-
1
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H, (2003) Translational selection and yeast proteome evolution. Genetics, 164, 1291-1303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
33646244720
-
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome
-
Arbiza L, Dopazo J, Dopazo H, (2006) Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Computational Biology, 2, e38.
-
(2006)
PLoS Computational Biology
, vol.2
, pp. e38
-
-
Arbiza, L.1
Dopazo, J.2
Dopazo, H.3
-
5
-
-
44249091879
-
Genome-scale proteomics reveals arabidopsis thaliana gene models and proteome dynamics
-
Baerenfaller K, Grossmann J, Grobei MA, et al,. (2008) Genome-scale proteomics reveals arabidopsis thaliana gene models and proteome dynamics. Science, 320, 938-941.
-
(2008)
Science
, vol.320
, pp. 938-941
-
-
Baerenfaller, K.1
Grossmann, J.2
Grobei, M.A.3
-
6
-
-
34250659350
-
More genes underwent positive selection in chimpanzee evolution than in human evolution
-
Bakewell MA, Shi P, Zhang J, (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences, 104, 7489-7494.
-
(2007)
Proceedings of the National Academy of Sciences
, vol.104
, pp. 7489-7494
-
-
Bakewell, M.A.1
Shi, P.2
Zhang, J.3
-
7
-
-
3042672020
-
Functional annotation of the Arabidopsis genome using controlled vocabularies
-
Berardini TZ, Mundodi S, Reiser L, et al,. (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiology, 135, 745-755.
-
(2004)
Plant Physiology
, vol.135
, pp. 745-755
-
-
Berardini, T.Z.1
Mundodi, S.2
Reiser, L.3
-
8
-
-
0034161419
-
Exonic splicing enhancers: Mechanism of action, diversity and role in human genetic diseases
-
Blencowe BJ, (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends in Biochemical Sciences, 25, 106-110.
-
(2000)
Trends in Biochemical Sciences
, vol.25
, pp. 106-110
-
-
Blencowe, B.J.1
-
9
-
-
0027249595
-
DbEST - Database for expressed sequence tags
-
Boguski MS, Lowe TMJ, Tolstoshev CM, (1993) dbEST-database for expressed sequence tags. Nature Genetics, 4, 332-333.
-
(1993)
Nature Genetics
, vol.4
, pp. 332-333
-
-
Boguski, M.S.1
Lowe, T.M.J.2
Tolstoshev, C.M.3
-
10
-
-
0034130561
-
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays
-
Brenner S, Johnson M, Bridgham J, et al,. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18, 630-634.
-
(2000)
Nature Biotechnology
, vol.18
, pp. 630-634
-
-
Brenner, S.1
Johnson, M.2
Bridgham, J.3
-
11
-
-
67649130520
-
Why do species vary in their rate of molecular evolution?
-
Bromham L, (2009) Why do species vary in their rate of molecular evolution? Biology Letters, 5, 401-404.
-
(2009)
Biology Letters
, vol.5
, pp. 401-404
-
-
Bromham, L.1
-
12
-
-
84890527710
-
The evolution, impact and properties of exonic splice enhancers
-
Caceres EF, Hurst LD, (2013) The evolution, impact and properties of exonic splice enhancers. Genome Biology, 14, R143.
-
(2013)
Genome Biology
, vol.14
, pp. R143
-
-
Caceres, E.F.1
Hurst, L.D.2
-
13
-
-
80053384429
-
Whole-genome sequencing of multiple Arabidopsis thaliana populations
-
Cao J, Schneeberger K, Ossowski S, et al,. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics, 43, 956-963.
-
(2011)
Nature Genetics
, vol.43
, pp. 956-963
-
-
Cao, J.1
Schneeberger, K.2
Ossowski, S.3
-
14
-
-
31844449496
-
Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers
-
Carlini DB, Genut JE, (2006) Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. Journal of Molecular Evolution, 62, 89-98.
-
(2006)
Journal of Molecular Evolution
, vol.62
, pp. 89-98
-
-
Carlini, D.B.1
Genut, J.E.2
-
15
-
-
58549101102
-
Discovery and revision of Arabidopsis genes by proteogenomics
-
Castellana NE, Payne SH, Shen Z, et al,. (2008) Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences USA, 105, 21034-21038.
