-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
Arabidopsis Genome Initiative
-
Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
3
-
-
0011542799
-
The Pfam protein families
-
Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
-
(2002)
Database Nucleic Acids Res
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
4
-
-
0033869323
-
Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions
-
Bennetzen, J.L. 2000a. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
-
(2000)
Plant Cell
, vol.12
, pp. 1021-1029
-
-
Bennetzen, J.L.1
-
5
-
-
0033976643
-
Transposable element contributions to plant gene and genome evolution
-
Bennetzen, J.L. 2000b. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
-
(2000)
Plant Mol. Biol
, vol.42
, pp. 251-269
-
-
Bennetzen, J.L.1
-
6
-
-
0037023308
-
The rice genome. Opening the door to comparative plant biology
-
Bennetzen, J.L. 2002. The rice genome. Opening the door to comparative plant biology. Science 296: 60-63.
-
(2002)
Science
, vol.296
, pp. 60-63
-
-
Bennetzen, J.L.1
-
7
-
-
0000637348
-
Do plants have a one-way ticket to genomic obesity?
-
Bennetzen, J.L. and Kellog, E. 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 7: 1509-1514.
-
(1997)
Plant Cell
, vol.7
, pp. 1509-1514
-
-
Bennetzen, J.L.1
Kellog, E.2
-
8
-
-
0030466156
-
Sequence composition and organization in the Sh2/A1-homologous region of rice
-
Chen, M. and Bennetzen, J.L. 1996. Sequence composition and organization in the Sh2/A1-homologous region of rice. Plant Mol. Biol. 32: 999-1001.
-
(1996)
Plant Mol. Biol
, vol.32
, pp. 999-1001
-
-
Chen, M.1
Bennetzen, J.L.2
-
9
-
-
0030908359
-
Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes
-
Chen, M., SanMiguel, P., de Oliveira, A.C., Woo, S.S., Zhang, H., Wing, R., and Bennetzen, J.L. 1997. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. 94: 3431-3435.
-
(1997)
Proc. Natl. Acad. Sci
, vol.94
, pp. 3431-3435
-
-
Chen, M.1
SanMiguel, P.2
de Oliveira, A.C.3
Woo, S.S.4
Zhang, H.5
Wing, R.6
Bennetzen, J.L.7
-
10
-
-
0031239091
-
Comparative genetics in the grasses
-
Devos, K.M. and Gale, M.D. 1997. Comparative genetics in the grasses. Plant Mol. Biol. 35: 3-15.
-
(1997)
Plant Mol. Biol
, vol.35
, pp. 3-15
-
-
Devos, K.M.1
Gale, M.D.2
-
11
-
-
0001272136
-
Chromosomal rearrangements in the rye genome relative to that of wheat
-
Devos, K.M., Atkinson, M.D., Chinoy, C.N., Harcourt, R.L., Koebner, R.M.D., Liu, C.J., Masojc, P., Xie, D.X., and Gale, M.D. 1993. Chromosomal rearrangements in the rye genome relative to that of wheat. Theor. Appl. Genet. 85: 673-680.
-
(1993)
Theor. Appl. Genet
, vol.85
, pp. 673-680
-
-
Devos, K.M.1
Atkinson, M.D.2
Chinoy, C.N.3
Harcourt, R.L.4
Koebner, R.M.D.5
Liu, C.J.6
Masojc, P.7
Xie, D.X.8
Gale, M.D.9
-
12
-
-
0032855945
-
Arabidopsis-rice: Will colinearity allow gene prediction across the eudicot-monocot divide?
-
Devos, K.M., Beales, J., Nagamura, Y., and Sasaki, T. 1999. Arabidopsis-rice: Will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res. 9: 825-829.
-
(1999)
Genome Res
, vol.9
, pp. 825-829
-
-
Devos, K.M.1
Beales, J.2
Nagamura, Y.3
Sasaki, T.4
-
13
-
-
0034691159
-
Transposons and genome evolution in plants
-
Fedoroff, N. 2000. Transposons and genome evolution in plants. Proc. Natl. Acad. Sci. 97: 7002-7007.
-
(2000)
Proc. Natl. Acad. Sci
, vol.97
, pp. 7002-7007
-
-
Fedoroff, N.1
-
14
-
-
0033529227
-
High gene density is conserved at syntenic loci of small and large grass genomes
-
Feuillet, C. and Keller, B. 1999. High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. 96: 8265-8270.
