-
1
-
-
70350504436
-
A transposon-induced epigenetic change leads to sex determination in melon
-
Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, et al. (2009) A transposon-induced epigenetic change leads to sex determination in melon. Nature 461: 1135–1138.
-
(2009)
Nature
, vol.461
, pp. 1135-1138
-
-
Martin, A.1
Troadec, C.2
Boualem, A.3
Rajab, M.4
Fernandez, R.5
-
2
-
-
84874782723
-
Transposon variants and their effects on gene expression in Arabidopsis
-
Wang X, Weigel D, Smith LM, (2013) Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet 9: e1003255.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003255
-
-
Wang, X.1
Weigel, D.2
Smith, L.M.3
-
3
-
-
0028885673
-
Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis
-
Bender J, Fink GR, (1995) Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83: 725–734.
-
(1995)
Cell
, vol.83
, pp. 725-734
-
-
Bender, J.1
Fink, G.R.2
-
4
-
-
0032829710
-
Arabidopsis PAI gene arrangements, cytosine methylation and expression
-
Melquist S, Luff B, Bender J, (1999) Arabidopsis PAI gene arrangements, cytosine methylation and expression. Genetics 153: 401–413.
-
(1999)
Genetics
, vol.153
, pp. 401-413
-
-
Melquist, S.1
Luff, B.2
Bender, J.3
-
5
-
-
84876875629
-
Extensive natural epigenetic variation at a de novo originated gene
-
Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LE, et al. (2013) Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet 9: e1003437.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003437
-
-
Silveira, A.B.1
Trontin, C.2
Cortijo, S.3
Barau, J.4
Del Bem, L.E.5
-
6
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419–423.
-
(2011)
Nature
, vol.477
, pp. 419-423
-
-
Gan, X.1
Stegle, O.2
Behr, J.3
Steffen, J.G.4
Drewe, P.5
-
7
-
-
80053384429
-
Whole-genome sequencing of multiple Arabidopsis thaliana populations
-
Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, et al. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43: 956–963.
-
(2011)
Nat Genet
, vol.43
, pp. 956-963
-
-
Cao, J.1
Schneeberger, K.2
Ossowski, S.3
Gunther, T.4
Bender, S.5
-
8
-
-
79959974750
-
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
-
Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, et al. (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci USA 108: 10249–10254.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 10249-10254
-
-
Schneeberger, K.1
Ossowski, S.2
Ott, F.3
Klein, J.D.4
Wang, X.5
-
9
-
-
84881026985
-
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
-
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, et al. (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45: 884–890.
-
(2013)
Nat Genet
, vol.45
, pp. 884-890
-
-
Long, Q.1
Rabanal, F.A.2
Meng, D.3
Huber, C.D.4
Farlow, A.5
-
10
-
-
84874991260
-
Patterns of population epigenomic diversity
-
Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, et al. (2013) Patterns of population epigenomic diversity. Nature 495: 193–198.
-
(2013)
Nature
, vol.495
, pp. 193-198
-
-
Schmitz, R.J.1
Schultz, M.D.2
Urich, M.A.3
Nery, J.R.4
Pelizzola, M.5
-
11
-
-
33646193822
-
Inherited epigenetic variation – revisiting soft inheritance
-
Richards EJ, (2006) Inherited epigenetic variation – revisiting soft inheritance. Nature reviews Genetics 7: 395–401.
-
(2006)
Nature reviews Genetics
, vol.7
, pp. 395-401
-
-
Richards, E.J.1
-
12
-
-
80054718602
-
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
-
Becker C, Hagmann J, Müller J, Koenig D, Stegle O, et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245–249.
-
(2011)
Nature
, vol.480
, pp. 245-249
-
-
Becker, C.1
Hagmann, J.2
Müller, J.3
Koenig, D.4
Stegle, O.5
-
13
-
-
80054837794
-
Transgenerational epigenetic instability is a source of novel methylation variants
-
Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, et al. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334: 369–373.