-
(2008)
Proceedings of the National Academy of Sciences USA
, vol.105
, pp. 21034-21038
-
-
Castellana, N.E.1
Payne, S.H.2
Shen, Z.3
-
16
-
-
0036699596
-
Selection for short introns in highly expressed genes
-
Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA, (2002) Selection for short introns in highly expressed genes. Nature Genetics, 31, 415-418.
-
(2002)
Nature Genetics
, vol.31
, pp. 415-418
-
-
Castillo-Davis, C.I.1
Mekhedov, S.L.2
Hartl, D.L.3
Koonin, E.V.4
Kondrashov, F.A.5
-
17
-
-
0038365368
-
Analysis of microarray data using Z score transformation
-
Cheadle C, Vawter MP, Freed WJ, Becker KG, (2003) Analysis of microarray data using Z score transformation. Journal of Molecular Diagnostics, 5, 73-81.
-
(2003)
Journal of Molecular Diagnostics
, vol.5
, pp. 73-81
-
-
Cheadle, C.1
Vawter, M.P.2
Freed, W.J.3
Becker, K.G.4
-
18
-
-
84901431283
-
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity
-
Chen L, Bush SJ, Tovar-Corona JM, Castillo-Morales A, Urrutia AO, (2014) Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Molecular Biology and Evolution, 31, 1402-1413.
-
(2014)
Molecular Biology and Evolution
, vol.31
, pp. 1402-1413
-
-
Chen, L.1
Bush, S.J.2
Tovar-Corona, J.M.3
Castillo-Morales, A.4
Urrutia, A.O.5
-
19
-
-
84881530250
-
Alternative splicing: A potential source of functional innovation in the eukaryotic genome
-
Chen L, Tovar-Corona JM, Urrutia AO, (2012) Alternative splicing: a potential source of functional innovation in the eukaryotic genome. International Journal of Evolutionary Biology, 2012, 10.
-
(2012)
International Journal of Evolutionary Biology
, vol.2012
, pp. 10
-
-
Chen, L.1
Tovar-Corona, J.M.2
Urrutia, A.O.3
-
20
-
-
79952196607
-
Expression level, evolutionary rate, and the cost of expression
-
Cherry JL, (2010a) Expression level, evolutionary rate, and the cost of expression. Genome Biology and Evolution, 2, 757-769.
-
(2010)
Genome Biology and Evolution
, vol.2
, pp. 757-769
-
-
Cherry, J.L.1
-
21
-
-
77249122086
-
Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins
-
Cherry JL, (2010b) Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins. Molecular Biology and Evolution, 27, 735-741.
-
(2010)
Molecular Biology and Evolution
, vol.27
, pp. 735-741
-
-
Cherry, J.L.1
-
22
-
-
0034666040
-
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
-
Coghlan A, Wolfe KH, (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast, 16, 1131-1145.
-
(2000)
Yeast
, vol.16
, pp. 1131-1145
-
-
Coghlan, A.1
Wolfe, K.H.2
-
23
-
-
27844577664
-
Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila
-
Comeron JM, Guthrie TB, (2005) Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila. Molecular Biology and Evolution, 22, 2519-2530.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 2519-2530
-
-
Comeron, J.M.1
Guthrie, T.B.2
-
24
-
-
0141853996
-
Asymmetric sequence divergence of duplicate genes
-
Conant GC, Wagner A, (2003) Asymmetric sequence divergence of duplicate genes. Genome Research, 13, 2052-2058.
-
(2003)
Genome Research
, vol.13
, pp. 2052-2058
-
-
Conant, G.C.1
Wagner, A.2
-
25
-
-
80052272774
-
The genome of the extremophile crucifer Thellungiella parvula
-
Dassanayake M, Oh DH, Haas JS, et al,. (2011) The genome of the extremophile crucifer Thellungiella parvula. Nature Genetics, 43, 913-918.
-
(2011)
Nature Genetics
, vol.43
, pp. 913-918
-
-
Dassanayake, M.1
Oh, D.H.2
Haas, J.S.3
-
26
-
-
26444621352
-
Why highly expressed proteins evolve slowly
-
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH, (2005) Why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences USA, 102, 14338-14343.
-
(2005)
Proceedings of the National Academy of Sciences USA
, vol.102
, pp. 14338-14343
-
-
Drummond, D.A.1
Bloom, J.D.2
Adami, C.3
Wilke, C.O.4
Arnold, F.H.5
-
27
-
-
0033977618
-
Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
-
Duret L, Mouchiroud D, (2000) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Molecular Biology and Evolution, 17, 68-070.
