-
1
-
-
70149103623
-
CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis
-
Aichinger, E., Villar, C.B.R., Farrona, S., Reyes, J.C., Hennig, L., and Köhler, C. (2009). CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis. PLoS Genet. 5: e1000605.
-
(2009)
Plos Genet
, vol.5
-
-
Aichinger, E.1
Villar, C.B.R.2
Farrona, S.3
Reyes, J.C.4
Hennig, L.5
Köhler, C.6
-
2
-
-
84900474211
-
E. (2014). “Onecodetofind them all”: A Perl tool to conveniently parse RepeatMasker output files. Mob
-
Bailly-Bechet, M., Haudry, A., and Lerat, E. (2014). “Onecodetofind them all”: a Perl tool to conveniently parse RepeatMasker output files. Mob. DNA 5: 13.
-
DNA
, vol.5
, pp. 13
-
-
Bailly-Bechet, M.1
Haudry, A.2
-
3
-
-
33748173668
-
The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr
-
Bechsgaard, J.S., Castric, V., Charlesworth, D., Vekemans, X., and Schierup, M.H. (2006). The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr. Mol. Biol. Evol. 23: 1741–1750.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 1741-1750
-
-
Bechsgaard, J.S.1
Castric, V.2
Charlesworth, D.3
Vekemans, X.4
Schierup, M.H.5
-
4
-
-
84873135198
-
Comprehensive developmental profiles of gene activity in regions andsubregionsoftheArabidopsis seed
-
Belmonte, M.F., et al. (2013). Comprehensive developmental profiles of gene activity in regions andsubregionsoftheArabidopsis seed. Proc.Natl.Acad.Sci.USA110: E435–E444.
-
(2013)
Proc.Natl.Acad.Sci.Usa
, vol.110
, pp. E435-E444
-
-
Belmonte, M.F.1
-
5
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
6
-
-
77950380766
-
Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana
-
Bomblies, K., Yant, L., Laitinen, R.A., Kim, S.-T., Hollister, J.D., Warthmann, N., Fitz, J., and Weigel, D. (2010). Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana. PLoS Genet. 6: e1000890.
-
(2010)
Plos Genet
, vol.6
-
-
Bomblies, K.1
Yant, L.2
Laitinen, R.A.3
Kim, S.-T.4
Hollister, J.D.5
Warthmann, N.6
Fitz, J.7
Weigel, D.8
-
7
-
-
84892974070
-
Small RNAs and heritable epigenetic variation in plants
-
Bond, D.M., and Baulcombe, D.C. (2014). Small RNAs and heritable epigenetic variation in plants. Trends Cell Biol. 24: 100–107.
-
(2014)
Trends Cell Biol
, vol.24
, pp. 100-107
-
-
Bond, D.M.1
Baulcombe, D.C.2
-
8
-
-
84867053720
-
Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA
-
Calarco, J.P., Borges, F., Donoghue, M.T.A., Van Ex, F., Jullien, P.E., Lopes, T., Gardner, R., Berger, F., Feijó, J.A., Becker, J.D., and Martienssen, R.A. (2012). Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151: 194–205.
-
(2012)
Cell
, vol.151
, pp. 194-205
-
-
Calarco, J.P.1
Borges, F.2
Donoghue, M.T.A.3
Van Ex, F.4
Jullien, P.E.5
Lopes, T.6
Gardner, R.7
Berger, F.8
Feijó, J.A.9
Becker, J.D.10
Martienssen, R.A.11
-
9
-
-
84864679478
-
Widespread dynamic DNA methylation in response to biotic stress
-
Dowen, R.H., Pelizzola, M., Schmitz, R.J., Lister, R., Dowen, J.M., Nery, J.R., Dixon, J.E., and Ecker, J.R. (2012). Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl. Acad. Sci. USA 109: E2183–E2191.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. E2183-E2191
-
-
Dowen, R.H.1
Pelizzola, M.2
Schmitz, R.J.3
Lister, R.4
Dowen, J.M.5
Nery, J.R.6
Dixon, J.E.7
Ecker, J.R.8
-
10
-
-
68949202924
-
Estimating the rate of adaptive molecular evolution in the presenceofslightlydeleterious mutations and population size change. Mol. Biol
-
Eyre-Walker, A., and Keightley, P.D. (2009). Estimating the rate of adaptive molecular evolution in the presenceofslightlydeleterious mutations and population size change. Mol. Biol. Evol. 26: 2097–2108.
