-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
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
-
-
0033891353
-
Extensive duplication and reshuffling in the Arabidopsis genome
-
Blanc, G., Barakat, A., Guyot, R., Cooke, R., and Delseny, M. (2000). Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12, 1093-1101.
-
(2000)
Plant Cell
, vol.12
, pp. 1093-1101
-
-
Blanc, G.1
Barakat, A.2
Guyot, R.3
Cooke, R.4
Delseny, M.5
-
4
-
-
0037313579
-
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
-
Blanc, G., Hokamp, K., and Wolfe, K.H. (2003). A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13, 137-144.
-
(2003)
Genome Res.
, vol.13
, pp. 137-144
-
-
Blanc, G.1
Hokamp, K.2
Wolfe, K.H.3
-
5
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., and Schneider, M. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
6
-
-
0037468758
-
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
-
Bowers, J.E., Chapman, B.A., Rong, J., and Paterson, A.H. (2003). Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433-438.
-
(2003)
Nature
, vol.422
, pp. 433-438
-
-
Bowers, J.E.1
Chapman, B.A.2
Rong, J.3
Paterson, A.H.4
-
7
-
-
0036009912
-
An integrated physical and genetic map of the rice genome
-
Chen, M., et al. (2002). An integrated physical and genetic map of the rice genome. Plant Cell 14, 537-545.
-
(2002)
Plant Cell
, vol.14
, pp. 537-545
-
-
Chen, M.1
-
8
-
-
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.A., and Bennetzen, J.L. (1997). Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. USA 94, 3431-3435.
-
(1997)
Proc. Natl. Acad. Sci. USA
, 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.A.6
Bennetzen, J.L.7
-
9
-
-
0037213551
-
Vertebrate evolution: Doubling and shuffling with a full deck
-
Durand, D. (2003). Vertebrate evolution: Doubling and shuffling with a full deck. Trends Genet. 19, 2-5.
-
(2003)
Trends Genet.
, vol.19
, pp. 2-5
-
-
Durand, D.1
-
10
-
-
0037153127
-
Sequence and analysis of rice chromosome 4
-
Feng, Q., et al. (2002). Sequence and analysis of rice chromosome 4. Nature 420, 316-320.
-
(2002)
Nature
, vol.420
, pp. 316-320
-
-
Feng, Q.1
-
11
-
-
0032478340
-
Comparative genetics in the grasses
-
Gale, M.D., and Devos, K.M. (1998). Comparative genetics in the grasses. Proc. Natl. Acad. Sci. USA 95, 1971-1974.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 1971-1974
-
-
Gale, M.D.1
Devos, K.M.2
-
12
-
-
0035147066
-
Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses
-
Gaut, B.S. (2001). Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 11, 55-66.
-
(2001)
Genome Res.
, vol.11
, pp. 55-66
-
-
Gaut, B.S.1
-
13
-
-
0036213939
-
Evolutionary dynamics of grass genomes
-
Gaut, B.S. (2002). Evolutionary dynamics of grass genomes. New Phytol. 154, 15-28.
-
(2002)
New Phytol.
, vol.154
, pp. 15-28
-
-
Gaut, B.S.1
-
14
-
-
0029812835
-
Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
-
Gaut, B.S., Morton, B.R., McCaig, B.C., and Clegg, M.T. (1996). Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274-10279.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 10274-10279
-
-
Gaut, B.S.1
Morton, B.R.2
McCaig, B.C.3
Clegg, M.T.4
-
15
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
Goff, S.A., 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.A.1
-
17
-
-
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
-
18
-
-
0035103949
-
Evolutionary history of the grasses
-
Kellogg, E.A. (2001). Evolutionary history of the grasses. Plant Physiol. 125, 1198-1205.
-
(2001)
Plant Physiol.
, vol.125
, pp. 1198-1205
-
-
Kellogg, E.A.1
-
19
-
-
0028141195
-
Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions
-
Kishimoto, N., Higo, H., Abe, K., Arai, S., Saito, A., and Higo, K. (1994). Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor. Appl. Genet. 88, 722-726.
-
(1994)
Theor. Appl. Genet.
, vol.88
, pp. 722-726
-
-
Kishimoto, N.1
Higo, H.2
Abe, K.3
Arai, S.4
Saito, A.5
Higo, K.6
-
20
-
-
0036918868
-
The impact of polyploidy on grass genome evolution
-
Levy, A.A., and Feldman, M. (2002). The impact of polyploidy on grass genome evolution. Plant Physiol. 130, 1587-1593.