-
(2011)
Science
, vol.334
, pp. 369-373
-
-
Schmitz, R.J.1
Schultz, M.D.2
Lewsey, M.G.3
O'Malley, R.C.4
Urich, M.A.5
-
14
-
-
84857430552
-
Chromatin replication and epigenome maintenance
-
Alabert C, Groth A, (2012) Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol 13: 153–167.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, pp. 153-167
-
-
Alabert, C.1
Groth, A.2
-
15
-
-
17644368221
-
A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns
-
Genereux DP, Miner BE, Bergstrom CT, Laird CD, (2005) A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns. Proc Natl Acad Sci USA 102: 5802–5807.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5802-5807
-
-
Genereux, D.P.1
Miner, B.E.2
Bergstrom, C.T.3
Laird, C.D.4
-
16
-
-
79955084771
-
The coupling of epigenome replication with DNA replication
-
Liu Q, Gong Z, (2011) The coupling of epigenome replication with DNA replication. Curr Opin Plant Biol 14: 187–194.
-
(2011)
Curr Opin Plant Biol
, vol.14
, pp. 187-194
-
-
Liu, Q.1
Gong, Z.2
-
17
-
-
77249170184
-
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
-
Law JA, Jacobsen SE, (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
-
18
-
-
84867053720
-
Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA
-
Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, et al. (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.3
Van Ex, F.4
Jullien, P.E.5
-
19
-
-
62549160981
-
A role for RNAi in the selective correction of DNA methylation defects
-
Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, et al. (2009) A role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600–1604.
-
(2009)
Science
, vol.323
, pp. 1600-1604
-
-
Teixeira, F.K.1
Heredia, F.2
Sarazin, A.3
Roudier, F.4
Boccara, M.5
-
20
-
-
84889251436
-
Epigenetic diversity increases the productivity and stability of plant populations
-
Latzel V, Allan E, Bortolini Silveira A, Colot V, Fischer M, et al. (2013) Epigenetic diversity increases the productivity and stability of plant populations. Nat Commun 4: 2875.
-
(2013)
Nat Commun
, vol.4
, pp. 2875
-
-
Latzel, V.1
Allan, E.2
Bortolini Silveira, A.3
Colot, V.4
Fischer, M.5
-
21
-
-
80051565958
-
Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature
-
Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, et al. (2011) Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics 188: 1015–1017.
-
(2011)
Genetics
, vol.188
, pp. 1015-1017
-
-
Roux, F.1
Colomé-Tatché, M.2
Edelist, C.3
Wardenaar, R.4
Guerche, P.5
-
22
-
-
84924429296
-
-
Cortijo S, Wardenaar R, Colome-Tatche M, Gilly A, Etcheverry M, et al. (2014) Mapping the epigenetic basis of complex traits. Science: ePub Feb 06, 2014.
-
-
-
-
23
-
-
84864679478
-
Widespread dynamic DNA methylation in response to biotic stress
-
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, et al. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 109: E2183–2191.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 2183-2191
-
-
Dowen, R.H.1
Pelizzola, M.2
Schmitz, R.J.3
Lister, R.4
Dowen, J.M.5
-
24
-
-
84861330906
-
Rethinking heredity, again
-
Bonduriansky R, (2012) Rethinking heredity, again. Trends Ecol Evol 27: 330–336.
-
(2012)
Trends Ecol Evol
, vol.27
, pp. 330-336
-
-
Bonduriansky, R.1
-
26
-
-
79959439333
-
Beyond DNA: integrating inclusive inheritance into an extended theory of evolution
-
Danchin E, Charmantier A, Champagne FA, Mesoudi A, Pujol B, et al. (2011) Beyond DNA: integrating inclusive inheritance into an extended theory of evolution. Nat Rev Genet 12: 475–486.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 475-486
-
-
Danchin, E.1
Charmantier, A.2
Champagne, F.A.3
Mesoudi, A.4
Pujol, B.5
-
27
-
-
68049107038
-
Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution
-
Jablonka E, Raz G, (2009) Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. Q Rev Biol 84: 131–176.
