-
1
-
-
84876572464
-
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network
-
Alvarez-Ponce, D., and Fares, M.A. (2012). Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biol. Evol. 4: 1263–1274.
-
(2012)
Genome Biol. Evol
, vol.4
, pp. 1263-1274
-
-
Alvarez-Ponce, D.1
Fares, M.A.2
-
2
-
-
84890829647
-
The Amborella genome and the evolution of flowering plants
-
Amborella Genome Project
-
Amborella Genome Project (2013). The Amborella genome and the evolution of flowering plants. Science 342: 1241089.
-
(2013)
Science
, vol.342
-
-
-
3
-
-
33745256005
-
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
-
Anisimova, M., and Gascuel, O. (2006). Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55: 539–552.
-
(2006)
Syst. Biol
, vol.55
, pp. 539-552
-
-
Anisimova, M.1
Gascuel, O.2
-
4
-
-
84873250550
-
PYRABACTIN RESISTANCE1-LIKE8 plays an important role for the regulation of abscisic acid signaling in root
-
Antoni, R., Gonzalez-Guzman, M., Rodriguez, L., Peirats-Llobet, M., Pizzio, G.A., Fernandez, M.A., De Winne, N., De Jaeger, G., Dietrich, D., Bennett, M.J., and Rodriguez, P.L. (2013). PYRABACTIN RESISTANCE1-LIKE8 plays an important role for the regulation of abscisic acid signaling in root. Plant Physiol. 161: 931–941.
-
(2013)
Plant Physiol
, vol.161
, pp. 931-941
-
-
Antoni, R.1
Gonzalez-Guzman, M.2
Rodriguez, L.3
Peirats-Llobet, M.4
Pizzio, G.A.5
Fernandez, M.A.6
De Winne, N.7
De Jaeger, G.8
Dietrich, D.9
Bennett, M.J.10
Rodriguez, P.L.11
-
5
-
-
55149108740
-
Unique genes in plants: Specificities and conserved features throughout evolution
-
Armisén, D., Lecharny, A., and Aubourg, S. (2008). Unique genes in plants: specificities and conserved features throughout evolution. BMC Evol. Biol. 8: 280.
-
(2008)
BMC Evol. Biol
, vol.8
, pp. 280
-
-
Armisén, D.1
Lecharny, A.2
Aubourg, S.3
-
6
-
-
33750858684
-
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
-
Aury, J.M., 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
-
8
-
-
54149092976
-
Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years
-
Barker, M.S., Kane, N.C., Matvienko, M., Kozik, A., Michelmore, R.W., Knapp, S.J., and Rieseberg, L.H. (2008). Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25: 2445–2455.
-
(2008)
Mol. Biol. Evol
, vol.25
, pp. 2445-2455
-
-
Barker, M.S.1
Kane, N.C.2
Matvienko, M.3
Kozik, A.4
Michelmore, R.W.5
Knapp, S.J.6
Rieseberg, L.H.7
-
9
-
-
84871883667
-
Protein-protein and protein-membrane associations in the lignin pathway
-
Bassard, J.E., et al. (2012). Protein-protein and protein-membrane associations in the lignin pathway. Plant Cell 24: 4465–4482.
-
(2012)
Plant Cell
, vol.24
, pp. 4465-4482
-
-
Bassard, J.E.1
-
10
-
-
79959858471
-
Twophase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints
-
Bekaert, M., Edger, P.P., Pires, J.C., and Conant, G.C. (2011). Twophase 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
-
11
-
-
0001677717
-
Controlling the false discovery rate - A practical and powerful approach to multiple testing
-
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B Met. 57: 289–300.
-
(1995)
J. Roy. Stat. Soc. B Met
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
12
-
-
15244350824
-
Dosage balance in gene regulation: Biological implications
-
Birchler, J.A., Riddle, N.C., Auger, D.L., and Veitia, R.A. (2005). Dosage balance in gene regulation: biological implications. Trends Genet. 21: 219–226.
-
(2005)
Trends Genet
, vol.21
, pp. 219-226
-
-
Birchler, J.A.1
Riddle, N.C.2
Auger, D.L.3
Veitia, R.A.4
-
13
-
-
34250632677
-
The gene balance hypothesis: From classical genetics to modern genomics
-
Birchler, J.A., and Veitia, R.A. (2007). The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19: 395–402.
-
(2007)
Plant Cell
, vol.19
, pp. 395-402
-
-
Birchler, J.A.1
Veitia, R.A.2
-
14
-
-
84866294456
-
Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines
-
Birchler, J.A., and Veitia, R.A. (2012). Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc. Natl. Acad. Sci. USA 109: 14746–14753.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 14746-14753
-
-
Birchler, J.A.1
Veitia, R.A.2
-
15
-
-
3142732892
-
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution
-
Blanc, G., and Wolfe, K.H. (2004a). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679–1691.
-
(2004)
Plant Cell
, vol.16
, pp. 1679-1691
-
-
Blanc, G.1
Wolfe, K.H.2
-
16
-
-
3142700743
-
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
-
Blanc, G., and Wolfe, K.H. (2004b). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667–1678.
-
(2004)
Plant Cell
, vol.16
, pp. 1667-1678
-
-
Blanc, G.1
Wolfe, K.H.2
-
17
-
-
70350218974
-
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
-
Bremer, B., et al. (2009). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 161: 105–121.
-
(2009)
Bot. J. Linn. Soc
, vol.161
, pp. 105-121
-
-
Bremer, B.1
-
18
-
-
52949135190
-
Evolution of a new function by degenerative mutation in cephalochordate steroid receptors
-
Bridgham, J.T., Brown, J.E., Rodríguez-Marí, A., Catchen, J.M., and Thornton, J.W. (2008). Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet. 4: e1000191.
