-
1
-
-
79952152627
-
Nuclear DNA amounts in angiosperms: targets, trends and tomorrow
-
Bennett MD, Leitch IJ. Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann Bot. 2011;107:467-590.
-
(2011)
Ann Bot
, vol.107
, pp. 467-590
-
-
Bennett, M.D.1
Leitch, I.J.2
-
2
-
-
42949157236
-
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
-
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991-6.
-
(2008)
Nature
, vol.452
, pp. 991-996
-
-
Ming, R.1
Hou, S.2
Feng, Y.3
Yu, Q.4
Dionne-Laporte, A.5
Saw, J.H.6
-
3
-
-
84939168087
-
-
CoGePedia. [ http://genomevolution.org/wiki/index.php/Main_Page ]
-
-
-
-
4
-
-
76749150030
-
Genome sequencing and analysis of the model grass Brachypodium distachyon
-
The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763-8.
-
(2010)
Nature
, vol.463
, pp. 763-768
-
-
-
5
-
-
34848886909
-
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
-
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449:463-7.
-
(2007)
Nature
, vol.449
, pp. 463-467
-
-
Jaillon, O.1
Aury, J.M.2
Noel, B.3
Policriti, A.4
Clepet, C.5
Casagrande, A.6
-
6
-
-
33748760611
-
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
-
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006;313:1596-604.
-
(2006)
Science
, vol.313
, pp. 1596-1604
-
-
Tuskan, G.A.1
Difazio, S.2
Jansson, S.3
Bohlmann, J.4
Grigoriev, I.5
Hellsten, U.6
-
7
-
-
74549221016
-
Genome sequence of the palaeopolyploid soybean
-
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463:178-83.
-
(2010)
Nature
, vol.463
, pp. 178-183
-
-
Schmutz, J.1
Cannon, S.B.2
Schlueter, J.3
Ma, J.4
Mitros, T.5
Nelson, W.6
-
8
-
-
70450202132
-
The B73 maize genome: complexity, diversity, and dynamics
-
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112-5.
-
(2009)
Science
, vol.326
, pp. 1112-1115
-
-
Schnable, P.S.1
Ware, D.2
Fulton, R.S.3
Stein, J.C.4
Wei, F.5
Pasternak, S.6
-
9
-
-
0038104857
-
Genomic gene clustering analysis of pathways in eukaryotes
-
Lee JM, Sonnhammer EL. Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 2003;13:875-82.
-
(2003)
Genome Res
, vol.13
, pp. 875-882
-
-
Lee, J.M.1
Sonnhammer, E.L.2
-
10
-
-
63649155506
-
Evolutionary conservation of neighbouring gene pairs in plants
-
Liu X, Han B. Evolutionary conservation of neighbouring gene pairs in plants. Gene. 2009;437:71-9.
-
(2009)
Gene
, vol.437
, pp. 71-79
-
-
Liu, X.1
Han, B.2
-
11
-
-
26944466421
-
Local coexpression domains of two to four genes in the genome of Arabidopsis
-
Ren XY, Fiers MW, Stiekema WJ, Nap JP. Local coexpression domains of two to four genes in the genome of Arabidopsis. Plant Physiol. 2005;138:923-34.
-
(2005)
Plant Physiol
, vol.138
, pp. 923-934
-
-
Ren, X.Y.1
Fiers, M.W.2
Stiekema, W.J.3
Nap, J.P.4
-
12
-
-
34848897175
-
Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains
-
Ren XY, Stiekema WJ, Nap JP. Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains. Plant Mol Biol. 2007;65:205-17.
-
(2007)
Plant Mol Biol
, vol.65
, pp. 205-217
-
-
Ren, X.Y.1
Stiekema, W.J.2
Nap, J.P.3
-
13
-
-
3042569650
-
Coexpression of neighboring genes in the genome of Arabidopsis thaliana
-
Williams EJ, Bowles DJ. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res. 2004;14:1060-7.
-
(2004)
Genome Res
, vol.14
, pp. 1060-1067
-
-
Williams, E.J.1
Bowles, D.J.2
-
14
-
-
49549105303
-
Gene-rich islands for fiber development in the cotton genome
-
Xu Z, Kohel RJ, Song G, Cho J, Alabady M, Yu J, et al. Gene-rich islands for fiber development in the cotton genome. Genomics. 2008;92:173-83.
