-
1
-
-
69449089723
-
More than just orphans: are taxonomically-restricted genes important in evolution?
-
Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG, (2009) More than just orphans: are taxonomically-restricted genes important in evolution? Trends in Genetics 25: 404-413.
-
(2009)
Trends in Genetics
, vol.25
, pp. 404-413
-
-
Khalturin, K.1
Hemmrich, G.2
Fraune, S.3
Augustin, R.4
Bosch, T.C.G.5
-
3
-
-
80052969570
-
The evolutionary origin of orphan genes
-
Tautz D, Domazet-Loso T, (2011) The evolutionary origin of orphan genes. Nat Rev Genet 12: 692-702.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 692-702
-
-
Tautz, D.1
Domazet-Loso, T.2
-
4
-
-
78650385315
-
New genes in Drosophila quickly become essential
-
Chen S, Zhang YE, Long M, (2010) New genes in Drosophila quickly become essential. Science (New York, N Y) 330: 1682-1685.
-
(2010)
Science (New York, N Y)
, vol.330
, pp. 1682-1685
-
-
Chen, S.1
Zhang, Y.E.2
Long, M.3
-
5
-
-
80055025720
-
Accelerated recruitment of new brain development genes into the human genome
-
Zhang YE, Landback P, Vibranovski MD, Long M, (2011) Accelerated recruitment of new brain development genes into the human genome. PLoS Biol 9: e1001179.
-
(2011)
PLoS Biol
, vol.9
-
-
Zhang, Y.E.1
Landback, P.2
Vibranovski, M.D.3
Long, M.4
-
6
-
-
78650690861
-
A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes
-
Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, et al. (2010) A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genetics 6: e1001255.
-
(2010)
PLoS Genetics
, vol.6
-
-
Ding, Y.1
Zhao, L.2
Yang, S.3
Jiang, Y.4
Chen, Y.5
-
7
-
-
0036544871
-
Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey
-
Zhang J, Zhang Y-p, Rosenberg HF, (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet 30: 411-415.
-
(2002)
Nat Genet
, vol.30
, pp. 411-415
-
-
Zhang, J.1
Zhang, Y.-P.2
Rosenberg, H.F.3
-
8
-
-
84865298207
-
Assembly of an evolutionarily new pathway for alpha-pyrone biosynthesis in Arabidopsis
-
Weng JK, Li Y, Mo H, Chapple C, (2012) Assembly of an evolutionarily new pathway for alpha-pyrone biosynthesis in Arabidopsis. Science 337: 960-964.
-
(2012)
Science
, vol.337
, pp. 960-964
-
-
Weng, J.K.1
Li, Y.2
Mo, H.3
Chapple, C.4
-
9
-
-
46649113144
-
A role for gene duplication and natural variation of gene expression in the evolution of metabolism
-
Kliebenstein DJ, (2008) A role for gene duplication and natural variation of gene expression in the evolution of metabolism. PLoS One 3: e1838.
-
(2008)
PLoS One
, vol.3
-
-
Kliebenstein, D.J.1
-
10
-
-
0347925092
-
Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection
-
Ferrari S, Vairo D, Ausubel FM, Cervone F, De Lorenzo G, (2003) Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection. Plant Cell 15: 93-106.
-
(2003)
Plant Cell
, vol.15
, pp. 93-106
-
-
Ferrari, S.1
Vairo, D.2
Ausubel, F.M.3
Cervone, F.4
De Lorenzo, G.5
-
11
-
-
30744464824
-
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
-
Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, et al. (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol 23: 469-478.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 469-478
-
-
Duarte, J.M.1
Cui, L.2
Wall, P.K.3
Zhang, Q.4
Zhang, X.5
-
12
-
-
57749085421
-
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli
-
Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH, (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148: 993-1003.
