-
1
-
-
84890829647
-
The Amborella genome and the evolution of flowering plants
-
Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science 342: 1241089.
-
(2013)
Science
, vol.342
, pp. 1241089
-
-
Genome Project, A.1
-
2
-
-
77649268965
-
Posttranslational regulation impacts the fate of duplicated genes
-
Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y. 2010. Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci 107: 2967-2971.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 2967-2971
-
-
Amoutzias, G.D.1
He, Y.2
Gordon, J.3
Mossialos, D.4
Oliver, S.G.5
Van De Peer, Y.6
-
3
-
-
78651325661
-
ParameciumDB in 2011: New tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
-
Arnaiz O, Sperling L. 2011. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res (Suppl 1) 39: D635-D636.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D635-D636
-
-
Arnaiz, O.1
Sperling, L.2
-
4
-
-
33750858684
-
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
-
Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel B, Segurens B, Daubin V, Anthouard V, Aiach N, et al. 2006. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
-
(2006)
Nature
, vol.444
, pp. 171-178
-
-
Aury, J.-M.1
Jaillon, O.2
Duret, L.3
Noel, B.4
Jubin, C.5
Porcel, B.6
Segurens, B.7
Daubin, V.8
Anthouard, V.9
Aiach, N.10
-
5
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57: 289-300.
-
(1995)
J R Stat Soc Series B Stat Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
59149093200
-
Divergent evolution of duplicate genes leads to genetic incompatibilities within A. Thaliana
-
Bikard D, Patel D, Le Mette C, Giorgi V, Camilleri C, Bennett MJ, Loudet O. 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
Bennett, M.J.6
Loudet, O.7
-
8
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
9
-
-
58449122276
-
Genetic diversity in the Paramecium aurelia species complex
-
Catania F,Wurmser F, PotekhinAA, Przybos E, LynchM. 2009. Genetic diversity in the Paramecium aurelia species complex.Mol Biol Evol 26: 421-431.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 421-431
-
-
Catania, F.1
Wurmser, F.2
Potekhin, A.A.3
Przybos, E.4
Lynch, M.5
-
10
-
-
33644499450
-
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
-
Chapman BA, Bowers JE, Feltus FA, Paterson AH. 2006. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci 103: 2730-2735.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 2730-2735
-
-
Chapman, B.A.1
Bowers, J.E.2
Feltus, F.A.3
Paterson, A.H.4
-
11
-
-
52049091231
-
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
-
Conant GC, Wolfe KH. 2008. Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. Genetics 179: 1681-1692.
-
(2008)
Genetics
, vol.179
, pp. 1681-1692
-
-
Conant, G.C.1
Wolfe, K.H.2
-
12
-
-
84884414234
-
Insight from the lamprey genome: Glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropinreleasing hormone (GnRH)
-
Decatur WA, Hall JA, Smith JJ, Li W, Sower SA. 2013. Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropinreleasing hormone (GnRH). Gen Comp Endocrinol 192: 237-245.
-
(2013)
Gen Comp Endocrinol
, vol.192
, pp. 237-245
-
-
Decatur, W.A.1
Hall, J.A.2
Smith, J.J.3
Li, W.4
Sower, S.A.5
-
13
-
-
0002594984
-
A rapid DNA isolation procedure for small quantities of fresh leaf tissue
-
Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bull 19: 11-15.
-
(1987)
Phytochemical Bull
, vol.19
, pp. 11-15
-
-
Doyle, J.J.1
Doyle, J.L.2
-
14
-
-
70350236484
-
Biased gene conversion and the evolution of mammalian genomic landscapes
-
Duret L, Galtier N. 2009. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10: 285-311.
-
(2009)
Annu Rev Genomics Hum Genet
, vol.10
, pp. 285-311
-
-
Duret, L.1
Galtier, N.2
-
15
-
-
41649113803
-
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline
-
Duret L, Cohen J, Jubin C, Dessen P, Gout JF, Mousset S, Aury JM, Jaillon O, Noel B, Arnaiz O, et al. 2008. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res 18: 585-596.