-
(2009)
Evol
, vol.26
, pp. 2097-2108
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
11
-
-
84947968595
-
Auxin production couples endosperm development to fertilization
-
Figueiredo, D.D., Batista, R.A., Roszak, P.J., and Köhler, C. (2015). Auxin production couples endosperm development to fertilization. Nat Plants 1: 15184.
-
(2015)
Nat Plants
, vol.1
, pp. 15184
-
-
Figueiredo, D.D.1
Batista, R.A.2
Roszak, P.J.3
Köhler, C.4
-
12
-
-
65249150257
-
Recent speciation associated with the evolution of selfing in Capsella
-
Foxe, J.P., Slotte, T., Stahl, E.A., Neuffer, B., Hurka, H., and Wright, S.I. (2009). Recent speciation associated with the evolution of selfing in Capsella. Proc.Natl.Acad.Sci.USA106: 5241–5245.
-
(2009)
Proc.Natl.Acad.Sci.Usa
, vol.106
, pp. 5241-5245
-
-
Foxe, J.P.1
Slotte, T.2
Stahl, E.A.3
Neuffer, B.4
Hurka, H.5
Wright, S.I.6
-
14
-
-
0030959648
-
DNA sequence evidence for the segmental allotetraploid origin of maize
-
Gaut, B.S., and Doebley, J.F. (1997). DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94: 6809–6814.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 6809-6814
-
-
Gaut, B.S.1
Doebley, J.F.2
-
15
-
-
67149086996
-
Extensive demethylation of repetitive elements during seed development underlies gene imprinting
-
Gehring, M., Bubb, K.L., and Henikoff, S. (2009). Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447–1451.
-
(2009)
Science
, vol.324
, pp. 1447-1451
-
-
Gehring, M.1
Bubb, K.L.2
Henikoff, S.3
-
16
-
-
80051745935
-
Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds
-
Gehring, M., Missirian, V., and Henikoff, S. (2011). Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS One 6: e23687.
-
(2011)
Plos One
, vol.6
-
-
Gehring, M.1
Missirian, V.2
Henikoff, S.3
-
17
-
-
77954969511
-
Genomewideanalysesreveallittleevidenceforadaptive evolution in many plant species. Mol. Biol
-
Gossmann, T.I., Song, B.-H., Windsor, A.J., Mitchell-Olds, T., Dixon, C.J., Kapralov, M.V., Filatov, D.A., and Eyre-Walker, A. (2010).Genomewideanalysesreveallittleevidenceforadaptive evolution in many plant species. Mol. Biol. Evol. 27: 1822–1832.
-
(2010)
Evol
, vol.27
, pp. 1822-1832
-
-
Gossmann, T.I.1
Song, B.-H.2
Windsor, A.J.3
Mitchell-Olds, T.4
Dixon, C.J.5
Kapralov, M.V.6
Filatov, D.A.7
Eyre-Walker, A.8
-
18
-
-
65249092034
-
Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck
-
Guo, Y.-L., Bechsgaard, J.S., Slotte, T., Neuffer, B., Lascoux, M., Weigel, D., and Schierup, M.H. (2009). Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc. Natl. Acad. Sci. USA 106: 5246–5251.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 5246-5251
-
-
Guo, Y.-L.1
Bechsgaard, J.S.2
Slotte, T.3
Neuffer, B.4
Lascoux, M.5
Weigel, D.6
Schierup, M.H.7
-
19
-
-
67149119197
-
Genome-wide demethylation of Arabidopsis endosperm
-
Hsieh, T.-F., Ibarra, C.A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R.L., and Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451–1454.
-
(2009)
Science
, vol.324
, pp. 1451-1454
-
-
Hsieh, T.-F.1
Ibarra, C.A.2
Silva, P.3
Zemach, A.4
Eshed-Williams, L.5
Fischer, R.L.6
Zilberman, D.7
-
20
-
-
79952143430
-
Regulation of imprinted gene expression in Arabidopsis endosperm
-
Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M.J., Hashimoto, M., Kirkbride, R.C., Harada, J.J., Zilberman, D., and Fischer, R.L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proc. Natl. Acad. Sci. USA 108: 1755–1762.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 1755-1762
-
-
Hsieh, T.-F.1
Shin, J.2
Uzawa, R.3
Silva, P.4
Cohen, S.5
Bauer, M.J.6
Hashimoto, M.7
Kirkbride, R.C.8
Harada, J.J.9
Zilberman, D.10
Fischer, R.L.11
-
21
-
-
84866140080
-
Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
-
Ibarra, C.A., et al. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337: 1360–1364.