-
(2008)
Plos Genet
, vol.4
-
-
Bridgham, J.T.1
Brown, J.E.2
Rodríguez-Marí, A.3
Catchen, J.M.4
Thornton, J.W.5
-
19
-
-
33748183184
-
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes
-
Brunet, F.G., Roest Crollius, H., Paris, M., Aury, J.M., Gibert, P., Jaillon, O., Laudet, V., and Robinson-Rechavi, M. (2006). Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol. Biol. Evol. 23: 1808–1816.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 1808-1816
-
-
Brunet, F.G.1
Roest Crollius, H.2
Paris, M.3
Aury, J.M.4
Gibert, P.5
Jaillon, O.6
Laudet, V.7
Robinson-Rechavi, M.8
-
20
-
-
84862777707
-
Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin
-
Buggs, R.J., Chamala, S., Wu, W., Tate, J.A., Schnable, P.S., Soltis, D.E., Soltis, P.S., and Barbazuk, W.B. (2012). Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr. Biol. 22: 248–252.
-
(2012)
Curr. Biol
, vol.22
, pp. 248-252
-
-
Buggs, R.J.1
Chamala, S.2
Wu, W.3
Tate, J.A.4
Schnable, P.S.5
Soltis, D.E.6
Soltis, P.S.7
Barbazuk, W.B.8
-
21
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in largescale phylogenetic analyses
-
Capella-Gutiérrez, S., Silla-Martínez, J.M., and Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in largescale phylogenetic analyses. Bioinformatics 25: 1972–1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
22
-
-
84867775180
-
Evolutionary dynamics and functional specialization of plant paralogs formed by whole and small-scale genome duplications
-
Carretero-Paulet, L., and Fares, M.A. (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
-
23
-
-
84859896621
-
Towards understanding how molecular networks evolve in plants
-
Chae, L., Lee, I., Shin, J., and Rhee, S.Y. (2012). Towards understanding how molecular networks evolve in plants. Curr. Opin. Plant Biol. 15: 177–184.
-
(2012)
Curr. Opin. Plant Biol
, vol.15
, pp. 177-184
-
-
Chae, L.1
Lee, I.2
Shin, J.3
Rhee, S.Y.4
-
24
-
-
84881243153
-
Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis
-
Chao, D.Y., Dilkes, B., Luo, H., Douglas, A., Yakubova, E., Lahner, B., and Salt, D.E. (2013). Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science 341: 658–659.
-
(2013)
Science
, vol.341
, pp. 658-659
-
-
Chao, D.Y.1
Dilkes, B.2
Luo, H.3
Douglas, A.4
Yakubova, E.5
Lahner, B.6
Salt, D.E.7
-
25
-
-
84874947727
-
The BioGRID interaction database: 2013 update
-
Chatr-Aryamontri, A., et al. (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Res. 41: D816–D823.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D816-D823
-
-
Chatr-Aryamontri, A.1
-
26
-
-
84925003517
-
Comparative genomics as a time machine: How relative gene dosage and metabolic requirements shaped the timedependent resolution of yeast polyploidy
-
Conant, G.C. (2014). Comparative genomics as a time machine: how relative gene dosage and metabolic requirements shaped the timedependent resolution of yeast polyploidy. Mol. Biol. Evol. 31: 3184–3193.
-
(2014)
Mol. Biol. Evol
, vol.31
, pp. 3184-3193
-
-
Conant, G.C.1
-
27
-
-
84901818848
-
Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time
-
Conant, G.C., Birchler, J.A., and Pires, J.C. (2014). Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Curr. Opin. Plant Biol. 19: 91–98.
-
(2014)
Curr. Opin. Plant Biol
, vol.19
, pp. 91-98
-
-
Conant, G.C.1
Birchler, J.A.2
Pires, J.C.3
-
28
-
-
84887146454
-
Centromeric cohesion is protected twice at meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis
-
Cromer, L., Jolivet, S., Horlow, C., Chelysheva, L., Heyman, J., De Jaeger, G., Koncz, C., De Veylder, L., and Mercier, R. (2013). Centromeric cohesion is protected twice at meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis. Curr. Biol. 23: 2090–2099.
-
(2013)
Curr. Biol
, vol.23
, pp. 2090-2099
-
-
Cromer, L.1
Jolivet, S.2
Horlow, C.3
Chelysheva, L.4
Heyman, J.5
De Jaeger, G.6
Koncz, C.7
De Veylder, L.8
Mercier, R.9
-
29
-
-
79955555644
-
Modification of gene duplicability during the evolution of protein interaction network. PLOS Comput
-
D’Antonio, M., and Ciccarelli, F.D. (2011). Modification of gene duplicability during the evolution of protein interaction network. PLOS Comput. Biol. 7: e1002029.
-
(2011)
Biol
, vol.7
-
-
D’Antonio, M.1
Ciccarelli, F.D.2
-
30
-
-
19344363466
-
Preferential duplication of conserved proteins in eukaryotic genomes
-
Davis, J.C., and Petrov, D.A. (2004). Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2: E55.
-
(2004)
Plos Biol
, vol.2
-
-
Davis, J.C.1
Petrov, D.A.2
-
31
-
-
48249132857
-
Pervasive and persistent redundancy among duplicated genes in yeast
-
Dean, E.J., Davis, J.C., Davis, R.W., and Petrov, D.A. (2008). Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet. 4: e1000113.
-
(2008)
Plos Genet
, vol.4
-
-
Dean, E.J.1
Davis, J.C.2
Davis, R.W.3
Petrov, D.A.4
-
32
-
-
84863780541
-
CORNET 2.0: Integrating plant coexpression, protein- protein interactions, regulatory interactions, gene associations and functional annotations
-
De Bodt, S., Hollunder, J., Nelissen, H., Meulemeester, N., and Inzé, D. (2012). CORNET 2.0: integrating plant coexpression, protein- protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol. 195: 707–720.
-
(2012)
New Phytol
, vol.195
, pp. 707-720
-
-
De Bodt, S.1
Hollunder, J.2
Nelissen, H.3
Meulemeester, N.4
Inzé, D.5
-
33
-
-
84874229463
-
Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
-
De Smet, R., Adams, K.L., Vandepoele, K., Van Montagu, M.C., Maere, S., and Van de Peer, Y. (2013). Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl. Acad. Sci. USA 110: 2898–2903.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 2898-2903
-
-
De Smet, R.1
Adams, K.L.2
Vandepoele, K.3
Van Montagu, M.C.4
Maere, S.5
Van De Peer, Y.6
-
34
-
-
84884683279
-
The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid insensitive1 in Arabidopsis
-
Di Rubbo, S., et al. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid insensitive1 in Arabidopsis. Plant Cell 25: 2986–2997.
