-
1
-
-
0034576561
-
Count me out
-
comment1006
-
Petsko G.A. Count me out. Genome Biol 1 (2000) comment1006
-
(2000)
Genome Biol
, vol.1
-
-
Petsko, G.A.1
-
2
-
-
0036733640
-
Computational prediction of eukaryotic protein-coding genes
-
Zhang M.Q. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 3 (2002) 698-710
-
(2002)
Nat Rev Genet
, vol.3
, pp. 698-710
-
-
Zhang, M.Q.1
-
3
-
-
0036796369
-
Current methods of gene prediction, their strengths and weaknesses
-
Mathé C., Sagot M.F., Schiex T., and Rouzé P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 30 (2002) 4103-4117
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4103-4117
-
-
Mathé, C.1
Sagot, M.F.2
Schiex, T.3
Rouzé, P.4
-
4
-
-
33748641351
-
EGASP: the human ENCODE genome annotation assessment project
-
Roderic G., Flicek P., Abril J.F., Reymond A., Lagarde J., Denoeud F., Antonarakis S., Ashburner M., Bajic V.B., Birney E., et al. EGASP: the human ENCODE genome annotation assessment project. Genome Biol 7 Suppl I (2006) S21-S31
-
(2006)
Genome Biol
, vol.7
, Issue.SUPPL. I
-
-
Roderic, G.1
Flicek, P.2
Abril, J.F.3
Reymond, A.4
Lagarde, J.5
Denoeud, F.6
Antonarakis, S.7
Ashburner, M.8
Bajic, V.B.9
Birney, E.10
-
5
-
-
6044226955
-
Consistent over-estimation of gene number in complex plant genomes
-
Bennetzen J.L., Coleman C., Liu R., Ma J., and Ramakrishna W. Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7 (2004) 1-5
-
(2004)
Curr Opin Plant Biol
, vol.7
, pp. 1-5
-
-
Bennetzen, J.L.1
Coleman, C.2
Liu, R.3
Ma, J.4
Ramakrishna, W.5
-
6
-
-
33344476905
-
Annotating the genome of Medicago truncatula
-
Town C.D. Annotating the genome of Medicago truncatula. Curr Opin Plant Biol 9 (2006) 122-127
-
(2006)
Curr Opin Plant Biol
, vol.9
, pp. 122-127
-
-
Town, C.D.1
-
7
-
-
20144366003
-
The genomes of Oryza sativa: a history of duplications
-
Yu J., Wang J., Lin W., Li S., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol 3 (2005) e38
-
(2005)
PLoS Biol
, vol.3
-
-
Yu, J.1
Wang, J.2
Lin, W.3
Li, S.4
Zhou, J.5
Ni, P.6
Dong, W.7
Hu, S.8
Zeng, C.9
Zhang, J.10
-
8
-
-
25844507235
-
Differential methylation of genes and repeats in land plants
-
The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration. The authors discuss the results of pilot methylation filtration sequencing projects in several plant species. They estimated the gene content of different plant genomes by analyzing their whole-genome shotgun sequence set. In general, they report that most plant species have large numbers of genes.
-
Rabinowicz P.D., Citek R., Budiman M.A., Nunberg A., Bedell J.A., Lakey N., O'Shaughnessy A.L., Nascimento L.U., McCombie W.R., and Martienssen R.A. Differential methylation of genes and repeats in land plants. Genome Res 15 (2005) 1431-1440. The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration. The authors discuss the results of pilot methylation filtration sequencing projects in several plant species. They estimated the gene content of different plant genomes by analyzing their whole-genome shotgun sequence set. In general, they report that most plant species have large numbers of genes.
-
(2005)
Genome Res
, vol.15
, pp. 1431-1440
-
-
Rabinowicz, P.D.1
Citek, R.2
Budiman, M.A.3
Nunberg, A.4
Bedell, J.A.5
Lakey, N.6
O'Shaughnessy, A.L.7
Nascimento, L.U.8
McCombie, W.R.9
Martienssen, R.A.10
-
9
-
-
33749532842
-
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
-
A comparative study of the partial genome sequences of two legumes. Gene prediction and annotation of approximately half of the sequenced genomes suggest the existence of more than 40 000 genes in both species. There is also evidence that a genome duplication occurred before the divergence of Medicago and Lotus.
