-
1
-
-
84984784783
-
Are we there yet? Reliably estimating the completeness of plant genome sequences
-
Veeckman, E., Ruttink, T. & Vandepoele, K. Are we there yet? Reliably estimating the completeness of plant genome sequences. Plant Cell 28, 1759-1768 (2016).
-
(2016)
Plant Cell
, vol.28
, pp. 1759-1768
-
-
Veeckman, E.1
Ruttink, T.2
Vandepoele, K.3
-
2
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
3
-
-
84868534630
-
Transposable elements, epigenetics and genome evolution
-
Fedoroff, N.V. Transposable elements, epigenetics and genome evolution. Science 338, 758-767 (2012).
-
(2012)
Science
, vol.338
, pp. 758-767
-
-
Fedoroff, N.V.1
-
4
-
-
84866181273
-
The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments
-
Chénais, B., Caruso, A., Hiard, S. & Casse, N. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509, 7-15 (2012).
-
(2012)
Gene
, vol.509
, pp. 7-15
-
-
Chénais, B.1
Caruso, A.2
Hiard, S.3
Casse, N.4
-
5
-
-
84871329875
-
How important are transposons for plant evolution?
-
Lisch, D. How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49-61 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 49-61
-
-
Lisch, D.1
-
6
-
-
77957560949
-
The genome of the domesticated apple (Malus × domestica Borkh.)
-
Velasco, R. et al. The genome of the domesticated apple (Malus × domestica Borkh.). Nat. Genet. 42, 833-839 (2010).
-
(2010)
Nat. Genet.
, vol.42
, pp. 833-839
-
-
Velasco, R.1
-
7
-
-
84868353666
-
A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome
-
Khan, M.A., Han, Y., Zhao, Y.F., Troggio, M. & Korban, S.S. A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS One 7, e47864 (2012).
-
(2012)
PLoS One
, vol.7
, pp. e47864
-
-
Khan, M.A.1
Han, Y.2
Zhao, Y.F.3
Troggio, M.4
Korban, S.S.5
-
8
-
-
85028746770
-
Next-generation DNA sequencing (II): Techniques, applications
-
Ansorge, W.J. Next-generation DNA sequencing (II): techniques, applications. Next Generat. Sequenc. & Applic. 1, 1-10 (2016).
-
(2016)
Next Generat. Sequenc. & Applic.
, vol.1
, pp. 1-10
-
-
Ansorge, W.J.1
-
9
-
-
85006197282
-
Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)
-
Zhang, G. et al. Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge). Gigascience 4, 62 (2015).
-
(2015)
Gigascience
, vol.4
, pp. 62
-
-
Zhang, G.1
-
10
-
-
84948440327
-
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
-
VanBuren, R. et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527, 508-511 (2015).
-
(2015)
Nature
, vol.527
, pp. 508-511
-
-
VanBuren, R.1
-
11
-
-
84978159862
-
Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms
-
Zapata, L. et al. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proc. Natl. Acad. Sci. USA 113, E4052-E4060 (2016).
-
(2016)
Proc. Natl. Acad. Sci. USA
, vol.113
, pp. E4052-E4060
-
-
Zapata, L.1
-
12
-
-
84991713156
-
The draft genome of MD-2 pineapple using hybrid error correction of long reads
-
Redwan, R.M., Saidin, A. & Kumar, S.V. The draft genome of MD-2 pineapple using hybrid error correction of long reads. DNA Res. 23, 427-439 (2016).
-
(2016)
DNA Res.
, vol.23
, pp. 427-439
-
-
Redwan, R.M.1
Saidin, A.2
Kumar, S.V.3
-
13
-
-
84961182921
-
Indica rice genome assembly, annotation and mining of blast-disease-resistance genes
-
Mahesh, H.B. et al. Indica rice genome assembly, annotation and mining of blast-disease-resistance genes. BMC Genomics 17, 242 (2016).