-
(2013)
Plant Cell
, vol.25
, pp. 2986-2997
-
-
Di Rubbo, S.1
-
35
-
-
84865311917
-
Evidence for a role of Arabidopsis CDT1 proteins in gametophyte development and maintenance of genome integrity
-
Domenichini, S., Benhamed, M., De Jaeger, G., Van De Slijke, E., Blanchet, S., Bourge, M., De Veylder, L., Bergounioux, C., and Raynaud, C. (2012). Evidence for a role of Arabidopsis CDT1 proteins in gametophyte development and maintenance of genome integrity. Plant Cell 24: 2779–2791.
-
(2012)
Plant Cell
, vol.24
, pp. 2779-2791
-
-
Domenichini, S.1
Benhamed, M.2
De Jaeger, G.3
Van De Slijke, E.4
Blanchet, S.5
Bourge, M.6
De Veylder, L.7
Bergounioux, C.8
Raynaud, C.9
-
36
-
-
84924083242
-
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
-
Douglas, G.M., et al. (2015). Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proc. Natl. Acad. Sci. USA 112: 2806–2811.
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 2806-2811
-
-
Douglas, G.M.1
-
37
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond, D.A., and Wilke, C.O. (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341–352.
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
38
-
-
77950191132
-
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol
-
Duarte, J.M., Wall, P.K., Edger, P.P., Landherr, L.L., Ma, H., Pires, J.C., Leebens-Mack, J., and dePamphilis, C.W. (2010). Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol. Biol. 10: 61.
-
(2010)
Biol
, vol.10
-
-
Duarte, J.M.1
Wall, P.K.2
Edger, P.P.3
Landherr, L.L.4
Ma, H.5
Pires, J.C.6
Leebens-Mack, J.7
Depamphilis, C.W.8
-
39
-
-
0037058930
-
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae
-
Dunham, M.J., Badrane, H., Ferea, T., Adams, J., Brown, P.O., Rosenzweig, F., and Botstein, D. (2002). Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99: 16144–16149.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16144-16149
-
-
Dunham, M.J.1
Badrane, H.2
Ferea, T.3
Adams, J.4
Brown, P.O.5
Rosenzweig, F.6
Botstein, D.7
-
40
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. (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
-
41
-
-
70349682921
-
Gene and genome duplications: The impact of dosage-sensitivity on the fate of nuclear genes
-
Edger, P.P., and Pires, J.C. (2009). Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 17: 699–717.
-
(2009)
Chromosome Res
, vol.17
, pp. 699-717
-
-
Edger, P.P.1
Pires, J.C.2
-
42
-
-
84865281034
-
SAMBA, a plant-specific anaphase-promoting complex/cyclosome regulator is involved in early development and A-type cyclin stabilization
-
Eloy, N.B., et al. (2012). SAMBA, a plant-specific anaphase-promoting complex/cyclosome regulator is involved in early development and A-type cyclin stabilization. Proc. Natl. Acad. Sci. USA 109: 13853–13858.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 13853-13858
-
-
Eloy, N.B.1
-
43
-
-
84899857140
-
BHLH003, bHLH013 and bHLH017 are new targets of JAZ repressors negatively regulating JA responses
-
Fonseca, S., Fernández-Calvo, P., Fernández, G.M., Díez-Díaz, M., Gimenez-Ibanez, S., López-Vidriero, I., Godoy, M., Fernández- Barbero, G., Van Leene, J., De Jaeger, G., Franco-Zorrilla, J.M., and Solano, R. (2014). bHLH003, bHLH013 and bHLH017 are new targets of JAZ repressors negatively regulating JA responses. PLoS One 9: e86182.
-
(2014)
Plos One
, vol.9
-
-
Fonseca, S.1
Fernández-Calvo, P.2
Fernández, G.M.3
Díez-Díaz, M.4
Gimenez-Ibanez, S.5
López-Vidriero, I.6
Godoy, M.7
Fernández- Barbero, G.8
Van Leene, J.9
De Jaeger, G.10
Franco-Zorrilla, J.M.11
Solano, R.12
-
44
-
-
84876515907
-
STRING v9.1: Protein-protein interaction networks, with increased coverage and integration
-
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., and Jensen, L.J. (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41: D808–D815.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
Lin, J.7
Minguez, P.8
Bork, P.9
Von Mering, C.10
Jensen, L.J.11
-
45
-
-
67651039811
-
Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition
-
Freeling, M. (2009). Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60: 433–453.
-
(2009)
Annu. Rev. Plant Biol
, vol.60
, pp. 433-453
-
-
Freeling, M.1
-
46
-
-
57149120510
-
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
-
Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R., and Lisch, D. (2008). Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18: 1924–1937.
-
(2008)
Genome Res
, vol.18
, pp. 1924-1937
-
-
Freeling, M.1
Lyons, E.2
Pedersen, B.3
Alam, M.4
Ming, R.5
Lisch, D.6
-
47
-
-
33745610025
-
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
-
Freeling, M., and Thomas, B.C. (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
-
48
-
-
84894205984
-
The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants
-
Gadeyne, A., et al. (2014). The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156: 691–704.
-
(2014)
Cell
, vol.156
, pp. 691-704
-
-
Gadeyne, A.1
-
49
-
-
84877790509
-
CodonPhyML: Fast maximum likelihood phylogeny estimation under codon substitution models
-
Gil, M., Zanetti, M.S., Zoller, S., and Anisimova, M. (2013). CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol. Biol. Evol. 30: 1270–1280.