-
Cannon S.B., Sterck L., Rombauts S., Sato S., Cheung F., Gouzy J., Wang X., Mudge J., Vasdewani J., Schiex T., et al. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103 (2006) 14959-14964. A comparative study of the partial genome sequences of two legumes. Gene prediction and annotation of approximately half of the sequenced genomes suggest the existence of more than 40 000 genes in both species. There is also evidence that a genome duplication occurred before the divergence of Medicago and Lotus.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 14959-14964
-
-
Cannon, S.B.1
Sterck, L.2
Rombauts, S.3
Sato, S.4
Cheung, F.5
Gouzy, J.6
Wang, X.7
Mudge, J.8
Vasdewani, J.9
Schiex, T.10
-
10
-
-
33748760611
-
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw)
-
The authors publish the poplar genome sequence, the second one of a dicot plant. There is evidence for three whole-genome duplications, two of which were most probably shared with Arabidopsis, whereas one occurred more recently, after the divergence of Arabidopsis and poplar. Although both species have experienced three whole-genome duplications, poplar has retained many more protein-coding genes than Arabidopsis. On average, poplar has from 1.4 to 1.6 copies for every Arabidopsis gene, although the number of different protein domains is similar in each genome.
-
Tuskan G., DiFazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313 (2006) 1596-1604. The authors publish the poplar genome sequence, the second one of a dicot plant. There is evidence for three whole-genome duplications, two of which were most probably shared with Arabidopsis, whereas one occurred more recently, after the divergence of Arabidopsis and poplar. Although both species have experienced three whole-genome duplications, poplar has retained many more protein-coding genes than Arabidopsis. On average, poplar has from 1.4 to 1.6 copies for every Arabidopsis gene, although the number of different protein domains is similar in each genome.
-
(2006)
Science
, vol.313
, pp. 1596-1604
-
-
Tuskan, G.1
DiFazio, S.2
Jansson, S.3
Bohlmann, J.4
Grigoriev, I.5
Hellsten, U.6
Putnam, N.7
Ralph, S.8
Rombauts, S.9
Salamov, A.10
-
11
-
-
27144519666
-
Genome duplication and the origin of angiosperms
-
De Bodt S., Maere S., and Van de Peer Y. Genome duplication and the origin of angiosperms. Trends Ecol Evol 20 (2005) 591-597
-
(2005)
Trends Ecol Evol
, vol.20
, pp. 591-597
-
-
De Bodt, S.1
Maere, S.2
Van de Peer, Y.3
-
12
-
-
33744822985
-
Widespread genome duplications throughout the history of flowering plants
-
Genome duplications have been demonstrated for core eudicots, such as Arabidopsis and poplar, and for Poaceae, such as rice. However, this study uses EST data to show that genome duplications have also occurred in more basal angiosperm lineages. The authors also provide evidence for ancient polyploidy in the Gnetales, but there is no evidence for genome duplications in pine.
-
Ciu L., Wall P.K., Heebens-Mack J.H., Lindsay B.G., Soltis D.E., Doyle J.J., Soltis P.S., Carlson J.E., Arumuganathan K., Barakat A., et al. Widespread genome duplications throughout the history of flowering plants. Genome Res 16 (2006) 738-749. Genome duplications have been demonstrated for core eudicots, such as Arabidopsis and poplar, and for Poaceae, such as rice. However, this study uses EST data to show that genome duplications have also occurred in more basal angiosperm lineages. The authors also provide evidence for ancient polyploidy in the Gnetales, but there is no evidence for genome duplications in pine.