-
(2016)
BMC Genomics
, vol.17
, pp. 242
-
-
Mahesh, H.B.1
-
14
-
-
84939453825
-
Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae
-
Badouin, H. et al. Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae. Genetics 200, 1275-1284 (2015).
-
(2015)
Genetics
, vol.200
, pp. 1275-1284
-
-
Badouin, H.1
-
15
-
-
33744822985
-
Widespread genome duplications throughout the history of fowering plants
-
Cui, L. et al. Widespread genome duplications throughout the history of fowering plants. Genome Res. 16, 738-749 (2006).
-
(2006)
Genome Res.
, vol.16
, pp. 738-749
-
-
Cui, L.1
-
16
-
-
70350225295
-
Chromatin indexing in Arabidopsis: An epigenomic tale of tails and more
-
Roudier, F. , Teixeira, F.K. & Colot, V. Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet. 25, 511-517 (2009).
-
(2009)
Trends Genet.
, vol.25
, pp. 511-517
-
-
Roudier Teixeira F, F.K.1
Colot, V.2
-
17
-
-
79955592294
-
The epigenome and plant development
-
He, G., Elling, A.A. & Deng, X.W. The epigenome and plant development. Annu. Rev. Plant Biol. 62, 411-435 (2011).
-
(2011)
Annu. Rev. Plant Biol.
, vol.62
, pp. 411-435
-
-
He, G.1
Elling, A.A.2
Deng, X.W.3
-
18
-
-
0033539183
-
An epigenetic mutation responsible for natural variation in foral symmetry
-
Cubas, P., Vincent, C. & Coen, E. An epigenetic mutation responsible for natural variation in foral symmetry. Nature 401, 157-161 (1999).
-
(1999)
Nature
, vol.401
, pp. 157-161
-
-
Cubas, P.1
Vincent, C.2
Coen, E.3
-
19
-
-
80054718602
-
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
-
Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245-249 (2011).
-
(2011)
Nature
, vol.480
, pp. 245-249
-
-
Becker, C.1
-
20
-
-
84942540296
-
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
-
Ong-Abdullah, M. et al. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533-537 (2015).
-
(2015)
Nature
, vol.525
, pp. 533-537
-
-
Ong-Abdullah, M.1
-
21
-
-
84963959883
-
Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifes a gene network module highly associated with anthocyanin and epigenetic regulation
-
El-Sharkawy, I., Liang, D. & Xu, K. Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifes a gene network module highly associated with anthocyanin and epigenetic regulation. J. Exp. Bot. 66, 7359-7376 (2015).
-
(2015)
J. Exp. Bot.
, vol.66
, pp. 7359-7376
-
-
El-Sharkawy, I.1
Liang, D.2
Xu, K.3
-
22
-
-
79956201630
-
Apple skin patterning is associated with differential expression of MYB10
-
Telias, A. et al. Apple skin patterning is associated with differential expression of MYB10. BMC Plant Biol. 11, 93 (2011).
-
(2011)
BMC Plant Biol.
, vol.11
, pp. 93
-
-
Telias, A.1
-
23
-
-
84997108992
-
A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species
-
Di Pierro, E.A. et al. A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species. Hortic. Res. 3, 16057 (2016).
-
(2016)
Hortic. Res.
, vol.3
, pp. 16057
-
-
Di Pierro, E.A.1
-
24
-
-
84879225756
-
Haploidy in apple and pear
-
Lespinasse, Y., Bouvier, L., Djulbic, M. & Chevreau, E. Haploidy in apple and pear. Acta Hortic. 484, 49-54 (1998).
-
(1998)
Acta Hortic.
, vol.484
, pp. 49-54
-
-
Lespinasse, Y.1
Bouvier, L.2
Djulbic, M.3
Chevreau, E.4
-
25
-
-
84942887758
-
SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
-
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
-
(2012)
Gigascience
, vol.1
, pp. 18
-
-
Luo, R.1
-
26
-
-
84984824728
-
DBG2OLC: Efficient assembly of large genomes using long erroneous reads of the third-generation sequencing technologies
-
Ye, C., Hill, C.M., Wu, S., Ruan, J. & Ma, Z.S. DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third-generation sequencing technologies. Sci. Rep. 6, 31900 (2016).