-
(2000)
Molecular Biology and Evolution
, vol.17
, pp. 68-070
-
-
Duret, L.1
Mouchiroud, D.2
-
28
-
-
48449101412
-
Standard and generalized McDonald-Kreitman test: A website to detect selection by comparing different classes of DNA sites
-
Egea R, Casillas S, Barbadilla A, (2008) Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. Nucleic Acids Research, 36, W157-W162.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. W157-W162
-
-
Egea, R.1
Casillas, S.2
Barbadilla, A.3
-
30
-
-
45849116820
-
Selection on amino acid substitutions in Arabidopsis
-
Foxe JP, V-u-N Dar, Zheng H, et al,. (2008) Selection on amino acid substitutions in Arabidopsis. Molecular Biology and Evolution, 25, 1375-1383.
-
(2008)
Molecular Biology and Evolution
, vol.25
, pp. 1375-1383
-
-
Foxe, J.P.1
V-U-N, D.2
Zheng, H.3
-
31
-
-
2942678187
-
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
-
Fraser H, Hirsh A, (2004) Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evolutionary Biology, 4, 13.
-
(2004)
BMC Evolutionary Biology
, vol.4
, pp. 13
-
-
Fraser, H.1
Hirsh, A.2
-
32
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
Gan X, Stegle O, Behr J, 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
-
33
-
-
35549007506
-
Mating systems and the efficacy of selection at the molecular level
-
Glémin S, (2007) Mating systems and the efficacy of selection at the molecular level. Genetics, 177, 905-916.
-
(2007)
Genetics
, vol.177
, pp. 905-916
-
-
Glémin, S.1
-
34
-
-
84903442692
-
Mating systems and selection efficacy: A test using chloroplastic sequence data in Angiosperms
-
Glemin S, Muyle A, (2014) Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms. Journal of Evolutionary Biology, 27, 1386-1399.
-
(2014)
Journal of Evolutionary Biology
, vol.27
, pp. 1386-1399
-
-
Glemin, S.1
Muyle, A.2
-
35
-
-
77954969511
-
Genome wide analyses reveal little evidence for adaptive evolution in many plant species
-
Gossmann TI, Song B-H, Windsor AJ, et al,. (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Molecular Biology and Evolution, 27, 1822-1832.
-
(2010)
Molecular Biology and Evolution
, vol.27
, pp. 1822-1832
-
-
Gossmann, T.I.1
Song, B.-H.2
Windsor, A.J.3
-
36
-
-
16344381521
-
Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
-
Hahn MW, Kern AD, (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biology and Evolution, 22, 803-806.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 803-806
-
-
Hahn, M.W.1
Kern, A.D.2
-
37
-
-
77049310401
-
The estimation and significance of the logarithm of a ratio of frequencies
-
Haldane JB, (1956) The estimation and significance of the logarithm of a ratio of frequencies. Annals of Human Genetics, 20, 309-311.
-
(1956)
Annals of Human Genetics
, vol.20
, pp. 309-311
-
-
Haldane, J.B.1
-
38
-
-
33745423085
-
Challenges of detecting directional selection after a bottleneck: Lessons from Sorghum bicolor
-
Hamblin MT, Casa AM, Sun H, et al,. (2006) Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics, 173, 953-964.
-
(2006)
Genetics
, vol.173
, pp. 953-964
-
-
Hamblin, M.T.1
Casa, A.M.2
Sun, H.3
-
39
-
-
79955468851
-
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
-
Hu TT, Pattyn P, Bakker EG, et al,. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics, 43, 476-481.
-
(2011)
Nature Genetics
, vol.43
, pp. 476-481
-
-
Hu, T.T.1
Pattyn, P.2
Bakker, E.G.3
-
40
-
-
0036720020
-
The Ka/Ks ratio: Diagnosing the form of sequence evolution
-
Hurst LD, (2002) The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends in Genetics, 18, 486.
-
(2002)
Trends in Genetics
, vol.18
, pp. 486
-
-
Hurst, L.D.1
-
41
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. Coli translational system
-
Ikemura T, (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. Journal of Molecular Biology, 151, 389-409.
-
(1981)
Journal of Molecular Biology
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
42
-
-
34250790725
-
Estimating the annotation error rate of curated GO database sequence annotations
-
Jones C, Brown A, Baumann U, (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics, 8, 170.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 170
-
-
Jones, C.1
Brown, A.2
Baumann, U.3
-
43
-
-
33846675265
-
A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group
-
Kawahara Y, Imanishi T, (2007) A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evolutionary Biology, 7, 9.