-
(2006)
Genome Res
, vol.16
, pp. 738-749
-
-
Ciu, L.1
Wall, P.K.2
Heebens-Mack, J.H.3
Lindsay, B.G.4
Soltis, D.E.5
Doyle, J.J.6
Soltis, P.S.7
Carlson, J.E.8
Arumuganathan, K.9
Barakat, A.10
-
13
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
This paper describes a mathematical model that simulates the birth and death dynamics of genes. By simulating age distributions of duplicated genes in the Arabidopsis genome, and then distinguishing between different classes of genes, the authors show that regulatory genes are mainly retained following whole-genome duplications. In contrast, there is selection against the retention of such genes when they are duplicated individually. Other genes, for instance those involved in responses to biotic stress or in secondary metabolism, have similar probabilities of being retained however they are duplicated.
-
Maere S., De Bodt S., Raes J., Casneuf T., Van Montagu M., Kuiper M., and Van de Peer Y. Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102 (2005) 5454-5459. This paper describes a mathematical model that simulates the birth and death dynamics of genes. By simulating age distributions of duplicated genes in the Arabidopsis genome, and then distinguishing between different classes of genes, the authors show that regulatory genes are mainly retained following whole-genome duplications. In contrast, there is selection against the retention of such genes when they are duplicated individually. Other genes, for instance those involved in responses to biotic stress or in secondary metabolism, have similar probabilities of being retained however they are duplicated.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
De Bodt, S.2
Raes, J.3
Casneuf, T.4
Van Montagu, M.5
Kuiper, M.6
Van de Peer, Y.7
-
14
-
-
20144386497
-
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
-
Stolc V., Samanta M.P., Tongprasit W., Sethi H., Liang S., Nelson D.C., Hegeman A., Nelson C., Rancour D., and Beddnarek S. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA 102 (2006) 4453-4458
-
(2006)
Proc Natl Acad Sci USA
, vol.102
, pp. 4453-4458
-
-
Stolc, V.1
Samanta, M.P.2
Tongprasit, W.3
Sethi, H.4
Liang, S.5
Nelson, D.C.6
Hegeman, A.7
Nelson, C.8
Rancour, D.9
Beddnarek, S.10
-
15
-
-
24644490196
-
Elucidation of the small RNA component of the transcriptome
-
Lu C., Tej S.S., Luo S., Haudenschild C.D., Meyer B.C., and Green P.J. Elucidation of the small RNA component of the transcriptome. Science 309 (2005) 1567-1569
-
(2005)
Science
, vol.309
, pp. 1567-1569
-
-
Lu, C.1
Tej, S.S.2
Luo, S.3
Haudenschild, C.D.4
Meyer, B.C.5
Green, P.J.6
-
16
-
-
84959057192
-
Eugene: a eukaryotic gene finder that combines several sources of evidence
-
Schiex T., Moisan A., and Rouzé P. Eugene: a eukaryotic gene finder that combines several sources of evidence. Lect Notes Comput Sci 2066 (2001) 111-125
-
(2001)
Lect Notes Comput Sci
, vol.2066
, pp. 111-125
-
-
Schiex, T.1
Moisan, A.2
Rouzé, P.3
-
17
-
-
0037268583
-
Comparative gene prediction in human and mouse
-
Parra G., Agarwal P., Abril J.F., Wiehe T., Fickett J.W., and Guigo R. Comparative gene prediction in human and mouse. Genome Res 13 (2003) 108-117
-
(2003)
Genome Res
, vol.13
, pp. 108-117
-
-
Parra, G.1
Agarwal, P.2
Abril, J.F.3
Wiehe, T.4
Fickett, J.W.5
Guigo, R.6
-
18
-
-
8844252293
-
TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders
-
Majoros W.H., Pertea M., and Slazberg S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders. Bioinformatics 20 (2004) 2878-2879
-
(2004)
Bioinformatics
, vol.20
, pp. 2878-2879
-
-
Majoros, W.H.1
Pertea, M.2
Slazberg, S.L.3
-
19
-
-
24644485994
-
JIGSAW: integration of multiple sources of evidence for gene prediction
-
Allen J.E., and Salzberg S.L. JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21 (2005) 3596-3603
-
(2005)
Bioinformatics
, vol.21
, pp. 3596-3603
-
-
Allen, J.E.1
Salzberg, S.L.2
-
21
-
-
27544456832
-
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
-
The authors describe the efforts to re-annotate the Arabidopsis genome since its original publication. To further improve the annotations, new pipelines with an emphasis on utilizing full-length cDNAs and EST sequences have been set up to automate gene structure annotation.