-
(2008)
Plant Physiol
, vol.148
, pp. 993-1003
-
-
Hanada, K.1
Zou, C.2
Lehti-Shiu, M.D.3
Shinozaki, K.4
Shiu, S.H.5
-
13
-
-
59149093200
-
Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana
-
Bikard D, Patel D, Le Mette C, Giorgi V, Camilleri C, et al. (2009) Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana. Science 323: 623-626.
-
(2009)
Science
, vol.323
, pp. 623-626
-
-
Bikard, D.1
Patel, D.2
Le Mette, C.3
Giorgi, V.4
Camilleri, C.5
-
14
-
-
68249119181
-
Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana
-
Zou C, Lehti-Shiu MD, Thomashow M, Shiu SH, (2009) Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet 5: e1000581.
-
(2009)
PLoS Genet
, vol.5
-
-
Zou, C.1
Lehti-Shiu, M.D.2
Thomashow, M.3
Shiu, S.H.4
-
15
-
-
77958497573
-
Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes
-
Cai JJ, Petrov DA, (2010) Relaxed Purifying Selection and Possibly High Rate of Adaptation in Primate Lineage-Specific Genes. Genome Biol Evol 2: 393-409.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 393-409
-
-
Cai, J.J.1
Petrov, D.A.2
-
16
-
-
67749145754
-
Global discovery of primate-specific genes in the human genome
-
Tay SK, Blythe J, Lipovich L, (2009) Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci U S A 106: 12019-12024.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 12019-12024
-
-
Tay, S.K.1
Blythe, J.2
Lipovich, L.3
-
17
-
-
0034754788
-
The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes
-
Schmid KJ, Aquadro CF, (2001) The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. Genetics 159: 589-598.
-
(2001)
Genetics
, vol.159
, pp. 589-598
-
-
Schmid, K.J.1
Aquadro, C.F.2
-
18
-
-
36849012677
-
Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome
-
Guo WJ, Li P, Ling J, Ye SP (2007) Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome. Comparative and Functional Genomics.
-
(2007)
Comparative and Functional Genomics
-
-
Guo, W.J.1
Li, P.2
Ling, J.3
Ye, S.P.4
-
19
-
-
0033974956
-
Genome evolution in polyploids
-
Wendel JF, (2000) Genome evolution in polyploids. Plant Mol Biol 42: 225-249.
-
(2000)
Plant Mol Biol
, vol.42
, pp. 225-249
-
-
Wendel, J.F.1
-
20
-
-
0034671866
-
The origins of genomic duplications in Arabidopsis
-
Vision TJ, Brown DG, Tanksley SD, (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
-
21
-
-
0037313579
-
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
-
Blanc G, Hokamp K, Wolfe KH, (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
-
22
-
-
79959858471
-
Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints
-
Bekaert M, Edger PP, Pires JC, Conant GC, (2011) Two-Phase Resolution of Polyploidy in the Arabidopsis Metabolic Network Gives Rise to Relative and Absolute Dosage Constraints. Plant Cell 23: 1719-1728.
-
(2011)
Plant Cell
, vol.23
, pp. 1719-1728
-
-
Bekaert, M.1
Edger, P.P.2
Pires, J.C.3
Conant, G.C.4
-
23
-
-
84858779019
-
Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications
-
Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC, (2011) Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications. Genome Biology and Evolution 3: 1369-1380.
-
(2011)
Genome Biology and Evolution
, vol.3
, pp. 1369-1380
-
-
Hudson, C.M.1
Puckett, E.E.2
Bekaert, M.3
Pires, J.C.4
Conant, G.C.5
-
24
-
-
34347225545
-
A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza
-
Fan C, Vibranovski MD, Chen Y, Long M (2007) A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza. Journal of Integrative Plant Biology 49.
-
(2007)
Journal of Integrative Plant Biology 49
-
-
Fan, C.1
Vibranovski, M.D.2
Chen, Y.3
Long, M.4
-
25
-
-
26944438711
-
Computational identification of 69 retroposons in Arabidopsis
-
Zhang YJ, Wu YR, Liu YL, Han B, (2005) Computational identification of 69 retroposons in Arabidopsis. Plant Physiol 138: 935-948.