-
(2012)
Science
, vol.337
, pp. 1360-1364
-
-
Ibarra, C.A.1
-
22
-
-
84865502020
-
Evolution, function, and regulation of genomic imprinting in plant seed development
-
Jiang, H., and Köhler, C. (2012). Evolution, function, and regulation of genomic imprinting in plant seed development. J. Exp. Bot. 63: 4713–4722.
-
(2012)
J. Exp. Bot
, vol.63
, pp. 4713-4722
-
-
Jiang, H.1
Köhler, C.2
-
23
-
-
16244366488
-
Genome evolution among cruciferous plants: A lecture from the comparison of the genetic maps of three diploid species–Capsella rubella, Arabidopsis lyrata subsp. petraea, and
-
Koch, M.A., and Kiefer, M. (2005). Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species–Capsella rubella, Arabidopsis lyrata subsp. petraea, and. Am. J. Bot. 92: 761–767.
-
(2005)
Am. J. Bot
, vol.92
, pp. 761-767
-
-
Koch, M.A.1
Kiefer, M.2
-
24
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F., and Andrews, S.R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571–1572.
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
25
-
-
5144230950
-
Gene loss and movement in the maize genome
-
Lai, J., Ma, J., Swigonová, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B., Park, Y.-J., Jeong, O.-Y., Bennetzen, J.L., and Messing, J. (2004). Gene loss and movement in the maize genome. Genome Res. 14: 1924–1931.
-
(2004)
Genome Res
, vol.14
, pp. 1924-1931
-
-
Lai, J.1
Ma, J.2
Swigonová, Z.3
Ramakrishna, W.4
Linton, E.5
Llaca, V.6
Tanyolac, B.7
Park, Y.-J.8
Jeong, O.-Y.9
Bennetzen, J.L.10
Messing, J.11
-
26
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
27
-
-
77249170184
-
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
-
Law, J.A., and Jacobsen, S.E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11: 204–220.
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 204-220
-
-
Law, J.A.1
Jacobsen, S.E.2
-
28
-
-
77952670452
-
Identifying repeats and transposable elements in sequenced genomes: How to find your way through the dense forest of programs
-
Lerat, E. (2010). Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb) 104: 520–533.
-
(2010)
Heredity (Edinb)
, vol.104
, pp. 520-533
-
-
Lerat, E.1
-
29
-
-
84862519067
-
Endosperm: Food for humankind and fodder for scientific discoveries
-
Li, J., and Berger, F. (2012). Endosperm: food for humankind and fodder for scientific discoveries. New Phytol. 195: 290–305.
-
(2012)
New Phytol
, vol.195
, pp. 290-305
-
-
Li, J.1
Berger, F.2
-
30
-
-
79959818388
-
A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm
-
Luo, M., Taylor, J.M., Spriggs, A., Zhang, H., Wu, X., Russell, S., Singh, M., and Koltunow, A. (2011). A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet. 7: e1002125.
-
(2011)
Plos Genet
, vol.7
-
-
Luo, M.1
Taylor, J.M.2
Spriggs, A.3
Zhang, H.4
Wu, X.5
Russell, S.6
Singh, M.7
Koltunow, A.8
-
31
-
-
84903156536
-
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat
-
Maumus, F., and Quesneville, H. (2014). Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nat. Commun. 5: 4104.
-
(2014)
Commun
, vol.5
, pp. 4104
-
-
Maumus, F.1
Quesneville, H.2
-
32
-
-
0035576277
-
Arabidopsis thaliana and its wild relatives: A model system for ecology and evolution
-
Mitchell-Olds, T. (2001). Arabidopsis thaliana and its wild relatives: a model system for ecology and evolution. Trends Ecol. Evol. 16: 693–700.
-
(2001)
Trends Ecol. Evol
, vol.16
, pp. 693-700
-
-
Mitchell-Olds, T.1
-
33
-
-
0025958320
-
Genomic imprinting in mammalian development: A parental tug-of-war
-
Moore, T., and Haig, D. (1991). Genomic imprinting in mammalian development: a parental tug-of-war. Trends Genet. 7: 45–49.