-
Haas B.J., Wortman J.R., Ronning C.M., Hannick L.I., Smith Jr. R.K., Maiti R., Chan A.P., Yu C., Farzad M., Wu D., White O., and Town C.D. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 3 (2005) 7. The authors describe the efforts to re-annotate the Arabidopsis genome since its original publication. To further improve the annotations, new pipelines with an emphasis on utilizing full-length cDNAs and EST sequences have been set up to automate gene structure annotation.
-
(2005)
BMC Biol
, vol.3
, pp. 7
-
-
Haas, B.J.1
Wortman, J.R.2
Ronning, C.M.3
Hannick, L.I.4
Smith Jr., R.K.5
Maiti, R.6
Chan, A.P.7
Yu, C.8
Farzad, M.9
Wu, D.10
White, O.11
Town, C.D.12
-
22
-
-
28844444029
-
Combined evidence annotation of transposable elements in genome sequences
-
Quesneville H., Bergman C.M., Andrieu O., Autard D., Nouaud D., Ashburner M., and Anxolabehere D. Combined evidence annotation of transposable elements in genome sequences. PLoS Comp Biol 1 (2005) 166-175
-
(2005)
PLoS Comp Biol
, vol.1
, pp. 166-175
-
-
Quesneville, H.1
Bergman, C.M.2
Andrieu, O.3
Autard, D.4
Nouaud, D.5
Ashburner, M.6
Anxolabehere, D.7
-
23
-
-
33645897982
-
Comparative genomics as a tool for gene discovery
-
Windsor A.J., and Mitchell-Olds T. Comparative genomics as a tool for gene discovery. Curr Opin Biotechnol 17 (2006) 1-7
-
(2006)
Curr Opin Biotechnol
, vol.17
, pp. 1-7
-
-
Windsor, A.J.1
Mitchell-Olds, T.2
-
24
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
The Arabidopsis Genome Initiative1
-
25
-
-
33644840915
-
Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants
-
Xiao Y.-L., Smith S.R., Ishmael N., Redman J.C., Kumar N., Monaghan E.L., Ayele M., Haas B.J., Wu H.C., and Town C.D. Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol 139 (2005) 1323-1337
-
(2005)
Plant Physiol
, vol.139
, pp. 1323-1337
-
-
Xiao, Y.-L.1
Smith, S.R.2
Ishmael, N.3
Redman, J.C.4
Kumar, N.5
Monaghan, E.L.6
Ayele, M.7
Haas, B.J.8
Wu, H.C.9
Town, C.D.10
-
26
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
Rhee S.Y., Beavis W., Berardini T.Z., Chen G., Dixon D., Doyle A., Garcia-Hernandez M., Huala E., Lander G., and Montoya M. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31 (2003) 224-228
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 224-228
-
-
Rhee, S.Y.1
Beavis, W.2
Berardini, T.Z.3
Chen, G.4
Dixon, D.5
Doyle, A.6
Garcia-Hernandez, M.7
Huala, E.8
Lander, G.9
Montoya, M.10
-
27
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
Goff S.A., Ricke D., Lan T.H., Presting G., Wang R., Dunn M., Glazebrook J., Sessions A., Oeller P., Varma H., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296 (2002) 92-100
-
(2002)
Science
, vol.296
, pp. 92-100
-
-
Goff, S.A.1
Ricke, D.2
Lan, T.H.3
Presting, G.4
Wang, R.5
Dunn, M.6
Glazebrook, J.7
Sessions, A.8
Oeller, P.9
Varma, H.10
-
28
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
Yu J., Hu S., Wang J., Wong G.K.-S., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002) 79-92
-
(2002)
Science
, vol.296
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.-S.4
Li, S.5
Liu, B.6
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
-
29
-
-
18744378026
-
Exploring the plant transcriptome through phylogenetic profiling
-
Vandepoele K., and Van de Peer Y. Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol 137 (2005) 31-42
-
(2005)
Plant Physiol
, vol.137
, pp. 31-42
-
-
Vandepoele, K.1
Van de Peer, Y.2
-
30
-
-
33646484347
-
Genomewide comparative analysis of alternative splicing in plants
-
In this study, the authors show that more than 20% of both Arabidopsis and rice genes with EST or cDNA evidence are alternatively spliced. Although not all splice variants will be biologically functional, alternative splicing undoubtedly plays an important role in adding to plant proteome diversity.