-
(2005)
Plant Physiol
, vol.138
, pp. 935-948
-
-
Zhang, Y.J.1
Wu, Y.R.2
Liu, Y.L.3
Han, B.4
-
26
-
-
33747465505
-
High rate of chimeric gene origination by retroposition in plant genomes
-
Wang W, Zheng H, Fan C, Li J, Shi J, et al. (2006) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802.
-
(2006)
Plant Cell
, vol.18
, pp. 1791-1802
-
-
Wang, W.1
Zheng, H.2
Fan, C.3
Li, J.4
Shi, J.5
-
27
-
-
33749357831
-
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice
-
Rizzon C, Ponger L, Gaut BS, (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol 2: e115.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Rizzon, C.1
Ponger, L.2
Gaut, B.S.3
-
28
-
-
57749177443
-
RNA-based gene duplication: mechanistic and evolutionary insights
-
Kaessmann H, Vinckenbosch N, Long M, (2009) RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 10: 19-31.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 19-31
-
-
Kaessmann, H.1
Vinckenbosch, N.2
Long, M.3
-
29
-
-
0242354129
-
The origin of new genes: glimpses from the young and old
-
Long M, Betran E, Thornton K, Wang W, (2003) The origin of new genes: glimpses from the young and old. Nat Rev Genet 4: 865-875.
-
(2003)
Nat Rev Genet
, vol.4
, pp. 865-875
-
-
Long, M.1
Betran, E.2
Thornton, K.3
Wang, W.4
-
30
-
-
56549119570
-
Turning a hobby into a job: how duplicated genes find new functions
-
Conant GC, Wolfe KH, (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938-950.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 938-950
-
-
Conant, G.C.1
Wolfe, K.H.2
-
31
-
-
84860178352
-
The origin and evolution of new genes
-
Cardoso-Moreira M, Long M, (2012) The origin and evolution of new genes. Methods Mol Biol 856: 161-186.
-
(2012)
Methods Mol Biol
, vol.856
, pp. 161-186
-
-
Cardoso-Moreira, M.1
Long, M.2
-
32
-
-
84861229453
-
Newly evolved genes: Moving from comparative genomics to functional studies in model systems: How important is genetic novelty for species adaptation and diversification?
-
Ranz JM, Parsch J (2012) Newly evolved genes: Moving from comparative genomics to functional studies in model systems: How important is genetic novelty for species adaptation and diversification? Bioessays.
-
(2012)
Bioessays
-
-
Ranz, J.M.1
Parsch, J.2
-
33
-
-
0003515251
-
-
Berlin, New York,: Springer-Verlag. xv
-
Ohno S (1970) Evolution by gene duplication. Berlin, New York,: Springer-Verlag. xv, 160 p. p.
-
(1970)
Evolution by gene duplication
, pp. 160
-
-
Ohno, S.1
-
34
-
-
0024356364
-
Role of gene duplication in evolution
-
Ohta T, (1989) Role of gene duplication in evolution. Genome 31: 304-310.
-
(1989)
Genome
, vol.31
, pp. 304-310
-
-
Ohta, T.1
-
35
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch M, Conery JS, (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
-
36
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, et al. (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A 102: 5454-5459.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
De Bodt, S.2
Raes, J.3
Casneuf, T.4
Van Montagu, M.5
-
37
-
-
0032893932
-
Preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (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
-
38
-
-
79951566081
-
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana
-
Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C, (2011) Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol 11: 47.
-
(2011)
BMC Evol Biol
, vol.11
, pp. 47
-
-
Donoghue, M.T.1
Keshavaiah, C.2
Swamidatta, S.H.3
Spillane, C.4
-
39
-
-
77649223105
-
Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana
-
Lin HN, Moghe G, Ouyang S, Iezzoni A, Shiu SH, et al. (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol 10.