-
(2009)
Q Rev Biol
, vol.84
, pp. 131-176
-
-
Jablonka, E.1
Raz, G.2
-
28
-
-
84875129831
-
DNA methylation dynamics in health and disease
-
Bergman Y, Cedar H, (2013) DNA methylation dynamics in health and disease. Nat Struct Mol Biol 20: 274–281.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 274-281
-
-
Bergman, Y.1
Cedar, H.2
-
29
-
-
84855956247
-
Epigenetics and the environment: emerging patterns and implications
-
Feil R, Fraga MF, (2011) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13: 97–109.
-
(2011)
Nat Rev Genet
, vol.13
, pp. 97-109
-
-
Feil, R.1
Fraga, M.F.2
-
30
-
-
84856150750
-
Population-epigenetic models of selection
-
Geoghegan JL, Spencer HG, (2012) Population-epigenetic models of selection. Theor Popul Biol 81: 232–242.
-
(2012)
Theor Popul Biol
, vol.81
, pp. 232-242
-
-
Geoghegan, J.L.1
Spencer, H.G.2
-
31
-
-
84857189974
-
Understanding transgenerational epigenetic inheritance via the gametes in mammals
-
Daxinger L, Whitelaw E, (2012) Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 13: 153–162.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 153-162
-
-
Daxinger, L.1
Whitelaw, E.2
-
32
-
-
79957679448
-
Epigenetic contribution to stress adaptation in plants
-
Mirouze M, Paszkowski J, (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14: 267–274.
-
(2011)
Curr Opin Plant Biol
, vol.14
, pp. 267-274
-
-
Mirouze, M.1
Paszkowski, J.2
-
33
-
-
79955086529
-
Selected aspects of transgenerational epigenetic inheritance and resetting in plants
-
Paszkowski J, Grossniklaus U, (2011) Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Curr Opin Plant Biol 14: 195–203.
-
(2011)
Curr Opin Plant Biol
, vol.14
, pp. 195-203
-
-
Paszkowski, J.1
Grossniklaus, U.2
-
34
-
-
84869496854
-
Epigenetic variation: origin and transgenerational inheritance
-
Becker C, Weigel D, (2012) Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol 15: 562–567.
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 562-567
-
-
Becker, C.1
Weigel, D.2
-
35
-
-
77649215261
-
The scale of population structure in Arabidopsis thaliana
-
Platt A, Horton M, Huang YS, Li Y, Anastasio AE, et al. (2010) The scale of population structure in Arabidopsis thaliana. PLoS Genet 6: e1000843.
-
(2010)
PLoS Genet
, vol.6
, pp. e1000843
-
-
Platt, A.1
Horton, M.2
Huang, Y.S.3
Li, Y.4
Anastasio, A.E.5
-
36
-
-
74849090833
-
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
-
Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92–94.
-
(2010)
Science
, vol.327
, pp. 92-94
-
-
Ossowski, S.1
Schneeberger, K.2
Lucas-Lledo, J.I.3
Warthmann, N.4
Clark, R.M.5
-
37
-
-
2642638791
-
A synopsis of Arabidopsis (Brassicaceae)
-
O'Kane SL, Al-Shehbaz IA, (1997) A synopsis of Arabidopsis (Brassicaceae). Novon 7: 323–327.
-
(1997)
Novon
, vol.7
, pp. 323-327
-
-
O'Kane, S.L.1
Al-Shehbaz, I.A.2
-
38
-
-
33748629119
-
Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis
-
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189–1201.
-
(2006)
Cell
, vol.126
, pp. 1189-1201
-
-
Zhang, X.1
Yazaki, J.2
Sundaresan, A.3
Cokus, S.4
Chan, S.W.5
-
39
-
-
84924405710
-
Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations
-
Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD, et al. (2014) Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Res 24: 1821–1829.
-
(2014)
Genome Res
, vol.24
, pp. 1821-1829
-
-
Jiang, C.1
Mithani, A.2
Belfield, E.J.3
Mott, R.4
Hurst, L.D.5
-
40
-
-
84869397620
-
MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
-
Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, et al. (2012) MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics 28: 2930–2939.