-
(2007)
BMC Evolutionary Biology
, vol.7
, pp. 9
-
-
Kawahara, Y.1
Imanishi, T.2
-
44
-
-
33846681383
-
Different levels of alternative splicing among eukaryotes
-
Kim E, Magen A, Ast G, (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Research, 35, 125-131.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 125-131
-
-
Kim, E.1
Magen, A.2
Ast, G.3
-
45
-
-
33646588998
-
Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae
-
Kim SH, Yi SV, (2006) Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae. Molecular Biology and Evolution, 23, 1068-1075.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 1068-1075
-
-
Kim, S.H.1
Yi, S.V.2
-
46
-
-
34548539463
-
Understanding relationship between sequence and functional evolution in yeast proteins
-
Kim SH, Yi SV, (2007) Understanding relationship between sequence and functional evolution in yeast proteins. Genetica, 131, 151-156.
-
(2007)
Genetica
, vol.131
, pp. 151-156
-
-
Kim, S.H.1
Yi, S.V.2
-
47
-
-
79953064734
-
Evolution of exon-intron structure and alternative splicing
-
Koralewski TE, Krutovsky KV, (2011) Evolution of exon-intron structure and alternative splicing. PLoS ONE, 6, e18055.
-
(2011)
PLoS ONE
, vol.6
, pp. e18055
-
-
Koralewski, T.E.1
Krutovsky, K.V.2
-
48
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov DM, Wolf YI, Rogozin IB, Koonin EV, (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Research, 13, 2229-2235.
-
(2003)
Genome Research
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
49
-
-
39749084483
-
Evolution of protein-coding genes in Drosophila
-
Larracuente AM, Sackton TB, Greenberg AJ, et al,. (2008) Evolution of protein-coding genes in Drosophila. Trends in Genetics, 24, 114-123.
-
(2008)
Trends in Genetics
, vol.24
, pp. 114-123
-
-
Larracuente, A.M.1
Sackton, T.B.2
Greenberg, A.J.3
-
50
-
-
17744376961
-
Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
-
Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL, (2005) Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Molecular Biology and Evolution, 22, 1345-1354.
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 1345-1354
-
-
Lemos, B.1
Bettencourt, B.R.2
Meiklejohn, C.D.3
Hartl, D.L.4
-
51
-
-
3042616134
-
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile
-
Lercher MJ, Chamary JV, Hurst LD, (2004) Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Research, 14, 1002-1013.
-
(2004)
Genome Research
, vol.14
, pp. 1002-1013
-
-
Lercher, M.J.1
Chamary, J.V.2
Hurst, L.D.3
-
52
-
-
0036613754
-
Clustering of housekeeping genes provides a unified model of gene order in the human genome
-
Lercher MJ, Urrutia AO, Hurst LD, (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genetics, 31, 180-183.
-
(2002)
Nature Genetics
, vol.31
, pp. 180-183
-
-
Lercher, M.J.1
Urrutia, A.O.2
Hurst, L.D.3
-
53
-
-
0034748984
-
Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias
-
Lercher MJ, Williams EJ, Hurst LD, (2001) Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias. Molecular Biology and Evolution, 18, 2032-2039.
-
(2001)
Molecular Biology and Evolution
, vol.18
, pp. 2032-2039
-
-
Lercher, M.J.1
Williams, E.J.2
Hurst, L.D.3
-
54
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
Löytynoja A, Goldman N, (2008) Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632-1635.
-
(2008)
Science
, vol.320
, pp. 1632-1635
-
-
Löytynoja, A.1
Goldman, N.2
-
55
-
-
33644909094
-
The evolutionary rate of a protein is influenced by features of the interacting partners
-
Makino T, Gojobori T, (2006) The evolutionary rate of a protein is influenced by features of the interacting partners. Molecular Biology and Evolution, 23, 784-789.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 784-789
-
-
Makino, T.1
Gojobori, T.2
-
56
-
-
4143105022
-
Recombination and base composition: The case of the highly self-fertilizing plant Arabidopsis thaliana
-
Marais G, Charlesworth B, Wright SI, (2004) Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biology, 5, R45.
-
(2004)
Genome Biology
, vol.5
, pp. R45
-
-
Marais, G.1
Charlesworth, B.2
Wright, S.I.3
-
57
-
-
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
-
58
-
-
2942553957
-
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis
-
Meyers BC, Tej SS, Vu TH, et al,. (2004) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Research, 14, 1641-1653.