-
(2010)
BMC Evol Biol 10
-
-
Lin, H.N.1
Moghe, G.2
Ouyang, S.3
Iezzoni, A.4
Shiu, S.H.5
-
40
-
-
64149089393
-
Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus
-
Yang X, Jawdy S, Tschaplinski TJ, Tuskan GA, (2009) Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. Genomics 93: 473-480.
-
(2009)
Genomics
, vol.93
, pp. 473-480
-
-
Yang, X.1
Jawdy, S.2
Tschaplinski, T.J.3
Tuskan, G.A.4
-
41
-
-
60549090058
-
Duplicate genes increase expression diversity in closely related species and allopolyploids
-
Ha M, Kim ED, Chen ZJ, (2009) Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A 106: 2295-2300.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 2295-2300
-
-
Ha, M.1
Kim, E.D.2
Chen, Z.J.3
-
42
-
-
35348820582
-
Divergence in expression between duplicated genes in Arabidopsis
-
Ganko EW, Meyers BC, Vision TJ, (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 24: 2298-2309.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2298-2309
-
-
Ganko, E.W.1
Meyers, B.C.2
Vision, T.J.3
-
43
-
-
33646859550
-
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
-
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y, (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 7: R13.
-
(2006)
Genome Biol
, vol.7
-
-
Casneuf, T.1
De Bodt, S.2
Raes, J.3
Maere, S.4
Van de Peer, Y.5
-
44
-
-
84879686532
-
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
-
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet.
-
(2013)
Nat Genet
-
-
Slotte, T.1
Hazzouri, K.M.2
Agren, J.A.3
Koenig, D.4
Maumus, F.5
-
45
-
-
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
-
-
-
46
-
-
80053386792
-
The genome of the mesopolyploid crop species Brassica rapa
-
Wang X, Wang H, Wang J, Sun R, Wu J, et al. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43: 1035-1039.
-
(2011)
Nat Genet
, vol.43
, pp. 1035-1039
-
-
Wang, X.1
Wang, H.2
Wang, J.3
Sun, R.4
Wu, J.5
-
47
-
-
79955468851
-
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
-
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43: 476-481.
-
(2011)
Nat Genet
, vol.43
, pp. 476-481
-
-
Hu, T.T.1
Pattyn, P.2
Bakker, E.G.3
Cao, J.4
Cheng, J.F.5
-
48
-
-
0032954807
-
Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages
-
Yang YW, Lai KN, Tai PY, Li WH, (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
-
-
33745467604
-
Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy
-
Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, et al. (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18: 1348-1359.
-
(2006)
Plant Cell
, vol.18
, pp. 1348-1359
-
-
Town, C.D.1
Cheung, F.2
Maiti, R.3
Crabtree, J.4
Haas, B.J.5
-
50
-
-
16244366488
-
Genome evolution among cruciferous plants: A lecture from the comparison of the genetic maps of three diploid species - Capsella rubella, Arabidopsis lyrata subsp Petraea, and A. thaliana
-
Koch MA, Kiefer M, (2005) Genome evolution among cruciferous plants: A lecture from the comparison of the genetic maps of three diploid species- Capsella rubella, Arabidopsis lyrata subsp Petraea, and A. thaliana. American Journal of Botany 92: 761-767.
-
(2005)
American Journal of Botany
, vol.92
, pp. 761-767
-
-
Koch, M.A.1
Kiefer, M.2
-
51
-
-
0036729901
-
Rates and patterns of molecular evolution in inbred and outbred Arabidopsis
-
Wright SI, Lauga B, Charlesworth D, (2002) Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol Biol Evol 19: 1407-1420.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1407-1420
-
-
Wright, S.I.1
Lauga, B.2
Charlesworth, D.3
-
52
-
-
0033804889
-
Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)
-
Koch MA, Haubold B, Mitchell-Olds T, (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17: 1483-1498.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 1483-1498
-
-
Koch, M.A.1
Haubold, B.2
Mitchell-Olds, T.3
-
53
-
-
0001692896
-
Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences
-
Koch M, Haubold B, Mitchell-Olds T, (2001) Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences. Am J Bot 88: 534-544.