-
(2008)
Genomics
, vol.92
, pp. 173-183
-
-
Xu, Z.1
Kohel, R.J.2
Song, G.3
Cho, J.4
Alabady, M.5
Yu, J.6
-
15
-
-
33644871314
-
Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains
-
Zhan S, Horrocks J, Lukens LN. Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J. 2006;45:347-57.
-
(2006)
Plant J
, vol.45
, pp. 347-357
-
-
Zhan, S.1
Horrocks, J.2
Lukens, L.N.3
-
16
-
-
78149360928
-
A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes
-
Carmel L, Koonin EV. A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol. 2009;1:382-90.
-
(2009)
Genome Biol Evol
, vol.1
, pp. 382-390
-
-
Carmel, L.1
Koonin, E.V.2
-
17
-
-
33845631171
-
'Genome design' model and multicellular complexity: golden middle
-
Vinogradov AE. 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res. 2006;34:5906-14.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5906-5914
-
-
Vinogradov, A.E.1
-
18
-
-
78651408063
-
Gene expression patterns are correlated with genomic and genic structure in soybean
-
Woody JL, Severin AJ, Bolon Y-T, Joseph B, Diers BW, Farmer AD, et al. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 2011;54:10-8.
-
(2011)
Genome
, vol.54
, pp. 10-18
-
-
Woody, J.L.1
Severin, A.J.2
Bolon, Y.-T.3
Joseph, B.4
Diers, B.W.5
Farmer, A.D.6
-
19
-
-
84899103272
-
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
-
Neale D, Wegrzyn J, Stevens K, Zimin A, Puiu D, Crepeau M, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol. 2014;15:R59.
-
(2014)
Genome Biol
, vol.15
, pp. R59
-
-
Neale, D.1
Wegrzyn, J.2
Stevens, K.3
Zimin, A.4
Puiu, D.5
Crepeau, M.6
-
20
-
-
37249036997
-
Toward sequencing cotton (Gossypium) genomes
-
Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, Guo W, et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 2007;145:1303-10.
-
(2007)
Plant Physiol
, vol.145
, pp. 1303-1310
-
-
Chen, Z.J.1
Scheffler, B.E.2
Dennis, E.3
Triplett, B.A.4
Zhang, T.5
Guo, W.6
-
21
-
-
84875886528
-
Draft genome of the wheat A-genome progenitor Triticum urartu
-
Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, et al. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature. 2013;496:87-90.
-
(2013)
Nature
, vol.496
, pp. 87-90
-
-
Ling, H.Q.1
Zhao, S.2
Liu, D.3
Wang, J.4
Sun, H.5
Zhang, C.6
-
22
-
-
84875898037
-
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
-
Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature. 2013;496:91-5.
-
(2013)
Nature
, vol.496
, pp. 91-95
-
-
Jia, J.1
Zhao, S.2
Kong, X.3
Li, Y.4
Zhao, G.5
He, W.6
-
23
-
-
85048671720
-
Genome interplay in the grain transcriptome of hexaploid bread wheat
-
Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, et al. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science. 2014;345:1250091.
-
(2014)
Science
, vol.345
, pp. 1250091
-
-
Pfeifer, M.1
Kugler, K.G.2
Sandve, S.R.3
Zhan, B.4
Rudi, H.5
Hvidsten, T.R.6
-
24
-
-
84863595438
-
Gene expression in the developing aleurone and starchy endosperm of wheat
-
Gillies SA, Futardo A, Henry RJ. Gene expression in the developing aleurone and starchy endosperm of wheat. Plant Biotechnol J. 2012;10:668-79.
-
(2012)
Plant Biotechnol J
, vol.10
, pp. 668-679
-
-
Gillies, S.A.1
Futardo, A.2
Henry, R.J.3
-
25
-
-
84856395511
-
Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome
-
Pellny TK, Lovegrove A, Freeman J, Tosi P, Love CG, Knox JP, et al. Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome. Plant Physiol. 2012;158:612-27.