-
(2008)
Genome Res
, vol.18
, pp. 585-596
-
-
Duret, L.1
Cohen, J.2
Jubin, C.3
Dessen, P.4
Gout, J.F.5
Mousset, S.6
Aury, J.M.7
Jaillon, O.8
Noel, B.9
Arnaiz, O.10
-
16
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
17
-
-
79952199263
-
Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling
-
Evangelisti AM, Conant GC. 2010. Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling. Genome Biol Evol 2: 826-834.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 826-834
-
-
Evangelisti, A.M.1
Conant, G.C.2
-
18
-
-
66249109710
-
Genome annotation in plants and fungi: EuGene as a model platform
-
Foissac S, Gouzy J, Rombauts S, Mathe C, Amselem J, Sterk L, Van de Peer Y, Rouze P, Schiex T. 2008. Genome annotation in plants and fungi: EuGene as a model platform. Current Bioinformatics 3: 87-97.
-
(2008)
Current Bioinformatics
, vol.3
, pp. 87-97
-
-
Foissac, S.1
Gouzy, J.2
Rombauts, S.3
Mathe, C.4
Amselem, J.5
Sterk, L.6
Van De Peer, Y.7
Rouze, P.8
Schiex, T.9
-
19
-
-
0032893932
-
The preservation of duplicate genes by complementary, degenerative mutations
-
Force A, Lynch M, Pickett FB, Amores A, Yan Y-I, Postlethwait J. 1999. The 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.-I.5
Postlethwait, J.6
-
20
-
-
57149114784
-
The evolutionary position of subfunctionalization, downgraded
-
Freeling M. 2008. The evolutionary position of subfunctionalization, downgraded. Genome Dyn 4: 25-40.
-
(2008)
Genome Dyn
, vol.4
, pp. 25-40
-
-
Freeling, M.1
-
21
-
-
33745610025
-
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
-
Freeling M, Thomas BC. 2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16: 805-814.
-
(2006)
Genome Res
, vol.16
, pp. 805-814
-
-
Freeling, M.1
Thomas, B.C.2
-
22
-
-
0037303814
-
Gene conversion drives GC content evolution in mammalian histones
-
Galtier N. 2003. Gene conversion drives GC content evolution in mammalian histones. Trends Genet 19: 65-68.
-
(2003)
Trends Genet
, vol.19
, pp. 65-68
-
-
Galtier, N.1
-
23
-
-
0034766004
-
GC-content evolution in mammalian genomes: The biased gene conversion hypothesis
-
Galtier N, Piganeau G, Mouchiroud D, Duret L. 2001. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159: 907-911.
-
(2001)
Genetics
, vol.159
, pp. 907-911
-
-
Galtier, N.1
Piganeau, G.2
Mouchiroud, D.3
Duret, L.4
-
24
-
-
65349158393
-
Differential retention of metabolic genes following whole-genome duplication
-
Gout J-F, Duret L, Kahn D. 2009. Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol 26: 1067-1072.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1067-1072
-
-
Gout, J.-F.1
Duret, L.2
Kahn, D.3
-
25
-
-
77953212314
-
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
-
Gout J-F, Kahn D, Duret L. 2010. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet 6: e1000944.
-
(2010)
PLoS Genet
, vol.6
, pp. e1000944
-
-
Gout, J.-F.1
Kahn, D.2
Duret, L.3
-
26
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, HordijkW, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
27
-
-
66049128566
-
Distinguishing among evolutionary models for the maintenance of gene duplicates
-
Hahn MW. 2009. Distinguishing among evolutionary models for the maintenance of gene duplicates. J Hered 100: 605-617.
-
(2009)
J Hered
, vol.100
, pp. 605-617
-
-
Hahn, M.W.1
-
28
-
-
20144374141
-
Gene complexity and gene duplicability
-
He X, Zhang J. 2005. Gene complexity and gene duplicability. Curr Biol 15: 1016-1021.
-
(2005)
Curr Biol
, vol.15
, pp. 1016-1021
-
-
He, X.1
Zhang, J.2
-
30
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res 9: 868-877.
-
(1999)
Genome Res
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
31
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci 256: 119-124.
-
(1994)
Proc R Soc Lond B Biol Sci
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
32
-
-
54349113511
-
Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species
-
Hughes T, Liberles DA. 2008. Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. J Mol Evol 67: 343-357.