-
(2001)
Am J Bot
, vol.88
, pp. 534-544
-
-
Koch, M.1
Haubold, B.2
Mitchell-Olds, T.3
-
54
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
-
56
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
-
57
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (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
-
58
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent WJ, (2002) BLAT- The BLAST-like alignment tool. Genome Res 12: 656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
59
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang ZH, (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.H.1
-
60
-
-
0036906987
-
Retroposed new genes out of the X in Drosophila
-
Betran E, Thornton K, Long M, (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12: 1854-1859.
-
(2002)
Genome Res
, vol.12
, pp. 1854-1859
-
-
Betran, E.1
Thornton, K.2
Long, M.3
-
61
-
-
0003421005
-
-
Sunderland Massachusetts: Sinauer Associates
-
Li W-H (1997) Molecular Evolution. Sunderland Massachusetts: Sinauer Associates.
-
(1997)
Molecular Evolution
-
-
Li, W.-H.1
-
62
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
63
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang ZH, (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15: 568-573.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 568-573
-
-
Yang, Z.H.1
-
64
-
-
80052824121
-
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
-
Ranwez V, Harispe S, Delsuc F, Douzery EJ, (2011) MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 6: e22594.
-
(2011)
PLoS One
, vol.6
-
-
Ranwez, V.1
Harispe, S.2
Delsuc, F.3
Douzery, E.J.4
-
65
-
-
80053384429
-
Whole-genome sequencing of multiple Arabidopsis thaliana populations
-
Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, et al. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43: 956-963.
-
(2011)
Nat Genet
, vol.43
, pp. 956-963
-
-
Cao, J.1
Schneeberger, K.2
Ossowski, S.3
Gunther, T.4
Bender, S.5
-
66
-
-
0024313579
-
Statistical-Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism
-
Tajima F, (1989) Statistical-Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics 123: 585-595.
-
(1989)
Genetics
, vol.123
, pp. 585-595
-
-
Tajima, F.1
-
67
-
-
0027453041
-
Statistical tests of neutrality of mutations
-
Fu YX, Li WH, (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
-
(1993)
Genetics
, vol.133
, pp. 693-709
-
-
Fu, Y.X.1
Li, W.H.2
-
68
-
-
39749143325
-
Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana
-
Ramos-Onsins SE, Puerma E, Balana-Alcaide D, Salguero D, Aguade M, (2008) Multilocus analysis of variation using a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana. Molecular Ecology 17: 1211-1223.
-
(2008)
Molecular Ecology
, vol.17
, pp. 1211-1223
-
-
Ramos-Onsins, S.E.1
Puerma, E.2
Balana-Alcaide, D.3
Salguero, D.4
Aguade, M.5
-
69
-
-
22744434580
-
The pattern of polymorphism in Arabidopsis thaliana
-
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. Plos Biology 3: 1289-1299.
-
(2005)
Plos Biology
, vol.3
, pp. 1289-1299
-
-
Nordborg, M.1
Hu, T.T.2
Ishino, Y.3
Jhaveri, J.4
Toomajian, C.5
-
70
-
-
22744434580
-
The pattern of polymorphism in Arabidopsis thaliana
-
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196.
-
(2005)
PLoS Biol
, vol.3
-
-
Nordborg, M.1
Hu, T.T.2
Ishino, Y.3
Jhaveri, J.4
Toomajian, C.5
-
71
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald JH, Kreitman M, (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
72
-
-
84861858040
-
Retrogenes moved out of the z chromosome in the silkworm
-
Wang J, Long M, Vibranovski MD, (2012) Retrogenes moved out of the z chromosome in the silkworm. J Mol Evol 74: 113-126.