-
(2012)
Plant Physiol
, vol.158
, pp. 612-627
-
-
Pellny, T.K.1
Lovegrove, A.2
Freeman, J.3
Tosi, P.4
Love, C.G.5
Knox, J.P.6
-
26
-
-
53749101560
-
A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R
-
Bartoš J, Paux E, Kofler R, Havránková M, Kopecký D, Suchánková P, et al. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R. BMC Plant Biol. 2008;8:95.
-
(2008)
BMC Plant Biol
, vol.8
, pp. 95
-
-
Bartoš, J.1
Paux, E.2
Kofler, R.3
Havránková, M.4
Kopecký, D.5
Suchánková, P.6
-
28
-
-
77955908237
-
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
-
Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, et al. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell. 2010;22:1686-701.
-
(2010)
Plant Cell
, vol.22
, pp. 1686-1701
-
-
Choulet, F.1
Wicker, T.2
Rustenholz, C.3
Paux, E.4
Salse, J.5
Leroy, P.6
-
29
-
-
82855167376
-
A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat
-
Rustenholz C, Choulet F, Laugier C, Safár J, Simková H, Dolezel J, et al. A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol. 2011;157:1596-608.
-
(2011)
Plant Physiol
, vol.157
, pp. 1596-1608
-
-
Rustenholz, C.1
Choulet, F.2
Laugier, C.3
Safár, J.4
Simková, H.5
Dolezel, J.6
-
30
-
-
84890493574
-
The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
-
Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simkova H, et al. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol. 2013;14:R138.
-
(2013)
Genome Biol
, vol.14
, pp. R138
-
-
Raats, D.1
Frenkel, Z.2
Krugman, T.3
Dodek, I.4
Sela, H.5
Simkova, H.6
-
31
-
-
84904382612
-
A chromosome-based draft sequence of the hexaploid bread wheat genome
-
The International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat genome. Science. 2014;345:1251788.
-
(2014)
Science
, vol.345
, pp. 1251788
-
-
-
32
-
-
84870260198
-
Analysis of the bread wheat genome using whole-genome shotgun sequencing
-
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705-10.
-
(2012)
Nature
, vol.491
, pp. 705-710
-
-
Brenchley, R.1
Spannagl, M.2
Pfeifer, M.3
Barker, G.L.4
D'Amore, R.5
Allen, A.M.6
-
33
-
-
84904390032
-
Structural and functional partitioning of bread wheat chromosome 3B
-
Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, et al. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014;345:1249721.
-
(2014)
Science
, vol.345
, pp. 1249721
-
-
Choulet, F.1
Alberti, A.2
Theil, S.3
Glover, N.4
Barbe, V.5
Daron, J.6
-
34
-
-
84907150192
-
The map-based sequence of the rice genome
-
International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005;436:793-800.
-
(2005)
Nature
, vol.436
, pp. 793-800
-
-
-
35
-
-
58449137410
-
The Sorghum bicolor genome and the diversification of grasses
-
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457:551-6.
-
(2009)
Nature
, vol.457
, pp. 551-556
-
-
Paterson, A.H.1
Bowers, J.E.2
Bruggmann, R.3
Dubchak, I.4
Grimwood, J.5
Gundlach, H.6
-
36
-
-
76749150030
-
Genome sequencing and analysis of the model grass Brachypodium distachyon
-
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463:763-8.
-
(2010)
Nature
, vol.463
, pp. 763-768
-
-
Vogel, J.P.1
Garvin, D.F.2
Mockler, T.C.3
Schmutz, J.4
Rokhsar, D.5
Bevan, M.W.6
-
37
-
-
24344508130
-
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
-
Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, et al. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 2005;15:1274-83.
-
(2005)
Genome Res
, vol.15
, pp. 1274-1283
-
-
Ma, L.1
Chen, C.2
Liu, X.3
Jiao, Y.4
Su, N.5
Li, L.6
-
38
-
-
77956277181
-
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
-
Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010;20:1238-49.
-
(2010)
Genome Res
, vol.20
, pp. 1238-1249
-
-
Lu, T.1
Lu, G.2
Fan, D.3
Zhu, C.4
Li, W.5
Zhao, Q.6
-
39
-
-
79955875150
-
Genome-wide atlas of transcription during maize development
-
Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, et al. Genome-wide atlas of transcription during maize development. Plant J. 2011;66:553-63.