-
(1999)
Proc. Natl. Acad. Sci
, vol.96
, pp. 8265-8270
-
-
Feuillet, C.1
Keller, B.2
-
15
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., and Postlethwait, J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
-
(1999)
Genetics
, vol.151
, pp. 1531-1545
-
-
Force, A.1
Lynch, M.2
Pickett, F.B.3
Amores, A.4
Yan, Y.L.5
Postlethwait, J.6
-
16
-
-
0032561403
-
Plant comparative genetics after 10 years
-
Gale, M.D. and Devos, K.M. 1998. Plant comparative genetics after 10 years. Science 282: 656-659.
-
(1998)
Science
, vol.282
, pp. 656-659
-
-
Gale, M.D.1
Devos, K.M.2
-
17
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
Goff, S., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
-
(2002)
Science
, vol.296
, pp. 92-100
-
-
Goff, S.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
-
18
-
-
0026544795
-
Retroelements in higher plants
-
Grandbastien, M. 1992. Retroelements in higher plants. Trends Genet. 8: 103-108.
-
(1992)
Trends Genet
, vol.8
, pp. 103-108
-
-
Grandbastien, M.1
-
19
-
-
0034636168
-
Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis
-
Grant, D., Cregan, P., and Shoemaker, R.C. 2000. Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Acad. Sci. 97: 4168-4173.
-
(2000)
Proc. Natl. Acad. Sci
, vol.97
, pp. 4168-4173
-
-
Grant, D.1
Cregan, P.2
Shoemaker, R.C.3
-
21
-
-
0034213530
-
Colinearity and gene density in grass genomes
-
Keller, B. and Feuillet, C. 2000. Colinearity and gene density in grass genomes. Trends Plant Sci. 5: 246-251.
-
(2000)
Trends Plant Sci
, vol.5
, pp. 246-251
-
-
Keller, B.1
Feuillet, C.2
-
22
-
-
0031238680
-
Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle
-
Kilian, A., Chen, J., Han, F., Steffenson, B., and Kleinhofs, A. 1997. Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol. Biol. 35: 187-195.
-
(1997)
Plant Mol. Biol
, vol.35
, pp. 187-195
-
-
Kilian, A.1
Chen, J.2
Han, F.3
Steffenson, B.4
Kleinhofs, A.5
-
23
-
-
0034255126
-
Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
-
Ku, H.M., Vision, T., Liu, J., and Tanksley, S.D. 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl Acad. Sci. 97: 9121-9126.
-
(2000)
Proc. Natl Acad. Sci
, vol.97
, pp. 9121-9126
-
-
Ku, H.M.1
Vision, T.2
Liu, J.3
Tanksley, S.D.4
-
24
-
-
0033066718
-
REPuter: Fast computation of maximal repeats in complete genomes
-
Kurtz, S. and Schleiermacher, C. 1999. REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
-
(1999)
Bioinformatics
, vol.15
, pp. 426-427
-
-
Kurtz, S.1
Schleiermacher, C.2
-
25
-
-
1042307072
-
Transposon diversity in Arabidopsis thaliana
-
Le, Q.H., Wright, S., Yu, Z., and Bureau, T. 2000. Transposon diversity in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 97: 7376-7381.
-
(2000)
Proc. Natl. Acad. Sci
, vol.97
, pp. 7376-7381
-
-
Le, Q.H.1
Wright, S.2
Yu, Z.3
Bureau, T.4
-
26
-
-
0035107159
-
Mutator transposase is widespread in the grasses
-
Lisch, D.R., Freeling, M., Langham, R.J., and Choy, M.Y. 2001. Mutator transposase is widespread in the grasses. Plant Physiol. 125: 1293-1303.
-
(2001)
Plant Physiol
, vol.125
, pp. 1293-1303
-
-
Lisch, D.R.1
Freeling, M.2
Langham, R.J.3
Choy, M.Y.4
-
27
-
-
0035215379
-
Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order
-
Liu, H., Sachidanandam, R., and Stein, L. 2001. Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res. 11: 2020-2026.
-
(2001)
Genome Res
, vol.11
, pp. 2020-2026
-
-
Liu, H.1
Sachidanandam, R.2
Stein, L.3
-
28
-
-
0034917750
-
Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana
-
Mayer, K., Murphy, G., Tarchini, R., Wambutt, R., Volckaert, G., Pohl T., Dusterhoft, A., Stiekema, W., Entian, K.D., Terryn, N., et al. 2001. Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res. 11: 1167-1174.