-
(2012)
J Mol Evol
, vol.74
, pp. 113-126
-
-
Wang, J.1
Long, M.2
Vibranovski, M.D.3
-
73
-
-
48249130774
-
At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
-
Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, et al. (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 9: R112.
-
(2008)
Genome Biol
, vol.9
-
-
Laubinger, S.1
Zeller, G.2
Henz, S.R.3
Sachsenberg, T.4
Widmer, C.K.5
-
74
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
-
(2011)
Nature
, vol.477
, pp. 419-423
-
-
Gan, X.1
Stegle, O.2
Behr, J.3
Steffen, J.G.4
Drewe, P.5
-
75
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
76
-
-
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, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-U174.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 174-511
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
-
77
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
-
78
-
-
79957868920
-
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger F, Andrews SR, (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572.
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
79
-
-
84863103782
-
Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
-
Li X, Zhu J, Hu F, Ge S, Ye M, et al. (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13: 300.
-
(2012)
BMC Genomics
, vol.13
, pp. 300
-
-
Li, X.1
Zhu, J.2
Hu, F.3
Ge, S.4
Ye, M.5
-
80
-
-
51649122447
-
Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes
-
Hughes AL, Friedman R, Rivailler P, French JO, (2008) Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol 25: 2199-2209.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 2199-2209
-
-
Hughes, A.L.1
Friedman, R.2
Rivailler, P.3
French, J.O.4
-
81
-
-
84857745267
-
Database resources of the National Center for Biotechnology Information
-
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40: D13-D25.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
-
82
-
-
27144513515
-
The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells
-
Diaz-Trivino S, del Mar Castellano M, de la Paz Sanchez M, Ramirez-Parra E, Desvoyes B, et al. (2005) The genes encoding Arabidopsis ORC subunits are E2F targets and the two ORC1 genes are differently expressed in proliferating and endoreplicating cells. Nucleic Acids Res 33: 5404-5414.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5404-5414
-
-
Diaz-Trivino, S.1
del Mar Castellano, M.2
de la Paz Sanchez, M.3
Ramirez-Parra, E.4
Desvoyes, B.5
-
83
-
-
0035027750
-
Differential expression of triplicate phosphoribosylanthranilate isomerase isogenes in the tryptophan biosynthetic pathway of Arabidopsis thaliana (L.) Heynh
-
He Y, Li J, (2001) Differential expression of triplicate phosphoribosylanthranilate isomerase isogenes in the tryptophan biosynthetic pathway of Arabidopsis thaliana (L.) Heynh. Planta 212: 641-647.
-
(2001)
Planta
, vol.212
, pp. 641-647
-
-
He, Y.1
Li, J.2
-
84
-
-
57749119299
-
Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
-
Wang Y, Zhang WZ, Song LF, Zou JJ, Su Z, et al. (2008) Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol 148: 1201-1211.
-
(2008)
Plant Physiol
, vol.148
, pp. 1201-1211
-
-
Wang, Y.1
Zhang, W.Z.2
Song, L.F.3
Zou, J.J.4
Su, Z.5
-
85
-
-
3542996904
-
Identification of genes required for embryo development in Arabidopsis
-
Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, et al. (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206-1220.
-
(2004)
Plant Physiol
, vol.135
, pp. 1206-1220
-
-
Tzafrir, I.1
Pena-Muralla, R.2
Dickerman, A.3
Berg, M.4
Rogers, R.5
-
86
-
-
21344452782
-
Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response
-
Nikiforova VJ, Daub CO, Hesse H, Willmitzer L, Hoefgen R, (2005) Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response. J Exp Bot 56: 1887-1896.