-
(1991)
Trends Genet
, vol.7
, pp. 45-49
-
-
Moore, T.1
Haig, D.2
-
34
-
-
0038118635
-
Imprinting evolution and the price of silence
-
Murphy, S.K., and Jirtle, R.L. (2003). Imprinting evolution and the price of silence. BioEssays 25: 577–588.
-
(2003)
Bioessays
, vol.25
, pp. 577-588
-
-
Murphy, S.K.1
Jirtle, R.L.2
-
35
-
-
69449085281
-
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting
-
Pask, A.J., Papenfuss, A.T., Ager, E.I., McColl, K.A., Speed, T.P., and Renfree, M.B. (2009). Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol. 10: R1.
-
(2009)
Genome Biol
, vol.10
, pp. R1
-
-
Pask, A.J.1
Papenfuss, A.T.2
Ager, E.I.3
McColl, K.A.4
Speed, T.P.5
Renfree, M.B.6
-
36
-
-
58449137410
-
The Sorghum bicolor genome and the diversification of grasses
-
Paterson, A.H., et al. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556.
-
(2009)
Nature
, vol.457
, pp. 551-556
-
-
Paterson, A.H.1
-
37
-
-
84906325490
-
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
-
Pignatta, D., Erdmann, R.M., Scheer, E., Picard, C.L., Bell, G.W., and Gehring, M. (2014). Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. eLife 3: e03198.
-
(2014)
Elife
, vol.3
-
-
Pignatta, D.1
Erdmann, R.M.2
Scheer, E.3
Picard, C.L.4
Bell, G.W.5
Gehring, M.6
-
38
-
-
84906972426
-
Different yet similar: Evolution of imprinting in flowering plants and mammals
-
Pires, N.D., and Grossniklaus, U.(2014). Different yet similar: evolution of imprinting in flowering plants and mammals. F1000Prime Rep. 6: 63.
-
(2014)
F1000prime Rep
, vol.6
, pp. 63
-
-
Pires, N.D.1
Grossniklaus, U.2
-
39
-
-
84864689053
-
A survey of tissue-specific genomic imprinting in mammals. Mol. Genet
-
Prickett, A.R., and Oakey, R.J. (2012). A survey of tissue-specific genomic imprinting in mammals. Mol. Genet. Genomics 287: 621–630.
-
(2012)
Genomics
, vol.287
, pp. 621-630
-
-
Prickett, A.R.1
Oakey, R.J.2
-
40
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841– 842.
-
(2010)
Bioinformatics
, vol.26
-
-
Quinlan, A.R.1
Hall, I.M.2
-
41
-
-
84900988020
-
Deeptools: A flexible platform for exploring deep-sequencing data
-
Ramírez, F., Dündar, F., Diehl, S., Grüning, B.A., and Manke, T. (2014). Deeptools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42: W187–W191.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W187-W191
-
-
Ramírez, F.1
Dündar, F.2
Diehl, S.3
Grüning, B.A.4
Manke, T.5
-
42
-
-
84937807100
-
Non-reciprocal interspecies hybridization barriers in the Capsella genus are established in the endosperm
-
Rebernig, C.A., Lafon-Placette, C., Hatorangan, M.R., Slotte, T., and Köhler, C. (2015). Non-reciprocal interspecies hybridization barriers in the Capsella genus are established in the endosperm. PLoS Genet. 11: e1005295.
-
(2015)
Plos Genet
, vol.11
-
-
Rebernig, C.A.1
Lafon-Placette, C.2
Hatorangan, M.R.3
Slotte, T.4
Köhler, C.5
-
43
-
-
78651271733
-
Integrative genomics viewer
-
Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nat. Biotechnol. 29: 24–26.
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdóttir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
44
-
-
84855487016
-
Polycomb group proteins are required to couple seed coat initiation to fertilization
-
Roszak, P., and Köhler, C. (2011). Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc. Natl. Acad. Sci. USA 108: 20826–20831.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 20826-20831
-
-
Roszak, P.1
Köhler, C.2
-
45
-
-
84912100585
-
Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene
-
Sanchez, D.H., and Paszkowski, J. (2014). Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene. PLoS Genet. 10: e1004806.
-
(2014)
Plos Genet
, vol.10
-
-
Sanchez, D.H.1
Paszkowski, J.2
-
46
-
-
84912120604
-
Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization
-
Seymour, D.K., Koenig, D., Hagmann, J., Becker, C., and Weigel, D. (2014). Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet. 10: e1004785.