-
(2008)
J Mol Evol
, vol.67
, pp. 343-357
-
-
Hughes, T.1
Liberles, D.A.2
-
33
-
-
75549087305
-
The evolution of gene duplications: Classifying and distinguishing between models
-
Innan H, Kondrashov F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11: 97-108.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 97-108
-
-
Innan, H.1
Kondrashov, F.2
-
34
-
-
38349125022
-
Translational control of intron splicing in eukaryotes
-
Jaillon O, Bouhouche K, Gout JF, Aury JM, Noel B, Saudemont B, Nowacki M, Serrano V, Porcel BM, Segurens B, et al. 2008. Translational control of intron splicing in eukaryotes. Nature 451: 359-362.
-
(2008)
Nature
, vol.451
, pp. 359-362
-
-
Jaillon, O.1
Bouhouche, K.2
Gout, J.F.3
Aury, J.M.4
Noel, B.5
Saudemont, B.6
Nowacki, M.7
Serrano, V.8
Porcel, B.M.9
Segurens, B.10
-
35
-
-
79955630390
-
Ancestral polyploidy in seed plants and angiosperms
-
Jiao YN, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang HY, Soltis PS, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
-
(2011)
Nature
, vol.473
, pp. 97-100
-
-
Jiao, Y.N.1
Wickett, N.J.2
Ayyampalayam, S.3
Chanderbali, A.S.4
Landherr, L.5
Ralph, P.E.6
Tomsho, L.P.7
Hu, Y.8
Liang, H.Y.9
Soltis, P.S.10
-
36
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
37
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
38
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
39
-
-
77955090647
-
Evolution of the mutation rate
-
Lynch M. 2010. Evolution of the mutation rate. Trends Genet 26: 345-352.
-
(2010)
Trends Genet
, vol.26
, pp. 345-352
-
-
Lynch, M.1
-
40
-
-
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
-
41
-
-
0034529964
-
The origin of interspecific genomic incompatibility via gene duplication
-
Lynch M, Force AG. 2000. The origin of interspecific genomic incompatibility via gene duplication. Am Nat 156: 590-605.
-
(2000)
Am Nat
, vol.156
, pp. 590-605
-
-
Lynch, M.1
Force, A.G.2
-
42
-
-
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
-
43
-
-
84870517015
-
Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
-
Makino T, McLysaght A. 2012. Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant. Genome Res 22: 2427-2435.
-
(2012)
Genome Res
, vol.22
, pp. 2427-2435
-
-
Makino, T.1
McLysaght, A.2
-
44
-
-
33748490697
-
Gene transposition as a cause of hybrid sterility in Drosophila
-
Masly JP, Jones CD, Noor MAF, Locke J, Orr HA. 2006. Gene transposition as a cause of hybrid sterility in Drosophila. Science 313: 1448-1450.
-
(2006)
Science
, vol.313
, pp. 1448-1450
-
-
Masly, J.P.1
Jones, C.D.2
Noor, M.A.F.3
Locke, J.4
Orr, H.A.5
-
45
-
-
84872507663
-
Evolutionary significance of whole-genome duplication
-
(ed. Soltis PS, Soltis DE), Springer-Verlag, Berlin.
-
McGrath CL, Lynch M. 2012. Evolutionary significance of whole-genome duplication. In Polyploidy and genome evolution (ed. Soltis PS, Soltis DE), pp. 1-20. Springer-Verlag, Berlin.
-
(2012)
Polyploidy and Genome Evolution
, pp. 1-20
-
-
McGrath, C.L.1
Lynch, M.2
-
46
-
-
84905641351
-
Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence
-
McGrath CL, Gout JF, Doak TG, Yanagi A, Lynch M. 2014. Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. Genetics doi: 10.1534/genetics.114.163287.
-
(2014)
Genetics
-
-
McGrath, C.L.1
Gout, J.F.2
Doak, T.G.3
Yanagi, A.4
Lynch, M.5
-
47
-
-
26244444380
-
From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD)
-
Meyer A, Van de Peer Y. 2005. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27: 937-945.
-
(2005)
BioEssays
, vol.27
, pp. 937-945
-
-
Meyer, A.1
Van De Peer, Y.2
-
48
-
-
84874969184
-
PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
-
Mi H, Muruganujan A, Thomas PD. 2012. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 41: D377-D386.