-
(2012)
Bioinformatics
, vol.28
, pp. 2930-2939
-
-
Seifert, M.1
Cortijo, S.2
Colomé-Tatché, M.3
Johannes, F.4
Roudier, F.5
-
41
-
-
80052937538
-
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
-
Molaro A, Hodges E, Fang F, Song Q, McCombie WR, et al. (2011) Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146: 1029–1041.
-
(2011)
Cell
, vol.146
, pp. 1029-1041
-
-
Molaro, A.1
Hodges, E.2
Fang, F.3
Song, Q.4
McCombie, W.R.5
-
42
-
-
84868122260
-
Deposition of histone variant H2A. Z within gene bodies regulates responsive genes
-
Coleman-Derr D, Zilberman D, (2012) Deposition of histone variant H2A. Z within gene bodies regulates responsive genes. PLoS Genet 8: e1002988.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002988
-
-
Coleman-Derr, D.1
Zilberman, D.2
-
43
-
-
84872614860
-
Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome
-
Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE, (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152: 352–364.
-
(2013)
Cell
, vol.152
, pp. 352-364
-
-
Stroud, H.1
Greenberg, M.V.2
Feng, S.3
Bernatavichute, Y.V.4
Jacobsen, S.E.5
-
44
-
-
84857189974
-
Understanding transgenerational epigenetic inheritance via the gametes in mammals
-
Daxinger L, Whitelaw E, (2012) Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet 13: 153–162.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 153-162
-
-
Daxinger, L.1
Whitelaw, E.2
-
45
-
-
70349956433
-
Finding the missing heritability of complex diseases
-
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747–753.
-
(2009)
Nature
, vol.461
, pp. 747-753
-
-
Manolio, T.A.1
Collins, F.S.2
Cox, N.J.3
Goldstein, D.B.4
Hindorff, L.A.5
-
46
-
-
70349326221
-
Epigenetic inheritance and the missing heritability problem
-
Slatkin M, (2009) Epigenetic inheritance and the missing heritability problem. Genetics 182: 845–850.
-
(2009)
Genetics
, vol.182
, pp. 845-850
-
-
Slatkin, M.1
-
47
-
-
84912120604
-
Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization
-
Seymour DK, Koenig D, Hagmann J, Becker C, 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
, pp. e1004785
-
-
Seymour, D.K.1
Koenig, D.2
Hagmann, J.3
Becker, C.4
Weigel, D.5
-
48
-
-
84861062626
-
Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly
-
Takuno S, Gaut BS, (2012) Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol 29: 219–227.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 219-227
-
-
Takuno, S.1
Gaut, B.S.2
-
49
-
-
57149099394
-
Sequencing of natural strains of Arabidopsis thaliana with short reads
-
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18: 2024–2033.
-
(2008)
Genome Res
, vol.18
, pp. 2024-2033
-
-
Ossowski, S.1
Schneeberger, K.2
Clark, R.M.3
Lanz, C.4
Warthmann, N.5
-
50
-
-
76249113666
-
Simultaneous alignment of short reads against multiple genomes
-
Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol 10: R98.
-
(2009)
Genome Biol
, vol.10
, pp. R98
-
-
Schneeberger, K.1
Hagmann, J.2
Ossowski, S.3
Warthmann, N.4
Gesing, S.5
-
51
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470: 59–65.
-
(2011)
Nature
, vol.470
, pp. 59-65
-
-
Mills, R.E.1
Walter, K.2
Stewart, C.3
Handsaker, R.E.4
Chen, K.5
-
52
-
-
70350694443
-
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z, (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865–2871.
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-2871
-
-
Ye, K.1
Schulz, M.H.2
Long, Q.3
Apweiler, R.4
Ning, Z.5
-
53
-
-
84866440781
-
DELLY: structural variant discovery by integrated paired-end and split-read analysis
-
Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333–i339.
-
(2012)
Bioinformatics
, vol.28
, pp. i333-i339
-
-
Rausch, T.1
Zichner, T.2
Schlattl, A.3
Stütz, A.M.4
Benes, V.5
-
54
-
-
84874223315
-
Accurate indel prediction using paired-end short reads
-
Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K, (2013) Accurate indel prediction using paired-end short reads. BMC Genomics 14: 132.