-
(2011)
Plant J
, vol.66
, pp. 553-563
-
-
Sekhon, R.S.1
Lin, H.2
Childs, K.L.3
Hansey, C.N.4
Buell, C.R.5
Leon, N.6
-
40
-
-
84876533257
-
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays
-
Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, et al. Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One. 2013;8:e61005.
-
(2013)
PLoS One
, vol.8
, pp. e61005
-
-
Sekhon, R.S.1
Briskine, R.2
Hirsch, C.N.3
Myers, C.L.4
Springer, N.M.5
Buell, C.R.6
-
41
-
-
77954249340
-
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants
-
Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, et al. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J. 2010;63:86-99.
-
(2010)
Plant J
, vol.63
, pp. 86-99
-
-
Libault, M.1
Farmer, A.2
Joshi, T.3
Takahashi, K.4
Langley, R.J.5
Franklin, L.D.6
-
42
-
-
0037560724
-
Allopolyploidy alters gene expression in the highly stable hexaploid wheat
-
He P, Friebe B, Gill B, Zhou J-M. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol. 2003;52:401-14.
-
(2003)
Plant Mol Biol
, vol.52
, pp. 401-414
-
-
He, P.1
Friebe, B.2
Gill, B.3
Zhou, J.-M.4
-
43
-
-
59449095429
-
Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids
-
Xu Y, Zhong L, Wu X, Fang X, Wang J. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta. 2009;229:471-83.
-
(2009)
Planta
, vol.229
, pp. 471-483
-
-
Xu, Y.1
Zhong, L.2
Wu, X.3
Fang, X.4
Wang, J.5
-
44
-
-
70349225934
-
Evolutionary and expression signatures of pseudogenes in arabidopsis and rice
-
Zou C, Lehti-Shiu MD, Thibaud-Nissen F, Prakash T, Buell CR, Shiu S-H. Evolutionary and expression signatures of pseudogenes in arabidopsis and rice. Plant Physiol. 2009;151:3-15.
-
(2009)
Plant Physiol
, vol.151
, pp. 3-15
-
-
Zou, C.1
Lehti-Shiu, M.D.2
Thibaud-Nissen, F.3
Prakash, T.4
Buell, C.R.5
Shiu, S.-H.6
-
45
-
-
68849088292
-
Identification and characterization of pseudogenes in the rice gene complement
-
Thibaud-Nissen F, Ouyang S, Buell CR. Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics. 2009;10:317.
-
(2009)
BMC Genomics
, vol.10
, pp. 317
-
-
Thibaud-Nissen, F.1
Ouyang, S.2
Buell, C.R.3
-
46
-
-
77958149797
-
Transcriptional activity of transposable elements in maize
-
Vicient C. Transcriptional activity of transposable elements in maize. BMC Genomics. 2010;11:601.
-
(2010)
BMC Genomics
, vol.11
, pp. 601
-
-
Vicient, C.1
-
47
-
-
84876782990
-
Pseudogenes: pseudo or real functional elements?
-
Li W, Yang W, Wang X-J. Pseudogenes: pseudo or real functional elements? J Genet Genomics. 2013;40:171-7.
-
(2013)
J Genet Genomics
, vol.40
, pp. 171-177
-
-
Li, W.1
Yang, W.2
Wang, X.-J.3
-
48
-
-
84856766408
-
Pseudogenes are not pseudo any more
-
Wen Y-Z, Zheng L-L, Qu L-H, Ayala FJ, Lun Z-R. Pseudogenes are not pseudo any more. RNA Biol. 2012;9:27-32.
-
(2012)
RNA Biol
, vol.9
, pp. 27-32
-
-
Wen, Y.-Z.1
Zheng, L.-L.2
Qu, L.-H.3
Ayala, F.J.4
Lun, Z.-R.5
-
49
-
-
84871910383
-
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in arabidopsis
-
Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in arabidopsis. Plant Cell. 2012;24:4333-45.