-
Wang B.-B., and Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA 103 (2006) 7175-7180. In this study, the authors show that more than 20% of both Arabidopsis and rice genes with EST or cDNA evidence are alternatively spliced. Although not all splice variants will be biologically functional, alternative splicing undoubtedly plays an important role in adding to plant proteome diversity.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 7175-7180
-
-
Wang, B.-B.1
Brendel, V.2
-
32
-
-
0037109058
-
The hidden duplication past of Arabidopsis thaliana
-
Simillion C., Vandepoele K., Van Montagu M., Zabeau M., and Van de Peer Y. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99 (2002) 13627-13632
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 13627-13632
-
-
Simillion, C.1
Vandepoele, K.2
Van Montagu, M.3
Zabeau, M.4
Van de Peer, Y.5
-
33
-
-
0037468758
-
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
-
Bowers J.E., Chapman B.A., Rong J., and Paterson A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 (2003) 433-438
-
(2003)
Nature
, vol.422
, pp. 433-438
-
-
Bowers, J.E.1
Chapman, B.A.2
Rong, J.3
Paterson, A.H.4
-
34
-
-
3142732892
-
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution
-
Blanc G., and Wolfe K.H. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16 (2004) 1679-1691
-
(2004)
Plant Cell
, vol.16
, pp. 1679-1691
-
-
Blanc, G.1
Wolfe, K.H.2
-
35
-
-
4444363053
-
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
-
Seoighe C., and Gehring C. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20 (2004) 461-464
-
(2004)
Trends Genet
, vol.20
, pp. 461-464
-
-
Seoighe, C.1
Gehring, C.2
-
36
-
-
33745610025
-
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
-
Freeling M., and Thomas B.C. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16 (2006) 805-814
-
(2006)
Genome Res
, vol.16
, pp. 805-814
-
-
Freeling, M.1
Thomas, B.C.2
-
37
-
-
33646859550
-
Nonrandom divergence of gene expression following gene and genome duplications in plants
-
Casneuf T., De Bodt S., Raes J., Maere S., and Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in plants. Genome Biol 7 (2006) R13
-
(2006)
Genome Biol
, vol.7
-
-
Casneuf, T.1
De Bodt, S.2
Raes, J.3
Maere, S.4
Van de Peer, Y.5
-
38
-
-
0037313579
-
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
-
Blanc G., Hokamp K., and Wolfe K.H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13 (2003) 137-144
-
(2003)
Genome Res
, vol.13
, pp. 137-144
-
-
Blanc, G.1
Hokamp, K.2
Wolfe, K.H.3
-
39
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch M., and Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 290 (2000) 1151-1155
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
40
-
-
0037047055
-
Assaying gene content in Arabidopsis
-
Allen K.D. Assaying gene content in Arabidopsis. Proc Natl Acad Sci USA 99 (2002) 9568-9572
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 9568-9572
-
-
Allen, K.D.1
-
42
-
-
0141564555
-
Evidence that rice, and other cereals, are ancient aneuploids
-
Vandepoele K., Simillion C., and Van de Peer Y. Evidence that rice, and other cereals, are ancient aneuploids. Plant Cell 15 (2003) 2192-2202
-
(2003)
Plant Cell
, vol.15
, pp. 2192-2202
-
-
Vandepoele, K.1
Simillion, C.2
Van de Peer, Y.3
|