-
(2012)
Nucleic Acids Res
, vol.41
, pp. D377-D386
-
-
Mi, H.1
Muruganujan, A.2
Thomas, P.D.3
-
49
-
-
57249105124
-
Aggressive assembly of pyrosequencing reads with mates
-
Miller JR, Delcher AL, Koren S, Venter E,Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
-
(2008)
Bioinformatics
, vol.24
, pp. 2818-2824
-
-
Miller, J.R.1
Delcher, A.L.2
Koren, S.3
Venter, E.4
Walenz, B.P.5
Brownley, A.6
Johnson, J.7
Li, K.8
Mobarry, C.9
Sutton, G.10
-
50
-
-
78650576181
-
Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes
-
Mizuta Y, Harushima Y, Kurata N. 2010. Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci 107: 20417-20422.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 20417-20422
-
-
Mizuta, Y.1
Harushima, Y.2
Kurata, N.3
-
51
-
-
33744807179
-
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
-
Morin RD, Chang E, Petrescu A, Liao N, Griffith M, ChowW, Kirkpatrick R, Butterfield YS, Young AC, Stott J, et al. 2006. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res 16: 796-803.
-
(2006)
Genome Res
, vol.16
, pp. 796-803
-
-
Morin, R.D.1
Chang, E.2
Petrescu, A.3
Liao, N.4
Griffith, M.5
Chow, W.6
Kirkpatrick, R.7
Butterfield, Y.S.8
Young, A.C.9
Stott, J.10
-
53
-
-
85012783341
-
Functions and genetic bases of reproductive barriers
-
(ed. Oka HI), Japan Scientific Societies Press/Elsevier, Tokyo.
-
Oka HI. 1988. Functions and genetic bases of reproductive barriers. In Origin of cultivated rice (ed. Oka HI), pp. 181-209. Japan Scientific Societies Press/Elsevier, Tokyo.
-
(1988)
Origin of Cultivated Rice
, pp. 181-209
-
-
Oka, H.I.1
-
54
-
-
24644486449
-
Timing and mechanism of ancient vertebrate genome duplications-The adventure of a hypothesis
-
Panopoulou G, Poustka AJ. 2005. Timing and mechanism of ancient vertebrate genome duplications-the adventure of a hypothesis. Trends Genet 21: 559-567.
-
(2005)
Trends Genet
, vol.21
, pp. 559-567
-
-
Panopoulou, G.1
Poustka, A.J.2
-
55
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp B, Pal C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
-
(2003)
Nature
, vol.424
, pp. 194-197
-
-
Papp, B.1
Pal, C.2
Hurst, L.D.3
-
56
-
-
0034526131
-
Zebrafish comparative genomics and the origins of vertebrate chromosomes
-
Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10: 1890-1902.
-
(2000)
Genome Res
, vol.10
, pp. 1890-1902
-
-
Postlethwait, J.H.1
Woods, I.G.2
Ngo-Hazelett, P.3
Yan, Y.L.4
Kelly, P.D.5
Chu, F.6
Huang, H.7
Hill-Force, A.8
Talbot, W.S.9
-
57
-
-
45749086679
-
The amphioxus genome and the evolution of the chordate karyotype
-
Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu J-K, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-1071.
-
(2008)
Nature
, vol.453
, pp. 1064-1071
-
-
Putnam, N.H.1
Butts, T.2
Ferrier, D.E.K.3
Furlong, R.F.4
Hellsten, U.5
Kawashima, T.6
Robinson-Rechavi, M.7
Shoguchi, E.8
Terry, A.9
Yu, J.-K.10
-
58
-
-
33645023614
-
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
-
Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH. 2006. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440: 341-345.
-
(2006)
Nature
, vol.440
, pp. 341-345
-
-
Scannell, D.R.1
Byrne, K.P.2
Gordon, J.L.3
Wong, S.4
Wolfe, K.H.5
-
59
-
-
34347209089
-
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
-
Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH. 2007. Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci 104: 8397-8402.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 8397-8402
-
-
Scannell, D.R.1
Frank, A.C.2
Conant, G.C.3
Byrne, K.P.4
Woolfit, M.5
Wolfe, K.H.6
-
60
-
-
84959057192
-
EuGene: An eucaryotic gene finder that combines several sources of evidence
-
(ed. Gascuel O, Sagot M-F), Springer, Berlin
-
Schiex T, Moisan A, Rouze P. 2001. EuGene: an eucaryotic gene finder that combines several sources of evidence. In Computational biology (ed. Gascuel O, Sagot M-F), pp. 111-125. Springer, Berlin.