-
(2012)
Plant Cell
, vol.24
, pp. 4333-4345
-
-
Liu, J.1
Jung, C.2
Xu, J.3
Wang, H.4
Deng, S.5
Bernad, L.6
-
50
-
-
84907388006
-
Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa
-
Shuai P, Liang D, Tang S, Zhang Z, Ye C-Y, Su Y et al. Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot. 2014; doi:10.1093/jxb/eru256.
-
(2014)
J Exp Bot
-
-
Shuai, P.1
Liang, D.2
Tang, S.3
Zhang, Z.4
Ye, C.-Y.5
Su, Y.6
-
51
-
-
84880157749
-
Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE Library
-
Britto-Kido SA, Ferreira Neto JRC, Pandolfi V, Marcelino-Guimarães FC, Nepomuceno AL, Vilela Abdelnoor R, et al. Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE Library. Sci World J. 2013;2013:14.
-
(2013)
Sci World J
, vol.2013
, pp. 14
-
-
Britto-Kido, S.A.1
Ferreira Neto, J.R.C.2
Pandolfi, V.3
Marcelino-Guimarães, F.C.4
Nepomuceno, A.L.5
Vilela Abdelnoor, R.6
-
52
-
-
84879606358
-
Long noncoding RNAs: new regulators in plant development
-
Zhang Y-C, Chen Y-Q. Long noncoding RNAs: new regulators in plant development. Biochem Biophysical Res Commun. 2013;436:111-4.
-
(2013)
Biochem Biophysical Res Commun
, vol.436
, pp. 111-114
-
-
Zhang, Y.-C.1
Chen, Y.-Q.2
-
53
-
-
24644448635
-
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
-
Wang XJ, Gaasterland T, Chua NH. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol. 2005;6:R30.
-
(2005)
Genome Biol
, vol.6
, pp. R30
-
-
Wang, X.J.1
Gaasterland, T.2
Chua, N.H.3
-
54
-
-
67649096971
-
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array
-
Coram TE, Settles ML, Chen X. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics. 2009;10:253.
-
(2009)
BMC Genomics
, vol.10
, pp. 253
-
-
Coram, T.E.1
Settles, M.L.2
Chen, X.3
-
55
-
-
56349148789
-
Analysis of wheat sage tags reveals evidence for widespread antisense transcription
-
Poole RL, Barker GLA, Werner K, Biggi GF, Coghill J, Gibbings JG, et al. Analysis of wheat sage tags reveals evidence for widespread antisense transcription. BMC Genomics. 2008;9:475.
-
(2008)
BMC Genomics
, vol.9
, pp. 475
-
-
Poole, R.L.1
Barker, G.L.A.2
Werner, K.3
Biggi, G.F.4
Coghill, J.5
Gibbings, J.G.6
-
56
-
-
1442329649
-
Antisense transcripts with rice full-length cDNAs
-
Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, et al. Antisense transcripts with rice full-length cDNAs. Genome Biol. 2003;5:R5.
-
(2003)
Genome Biol
, vol.5
, pp. R5
-
-
Osato, N.1
Yamada, H.2
Satoh, K.3
Ooka, H.4
Yamamoto, M.5
Suzuki, K.6
-
57
-
-
84871390926
-
Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
-
Lu T, Zhu C, Lu G, Guo Y, Zhou Y, Zhang Z, et al. Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice. BMC Genomics. 2012;13:721.
-
(2012)
BMC Genomics
, vol.13
, pp. 721
-
-
Lu, T.1
Zhu, C.2
Lu, G.3
Guo, Y.4
Zhou, Y.5
Zhang, Z.6
-
58
-
-
84878328255
-
Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues
-
Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, et al. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol Plant. 2013;6:704-15.
-
(2013)
Mol Plant
, vol.6
, pp. 704-715
-
-
Zhang, X.1
Lii, Y.2
Wu, Z.3
Polishko, A.4
Zhang, H.5
Chinnusamy, V.6
-
59
-
-
0032487442
-
Transcription sites are not correlated with chromosome territories in wheat nuclei
-
Abranches R, Beven AF, Aragon-Alcaide L, Shaw PJ. Transcription sites are not correlated with chromosome territories in wheat nuclei. J Cell Biol. 1998;143:5-12.