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 1270-1280
-
-
Gil, M.1
Zanetti, M.S.2
Zoller, S.3
Anisimova, M.4
-
50
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman, N., and Yang, Z. (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725–736.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
51
-
-
58149166731
-
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
-
Gresham, D., Desai, M.M., Tucker, C.M., Jenq, H.T., Pai, D.A., Ward, A., DeSevo, C.G., Botstein, D., and Dunham, M.J. (2008). The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4: e1000303.
-
(2008)
Plos Genet
, vol.4
-
-
Gresham, D.1
Desai, M.M.2
Tucker, C.M.3
Jenq, H.T.4
Pai, D.A.5
Ward, A.6
Desevo, C.G.7
Botstein, D.8
Dunham, M.J.9
-
52
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0.Syst
-
Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., and 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)
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
-
53
-
-
84869786704
-
Increased phenotypic plasticity to climate may have boosted the invasion success of polyploid Centaurea stoebe
-
Hahn, M.A., van Kleunen, M., and Müller-Schärer, H. (2012). Increased phenotypic plasticity to climate may have boosted the invasion success of polyploid Centaurea stoebe. PLoS One 7: e50284.
-
(2012)
Plos One
, vol.7
-
-
Hahn, M.A.1
Van Kleunen, M.2
Müller-Schärer, H.3
-
54
-
-
37249034790
-
Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution
-
Hahn, M.W. (2007). Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biol. 8: R141.
-
(2007)
Genome Biol
, vol.8
-
-
Hahn, M.W.1
-
55
-
-
23744452485
-
Estimating the tempo and mode of gene family evolution from comparative genomic data
-
Hahn, M.W., De Bie, T., Stajich, J.E., Nguyen, C., and Cristianini, N. (2005). Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15: 1153–1160.
-
(2005)
Genome Res
, vol.15
, pp. 1153-1160
-
-
Hahn, M.W.1
De Bie, T.2
Stajich, J.E.3
Nguyen, C.4
Cristianini, N.5
-
57
-
-
84902707570
-
Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
-
Han, F., Peng, Y., Xu, L., and Xiao, P. (2014). Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes. BMC Genomics 15: 504.
-
(2014)
BMC Genomics
, vol.15
, pp. 504
-
-
Han, F.1
Peng, Y.2
Xu, L.3
Xiao, P.4
-
58
-
-
28944441407
-
Higher duplicability of less important genes in yeast genomes
-
He, X., and Zhang, J. (2006). Higher duplicability of less important genes in yeast genomes. Mol. Biol. Evol. 23: 144–151.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 144-151
-
-
He, X.1
Zhang, J.2
-
59
-
-
84890282620
-
Constitutively active UVR8 photoreceptor variant in Arabidopsis
-
Heijde, M., Binkert, M., Yin, R., Ares-Orpel, F., Rizzini, L., Van De Slijke, E., Persiau, G., Nolf, J., Gevaert, K., De Jaeger, G., and Ulm, R. (2013). Constitutively active UVR8 photoreceptor variant in Arabidopsis. Proc. Natl. Acad. Sci. USA 110: 20326–20331.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 20326-20331
-
-
Heijde, M.1
Binkert, M.2
Yin, R.3
Ares-Orpel, F.4
Rizzini, L.5
Van De Slijke, E.6
Persiau, G.7
Nolf, J.8
Gevaert, K.9
De Jaeger, G.10
Ulm, R.11
-
60
-
-
78649932630
-
2R and remodeling of vertebrate signal transduction engine
-
Huminiecki, L., and Heldin, C.H. (2010). 2R and remodeling of vertebrate signal transduction engine. BMC Biol. 8: 146.
-
(2010)
BMC Biol
, vol.8
-
-
Huminiecki, L.1
Heldin, C.H.2
-
61
-
-
84907351551
-
Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots
-
Jiao, Y., Li, J., Tang, H., and Paterson, A.H. (2014). Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell 26: 2792–2802.
-
(2014)
Plant Cell
, vol.26
, pp. 2792-2802
-
-
Jiao, Y.1
Li, J.2
Tang, H.3
Paterson, A.H.4
-
62
-
-
84951800983
-
Paralogue interference affects the dynamics after gene duplication
-
Kaltenegger, E., and Ober, D. (2015). Paralogue interference affects the dynamics after gene duplication. Trends Plant Sci. 20: 814–821.
-
(2015)
Trends Plant Sci
, vol.20
, pp. 814-821
-
-
Kaltenegger, E.1
Ober, D.2
-
63
-
-
7644238181
-
Biological robustness. Nat
-
Kitano, H. (2004). Biological robustness. Nat. Rev. Genet. 5: 826–837.
-
(2004)
Rev. Genet
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
64
-
-
16444381885
-
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
-
Koonin, E.V., et al. (2004). A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5: R7.
-
(2004)
Genome Biol
, vol.5
-
-
Koonin, E.V.1
-
65
-
-
0141519279
-
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
-
Li, L., Stoeckert, C.J., Jr., and Roos, D.S. (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178–2189.
-
(2003)
Genome Res
, vol.13
, pp. 2178-2189
-
-
Li, L.1
Stoeckert, C.J.2
Roos, D.S.3
-
66
-
-
38949158494
-
Protein under-wrapping causes dosage sensitivity and decreases gene duplicability
-
Liang, H., Plazonic, K.R., Chen, J., Li, W.H., and Fernández, A. (2008). Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet. 4: e11.
-
(2008)
Plos Genet
, vol.4
-
-
Liang, H.1
Plazonic, K.R.2
Chen, J.3
Li, W.H.4
Fernández, A.5
-
67
-
-
84903692243
-
Meiotic gene evolution: Can you teach a new dog new tricks? Mol. Biol
-
Lloyd, A.H., et al. (2014). Meiotic gene evolution: can you teach a new dog new tricks? Mol. Biol. Evol. 31: 1724–1727.
-
(2014)
Evol
, vol.31
, pp. 1724-1727
-
-
Lloyd, A.H.1
-
68
-
-
84857950845
-
A comprehensive dataset of genes with a loss-of-function mutant phenotype in Arabidopsis
-
Lloyd, J., and Meinke, D. (2012). A comprehensive dataset of genes with a loss-of-function mutant phenotype in Arabidopsis. Plant Physiol. 158: 1115–1129.