-
(2001)
Genome Res
, vol.11
, pp. 1167-1174
-
-
Mayer, K.1
Murphy, G.2
Tarchini, R.3
Wambutt, R.4
Volckaert, G.5
Pohl, T.6
Dusterhoft, A.7
Stiekema, W.8
Entian, K.D.9
Terryn, N.10
-
30
-
-
2642665514
-
A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome
-
Panstruga, R., Buschges, R., Piffanelli, P., and Schulze-Lefert, P. 1998. A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res. 26: 1056-1062.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1056-1062
-
-
Panstruga, R.1
Buschges, R.2
Piffanelli, P.3
Schulze-Lefert, P.4
-
31
-
-
0033381623
-
Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
-
Pavy, N., Rombauts, S., Déhais, P., Mathé, C., Ramana, D.V., Leroy, P., and Rouzé, P. 1999. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences. Bioinformatics 15: 887-899.
-
(1999)
Bioinformatics
, vol.15
, pp. 887-899
-
-
Pavy, N.1
Rombauts, S.2
Déhais, P.3
Mathé, C.4
Ramana, D.V.5
Leroy, P.6
Rouzé, P.7
-
32
-
-
0011543118
-
Investigating ancient duplication events in the Arabidopsis genome
-
(eds. A. Meyer and Y. Van de Peer). Kluwer Academic Publishers, Dordrecht, The Netherlands (in press)
-
Raes, J., Vandepoele, K., Simillion, C., Saeys, Y., and Van de Peer, T. 2002. Investigating ancient duplication events in the Arabidopsis genome. In Genome evolution (eds. A. Meyer and Y. Van de Peer). Kluwer Academic Publishers, Dordrecht, The Netherlands (in press).
-
(2002)
Genome Evolution
-
-
Raes, J.1
Vandepoele, K.2
Simillion, C.3
Saeys, Y.4
Van de Peer, T.5
-
33
-
-
0035032414
-
Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes
-
Rossberg, M., Theres, K., Acarkan, A., Herrero, R., Schmitt, T., Schumacher, K., Schmitz, G., and Schmidt, R. 2001. Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13: 979-988.
-
(2001)
Plant Cell
, vol.13
, pp. 979-988
-
-
Rossberg, M.1
Theres, K.2
Acarkan, A.3
Herrero, R.4
Schmitt, T.5
Schumacher, K.6
Schmitz, G.7
Schmidt, R.8
-
34
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 85-94.
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
35
-
-
0033118642
-
Genome annotation: Which tools do we have for it?
-
Rouzé, P., Pavy, N., and Rombauts, S. 1999. Genome annotation: Which tools do we have for it? Curr. Opin. Plant Biol. 2: 90-95.
-
(1999)
Curr. Opin. Plant Biol
, vol.2
, pp. 90-95
-
-
Rouzé, P.1
Pavy, N.2
Rombauts, S.3
-
36
-
-
0033635022
-
Artemis: Sequence visualization and annotation
-
Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M., and Barrell, B. 2000. Artemis: Sequence visualization and annotation. Bioinformatics 16: 944-945.
-
(2000)
Bioinformatics
, vol.16
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.6
Barrell, B.7
-
37
-
-
0036083902
-
RiceGAAS: An automated annotation system and database for rice genome sequence
-
Sakata, K., Nagamura, Y., Numa, H., Antonio, B., Nagasaki, H., Idonuma, A., Watanabe, W., Shimizu, Y., Horiuchi, I., Matsumoto, T., et al. 2002. RiceGAAS: An automated annotation system and database for rice genome sequence. Nucleic Acids Res. 30: 98-102.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 98-102
-
-
Sakata, K.1
Nagamura, Y.2
Numa, H.3
Antonio, B.4
Nagasaki, H.5
Idonuma, A.6
Watanabe, W.7
Shimizu, Y.8
Horiuchi, I.9
Matsumoto, T.10
-
38
-
-
0034013059
-
International Rice Genome Sequencing Project: The effort to completely sequence the rice genome
-
Sasaki, T. and Burr, B. 2000. International Rice Genome Sequencing Project: The effort to completely sequence the rice genome. Curr. Opin. Plant Biol. 3: 138-141.