-
(1998)
J Cell Biol
, vol.143
, pp. 5-12
-
-
Abranches, R.1
Beven, A.F.2
Aragon-Alcaide, L.3
Shaw, P.J.4
-
60
-
-
84907018247
-
The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression
-
Baker K, Bayer M, Cook N, Dreißig S, Dhillon T, Russell J, et al. The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. Plant J. 2014;79:981-92.
-
(2014)
Plant J
, vol.79
, pp. 981-992
-
-
Baker, K.1
Bayer, M.2
Cook, N.3
Dreißig, S.4
Dhillon, T.5
Russell, J.6
-
61
-
-
84884909700
-
Deep RNA-Seq uncovers the peach transcriptome landscape
-
Wang L, Zhao S, Gu C, Zhou Y, Zhou H, Ma J, et al. Deep RNA-Seq uncovers the peach transcriptome landscape. Plant Mol Biol. 2013;83:365-77.
-
(2013)
Plant Mol Biol
, vol.83
, pp. 365-377
-
-
Wang, L.1
Zhao, S.2
Gu, C.3
Zhou, Y.4
Zhou, H.5
Ma, J.6
-
62
-
-
84876315713
-
Biological functions of natural antisense transcripts
-
Werner A. Biological functions of natural antisense transcripts. BMC Biol. 2013;11:31.
-
(2013)
BMC Biol
, vol.11
, pp. 31
-
-
Werner, A.1
-
63
-
-
84860280329
-
Regulation of inducible gene expression by natural antisense transcripts
-
Nishizawa M, Okumura T, Ikeya Y, Kimura T. Regulation of inducible gene expression by natural antisense transcripts. Front Biosci. 2012;17:938-58.
-
(2012)
Front Biosci
, vol.17
, pp. 938-958
-
-
Nishizawa, M.1
Okumura, T.2
Ikeya, Y.3
Kimura, T.4
-
64
-
-
69249217649
-
Regulatory roles of natural antisense transcripts
-
Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol. 2009;10:637-43.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, pp. 637-643
-
-
Faghihi, M.A.1
Wahlestedt, C.2
-
65
-
-
34447263110
-
Selection for the miniaturization of highly expressed genes
-
Li SW, Feng L, Niu DK. Selection for the miniaturization of highly expressed genes. Biochem Biophys Res Commun. 2007;360:586-92.
-
(2007)
Biochem Biophys Res Commun
, vol.360
, pp. 586-592
-
-
Li, S.W.1
Feng, L.2
Niu, D.K.3
-
66
-
-
4744355710
-
Compactness of human housekeeping genes: selection for economy or genomic design?
-
Vinogradov AE. Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet. 2004;20:248-53.
-
(2004)
Trends Genet
, vol.20
, pp. 248-253
-
-
Vinogradov, A.E.1
-
67
-
-
84861890038
-
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
-
Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 2012;22:1184-95.
-
(2012)
Genome Res
, vol.22
, pp. 1184-1195
-
-
Marquez, Y.1
Brown, J.W.2
Simpson, C.3
Barta, A.4
Kalyna, M.5
-
68
-
-
84879157497
-
Genome-wide landscape of alternative splicing events in Brachypodium distachyon
-
Walters B, Lum G, Sablok G, Min XJ. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res. 2013;20:163-71.
-
(2013)
DNA Res
, vol.20
, pp. 163-171
-
-
Walters, B.1
Lum, G.2
Sablok, G.3
Min, X.J.4
-
69
-
-
84902301794
-
RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
-
Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, et al. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol. 2014;14:169.
-
(2014)
BMC Plant Biol
, vol.14
, pp. 169
-
-
Wang, L.1
Cao, C.2
Ma, Q.3
Zeng, Q.4
Wang, H.5
Cheng, Z.6
-
70
-
-
84870265846
-
A physical, genetic and functional sequence assembly of the barley genome
-
Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, et al. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491:711-6.
-
(2012)
Nature
, vol.491
, pp. 711-716
-
-
Mayer, K.F.1
Waugh, R.2
Brown, J.W.3
Schulman, A.4
Langridge, P.5
Platzer, M.6
-
71
-
-
84866843094
-
Alternative splicing in plants-coming of age
-
Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW. Alternative splicing in plants-coming of age. Trends Plant Sci. 2012;17:616-23.