-
(2012)
Plant Physiol
, vol.158
, pp. 1115-1129
-
-
Lloyd, J.1
Meinke, D.2
-
69
-
-
84941266791
-
Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes
-
Lloyd, J.P., Seddon, A.E., Moghe, G.D., Simenc, M.C., and Shiu, S.H. (2015). Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes. Plant Cell 27: 2133–2147.
-
(2015)
Plant Cell
, vol.27
, pp. 2133-2147
-
-
Lloyd, J.P.1
Seddon, A.E.2
Moghe, G.D.3
Simenc, M.C.4
Shiu, S.H.5
-
70
-
-
0034634395
-
The evolutionary fate and consequences of duplicate genes
-
Lynch, M., and Conery, J.S. (2000). The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155.
-
(2000)
Science
, vol.290
, pp. 1151-1155
-
-
Lynch, M.1
Conery, J.S.2
-
71
-
-
0037270015
-
The evolutionary demography of duplicate genes
-
Lynch, M., and Conery, J.S. (2003). The evolutionary demography of duplicate genes. J. Struct. Funct. Genomics 3: 35–44.
-
(2003)
J. Struct. Funct. Genomics
, vol.3
, pp. 35-44
-
-
Lynch, M.1
Conery, J.S.2
-
72
-
-
4744343021
-
The altered evolutionary trajectories of gene duplicates
-
Lynch, M., and Katju, V. (2004). The altered evolutionary trajectories of gene duplicates. Trends Genet. 20: 544–549.
-
(2004)
Trends Genet
, vol.20
, pp. 544-549
-
-
Lynch, M.1
Katju, V.2
-
73
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., and Van de Peer, Y. (2005a). Modeling gene and genome duplications in eukaryotes. Proc. Natl. Acad. Sci. USA 102: 5454–5459.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
De Bodt, S.2
Raes, J.3
Casneuf, T.4
Van Montagu, M.5
Kuiper, M.6
Van De Peer, Y.7
-
74
-
-
24044440971
-
BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
-
Maere, S., Heymans, K., and Kuiper, M. (2005b). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448–3449.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
75
-
-
63449086872
-
The complex relationship of gene duplication and essentiality
-
Makino, T., Hokamp, K., and McLysaght, A. (2009). The complex relationship of gene duplication and essentiality. Trends Genet. 25: 152–155.
-
(2009)
Trends Genet
, vol.25
, pp. 152-155
-
-
Makino, T.1
Hokamp, K.2
McLysaght, A.3
-
76
-
-
77952679366
-
Ohnologs in the human genome are dosage balanced and frequently associated with disease
-
Makino, T., and McLysaght, A. (2010). Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc. Natl. Acad. Sci. USA 107: 9270–9274.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 9270-9274
-
-
Makino, T.1
McLysaght, A.2
-
77
-
-
84872507663
-
Evolutionary significance of whole-genome duplication
-
P.S. Soltis and D.E. Soltis, eds (Berlin: Springer-Verlag
-
McGrath, C.L., and Lynch, M. (2012). Evolutionary significance of whole-genome duplication. In Polyploidy and Genome Evolution, P.S. Soltis and D.E. Soltis, eds (Berlin: Springer-Verlag), pp. 1–20.
-
(2012)
Polyploidy and Genome Evolution
, pp. 1-20
-
-
McGrath, C.L.1
Lynch, M.2
-
78
-
-
66449114096
-
Scaling laws in functional genome content across prokaryotic clades and lifestyles
-
Molina, N., and van Nimwegen, E. (2009). Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends Genet. 25: 243–247.
-
(2009)
Trends Genet
, vol.25
, pp. 243-247
-
-
Molina, N.1
Van Nimwegen, E.2
-
79
-
-
0038724494
-
Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data
-
Monti, S., Tamayo, P., Mesirov, J., and Golub, T. (2003). Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52: 91–118.
-
(2003)
Mach. Learn
, vol.52
, pp. 91-118
-
-
Monti, S.1
Tamayo, P.2
Mesirov, J.3
Golub, T.4
-
80
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse, S.V., and Gaut, B.S. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11: 715–724.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
81
-
-
84874240821
-
The Chloroplast Function Database II: A comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins
-
Myouga, F., Akiyama, K., Tomonaga, Y., Kato, A., Sato, Y., Kobayashi, M., Nagata, N., Sakurai, T., and Shinozaki, K. (2013). The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins. Plant Cell Physiol. 54: e2.
-
(2013)
Plant Cell Physiol
, vol.54
-
-
Myouga, F.1
Akiyama, K.2
Tomonaga, Y.3
Kato, A.4
Sato, Y.5
Kobayashi, M.6
Nagata, N.7
Sakurai, T.8
Shinozaki, K.9
-
82
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei, M., and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418–426.
-
(1986)
Mol. Biol. Evol
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
83
-
-
84885026474
-
Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods
-
Nguyen, T.H., Ranwez, V., Berry, V., and Scornavacca, C. (2013). Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PLoS One 8: e73667.
-
(2013)
Plos One
, vol.8
-
-
Nguyen, T.H.1
Ranwez, V.2
Berry, V.3
Scornavacca, C.4
-
85
-
-
24044471657
-
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
-
Oliver, T., Schmidt, B., Nathan, D., Clemens, R., and Maskell, D. (2005). Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics 21: 3431–3432.
-
(2005)
Bioinformatics
, vol.21
, pp. 3431-3432
-
-
Oliver, T.1
Schmidt, B.2
Nathan, D.3
Clemens, R.4
Maskell, D.5
-
86
-
-
0038157152
-
Dosage sensitivity and the evolution of gene families in yeast
-
Papp, B., Pál, C., and Hurst, L.D. (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
Pál, C.2
Hurst, L.D.3
-
87
-
-
33750173564
-
Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
-
Paterson, A.H., Chapman, B.A., Kissinger, J.C., Bowers, J.E., Feltus, F.A., and Estill, J.C. (2006). Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22: 597–602.