-
(2013)
BMC Genomics
, vol.14
, pp. 132
-
-
Grimm, D.1
Hagmann, J.2
Koenig, D.3
Weigel, D.4
Borgwardt, K.5
-
55
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
56
-
-
84942887758
-
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
-
Luo R, Liu B, Xie Y, Li Z, Huang W, et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1: 18.
-
(2012)
GigaScience
, vol.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
-
57
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821–829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
58
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
59
-
-
79957932376
-
Dindel: accurate indel calls from short-read data
-
Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, et al. (2011) Dindel: accurate indel calls from short-read data. Genome Res 21: 961–973.
-
(2011)
Genome Res
, vol.21
, pp. 961-973
-
-
Albers, C.A.1
Lunter, G.2
MacArthur, D.G.3
McVean, G.4
Ouwehand, W.H.5
-
60
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440–9445.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
61
-
-
65249148577
-
Estimating the number of unseen variants in the human genome
-
Ionita-Laza I, Lange C, N ML, (2009) Estimating the number of unseen variants in the human genome. Proc Natl Acad Sci USA 106: 5008–5013.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 5008-5013
-
-
Ionita-Laza, I.1
Lange, C.2
-
62
-
-
84884695071
-
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
-
Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, et al. (2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 23: 1651–1662.
-
(2013)
Genome Res
, vol.23
, pp. 1651-1662
-
-
Regulski, M.1
Lu, Z.2
Kendall, J.3
Donoghue, M.T.4
Reinders, J.5
-
63
-
-
77950301214
-
Variance component model to account for sample structure in genome-wide association studies
-
Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, et al. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42: 348–354.
-
(2010)
Nat Genet
, vol.42
, pp. 348-354
-
-
Kang, H.M.1
Sul, J.H.2
Service, S.K.3
Zaitlen, N.A.4
Kong, S.Y.5
-
64
-
-
80053372166
-
FaST linear mixed models for genome-wide association studies
-
Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, et al. (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8: 833–835.
-
(2011)
Nat Methods
, vol.8
, pp. 833-835
-
-
Lippert, C.1
Listgarten, J.2
Liu, Y.3
Kadie, C.M.4
Davidson, R.I.5
-
65
-
-
68349086946
-
SHOREmap: simultaneous mapping and mutation identification by deep sequencing
-
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, et al. (2009) SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6: 550–551.
-
(2009)
Nat Methods
, vol.6
, pp. 550-551
-
-
Schneeberger, K.1
Ossowski, S.2
Lanz, C.3
Juul, T.4
Petersen, A.H.5
-
66
-
-
0034118493
-
Inference of population structure using multilocus genotype data
-
Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
-
(2000)
Genetics
, vol.155
, pp. 945-959
-
-
Pritchard, J.K.1
Stephens, M.2
Donnelly, P.3
-
67
-
-
21244479740
-
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
-
Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611–2620.
-
(2005)
Mol Ecol
, vol.14
, pp. 2611-2620
-
-
Evanno, G.1
Regnaut, S.2
Goudet, J.3
-
68
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254–267.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
69
-
-
84879686532
-
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
-
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45: 831–835.
-
(2013)
Nat Genet
, vol.45
, pp. 831-835
-
-
Slotte, T.1
Hazzouri, K.M.2
Agren, J.A.3
Koenig, D.4
Maumus, F.5
-
70
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
-
71
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
72
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31: 46–53.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
Hendrickson, D.G.2
Sauvageau, M.3
Goff, L.4
Rinn, J.L.5
-
73
-
-
69649109364
-
Circos: an information aesthetic for comparative genomics
-
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645.
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
-
74
-
-
84867661862
-
Analysis of high-throughput plant image data with the information system IAP
-
Klukas C, Pape JM, Entzian A, (2012) Analysis of high-throughput plant image data with the information system IAP. J Integr Bioinform 9: 191.
-
(2012)
J Integr Bioinform
, vol.9
, pp. 191
-
-
Klukas, C.1
Pape, J.M.2
Entzian, A.3
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