-
(2004)
Genome Research
, vol.14
, pp. 1641-1653
-
-
Meyers, B.C.1
Tej, S.S.2
Vu, T.H.3
-
59
-
-
84906282269
-
Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: Searching for G × e effects
-
Morrison GD, Linder CR, (2014) Association mapping of germination traits in Arabidopsis thaliana under light and nutrient treatments: searching for G × E effects. G3 (Bethesda), 4, 1465-1478.
-
(2014)
G3 (Bethesda)
, vol.4
, pp. 1465-1478
-
-
Morrison, G.D.1
Linder, C.R.2
-
60
-
-
33644876658
-
Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA
-
Nakano M, Nobuta K, Vemaraju K, et al,. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research, 34, D731-D735.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D731-D735
-
-
Nakano, M.1
Nobuta, K.2
Vemaraju, K.3
-
61
-
-
29444452921
-
Molecular signatures of natural selection
-
Nielsen R, (2005) Molecular signatures of natural selection. Annual Review of Genetics, 39, 197-218.
-
(2005)
Annual Review of Genetics
, vol.39
, pp. 197-218
-
-
Nielsen, R.1
-
62
-
-
75849145292
-
Expansion of the eukaryotic proteome by alternative splicing
-
Nilsen TW, Graveley BR, (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463.
-
(2010)
Nature
, vol.463
, pp. 457-463
-
-
Nilsen, T.W.1
Graveley, B.R.2
-
63
-
-
0035207792
-
Does the recombination rate affect the efficiency of purifying selection? the yeast genome provides a partial answer
-
Pál C, Papp B, Hurst LD, (2001) Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Molecular Biology and Evolution, 18, 2323-2326.
-
(2001)
Molecular Biology and Evolution
, vol.18
, pp. 2323-2326
-
-
Pál, C.1
Papp, B.2
Hurst, L.D.3
-
64
-
-
77955223565
-
Expression breadth and expression abundance behave differently in correlations with evolutionary rates
-
Park S, Choi S, (2010) Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evolutionary Biology, 10, 241.
-
(2010)
BMC Evolutionary Biology
, vol.10
, pp. 241
-
-
Park, S.1
Choi, S.2
-
65
-
-
77749282952
-
Anopheles immune genes and amino acid sites evolving under the effect of positive selection
-
Parmakelis A, Moustaka M, Poulakakis N, et al,. (2010) Anopheles immune genes and amino acid sites evolving under the effect of positive selection. PLoS ONE, 5, e8885.
-
(2010)
PLoS ONE
, vol.5
, pp. e8885
-
-
Parmakelis, A.1
Moustaka, M.2
Poulakakis, N.3
-
66
-
-
30744469841
-
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
-
Parmley JL, Chamary JV, Hurst LD, (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Molecular Biology and Evolution, 23, 301-309.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 301-309
-
-
Parmley, J.L.1
Chamary, J.V.2
Hurst, L.D.3
-
67
-
-
34547709593
-
Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
-
Parmley JL, Hurst LD, (2007) Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Molecular Biology and Evolution, 24, 1600-1603.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1600-1603
-
-
Parmley, J.L.1
Hurst, L.D.2
-
68
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson WR, (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods in Molecular Biology, 132, 185-219.
-
(2000)
Methods in Molecular Biology
, vol.132
, pp. 185-219
-
-
Pearson, W.R.1
-
69
-
-
34249987613
-
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
-
Pertea M, Mount SM, Salzberg SL, (2007) A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics, 8, 159.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 159
-
-
Pertea, M.1
Mount, S.M.2
Salzberg, S.L.3
-
70
-
-
67349114852
-
Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution
-
Podder S, Mukhopadhyay P, Ghosh TC, (2009) Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution. Gene, 439, 11-16.
-
(2009)
Gene
, vol.439
, pp. 11-16
-
-
Podder, S.1
Mukhopadhyay, P.2
Ghosh, T.C.3
-
71
-
-
84863304598
-
-
R Development Core Team. R Foundation for Statistical Computing, Vienna, Austria.
-
R Development Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2012)
R: A Language and Environment for Statistical Computing
-
-
-
72
-
-
77957937001
-
-
Northwestern University, Evanston, Illinois, USA.
-
Revelle W, (2014) psych: Procedures for Psychological, Psychometric, and Personality Research. Northwestern University, Evanston, Illinois, USA.