-
(2012)
Trends Plant Sci
, vol.17
, pp. 616-623
-
-
Syed, N.H.1
Kalyna, M.2
Marquez, Y.3
Barta, A.4
Brown, J.W.5
-
72
-
-
50649109231
-
Genome-wide analyses of alternative splicing in plants: opportunities and challenges
-
Barbazuk WB, Fu Y, McGinnis KM. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 2008;18:1381-92.
-
(2008)
Genome Res
, vol.18
, pp. 1381-1392
-
-
Barbazuk, W.B.1
Fu, Y.2
McGinnis, K.M.3
-
73
-
-
77951120000
-
Alternative splicing and evolution: diversification, exon definition and function
-
Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet. 2010;11:345-55.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 345-355
-
-
Keren, H.1
Lev-Maor, G.2
Ast, G.3
-
74
-
-
33646484347
-
Genomewide comparative analysis of alternative splicing in plants
-
Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A. 2006;103:7175-80.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 7175-7180
-
-
Wang, B.B.1
Brendel, V.2
-
75
-
-
0038692119
-
Human housekeeping genes are compact
-
Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet. 2003;19:362-5.
-
(2003)
Trends Genet
, vol.19
, pp. 362-365
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
77
-
-
0142092546
-
The signature of selection mediated by expression on human genes
-
Urrutia AO, Hurst LD. The signature of selection mediated by expression on human genes. Genome Res. 2003;13:2260-4.
-
(2003)
Genome Res
, vol.13
, pp. 2260-2264
-
-
Urrutia, A.O.1
Hurst, L.D.2
-
78
-
-
33745638358
-
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
-
Seoighe C, Gehring C, Hurst LD. Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet. 2005;1:e13.
-
(2005)
PLoS Genet
, vol.1
, pp. e13
-
-
Seoighe, C.1
Gehring, C.2
Hurst, L.D.3
-
79
-
-
84858383903
-
Maize (Zea mays L) genome diversity as revealed by RNA-sequencing
-
Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR. Maize (Zea mays L) genome diversity as revealed by RNA-sequencing. PLoS One. 2012;7:e33071.
-
(2012)
PLoS One
, vol.7
, pp. e33071
-
-
Hansey, C.N.1
Vaillancourt, B.2
Sekhon, R.S.3
Leon, N.4
Kaeppler, S.M.5
Buell, C.R.6
-
80
-
-
33748195447
-
Evolutionary origin and maintenance of coexpressed gene clusters in mammals
-
Sémon M, Duret L. Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol. 2006;23:1715-23.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1715-1723
-
-
Sémon, M.1
Duret, L.2
-
81
-
-
0003328368
-
Evidence for large domains of similarly expressed genes in the Drosophila genome
-
Spellman PT, Rubin GM. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 2002;1:5.
-
(2002)
J Biol
, vol.1
, pp. 5
-
-
Spellman, P.T.1
Rubin, G.M.2
-
82
-
-
77951888464
-
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions
-
Chen WH, de Meaux J, Lercher MJ. Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions. BMC Genomics. 2010;11:178.
-
(2010)
BMC Genomics
, vol.11
, pp. 178
-
-
Chen, W.H.1
Meaux, J.2
Lercher, M.J.3
-
83
-
-
79952744855
-
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
-
Schnable JC, Springer NM, Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A. 2011;108:4069-74.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 4069-4074
-
-
Schnable, J.C.1
Springer, N.M.2
Freeling, M.3
-
84
-
-
84872611513
-
Homoeolog expression bias and expression level dominance in allopolyploid cotton
-
Yoo MJ, Szadkowski E, Wendel JF. Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity (Edinb). 2013;110:171-80.
-
(2013)
Heredity (Edinb)
, vol.110
, pp. 171-180
-
-
Yoo, M.J.1
Szadkowski, E.2
Wendel, J.F.3
-
85
-
-
84860424914
-
Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa
-
Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, et al. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One. 2012;7:e36442.