-
(2014)
Plos Genet
, vol.10
-
-
Seymour, D.K.1
Koenig, D.2
Hagmann, J.3
Becker, C.4
Weigel, D.5
-
47
-
-
84979781055
-
Chromatin dynamics during plant sexual reproduction. Front
-
She, W., and Baroux, C.(2014). Chromatin dynamics during plant sexual reproduction. Front. Plant Sci. 5: 354.
-
(2014)
Plant Sci
, vol.5
, pp. 354
-
-
She, W.1
Baroux, C.2
-
48
-
-
84905126894
-
The impact of linked selection on plant genomic variation. Brief. Funct
-
Slotte, T. (2014). The impact of linked selection on plant genomic variation. Brief. Funct. Genomics 13: 268–275.
-
(2014)
Genomics
, vol.13
, pp. 268-275
-
-
Slotte, T.1
-
49
-
-
77954966377
-
Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size
-
Slotte, T., Foxe, J.P., Hazzouri, K.M., and Wright, S.I.(2010). Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol. Biol. Evol. 27: 1813–1821.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 1813-1821
-
-
Slotte, T.1
Foxe, J.P.2
Hazzouri, K.M.3
Wright, S.I.4
-
50
-
-
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
-
51
-
-
84943406348
-
Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Mol. Biol
-
Steige, K.A., Reimegård, J., Koenig, D., Scofield, D.G., and Slotte, T. (2015). Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Mol. Biol. Evol. 32: 2501–2514.
-
(2015)
Evol
, vol.32
, pp. 2501-2514
-
-
Steige, K.A.1
Reimegård, J.2
Koenig, D.3
Scofield, D.G.4
Slotte, T.5
-
52
-
-
80051669931
-
Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
-
StOnge, K.R., Källman, T., Slotte, T., Lascoux, M., and Palmé, A.E. (2011). Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems. Mol. Ecol. 20: 3306–3320.
-
(2011)
Mol. Ecol
, vol.20
, pp. 3306-3320
-
-
Stonge, K.R.1
Källman, T.2
Slotte, T.3
Lascoux, M.4
Palmé, A.E.5
-
53
-
-
34250660148
-
Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting
-
Suzuki, S., et al. (2007). Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet. 3: e55.
-
(2007)
Plos Genet
, vol.3
-
-
Suzuki, S.1
-
54
-
-
12344321713
-
Genomic imprinting of IGF2, p57(KIP2) andPEG1/MEST in a marsupial, the tammar wallaby
-
Suzuki, S., Renfree, M.B., Pask, A.J., Shaw, G., Kobayashi, S., Kohda, T., Kaneko-Ishino, T., and Ishino, F. (2005). Genomic imprinting of IGF2, p57(KIP2) andPEG1/MEST in a marsupial, the tammar wallaby. Mech. Dev. 122: 213–222.
-
(2005)
Mech. Dev
, vol.122
, pp. 213-222
-
-
Suzuki, S.1
Renfree, M.B.2
Pask, A.J.3
Shaw, G.4
Kobayashi, S.5
Kohda, T.6
Kaneko-Ishino, T.7
Ishino, F.8
-
55
-
-
5144234363
-
Close split of sorghum and maize genome progenitors
-
Swigonová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. (2004). Close split of sorghum and maize genome progenitors. Genome Res. 14: 1916–1923.
-
(2004)
Genome Res
, vol.14
, pp. 1916-1923
-
-
Swigonová, Z.1
Lai, J.2
Ma, J.3
Ramakrishna, W.4
Llaca, V.5
Bennetzen, J.L.6
Messing, J.7
-
56
-
-
77955273950
-
A triptych of the evolution of plant transposable elements
-
Tenaillon, M.I., Hollister, J.D., and Gaut, B.S. (2010). A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15: 471–478.
-
(2010)
Trends Plant Sci
, vol.15
, pp. 471-478
-
-
Tenaillon, M.I.1
Hollister, J.D.2
Gaut, B.S.3
-
57
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.Nat.Protoc.7: 562–578.
-
(2012)
Nat.Protoc
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
58
-
-
66649122827
-
Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks
-
Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., and Van de Peer, Y. (2009). Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol. 150: 535–546.