-
(2014)
Psych: Procedures for Psychological, Psychometric, and Personality Research
-
-
Revelle, W.1
-
73
-
-
67650314824
-
Historical divergence and gene flow in the genus Zea
-
Ross-Ibarra J, Tenaillon M, Gaut BS, (2009) Historical divergence and gene flow in the genus Zea. Genetics, 181, 1399-1413.
-
(2009)
Genetics
, vol.181
, pp. 1399-1413
-
-
Ross-Ibarra, J.1
Tenaillon, M.2
Gaut, B.S.3
-
74
-
-
16244362244
-
A gene expression map of Arabidopsis thaliana development
-
Schmid M, Davison TS, Henz SR, et al,. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics, 37, 501-506.
-
(2005)
Nature Genetics
, vol.37
, pp. 501-506
-
-
Schmid, M.1
Davison, T.S.2
Henz, S.R.3
-
75
-
-
33745638358
-
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
-
Seoighe C, Gehring C, Hurst LD, (2005) Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genetics, 1, e13.
-
(2005)
PLoS Genetics
, vol.1
, pp. e13
-
-
Seoighe, C.1
Gehring, C.2
Hurst, L.D.3
-
76
-
-
77954679308
-
DNA repair and recombination in higher plants: Insights from comparative genomics of arabidopsis and rice
-
Singh S, Roy S, Choudhury S, Sengupta D, (2010) DNA repair and recombination in higher plants: insights from comparative genomics of arabidopsis and rice. BMC Genomics, 11, 443.
-
(2010)
BMC Genomics
, vol.11
, pp. 443
-
-
Singh, S.1
Roy, S.2
Choudhury, S.3
Sengupta, D.4
-
77
-
-
84859114543
-
Genomic determinants of protein evolution and polymorphism in Arabidopsis
-
Slotte T, Bataillon T, Hansen TT, et al,. (2011) Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution, 3, 1210-1219.
-
(2011)
Genome Biology and Evolution
, vol.3
, pp. 1210-1219
-
-
Slotte, T.1
Bataillon, T.2
Hansen, T.T.3
-
78
-
-
78651328883
-
The BioGRID interaction database: 2011 update
-
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, et al,. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Research, 39, D698-D704.
-
(2011)
Nucleic Acids Research
, vol.39
, pp. D698-D704
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-Aryamontri, A.3
-
79
-
-
33644873184
-
BioGRID: A general repository for interaction datasets
-
Stark C, Breitkreutz BJ, Reguly T, et al,. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Research, 34, D535-D539.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
-
80
-
-
33846786904
-
Synonymous codon usage in Escherichia coli: Selection for translational accuracy
-
Stoletzki N, Eyre-Walker A, (2007) Synonymous codon usage in Escherichia coli: selection for translational accuracy. Molecular Biology and Evolution, 24, 374-381.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 374-381
-
-
Stoletzki, N.1
Eyre-Walker, A.2
-
81
-
-
84902995537
-
Efficient purging of deleterious mutations in plants with haploid selfing
-
Szövényi P, Devos N, Weston DJ, et al,. (2014) Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biology and Evolution, 6, 1238-1252.
-
(2014)
Genome Biology and Evolution
, vol.6
, pp. 1238-1252
-
-
Szövényi, P.1
Devos, N.2
Weston, D.J.3
-
83
-
-
33750954198
-
Intron length and accelerated 3′ gene evolution
-
Tang CS, Zhao YZ, Smith DK, Epstein RJ, (2006) Intron length and accelerated 3′ gene evolution. Genomics, 88, 682-689.
-
(2006)
Genomics
, vol.88
, pp. 682-689
-
-
Tang, C.S.1
Zhao, Y.Z.2
Smith, D.K.3
Epstein, R.J.4
-
84
-
-
45449085031
-
Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence
-
Tennessen JA, (2008) Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence. Bioinformatics, 24, 1421-1425.
-
(2008)
Bioinformatics
, vol.24
, pp. 1421-1425
-
-
Tennessen, J.A.1
-
85
-
-
0037143745
-
Signature of balancing selection in Arabidopsis
-
Tian D, Araki H, Stahl E, Bergelson J, Kreitman M, (2002) Signature of balancing selection in Arabidopsis. Proceedings of the National Academy of Sciences USA, 99, 11525-11530.