-
(2005)
J Exp Bot
, vol.56
, pp. 1887-1896
-
-
Nikiforova, V.J.1
Daub, C.O.2
Hesse, H.3
Willmitzer, L.4
Hoefgen, R.5
-
87
-
-
84859630952
-
Birth, death and subfunctionalization in the Arabidopsis genome
-
Rutter MT, Cross KV, Van Woert PA, (2012) Birth, death and subfunctionalization in the Arabidopsis genome. Trends Plant Sci 17: 204-212.
-
(2012)
Trends Plant Sci
, vol.17
, pp. 204-212
-
-
Rutter, M.T.1
Cross, K.V.2
Van Woert, P.A.3
-
88
-
-
50649097020
-
On the origin of new genes in Drosophila
-
Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, et al. (2008) On the origin of new genes in Drosophila. Genome Res 18: 1446-1455.
-
(2008)
Genome Res
, vol.18
, pp. 1446-1455
-
-
Zhou, Q.1
Zhang, G.2
Zhang, Y.3
Xu, S.4
Zhao, R.5
-
89
-
-
0015722319
-
Slightly deleterious mutant substitutions in evolution
-
Ohta T, (1973) Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
-
(1973)
Nature
, vol.246
, pp. 96-98
-
-
Ohta, T.1
-
90
-
-
0027020232
-
The nearly neutral theory of molecular evolution
-
Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst: 263-286.
-
(1992)
Annu Rev Ecol Syst
, pp. 263-286
-
-
Ohta, T.1
-
91
-
-
0035697435
-
The probability of preservation of a newly arisen gene duplicate
-
Lynch M, O'Hely M, Walsh B, Force A, (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
-
(2001)
Genetics
, vol.159
, pp. 1789-1804
-
-
Lynch, M.1
O'Hely, M.2
Walsh, B.3
Force, A.4
-
92
-
-
0345306751
-
The origins of genome complexity
-
Lynch M, Conery JS, (2003) The origins of genome complexity. Science 302: 1401-1404.
-
(2003)
Science
, vol.302
, pp. 1401-1404
-
-
Lynch, M.1
Conery, J.S.2
-
93
-
-
84855440297
-
Functional evolution of duplicated odorant-binding protein genes, Obp57d and Obp57e, in Drosophila
-
Harada E, Nakagawa J, Asano T, Taoka M, Sorimachi H, et al. (2012) Functional evolution of duplicated odorant-binding protein genes, Obp57d and Obp57e, in Drosophila. PLoS One 7: e29710.
-
(2012)
PLoS One
, vol.7
-
-
Harada, E.1
Nakagawa, J.2
Asano, T.3
Taoka, M.4
Sorimachi, H.5
-
94
-
-
84857420366
-
Multiple routes to subfunctionalization and gene duplicate specialization
-
Proulx SR, (2012) Multiple routes to subfunctionalization and gene duplicate specialization. Genetics 190: 737-751.
-
(2012)
Genetics
, vol.190
, pp. 737-751
-
-
Proulx, S.R.1
-
95
-
-
35148863240
-
Gene duplication and the adaptive evolution of a classic genetic switch
-
Hittinger CT, Carroll SB, (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677-681.
-
(2007)
Nature
, vol.449
, pp. 677-681
-
-
Hittinger, C.T.1
Carroll, S.B.2
-
96
-
-
33144464980
-
Role of positive selection in the retention of duplicate genes in mammalian genomes
-
Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH, (2006) Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A 103: 2232-2236.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 2232-2236
-
-
Shiu, S.H.1
Byrnes, J.K.2
Pan, R.3
Zhang, P.4
Li, W.H.5
-
97
-
-
0018344224
-
Evolution of the differential regulation of duplicate genes after polyploidization
-
Ferris SD, Whitt GS, (1979) Evolution of the differential regulation of duplicate genes after polyploidization. J Mol Evol 12: 267-317.
-
(1979)
J Mol Evol
, vol.12
, pp. 267-317
-
-
Ferris, S.D.1
Whitt, G.S.2
-
98
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes AL, (1994) The evolution of functionally novel proteins after gene duplication. Proc Biol Sci 256: 119-124.