-
(2009)
Plant Physiol
, vol.150
, pp. 535-546
-
-
Vandepoele, K.1
Quimbaya, M.2
Casneuf, T.3
De Veylder, L.4
Van De Peer, Y.5
-
59
-
-
84888377186
-
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
-
Waters, A.J., Bilinski, P., Eichten, S.R., Vaughn, M.W., Ross-Ibarra, J., Gehring, M., and Springer, N.M. (2013). Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proc. Natl. Acad. Sci. USA 110: 19639–19644.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 19639-19644
-
-
Waters, A.J.1
Bilinski, P.2
Eichten, S.R.3
Vaughn, M.W.4
Ross-Ibarra, J.5
Gehring, M.6
Springer, N.M.7
-
60
-
-
84907587760
-
Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora
-
Williamson, R.J., Josephs, E.B., Platts, A.E., Hazzouri, K.M., Haudry, A., Blanchette, M., and Wright, S.I. (2014). Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PLoS Genet. 10: e1004622.
-
(2014)
Plos Genet
, vol.10
-
-
Williamson, R.J.1
Josephs, E.B.2
Platts, A.E.3
Hazzouri, K.M.4
Haudry, A.5
Blanchette, M.6
Wright, S.I.7
-
61
-
-
79959848590
-
High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm
-
Wolff, P., Weinhofer, I., Seguin, J., Roszak, P., Beisel, C., Donoghue, M.T.A., Spillane, C., Nordborg, M., Rehmsmeier, M., and Köhler, C.(2011). High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm. PLoS Genet. 7: e1002126.
-
(2011)
Plos Genet
, vol.7
-
-
Wolff, P.1
Weinhofer, I.2
Seguin, J.3
Roszak, P.4
Beisel, C.5
Donoghue, M.T.A.6
Spillane, C.7
Nordborg, M.8
Rehmsmeier, M.9
Köhler, C.10
-
62
-
-
33845511629
-
A maternal-offspring coadaptation theory for the evolution of genomic imprinting
-
Wolf, J.B., and Hager, R. (2006). A maternal-offspring coadaptation theory for the evolution of genomic imprinting. PLoS Biol. 4: e380.
-
(2006)
Plos Biol
, vol.4
-
-
Wolf, J.B.1
Hager, R.2
-
63
-
-
50849106398
-
Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis
-
Woo, H.R., Dittmer, T.A., and Richards, E.J. (2008). Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet. 4: e1000156.
-
(2008)
Plos Genet
, vol.4
-
-
Woo, H.R.1
Dittmer, T.A.2
Richards, E.J.3
-
64
-
-
84903186608
-
Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean
-
Xu, W., Dai, M., Li, F., and Liu, A. (2014). Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean. Nucleic Acids Res. 42: 6987–6998.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 6987-6998
-
-
Xu, W.1
Dai, M.2
Li, F.3
Liu, A.4
-
65
-
-
84873475717
-
Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense
-
Yu, A., Lepère, G., Jay, F., Wang, J., Bapaume, L., Wang, Y., Abraham, A.-L., Penterman, J., Fischer, R.L., Voinnet, O., and Navarro, L.(2013). Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc. Natl. Acad. Sci. USA 110: 2389–2394.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 2389-2394
-
-
Yu, A.1
Lepère, G.2
Jay, F.3
Wang, J.4
Bapaume, L.5
Wang, Y.6
Abraham, A.-L.7
Penterman, J.8
Fischer, R.L.9
Voinnet, O.10
Navarro, L.11
-
66
-
-
84956720580
-
Genome-wide screen of genes imprinted in sorghum endosperm and the roles of allelic differential cytosine methylation
-
Zhang, M., Li, N., He, W., Zhang, H., Yang, W., and Liu, B. (2016). Genome-wide screen of genes imprinted in sorghum endosperm and the roles of allelic differential cytosine methylation. Plant J. 85: 424–436.
-
(2016)
Plant J
, vol.85
, pp. 424-436
-
-
Zhang, M.1
Li, N.2
He, W.3
Zhang, H.4
Yang, W.5
Liu, B.6
-
67
-
-
84908180718
-
Ancient eudicot hexaploidy meets ancestral eurosid gene order
-
Zheng, C., Chen, E., Albert, V.A., Lyons, E., and Sankoff, D.(2013). Ancient eudicot hexaploidy meets ancestral eurosid gene order. BMC Genomics 14: S3.
-
(2013)
BMC Genomics
, vol.14
, pp. S3
-
-
Zheng, C.1
Chen, E.2
Albert, V.A.3
Lyons, E.4
Sankoff, D.5
-
68
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T., and Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39: 61–69.
-
(2007)
Nat. Genet
, vol.39
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
|