-
(2012)
PLoS One
, vol.7
, pp. e36442
-
-
Cheng, F.1
Wu, J.2
Fang, L.3
Sun, S.4
Liu, B.5
Lin, K.6
-
86
-
-
4844223232
-
Tissue-specific spatial organization of genomes
-
Parada L, McQueen P, Misteli T. Tissue-specific spatial organization of genomes. Genome Biol. 2004;5:R44.
-
(2004)
Genome Biol
, vol.5
, pp. R44
-
-
Parada, L.1
McQueen, P.2
Misteli, T.3
-
87
-
-
33847386173
-
Chromosome organization: new facts, new models
-
Branco MR, Pombo A. Chromosome organization: new facts, new models. Trends Cell Biol. 2007;17:127-34.
-
(2007)
Trends Cell Biol
, vol.17
, pp. 127-134
-
-
Branco, M.R.1
Pombo, A.2
-
88
-
-
76449120030
-
Exploring the relationship between interphase gene positioning, transcriptional regulation and the nuclear matrix
-
Elcock LS, Bridger JM. Exploring the relationship between interphase gene positioning, transcriptional regulation and the nuclear matrix. Biochem Soc Trans. 2010;38:263-7.
-
(2010)
Biochem Soc Trans
, vol.38
, pp. 263-267
-
-
Elcock, L.S.1
Bridger, J.M.2
-
89
-
-
0031762360
-
Non-Rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells
-
Dong F, Jiang J. Non-Rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res. 1998;6:551-8.
-
(1998)
Chromosome Res
, vol.6
, pp. 551-558
-
-
Dong, F.1
Jiang, J.2
-
90
-
-
0035108110
-
The polar arrangement of telomeres in interphase and meiosis. Rabl Organization and the Bouquet
-
Cowan CR, Carlton PM, Cande WZ. The polar arrangement of telomeres in interphase and meiosis. Rabl Organization and the Bouquet. Plant Physiol. 2001;125:532-8.
-
(2001)
Plant Physiol
, vol.125
, pp. 532-538
-
-
Cowan, C.R.1
Carlton, P.M.2
Cande, W.Z.3
-
91
-
-
0036902097
-
The architecture of interphase chromosomes and gene positioning are altered by changes in DNA methylation and histone acetylation
-
Santos AP, Abranches R, Stoger E, Beven A, Viegas W, Shaw PJ. The architecture of interphase chromosomes and gene positioning are altered by changes in DNA methylation and histone acetylation. J Cell Sci. 2002;115:4597-605.
-
(2002)
J Cell Sci
, vol.115
, pp. 4597-4605
-
-
Santos, A.P.1
Abranches, R.2
Stoger, E.3
Beven, A.4
Viegas, W.5
Shaw, P.J.6
-
92
-
-
84939123559
-
-
FastQC. [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc ]
-
-
-
-
93
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-5.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Baren, M.J.6
-
94
-
-
84939172237
-
-
TopHat. [ http://ccb.jhu.edu/software/tophat/index.shtml ]
-
-
-
-
95
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
96
-
-
68549104404
-
The sequence alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
97
-
-
84939200934
-
-
Cufflinks. [ http://cole-trapnell-lab.github.io/cufflinks/ ]
-
-
-
-
98
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002;296:79-92.
-
(2002)
Science
, vol.296
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.4
Li, S.5
Liu, B.6
-
99
-
-
84880266648
-
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494-512.
-
(2013)
Nat Protoc
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
Bowden, J.6
-
100
-
-
84939207013
-
-
Changepoint-package. [ http://www.inside-r.org/packages/cran/changepoint/docs/changepoint ]
-
-
-
-
101
-
-
84939123031
-
-
R software. [ www.r-project.org ]
-
-
-
-
102
-
-
84939210556
-
-
Hierarchical clustering explorer software. [ http://www.cs.umd.edu/hcil/hce/ ]
-
-
-
-
103
-
-
31344469004
-
GOBU: toward an integration interface for biological object
-
Lin W, Chen Y, Ho J, Hsiao C. GOBU: toward an integration interface for biological object. J Information Sci Eng. 2006;22:19-30.
-
(2006)
J Information Sci Eng
, vol.22
, pp. 19-30
-
-
Lin, W.1
Chen, Y.2
Ho, J.3
Hsiao, C.4
|