-
(1994)
Proc Biol Sci
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
99
-
-
0026326815
-
The recruitment of crystal-lins: new functions precede gene duplication
-
Piatigorsky J, Wistow G, (1991) The recruitment of crystal-lins: new functions precede gene duplication. Science 252: 1078-1079.
-
(1991)
Science
, vol.252
, pp. 1078-1079
-
-
Piatigorsky, J.1
Wistow, G.2
-
100
-
-
67649854463
-
Seed banks cause elevated generation times and effective population sizes of Arabidopsis thaliana in northern Europe
-
Lundemo S, Falahati-Anbaran M, Stenoien HK, (2009) Seed banks cause elevated generation times and effective population sizes of Arabidopsis thaliana in northern Europe. Mol Ecol 18: 2798-2811.
-
(2009)
Mol Ecol
, vol.18
, pp. 2798-2811
-
-
Lundemo, S.1
Falahati-Anbaran, M.2
Stenoien, H.K.3
-
101
-
-
80052081034
-
Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations
-
Gomaa NH, Montesinos-Navarro A, Alonso-Blanco C, Pico FX, (2011) Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations. Mol Ecol 20: 3540-3554.
-
(2011)
Mol Ecol
, vol.20
, pp. 3540-3554
-
-
Gomaa, N.H.1
Montesinos-Navarro, A.2
Alonso-Blanco, C.3
Pico, F.X.4
-
102
-
-
34147128526
-
Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila
-
Bai YS, Casola C, Feschotte C, Betran E (2007) Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol 8.
-
(2007)
Genome Biol 8
-
-
Bai, Y.S.1
Casola, C.2
Feschotte, C.3
Betran, E.4
-
103
-
-
1642475221
-
Extensive gene traffic on the mammalian X chromosome
-
Emerson JJ, Kaessmann H, Betran E, Long MY, (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540.
-
(2004)
Science
, vol.303
, pp. 537-540
-
-
Emerson, J.J.1
Kaessmann, H.2
Betran, E.3
Long, M.Y.4
-
105
-
-
27844557002
-
Emergence of young human genes after a burst of retroposition in primates
-
Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H, (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3: e357.
-
(2005)
PLoS Biol
, vol.3
-
-
Marques, A.C.1
Dupanloup, I.2
Vinckenbosch, N.3
Reymond, A.4
Kaessmann, H.5
-
106
-
-
33746438091
-
A novel approach for characterizing expression levels of genes duplicated by polyploidy
-
Udall JA, Swanson JM, Nettleton D, Percifield RJ, Wendel JF, (2006) A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173: 1823-1827.
-
(2006)
Genetics
, vol.173
, pp. 1823-1827
-
-
Udall, J.A.1
Swanson, J.M.2
Nettleton, D.3
Percifield, R.J.4
Wendel, J.F.5
-
107
-
-
34248195475
-
The plant genome's methylation status and response to stress: implications for plant improvement
-
Lukens LN, Zhan SH, (2007) The plant genome's methylation status and response to stress: implications for plant improvement. Current Opinion in Plant Biology 10: 317-322.
-
(2007)
Current Opinion in Plant Biology
, vol.10
, pp. 317-322
-
-
Lukens, L.N.1
Zhan, S.H.2
-
108
-
-
79952846249
-
Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)
-
Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, et al. (2011) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). Journal of Experimental Botany 62: 1951-1960.
-
(2011)
Journal of Experimental Botany
, vol.62
, pp. 1951-1960
-
-
Wang, W.S.1
Pan, Y.J.2
Zhao, X.Q.3
Dwivedi, D.4
Zhu, L.H.5
-
109
-
-
84867775180
-
Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications
-
Carretero-Paulet L, Fares MA, (2012) Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications. Mol Biol Evol 29: 3541-3551.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3541-3551
-
-
Carretero-Paulet, L.1
Fares, M.A.2
|