-
(2002)
Proceedings of the National Academy of Sciences USA
, vol.99
, pp. 11525-11530
-
-
Tian, D.1
Araki, H.2
Stahl, E.3
Bergelson, J.4
Kreitman, M.5
-
86
-
-
0024596324
-
Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes
-
Ticher A, Graur D, (1989) Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes. Journal of Molecular Evolution, 28, 286-298.
-
(1989)
Journal of Molecular Evolution
, vol.28
, pp. 286-298
-
-
Ticher, A.1
Graur, D.2
-
87
-
-
78650453703
-
Lineage-specific variation in intensity of natural selection in mammals
-
Toll-Riera M, Laurie S, Albà MM, (2011) Lineage-specific variation in intensity of natural selection in mammals. Molecular Biology and Evolution, 28, 383-398.
-
(2011)
Molecular Biology and Evolution
, vol.28
, pp. 383-398
-
-
Toll-Riera, M.1
Laurie, S.2
Albà, M.M.3
-
88
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller T, Waldman YY, Kupiec M, Ruppin E, (2010) Translation efficiency is determined by both codon bias and folding energy. Proceedings of the National Academy of Sciences USA, 107, 3645-3650.
-
(2010)
Proceedings of the National Academy of Sciences USA
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
Waldman, Y.Y.2
Kupiec, M.3
Ruppin, E.4
-
89
-
-
0035671698
-
Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
-
Urrutia AO, Hurst LD, (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics, 159, 1191-1199.
-
(2001)
Genetics
, vol.159
, pp. 1191-1199
-
-
Urrutia, A.O.1
Hurst, L.D.2
-
90
-
-
0142092546
-
The signature of selection mediated by expression on human genes
-
Urrutia AO, Hurst LD, (2003) The signature of selection mediated by expression on human genes. Genome Research, 13, 2260-2264.
-
(2003)
Genome Research
, vol.13
, pp. 2260-2264
-
-
Urrutia, A.O.1
Hurst, L.D.2
-
91
-
-
0141854009
-
The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes
-
Versteeg R, van Schaik BD, van Batenburg MF, et al,. (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Research, 13, 1998-2004.
-
(2003)
Genome Research
, vol.13
, pp. 1998-2004
-
-
Versteeg, R.1
Van Schaik, B.D.2
Van Batenburg, M.F.3
-
92
-
-
79954489823
-
The effects of network neighbours on protein evolution
-
Wang GZ, Lercher MJ, (2011) The effects of network neighbours on protein evolution. PLoS ONE, 6, e18288.
-
(2011)
PLoS ONE
, vol.6
, pp. e18288
-
-
Wang, G.Z.1
Lercher, M.J.2
-
93
-
-
37549008368
-
Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster
-
Warnecke T, Hurst LD, (2007) Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Molecular Biology and Evolution, 24, 2755-2762.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 2755-2762
-
-
Warnecke, T.1
Hurst, L.D.2
-
94
-
-
48449087547
-
Gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the Plasmodium genus
-
Weedall GD, Polley SD, Conway DJ, (2008) Gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the Plasmodium genus. PLoS ONE, 3, e2281.
-
(2008)
PLoS ONE
, vol.3
, pp. e2281
-
-
Weedall, G.D.1
Polley, S.D.2
Conway, D.J.3
-
95
-
-
0034687371
-
The proteins of linked genes evolve at similar rates
-
Williams EJ, Hurst LD, (2000) The proteins of linked genes evolve at similar rates. Nature, 407, 900-903.
-
(2000)
Nature
, vol.407
, pp. 900-903
-
-
Williams, E.J.1
Hurst, L.D.2
-
96
-
-
0036218716
-
Clustering of tissue-specific genes underlies much of the similarity in rates of protein evolution of linked genes
-
Williams EJ, Hurst LD, (2002) Clustering of tissue-specific genes underlies much of the similarity in rates of protein evolution of linked genes. Journal of Molecular Evolution, 54, 511-518.
-
(2002)
Journal of Molecular Evolution
, vol.54
, pp. 511-518
-
-
Williams, E.J.1
Hurst, L.D.2
-
97
-
-
0347766006
-
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
-
Winter EE, Goodstadt L, Ponting CP, (2004) Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Research, 14, 54-61.
-
(2004)
Genome Research
, vol.14
, pp. 54-61
-
-
Winter, E.E.1
Goodstadt, L.2
Ponting, C.P.3
-
98
-
-
0025318864
-
The 'effective number of codons' used in a gene
-
Wright F, (1990) The 'effective number of codons' used in a gene. Gene, 87, 23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
99
-
-
33751351656
-
Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata
-
Wright SI, Foxe JP, DeRose-Wilson L, et al,. (2006) Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics, 174, 1421-1430.
