENNYWISE, regulates internode patterning in the Arabidopsis inflorescence
-
Smith, H.M.S., and, Hake, S., (2003) The interaction of two homeobox genes, BREVIPEDICELLUS and PENNYWISE, regulates internode patterning in the Arabidopsis inflorescence. Plant Cell, 15, 1717-1727.
-
(2003)
Plant Cell
, vol.15
, pp. 1717-1727
-
-
Smith, H.M.S.1
Hake, S.2
-
32
-
-
84925491555
-
An Arabidopsis gene regulatory network for secondary cell wall synthesis
-
Taylor-Teeples, M., Lin, L., de Lucas, M., et al. (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 517, 571-575.
-
(2015)
Nature
, vol.517
, pp. 571-575
-
-
Taylor-Teeples, M.1
Lin, L.2
De Lucas, M.3
-
33
-
-
84895794723
-
Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets
-
Teng, L., He, B., Gao, P., Gao, L., and, Tan, K., (2014) Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. Nucleic Acids Res. 42, e24.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. e24
-
-
Teng, L.1
He, B.2
Gao, P.3
Gao, L.4
Tan, K.5
-
34
-
-
84898030115
-
A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms
-
Van de Poel, B., Bulens, I., Hertog, M.L., Nicolai, B.M., and, Geeraerd, A.H., (2014) A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms. New Phytol. 202, 952-963.
-
(2014)
New Phytol.
, vol.202
, pp. 952-963
-
-
Van De Poel, B.1
Bulens, I.2
Hertog, M.L.3
Nicolai, B.M.4
Geeraerd, A.H.5
-
35
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y., Liu, T., Meyer, C., et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137.
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.3
-
36
-
-
77951947707
-
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
-
Zhu, L.J., Gazin, C., Lawson, N.D., Pages, H., Lin, S.M., Lapointe, D.S., and, Green, M.R., (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics, 11, 237.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 237
-
-
Zhu, L.J.1
Gazin, C.2
Lawson, N.D.3
Pages, H.4
Lin, S.M.5
Lapointe, D.S.6
Green, M.R.7
|