-
(2002)
Plant Physiol.
, vol.130
, pp. 1587-1593
-
-
Levy, A.A.1
Feldman, M.2
-
21
-
-
0027403961
-
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
-
Li, W.H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 96-99
-
-
Li, W.H.1
-
22
-
-
0003421005
-
-
Sunderland, MA: Sinauer Associates
-
Li, W.H. (1997). Molecular Evolution. (Sunderland, MA: Sinauer Associates).
-
(1997)
Molecular Evolution
-
-
Li, W.H.1
-
23
-
-
0035865239
-
Evolutionary analyses of the human genome
-
Li, W.H., Gu, Z., Wang, H., and Nekrutenko, A. (2001). Evolutionary analyses of the human genome. Nature 409, 847-849.
-
(2001)
Nature
, vol.409
, pp. 847-849
-
-
Li, W.H.1
Gu, Z.2
Wang, H.3
Nekrutenko, A.4
-
24
-
-
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
-
25
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch, M., and Conery, J.S. (2000). The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
26
-
-
0034917750
-
Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana
-
Mayer, K., 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
-
27
-
-
0028850934
-
Conservation of duplicated segments between rice chromosome-11 and chromosome-12
-
Nagamura, Y., et al. (1995). Conservation of duplicated segments between rice chromosome-11 and chromosome-12. Breed. Sci. 45, 373-376.
-
(1995)
Breed. Sci.
, vol.45
, pp. 373-376
-
-
Nagamura, Y.1
-
29
-
-
0033784032
-
Comparative genomics of plant chromosomes
-
Paterson, A.H., Bowers, J.E., Burow, M.D., Draye, X., Elsik, C.G., Jiang, C.X., Katsar, C.S., Lan, T.H., Lin, Y.R., Ming, R., and Wright, R.J. (2000). Comparative genomics of plant chromosomes. Plant Cell 12, 1523-1540.
-
(2000)
Plant Cell
, vol.12
, pp. 1523-1540
-
-
Paterson, A.H.1
Bowers, J.E.2
Burow, M.D.3
Draye, X.4
Elsik, C.G.5
Jiang, C.X.6
Katsar, C.S.7
Lan, T.H.8
Lin, Y.R.9
Ming, R.10
Wright, R.J.11
-
30
-
-
16144364971
-
Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence
-
Paterson, A.H., et al. (1996). Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat. Genet. 14, 380-382.
-
(1996)
Nat. Genet.
, vol.14
, pp. 380-382
-
-
Paterson, A.H.1
-
31
-
-
0036845822
-
Splitting pairs: The diverging fates of duplicated genes
-
Prince, V.E., and Pickett, F.B. (2002). Splitting pairs: The diverging fates of duplicated genes. Nat. Rev. Genet. 3, 827-837.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 827-837
-
-
Prince, V.E.1
Pickett, F.B.2
-
32
-
-
0037266832
-
Investigating ancient duplication events in the Arabidopsis genome
-
Raes, J., Vandepoele, K., Simillion, C., Saeys, Y., and Van de Peer, Y. (2003). Investigating ancient duplication events in the Arabidopsis genome. J. Struct. Funct. Genomics 3, 117-129.
-
(2003)
J. Struct. Funct. Genomics
, vol.3
, pp. 117-129
-
-
Raes, J.1
Vandepoele, K.2
Simillion, C.3
Saeys, Y.4
Van De Peer, Y.5
-
33
-
-
0038581538
-
In-depth view of structure, activity, and evolution of rice chromosome 10
-
Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566-1569.
-
(2003)
Science
, vol.300
, pp. 1566-1569
-
-
-
34
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice, P., Longden, I., and Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
35
-
-
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
-
36
-
-
0036083902
-
RiceGAAS: An automated annotation system and database for rice genome sequence
-
Sakata, K., Nagamura, Y., Numa, H., Antonio, B.A., Nagasaki, H., Idonuma, A., Watanabe, W., Shimizu, Y., Horiuchi, I., Matsumoto, T., Sasaki, T., and Higo, K. (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.A.4
Nagasaki, H.5
Idonuma, A.6
Watanabe, W.7
Shimizu, Y.8
Horiuchi, I.9
Matsumoto, T.10
Sasaki, T.11
Higo, K.12
-
37
-
-
0036606406
-
Synteny between Arabidopsis thaliana and rice at the genome level: A tool to identify conservation in the ongoing rice genome sequencing project
-
Salse, J., Piegu, B., Cooke, R., and Delseny, M. (2002). Synteny between Arabidopsis thaliana and rice at the genome level: A tool to identify conservation in the ongoing rice genome sequencing project. Nucleic Acids Res. 30, 2316-2328.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2316-2328
-
-
Salse, J.1
Piegu, B.2
Cooke, R.3
Delseny, M.4
-
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
-
-
0037153190
-
The genome sequence and structure of rice chromosome 1
-
Sasaki, T., et al. (2002). The genome sequence and structure of rice chromosome 1. Nature 420, 312-316.