-
(2001)
Computational Biology
, pp. 111-125
-
-
Schiex, T.1
Moisan, A.2
Rouze, P.3
-
61
-
-
0023650543
-
The codon Adaptation Index-A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH. 1987. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15: 1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
62
-
-
23244439774
-
The role of deleterious mutations in allopatric speciation
-
Shpak M. 2005. The role of deleterious mutations in allopatric speciation. Evolution 59: 1389-1399.
-
(2005)
Evolution
, vol.59
, pp. 1389-1399
-
-
Shpak, M.1
-
63
-
-
0037109058
-
The hidden duplication past of Arabidopsis thaliana
-
Simillion C, Vandepoele K, Van Montagu C, ZabeauM, Van de Peer Y. 2002. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci 99: 13627-13632.
-
(2002)
Proc Natl Acad Sci
, vol.99
, pp. 13627-13632
-
-
Simillion, C.1
Vandepoele, K.2
Van Montagu, C.3
Zabeau, M.4
Van De Peer, Y.5
-
64
-
-
0000448959
-
The Paramecium aurelia complex of fourteen sibling species
-
Sonneborn TM. 1975. The Paramecium aurelia complex of fourteen sibling species. Trans Am Microsc Soc 94: 155-178.
-
(1975)
Trans Am Microsc Soc
, vol.94
, pp. 155-178
-
-
Sonneborn, T.M.1
-
65
-
-
40049091292
-
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
-
Stanke M, Diekhans M, Baertsch R, Haussler D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637-644.
-
(2008)
Bioinformatics
, vol.24
, pp. 637-644
-
-
Stanke, M.1
Diekhans, M.2
Baertsch, R.3
Haussler, D.4
-
66
-
-
84868579284
-
Extraordinary genome stability in the ciliate Paramecium tetraurelia
-
Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc Natl Acad Sci 109: 19339-19344.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 19339-19344
-
-
Sung, W.1
Tucker, A.E.2
Doak, T.G.3
Choi, E.4
Thomas, W.K.5
Lynch, M.6
-
67
-
-
56049116951
-
Preservation of a pseudogene by gene conversion and diversifying selection
-
Takuno S, Nishio T, Satta Y, Innan H. 2008. Preservation of a pseudogene by gene conversion and diversifying selection. Genetics 180: 517-531.
-
(2008)
Genetics
, vol.180
, pp. 517-531
-
-
Takuno, S.1
Nishio, T.2
Satta, Y.3
Innan, H.4
-
68
-
-
10944230777
-
Duplication and divergence: The evolution of new genes and old ideas
-
Taylor JS, Raes J. 2004. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38: 615-643.
-
(2004)
Annu Rev Genet
, vol.38
, pp. 615-643
-
-
Taylor, J.S.1
Raes, J.2
-
69
-
-
1942485886
-
The effect of gene conversion on the divergence between duplicated genes
-
Teshima KM, Innan H. 2004. The effect of gene conversion on the divergence between duplicated genes. Genetics 166: 1553-1560.
-
(2004)
Genetics
, vol.166
, pp. 1553-1560
-
-
Teshima, K.M.1
Innan, H.2
-
70
-
-
33745617700
-
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
-
Thomas BC, Pedersen B, Freeling M. 2006. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 16: 934-946.
-
(2006)
Genome Res
, vol.16
, pp. 934-946
-
-
Thomas, B.C.1
Pedersen, B.2
Freeling, M.3
-
71
-
-
20044383583
-
Resurrecting ancestral alcohol dehydrogenases from yeast
-
Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA. 2005. Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37: 630-635.
-
(2005)
Nat Genet
, vol.37
, pp. 630-635
-
-
Thomson, J.M.1
Gaucher, E.A.2
Burgan, M.F.3
De Kee, D.W.4
Li, T.5
Aris, J.P.6
Benner, S.A.7
-
72
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Lior P. 2012. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31: 46-53.