-
(2006)
Trends Genet
, vol.22
, pp. 597-602
-
-
Paterson, A.H.1
Chapman, B.A.2
Kissinger, J.C.3
Bowers, J.E.4
Feltus, F.A.5
Estill, J.C.6
-
88
-
-
77950439369
-
NINJA connects the co-repressor TOPLESS to jasmonate signalling
-
Pauwels, L., et al. (2010). NINJA connects the co-repressor TOPLESS to jasmonate signalling. Nature 464: 788–791.
-
(2010)
Nature
, vol.464
, pp. 788-791
-
-
Pauwels, L.1
-
89
-
-
84897087067
-
The Non-JAZ TIFY protein TIFY8 from Arabidopsis thaliana is a transcriptional repressor
-
Perez, A.C., Durand, A.N., Vanden Bossche, R., De Clercq, R., Persiau, G., Van Wees, S.C.M., Pieterse, C.M.J., Gevaert, K., De Jaeger, G., Goossens, A., and Pauwels, L. (2014). The Non-JAZ TIFY protein TIFY8 from Arabidopsis thaliana is a transcriptional repressor. PLoS One 9: e84891.
-
(2014)
Plos One
, vol.9
-
-
Perez, A.C.1
Durand, A.N.2
Vanden Bossche, R.3
De Clercq, R.4
Persiau, G.5
Van Wees, S.C.M.6
Pieterse, C.M.J.7
Gevaert, K.8
De Jaeger, G.9
Goossens, A.10
Pauwels, L.11
-
90
-
-
75549087883
-
PlnTFDB: Updated content and new features of the plant transcription factor database
-
Pérez-Rodríguez, P., Riaño-Pachón, D.M., Corrêa, L.G., Rensing, S.A., Kersten, B., and Mueller-Roeber, B. (2010). PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38: D822–D827.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Pérez-Rodríguez, P.1
Riaño-Pachón, D.M.2
Corrêa, L.G.3
Rensing, S.A.4
Kersten, B.5
Mueller-Roeber, B.6
-
91
-
-
84895736885
-
Detecting and locating whole genome duplications on a phylogeny: A probabilistic approach
-
Rabier, C.E., Ta, T., and Ané, C. (2014). Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Mol. Biol. Evol. 31: 750–762.
-
(2014)
Mol. Biol. Evol
, vol.31
, pp. 750-762
-
-
Rabier, C.E.1
Ta, T.2
Ané, C.3
-
92
-
-
49849100187
-
Low duplicability and network fragility of cancer genes
-
Rambaldi, D., Giorgi, F.M., Capuani, F., Ciliberto, A., and Ciccarelli, F.D. (2008). Low duplicability and network fragility of cancer genes. Trends Genet. 24: 427–430.
-
(2008)
Trends Genet
, vol.24
, pp. 427-430
-
-
Rambaldi, D.1
Giorgi, F.M.2
Capuani, F.3
Ciliberto, A.4
Ciccarelli, F.D.5
-
93
-
-
84855318177
-
Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
-
Rodgers-Melnick, E., Mane, S.P., Dharmawardhana, P., Slavov, G.T., Crasta, O.R., Strauss, S.H., Brunner, A.M., and Difazio, S.P. (2012). Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus. Genome Res. 22: 95–105.
-
(2012)
Genome Res
, vol.22
, pp. 95-105
-
-
Rodgers-Melnick, E.1
Mane, S.P.2
Dharmawardhana, P.3
Slavov, G.T.4
Crasta, O.R.5
Strauss, S.H.6
Brunner, A.M.7
Difazio, S.P.8
-
94
-
-
84878113118
-
Inferring ancient divergences requires genes with strong phylogenetic signals
-
Salichos, L., and Rokas, A. (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327–331.
-
(2013)
Nature
, vol.497
, pp. 327-331
-
-
Salichos, L.1
Rokas, A.2
-
95
-
-
84898641369
-
Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol
-
Salichos, L., Stamatakis, A., and Rokas, A. (2014). Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31: 1261–1271.
-
(2014)
Evol
, vol.31
, pp. 1261-1271
-
-
Salichos, L.1
Stamatakis, A.2
Rokas, A.3
-
96
-
-
74549221016
-
Genome sequence of the palaeopolyploid soybean
-
Schmutz, J., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183.
-
(2010)
Nature
, vol.463
, pp. 178-183
-
-
Schmutz, J.1
-
97
-
-
33746506280
-
Aneuploidy and isochromosome formation in drug-resistant Candida albicans
-
Selmecki, A., Forche, A., and Berman, J. (2006). Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Science 313: 367–370.
-
(2006)
Science
, vol.313
, pp. 367-370
-
-
Selmecki, A.1
Forche, A.2
Berman, J.3
-
98
-
-
84925009217
-
Polyploidy can drive rapid adaptation in yeast
-
Selmecki, A.M., Maruvka, Y.E., Richmond, P.A., Guillet, M., Shoresh, N., Sorenson, A.L., De, S., Kishony, R., Michor, F., Dowell, R., and Pellman, D. (2015). Polyploidy can drive rapid adaptation in yeast. Nature 519: 349–352.
-
(2015)
Nature
, vol.519
, pp. 349-352
-
-
Selmecki, A.M.1
Maruvka, Y.E.2
Richmond, P.A.3
Guillet, M.4
Shoresh, N.5
Sorenson, A.L.6
De, S.7
Kishony, R.8
Michor, F.9
Dowell, R.10
Pellman, D.11
-
99
-
-
4444363053
-
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
-
Seoighe, C., and Gehring, C. (2004). Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20: 461–464.
-
(2004)
Trends Genet
, vol.20
, pp. 461-464
-
-
Seoighe, C.1
Gehring, C.2
-
100
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection. Syst
-
Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51: 492–508.
-
(2002)
Biol
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
101
-
-
84868103798
-
New insights into the troubles of aneuploidy
-
Siegel, J.J., and Amon, A. (2012). New insights into the troubles of aneuploidy. Annu. Rev. Cell Dev. Biol. 28: 189–214.