-
(2006)
Genetics
, vol.174
, pp. 1421-1430
-
-
Wright, S.I.1
Foxe, J.P.2
Derose-Wilson, L.3
-
100
-
-
84879032810
-
Evolutionary consequences of self-fertilization in plants
-
Wright SI, Kalisz S, Slotte T, (2013) Evolutionary consequences of self-fertilization in plants. Proceedings of the Royal Society B: Biological Sciences, 280, 20130133.
-
(2013)
Proceedings of the Royal Society B: Biological Sciences
, vol.280
, pp. 20130133
-
-
Wright, S.I.1
Kalisz, S.2
Slotte, T.3
-
101
-
-
4143122090
-
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
-
Wright SI, Yau CBK, Looseley M, Meyers BC, (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Molecular Biology and Evolution, 21, 1719-1726.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 1719-1726
-
-
Wright, S.I.1
Yau, C.B.K.2
Looseley, M.3
Meyers, B.C.4
-
102
-
-
23244443123
-
Distribution of exonic splicing enhancer elements in human genes
-
Wu Y, Zhang Y, Zhang J, (2005) Distribution of exonic splicing enhancer elements in human genes. Genomics, 86, 329-336.
-
(2005)
Genomics
, vol.86
, pp. 329-336
-
-
Wu, Y.1
Zhang, Y.2
Zhang, J.3
-
103
-
-
10844290766
-
A model-based background adjustment for oligonucleotide expression arrays
-
Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F, (2004) A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association, 99, 909-917.
-
(2004)
Journal of the American Statistical Association
, vol.99
, pp. 909-917
-
-
Wu, Z.1
Irizarry, R.A.2
Gentleman, R.3
Martinez-Murillo, F.4
Spencer, F.5
-
104
-
-
67650904949
-
Integrated assessment of genomic correlates of protein evolutionary rate
-
Xia Y, Franzosa EA, Gerstein MB, (2009) Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Computational Biology, 5, e1000413.
-
(2009)
PLoS Computational Biology
, vol.5
, pp. e1000413
-
-
Xia, Y.1
Franzosa, E.A.2
Gerstein, M.B.3
-
105
-
-
0242300620
-
Empirical analysis of transcriptional activity in the Arabidopsis genome
-
Yamada K, Lim J, Dale JM, et al,. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842-846.
-
(2003)
Science
, vol.302
, pp. 842-846
-
-
Yamada, K.1
Lim, J.2
Dale, J.M.3
-
106
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai I, Benjamin H, Shmoish M, et al,. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics, 21, 650-659.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
-
107
-
-
72549117232
-
In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure
-
Yang H, (2009) In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure. Biology Direct, 4, 45.
-
(2009)
Biology Direct
, vol.4
, pp. 45
-
-
Yang, H.1
-
108
-
-
79961064486
-
Factors that contribute to variation in evolutionary rate among Arabidopsis genes
-
Yang L, Gaut BS, (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Molecular Biology and Evolution, 28, 2359-2369.
-
(2011)
Molecular Biology and Evolution
, vol.28
, pp. 2359-2369
-
-
Yang, L.1
Gaut, B.S.2
-
109
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586-1591.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
110
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP, (2000) Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution, 15, 496-503.
-
(2000)
Trends in Ecology & Evolution
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
111
-
-
1542286776
-
Mammalian housekeeping genes evolve more slowly than tissue-specific genes
-
Zhang L, Li WH, (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Molecular Biology and Evolution, 21, 236-239.
-
(2004)
Molecular Biology and Evolution
, vol.21
, pp. 236-239
-
-
Zhang, L.1
Li, W.H.2
-
112
-
-
1842635464
-
Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression
-
Zheng ZM, (2004) Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. Journal of Biomedical Science, 11, 278-294.
-
(2004)
Journal of Biomedical Science
, vol.11
, pp. 278-294
-
-
Zheng, Z.M.1
-
113
-
-
60549105899
-
Patterns of exon-intron architecture variation of genes in eukaryotic genomes
-
Zhu L, Zhang Y, Zhang W, et al,. (2009) Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics, 10, 47.
-
(2009)
BMC Genomics
, vol.10
, pp. 47
-
-
Zhu, L.1
Zhang, Y.2
Zhang, W.3
|