-
(2016)
Sci. Rep.
, vol.6
, pp. 31900
-
-
Ye, C.1
Hill, C.M.2
Wu, S.3
Ruan, J.4
Ma, Z.S.5
-
27
-
-
84953270832
-
Genetic diversity, population structure, parentage analysis and construction of core collections in the French apple germplasm based on SSR markers
-
Lassois, L. et al. Genetic diversity, population structure, parentage analysis and construction of core collections in the French apple germplasm based on SSR markers. Plant Mol. Biol. Rep. 34, 827-844 (2016).
-
(2016)
Plant Mol. Biol. Rep.
, vol.34
, pp. 827-844
-
-
Lassois, L.1
-
28
-
-
84962850091
-
Development and validation of the Axiom Apple480K SNP genotyping array
-
Bianco, L. et al. Development and validation of the Axiom Apple480K SNP genotyping array. Plant J. 86, 62-74 (2016).
-
(2016)
Plant J.
, vol.86
, pp. 62-74
-
-
Bianco, L.1
-
29
-
-
84931086162
-
A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'
-
Falginella, L. et al. A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'. BMC Plant Biol. 15, 150 (2015).
-
(2015)
BMC Plant Biol.
, vol.15
, pp. 150
-
-
Falginella, L.1
-
30
-
-
34249848751
-
CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes
-
Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061-1067 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 1061-1067
-
-
Parra, G.1
Bradnam, K.2
Korf, I.3
-
31
-
-
84991528460
-
Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam, K.R. et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2, 10 (2013).
-
(2013)
Gigascience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
-
32
-
-
66249109710
-
Genome annotation in plants and fungi: EuGene as a model platform
-
Foissac, S. et al. Genome annotation in plants and fungi: EuGene as a model platform. Curr. Bioinform. 3, 87-97 (2008).
-
(2008)
Curr. Bioinform.
, vol.3
, pp. 87-97
-
-
Foissac, S.1
-
33
-
-
85007305380
-
Improved hybrid de novo genome assembly of domesticated apple (Malus × domestica)
-
Li, X. et al. Improved hybrid de novo genome assembly of domesticated apple (Malus × domestica). Gigascience 5, 35 (2016).
-
(2016)
Gigascience
, vol.5
, pp. 35
-
-
Li, X.1
-
34
-
-
84940907209
-
BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
-
Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V. & Zdobnov, E.M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 3210-3212
-
-
Simão, F.A.1
Waterhouse, R.M.2
Ioannidis, P.3
Kriventseva, E.V.4
Zdobnov, E.M.5
-
35
-
-
84901585239
-
Widespread antisense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control
-
Celton, J.M. et al. Widespread antisense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control. New Phytol. 203, 287-299 (2014).
-
(2014)
New Phytol.
, vol.203
, pp. 287-299
-
-
Celton, J.M.1
-
36
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
-
37
-
-
79551624472
-
Considering transposable element diversification in de novo annotation approaches
-
Flutre, T., Duprat, E., Feuillet, C. & Quesneville, H. Considering transposable element diversification in de novo annotation approaches. PLoS One 6, e16526 (2011).
-
(2011)
PLoS One
, vol.6
, pp. e16526
-
-
Flutre, T.1
Duprat, E.2
Feuillet, C.3
Quesneville, H.4
-
38
-
-
28844444029
-
Combined evidence annotation of transposable elements in genome sequences
-
Quesneville, H. et al. Combined evidence annotation of transposable elements in genome sequences. PLOS Comput. Biol. 1, 166-175 (2005).
-
(2005)
PLOS Comput. Biol.