-
(2012)
Nat Biotechnol
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
Hendrickson, D.G.2
Sauvageau, M.3
Goff, L.4
Rinn, J.L.5
Lior, P.6
-
73
-
-
70349325524
-
The evolutionary significance of ancient genome duplications
-
Van de Peer Y, Maere S, Meyer A. 2009. The evolutionary significance of ancient genome duplications. Nat Rev Genet 10: 725-732.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 725-732
-
-
Van De Peer, Y.1
Maere, S.2
Meyer, A.3
-
74
-
-
0036008552
-
Exploring the etiology of haploinsufficiency
-
Veitia RA. 2002. Exploring the etiology of haploinsufficiency. BioEssays 24: 175-184.
-
(2002)
BioEssays
, vol.24
, pp. 175-184
-
-
Veitia, R.A.1
-
75
-
-
48949115115
-
Cellular reactions to gene dosage imbalance: Genomic, transcriptomic, and proteomic effects
-
Veitia RA, Bottani S, Birchler JA. 2008. Cellular reactions to gene dosage imbalance: genomic, transcriptomic, and proteomic effects. Trends Genet 24: 390-397.
-
(2008)
Trends Genet
, vol.24
, pp. 390-397
-
-
Veitia, R.A.1
Bottani, S.2
Birchler, J.A.3
-
76
-
-
0023449349
-
Sequence-dependent gene conversion: Can duplicated genes diverge fast enough to escape conversion?
-
Walsh JB. 1987. Sequence-dependent gene conversion: can duplicated genes diverge fast enough to escape conversion? Genetics 117: 543-557.
-
(1987)
Genetics
, vol.117
, pp. 543-557
-
-
Walsh, J.B.1
-
77
-
-
0001604836
-
A model for divergent, allopatric speciation of polyploid Pteridophytes resulting from silencing of duplicate-gene expression
-
Werth CR,Windham MD. 1991. A model for divergent, allopatric speciation of polyploid Pteridophytes resulting from silencing of duplicate-gene expression. Am Nat 137: 515-526.
-
(1991)
Am Nat
, vol.137
, pp. 515-526
-
-
Werth, C.R.1
Windham, M.D.2
-
78
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC. 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
-
79
-
-
77954741256
-
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs
-
Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Damon L, Shabarinath S, Freeling M. 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biol 8: 1-15.
-
(2010)
PLoS Biol
, vol.8
, pp. 1-15
-
-
Woodhouse, M.R.1
Schnable, J.C.2
Pedersen, B.S.3
Lyons, E.4
Damon, L.5
Shabarinath, S.6
Freeling, M.7
-
80
-
-
20044391996
-
The gene duplication that greased society's wheels
-
Woolfit M, Wolfe K. 2005. The gene duplication that greased society's wheels. Nat Genet 37: 566-567.
-
(2005)
Nat Genet
, vol.37
, pp. 566-567
-
-
Woolfit, M.1
Wolfe, K.2
-
81
-
-
77952253818
-
Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication
-
Wu X, Qi X. 2010. Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. BMC Evol Biol 10: 145.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 145
-
-
Wu, X.1
Qi, X.2
-
82
-
-
44649166423
-
The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution
-
Wu Y, Zhu Z, Ligeng M, Chen M. 2008. The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution. Mol Biol Evol 25: 1003-1006.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1003-1006
-
-
Wu, Y.1
Zhu, Z.2
Ligeng, M.3
Chen, M.4
-
83
-
-
76549125715
-
Mitochondrial gene in the nuclear genome induces reproductive barrier in rice
-
Yamagata Y, Yamamoto E, Aya K, Win KT, Doi K. Sobrizal, Tomoko I, Kanamori H,Wu J, Matsumoto T, et al. 2010. Mitochondrial gene in the nuclear genome induces reproductive barrier in rice. Proc Natl Acad Sci 107: 1494-1499.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 1494-1499
-
-
Yamagata, Y.1
Yamamoto, E.2
Aya, K.3
Win, K.T.4
Sobrizal, D.K.5
Tomoko, I.6
Kanamori, H.7
Wu, J.8
Matsumoto, T.9
-
84
-
-
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
-
-
Zh, Y.1
|