-
(2000)
Curr. Opin. Plant Biol
, vol.3
, pp. 138-141
-
-
Sasaki, T.1
Burr, B.2
-
39
-
-
0034096819
-
Synteny: Recent advances and future prospects
-
Schmidt, R. 2000. Synteny: Recent advances and future prospects. Curr. Opin. Plant Biol. 3: 97-102.
-
(2000)
Curr. Opin. Plant Biol
, vol.3
, pp. 97-102
-
-
Schmidt, R.1
-
40
-
-
0034084963
-
The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4
-
Tarchini, R., Biddle, P., Wineland, R., Tingey, S., and Rafalski, A. 2000. The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381-391.
-
(2000)
Plant Cell
, vol.12
, pp. 381-391
-
-
Tarchini, R.1
Biddle, P.2
Wineland, R.3
Tingey, S.4
Rafalski, A.5
-
41
-
-
0033594895
-
Colinearity and its exceptions in orthologous adh regions of maize and sorghum
-
Tikhonov, A.P., SanMiguel, P.J., Nakajima, Y., Gorenstein, N.M., Bennetzen, J.L., and Avramova, Z. 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl Acad. Sci. 96: 7409-7414.
-
(1999)
Proc. Natl Acad. Sci
, vol.96
, pp. 7409-7414
-
-
Tikhonov, A.P.1
SanMiguel, P.J.2
Nakajima, Y.3
Gorenstein, N.M.4
Bennetzen, J.L.5
Avramova, Z.6
-
42
-
-
0034819040
-
The ghost of selection past: Rates of evolution and functional divergence of anciently duplicated genes
-
Van de Peer, Y., Taylor, J.S., Braasch, I., and Meyer, A. 2001. The ghost of selection past: Rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53: 436-446.
-
(2001)
J. Mol. Evol
, vol.53
, pp. 436-446
-
-
Van de Peer, Y.1
Taylor, J.S.2
Braasch, I.3
Meyer, A.4
-
43
-
-
0033210688
-
Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana
-
van Dodeweerd, A.M., Hall, C.R., Bent, E.G., Johnson, S.J., Bevan, M.W., and Bancroft, I. 1999. Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana. Genome 42: 887-892.
-
(1999)
Genome
, vol.42
, pp. 887-892
-
-
van Dodeweerd, A.M.1
Hall, C.R.2
Bent, E.G.3
Johnson, S.J.4
Bevan, M.W.5
Bancroft, I.6
-
44
-
-
0035102628
-
Active retrotransposons are a common feature of grass genomes
-
Vicient, C.M., Jaaskelainen, M.J., Kalendar, R., and Schulman, A.H. 2001. Active retrotransposons are a common feature of grass genomes. Plant Physiol. 125: 1283-1292.
-
(2001)
Plant Physiol
, vol.125
, pp. 1283-1292
-
-
Vicient, C.M.1
Jaaskelainen, M.J.2
Kalendar, R.3
Schulman, A.H.4
-
45
-
-
0034671866
-
The origins of genomic duplications in Arabidopsis
-
Vision, T.J., Brown, D.G., and Tanksley, S.D. 2000. The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
-
(2000)
Science
, vol.290
, pp. 2114-2117
-
-
Vision, T.J.1
Brown, D.G.2
Tanksley, S.D.3
-
46
-
-
0033974956
-
Genome evolution in polyploids
-
Wendel, J.F. 2000. Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
-
(2000)
Plant Mol. Biol
, vol.42
, pp. 225-249
-
-
Wendel, J.F.1
-
47
-
-
0035823864
-
Evolution of the angiosperms: Calibrating the family tree
-
Wikström, N., Savolainen, V., and Chase, M.W. 2001. Evolution of the angiosperms: Calibrating the family tree. Proc. R. Soc. Lond. B Biol. Sci. 268: 2211-2220.
-
(2001)
Proc. R. Soc. Lond. B Biol. Sci
, vol.268
, pp. 2211-2220
-
-
Wikström, N.1
Savolainen, V.2
Chase, M.W.3
-
48
-
-
0032954807
-
Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages
-
Yang, Y.W., Lai, K.N., Tai, P.Y., and Li, W.H. 1999. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 48: 597-604.
-
(1999)
J. Mol. Evol
, vol.48
, pp. 597-604
-
-
Yang, Y.W.1
Lai, K.N.2
Tai, P.Y.3
Li, W.H.4
-
49
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 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
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
|