, vol.1
, pp. 166-175
-
-
Quesneville, H.1
-
39
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
-
(2005)
Cytogenet. Genome Res.
, vol.110
, pp. 462-467
-
-
Jurka, J.1
-
40
-
-
31044442399
-
Recombination, rearrangement, reshuffing and divergence in a centromeric region of rice
-
Ma, J. & Bennetzen, J.L. Recombination, rearrangement, reshuffing and divergence in a centromeric region of rice. Proc. Natl. Acad. Sci. USA 103, 383-388 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 383-388
-
-
Ma, J.1
Bennetzen, J.L.2
-
41
-
-
84949293478
-
Genome-wide annotation and comparative analysis of long-terminal-repeat retrotransposons between pear species of P. Bretschneideri and P. Communis
-
Yin, H. et al. Genome-wide annotation and comparative analysis of long-terminal-repeat retrotransposons between pear species of P. bretschneideri and P. communis. Sci. Rep. 5, 17644 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 17644
-
-
Yin, H.1
-
42
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
-
43
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
-
44
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008).
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
-
45
-
-
84901041535
-
RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
-
Matzke, M.A. & Mosher, R.A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394-408 (2014).
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 394-408
-
-
Matzke, M.A.1
Mosher, R.A.2
-
46
-
-
77249170184
-
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
-
Law, J.A. & Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204-220 (2010).
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 204-220
-
-
Law, J.A.1
Jacobsen, S.E.2
-
47
-
-
84922377811
-
Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage
-
Hagmann, J. et al. Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet. 11, e1004920 (2015).
-
(2015)
PLoS Genet.
, vol.11
, pp. e1004920
-
-
Hagmann, J.1
-
48
-
-
84925477292
-
Dramatic improvement in genome assembly achieved using doubled-haploid genomes
-
Zhang, H. et al. Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Sci. Rep. 4, 6780-6785 (2014).
-
(2014)
Sci. Rep.
, vol.4
, pp. 6780-6785
-
-
Zhang, H.1
-
49
-
-
84873386377
-
The genome of the pear (Pyrus bretschneideri Rehd.)
-
Wu, J. et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 23, 396-408 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 396-408
-
-
Wu, J.1
-
50
-
-
84916624307
-
Bursts of transposable elements as an evolutionary driving force
-
Belyayev, A. Bursts of transposable elements as an evolutionary driving force. J. Evol. Biol. 27, 2573-2584 (2014).
-
(2014)
J. Evol. Biol.
, vol.27
, pp. 2573-2584
-
-
Belyayev, A.1
-
52
-
-
84863661802
-
New insight into the history of domesticated apple: Secondary contribution of the European wild apple to the genome of cultivated varieties
-
Cornille, A. et al. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 8, e1002703 (2012).
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002703
-
-
Cornille, A.1
-
53
-
-
84873032132
-
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
-
Melters, D.P. et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 14, R10 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R10
-
-
Melters, D.P.1
-
54
-
-
84926496186
-
RNA-directed DNA methylation: The evolution of a complex epigenetic pathway in fowering plants
-
Matzke, M.A., Kanno, T. & Matzke, A.J.M. RNA-directed DNA methylation: the evolution of a complex epigenetic pathway in fowering plants. Annu. Rev. Plant Biol. 66, 243-267 (2015).
-
(2015)
Annu. Rev. Plant Biol.
, vol.66
, pp. 243-267
-
-
Matzke, M.A.1
Kanno, T.2
Matzke, A.J.M.3
-
55
-
-
84979284341
-
Unique cell-type-specifc patterns of DNA methylation in the root meristem
-
Kawakatsu, T. et al. Unique cell-type-specifc patterns of DNA methylation in the root meristem. Nat. Plants 2, 16058 (2016).