-
(2012)
Annu. Rev. Cell Dev. Biol
, vol.28
, pp. 189-214
-
-
Siegel, J.J.1
Amon, A.2
-
102
-
-
84879686532
-
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
-
Slotte, T., et al. (2013). The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat. Genet. 45: 831–835.
-
(2013)
Nat. Genet
, vol.45
, pp. 831-835
-
-
Slotte, T.1
-
103
-
-
53349160132
-
Rates of molecular evolution are linked to life history in flowering plants
-
Smith, S.A., and Donoghue, M.J. (2008). Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86–89.
-
(2008)
Science
, vol.322
, pp. 86-89
-
-
Smith, S.A.1
Donoghue, M.J.2
-
104
-
-
78149250431
-
What we still don’t know about polyploidy
-
Soltis, D.E., Buggs, R.J.A., Doyle, J.J., and Soltis, P.S. (2010). What we still don’t know about polyploidy. Taxon 59: 1387–1403.
-
(2010)
Taxon
, vol.59
, pp. 1387-1403
-
-
Soltis, D.E.1
Buggs, R.J.A.2
Doyle, J.J.3
Soltis, P.S.4
-
105
-
-
84878685777
-
A protein phosphatase 2A complex spatially controls plant cell division. Nat
-
Spinner, L., et al. (2013). A protein phosphatase 2A complex spatially controls plant cell division. Nat. Commun. 4: 1863.
-
(2013)
Commun
, vol.4
, pp. 1863
-
-
Spinner, L.1
-
106
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
107
-
-
84866458802
-
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
-
Stolzer, M., Lai, H., Xu, M., Sathaye, D., Vernot, B., and Durand, D. (2012). Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28: i409–i415.
-
(2012)
Bioinformatics
, vol.28
-
-
Stolzer, M.1
Lai, H.2
Xu, M.3
Sathaye, D.4
Vernot, B.5
Durand, D.6
-
108
-
-
84930668371
-
The fitness consequences of aneuploidy are driven by condition-dependent gene effects
-
Sunshine, A.B., Payen, C., Ong, G.T., Liachko, I., Tan, K.M., and Dunham, M.J. (2015). The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol. 13: e1002155.
-
(2015)
Plos Biol
, vol.13
-
-
Sunshine, A.B.1
Payen, C.2
Ong, G.T.3
Liachko, I.4
Tan, K.M.5
Dunham, M.J.6
-
109
-
-
33747847779
-
PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
-
Suyama, M., Torrents, D., and Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34: W609–W612.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Suyama, M.1
Torrents, D.2
Bork, P.3
-
110
-
-
46949090817
-
The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1
-
Takahashi, N., Lammens, T., Boudolf, V., Maes, S., Yoshizumi, T., De Jaeger, G., Witters, E., Inzé, D., and De Veylder, L. (2008). The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1. EMBO J. 27: 1840–1851.
-
(2008)
EMBO J
, vol.27
, pp. 1840-1851
-
-
Takahashi, N.1
Lammens, T.2
Boudolf, V.3
Maes, S.4
Yoshizumi, T.5
De Jaeger, G.6
Witters, E.7
Inzé, D.8
De Veylder, L.9
-
111
-
-
84555178065
-
The more the better? The role of polyploidy in facilitating plant invasions
-
te Beest, M., Le Roux, J.J., Richardson, D.M., Brysting, A.K., Suda, J., Kubesová, M., and Pysek, P. (2012). The more the better? The role of polyploidy in facilitating plant invasions. Ann. Bot. (Lond.) 109: 19–45.
-
(2012)
Ann. Bot. (Lond.)
, vol.109
, pp. 19-45
-
-
Te Beest, M.1
Le Roux, J.J.2
Richardson, D.M.3
Brysting, A.K.4
Suda, J.5
Kubesová, M.6
Pysek, P.7
-
112
-
-
70549110074
-
The flowering world: A tale of duplications
-
Van de Peer, Y., Fawcett, J.A., Proost, S., Sterck, L., and Vandepoele, K. (2009a). The flowering world: a tale of duplications. Trends Plant Sci. 14: 680–688.
-
(2009)
Trends Plant Sci
, vol.14
, pp. 680-688
-
-
Van De Peer, Y.1
Fawcett, J.A.2
Proost, S.3
Sterck, L.4
Vandepoele, K.5
-
113
-
-
70349325524
-
The evolutionary significance of ancient genome duplications. Nat
-
Van de Peer, Y., Maere, S., and Meyer, A. (2009b). The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10: 725–732.
-
(2009)
Rev. Genet
, vol.10
, pp. 725-732
-
-
Van De Peer, Y.1
Maere, S.2
Meyer, A.3
-
114
-
-
84876273527
-
Large-scale event extraction from literature with multi-level gene normalization
-
Van Landeghem, S., Björne, J., Wei, C.H., Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H.Y., Lu, Z., Salakoski, T., Van de Peer, Y., and Ginter, F. (2013). Large-scale event extraction from literature with multi-level gene normalization. PLoS One 8: e55814.
-
(2013)
Plos One
, vol.8
-
-
Van Landeghem, S.1
Björne, J.2
Wei, C.H.3
Hakala, K.4
Pyysalo, S.5
Ananiadou, S.6
Kao, H.Y.7
Lu, Z.8
Salakoski, T.9
Van De Peer, Y.10
Ginter, F.11
-
115
-
-
77955608634
-
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana
-
Van Leene, J., et al. (2010). Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 6: 397.
-
(2010)
Mol. Syst. Biol
, vol.6
-
-
Van Leene, J.1
-
116
-
-
84905647470
-
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary
-
Vanneste, K., Baele, G., Maere, S., and Van de Peer, Y. (2014a). Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. Genome Res. 24: 1334–1347.
-
(2014)
Genome Res
, vol.24
, pp. 1334-1347
-
-
Vanneste, K.1
Baele, G.2
Maere, S.3
Van De Peer, Y.4
-
117
-
-
84902983212
-
Tangled up in two: A burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution
-
Vanneste, K., Maere, S., and Van de Peer, Y. (2014b). Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 369: 20130353.