-
(2002)
Nature
, vol.420
, pp. 312-316
-
-
Sasaki, T.1
-
40
-
-
0030473920
-
Gen(om)e duplications in the evolution of early vertebrates
-
Sidow, A. (1996). Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Bev. 6, 715-722.
-
(1996)
Curr. Opin. Genet. Bev.
, vol.6
, pp. 715-722
-
-
Sidow, A.1
-
41
-
-
0037109058
-
The hidden duplication past of Arabidopsis thaliana
-
Simillion, C., Vandepoele, K., Van Montagu, M.C., Zabeau, M., and Van De Peer, Y. (2002). The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99, 13627-13632.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 13627-13632
-
-
Simillion, C.1
Vandepoele, K.2
Van Montagu, M.C.3
Zabeau, M.4
Van De Peer, Y.5
-
42
-
-
0000032326
-
Possible significance of duplication in evolution
-
Stephens, S.G. (1951). Possible significance of duplication in evolution. Adv. Genet. 4, 247-265.
-
(1951)
Adv. Genet.
, vol.4
, pp. 247-265
-
-
Stephens, S.G.1
-
43
-
-
0029100727
-
Phylogenetic test of the molecular clock and linearized trees
-
Takezaki, N., Rzhetsky, A., and Nei, M. (1995). Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823-833.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 823-833
-
-
Takezaki, N.1
Rzhetsky, A.2
Nei, M.3
-
44
-
-
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
-
45
-
-
0032979838
-
Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4
-
Terryn, N., et al. (1999). Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445, 237-245.
-
(1999)
FEBS Lett.
, vol.445
, pp. 237-245
-
-
Terryn, N.1
-
46
-
-
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. USA 96, 7409-7414.
-
(1999)
Proc. Natl. Acad. Sci. USA
, 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
-
47
-
-
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
-
48
-
-
0036852286
-
The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
-
Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., and Van de Peer, Y. (2002a). The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12, 1792-1801.
-
(2002)
Genome Res.
, vol.12
, pp. 1792-1801
-
-
Vandepoele, K.1
Saeys, Y.2
Simillion, C.3
Raes, J.4
Van De Peer, Y.5
-
49
-
-
0036889658
-
Detecting the undetectable: Uncovering duplicated segments in Arabidopsis by comparison with rice
-
Vandepoele, K., Simillion, C., and Van de Peer, Y. (2002b). Detecting the undetectable: Uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet. 18, 606-608.
-
(2002)
Trends Genet.
, vol.18
, pp. 606-608
-
-
Vandepoele, K.1
Simillion, C.2
Van De Peer, Y.3
-
50
-
-
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
-
51
-
-
0035344021
-
Yesterday's polyploids and the mystery of diploidization
-
Wolfe, K.H. (2001). Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2, 333-341.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 333-341
-
-
Wolfe, K.H.1
-
52
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe, K.H., and Shields, D.C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
53
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
Yu, J., 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
-
54
-
-
7344250636
-
The molecular clock revisited: The rate of synonymous vs. replacement change in Drosophila
-
Zeng, L.W., Comeron, J.M., Chen, B., and Kreitman, M. (1996). The molecular clock revisited: The rate of synonymous vs. replacement change in Drosophila. Genetica 103, 369-382.
-
(1996)
Genetica
, vol.103
, pp. 369-382
-
-
Zeng, L.W.1
Comeron, J.M.2
Chen, B.3
Kreitman, M.4
-
55
-
-
0036726239
-
Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana
-
Zhang, L., Vision, T.J., and Gaut, B.S. (2002). Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol. Biol. Evol. 19, 1464-1473.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1464-1473
-
-
Zhang, L.1
Vision, T.J.2
Gaut, B.S.3
|