-
(2014)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.369
-
-
Vanneste, K.1
Maere, S.2
Van De Peer, Y.3
-
118
-
-
84871822072
-
Inference of genome duplications from age distributions revisited
-
Vanneste, K., Van de Peer, Y., and Maere, S. (2013). Inference of genome duplications from age distributions revisited. Mol. Biol. Evol. 30: 177–190.
-
(2013)
Mol. Biol. Evol
, vol.30
, pp. 177-190
-
-
Vanneste, K.1
Van De Peer, Y.2
Maere, S.3
-
119
-
-
0041828241
-
Scaling laws in the functional content of genomes
-
van Nimwegen, E. (2003). Scaling laws in the functional content of genomes. Trends Genet. 19: 479–484.
-
(2003)
Trends Genet
, vol.19
, pp. 479-484
-
-
Van Nimwegen, E.1
-
120
-
-
84896899026
-
ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development
-
Vercruyssen, L., et al. (2014). ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 26: 210–229.
-
(2014)
Plant Cell
, vol.26
, pp. 210-229
-
-
Vercruyssen, L.1
-
121
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication- aware phylogenetic trees in vertebrates
-
Vilella, A.J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., and Birney, E. (2009). EnsemblCompara GeneTrees: Complete, duplication- aware phylogenetic trees in vertebrates. Genome Res. 19: 327–335.
-
(2009)
Genome Res
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
Birney, E.6
-
122
-
-
82555185713
-
Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms
-
Wang, Y., Wang, X., Tang, H., Tan, X., Ficklin, S.P., Feltus, F.A., and Paterson, A.H. (2011). Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One 6: e28150.
-
(2011)
Plos One
, vol.6
-
-
Wang, Y.1
Wang, X.2
Tang, H.3
Tan, X.4
Ficklin, S.P.5
Feltus, F.A.6
Paterson, A.H.7
-
123
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
Wapinski, I., Pfeffer, A., Friedman, N., and Regev, A. (2007). Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54–61.
-
(2007)
Nature
, vol.449
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
124
-
-
77954182362
-
ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking
-
Wilkerson, M.D., and Hayes, D.N. (2010). ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 26: 1572–1573.
-
(2010)
Bioinformatics
, vol.26
, pp. 1572-1573
-
-
Wilkerson, M.D.1
Hayes, D.N.2
-
125
-
-
84856480832
-
Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids
-
Woodhouse, M.R., Tang, H., and Freeling, M. (2011). Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell 23: 4241–4253.
-
(2011)
Plant Cell
, vol.23
, pp. 4241-4253
-
-
Woodhouse, M.R.1
Tang, H.2
Freeling, M.3
-
126
-
-
84878498140
-
Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses
-
Woods, S., Coghlan, A., Rivers, D., Warnecke, T., Jeffries, S.J., Kwon, T., Rogers, A., Hurst, L.D., and Ahringer, J. (2013). Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses. PLoS Genet. 9: e1003330.
-
(2013)
Plos Genet
, vol.9
-
-
Woods, S.1
Coghlan, A.2
Rivers, D.3
Warnecke, T.4
Jeffries, S.J.5
Kwon, T.6
Rogers, A.7
Hurst, L.D.8
Ahringer, J.9
-
127
-
-
84871822882
-
TreeFix: Statistically informed gene tree error correction using species trees
-
Wu, Y.C., Rasmussen, M.D., Bansal, M.S., and Kellis, M. (2013). TreeFix: statistically informed gene tree error correction using species trees. Syst. Biol. 62: 110–120.
-
(2013)
Syst. Biol
, vol.62
, pp. 110-120
-
-
Wu, Y.C.1
Rasmussen, M.D.2
Bansal, M.S.3
Kellis, M.4
-
128
-
-
84905995450
-
Evolution of physiological responses to salt stress in hexaploid wheat
-
Yang, C., Zhao, L., Zhang, H., Yang, Z., Wang, H., Wen, S., Zhang, C., Rustgi, S., von Wettstein, D., and Liu, B. (2014). Evolution of physiological responses to salt stress in hexaploid wheat. Proc. Natl. Acad. Sci. USA 111: 11882–11887.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 11882-11887
-
-
Yang, C.1
Zhao, L.2
Zhang, H.3
Yang, Z.4
Wang, H.5
Wen, S.6
Zhang, C.7
Rustgi, S.8
Von Wettstein, D.9
Liu, B.10
-
129
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl
-
Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555–556.
-
(1997)
Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
130
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol
-
Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586–1591.
-
(2007)
Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
131
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang, Z., and Nielsen, R. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17: 32–43.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
132
-
-
77249113749
-
Estimates of the effect of natural selection on protein-coding content
-
Yap, V.B., Lindsay, H., Easteal, S., and Huttley, G. (2010). Estimates of the effect of natural selection on protein-coding content. Mol. Biol. Evol. 27: 726–734.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 726-734
-
-
Yap, V.B.1
Lindsay, H.2
Easteal, S.3
Huttley, G.4
-
133
-
-
84871375832
-
Chromosomal duplication is a transient evolutionary solution to stress
-
Yona, A.H., Manor, Y.S., Herbst, R.H., Romano, G.H., Mitchell, A., Kupiec, M., Pilpel, Y., and Dahan, O. (2012). Chromosomal duplication is a transient evolutionary solution to stress. Proc. Natl. Acad. Sci. USA 109: 21010–21015.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 21010-21015
-
-
Yona, A.H.1
Manor, Y.S.2
Herbst, R.H.3
Romano, G.H.4
Mitchell, A.5
Kupiec, M.6
Pilpel, Y.7
Dahan, O.8
-
134
-
-
84931575424
-
Determinants of the rate of protein sequence evolution. Nat
-
Zhang, J., and Yang, J.R. (2015). Determinants of the rate of protein sequence evolution. Nat. Rev. Genet. 16: 409–420.
-
(2015)
Rev. Genet
, vol.16
, pp. 409-420
-
-
Zhang, J.1
Yang, J.R.2
|