-
(2016)
Nat. Plants
, vol.2
, pp. 16058
-
-
Kawakatsu, T.1
-
56
-
-
33746513103
-
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening
-
Manning, K. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948-952 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 948-952
-
-
Manning, K.1
-
57
-
-
84940536894
-
A DEMETER-like DNA demethylase governs tomato fruit ripening
-
Liu, R. et al. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl. Acad. Sci. USA 112, 10804-10809 (2015).
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 10804-10809
-
-
Liu, R.1
-
58
-
-
84975153630
-
DNA methylation and chromatin regulation during feshy fruit development and ripening
-
Gallusci, P. , Hodgman, C., Teyssier, E. & Seymour, G.B. DNA methylation and chromatin regulation during feshy fruit development and ripening. Front. Plant Sci. 7, 807 (2016).
-
(2016)
Front. Plant Sci.
, vol.7
, pp. 807
-
-
Gallusci Hodgman P, C.1
Teyssier, E.2
Seymour, G.B.3
-
59
-
-
79956053248
-
Cell number counts - The fw2.2 and CNR genes and implications for controlling plant fruit and organ size
-
Guo, M. & Simmons, C.R. Cell number counts-the fw2.2 and CNR genes and implications for controlling plant fruit and organ size. Plant Sci. 181, 1-7 (2011).
-
(2011)
Plant Sci.
, vol.181
, pp. 1-7
-
-
Guo, M.1
Simmons, C.R.2
-
60
-
-
84884688892
-
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
-
Schmitz, R.J. et al. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 23, 1663-1674 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 1663-1674
-
-
Schmitz, R.J.1
-
61
-
-
84913546864
-
Toward better understanding of artifacts in variant calling from high-coverage samples
-
Li, H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30, 2843-2851 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2843-2851
-
-
Li, H.1
-
62
-
-
84914689868
-
Pilon: An integrated tool for comprehensive microbial variant detection and genome- A ssembly improvement
-
Walker, B.J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome- A ssembly improvement. PLoS One 9, e112963 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e112963
-
-
Walker, B.J.1
-
63
-
-
84906826446
-
BESST-efficient scaffolding of large fragmented assemblies
-
Sahlin, K., Vezzi, F., Nystedt, B., Lundeberg, J. & Arvestad, L. BESST-efficient scaffolding of large fragmented assemblies. BMC Bioinformatics 15, 281 (2014).
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 281
-
-
Sahlin, K.1
Vezzi, F.2
Nystedt, B.3
Lundeberg, J.4
Arvestad, L.5
-
64
-
-
84907815005
-
Development and validation of a 20K single-nucleotide polymorphism (SNP) whole-genome genotyping array for apple (Malus × domestica Borkh)
-
Bianco, L. et al. Development and validation of a 20K single-nucleotide polymorphism (SNP) whole-genome genotyping array for apple (Malus × domestica Borkh). PLoS One 9, e110377 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e110377
-
-
Bianco, L.1
-
65
-
-
85090878417
-
LDheatmap: An R function for graphical display of pairwise linkage disequilibria between single-nucleotide polymorphisms
-
Shin, J.H., Blay, S., McNeney, B. & Graham, J. LDheatmap: an R function for graphical display of pairwise linkage disequilibria between single-nucleotide polymorphisms. J. Stat. Software 16, c03 (2006).
-
(2006)
J. Stat. Software
, vol.16
, pp. c03
-
-
Shin, J.H.1
Blay, S.2
McNeney, B.3
Graham, J.4
-
66
-
-
84900988020
-
DeepTools: A fexible platform for exploring deep-sequencing data
-
Ramírez, F., Dündar, F., Diehl, S., Grüning, B.A. & Manke, T. deepTools: a fexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187-W191 (2014).
-
(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
-
67
-
-
79960264362
-
Full-length transcriptome assembly from RNA-seq data without a reference genome
-
Grabherr, M.G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
-
68
-
-
84902474663
-
SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-seq reads
-
Xie, Y. et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-seq reads. Bioinformatics 30, 1660-1666 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1660-1666
-
-
Xie, Y.1
-
69
-
-
18744383071
-
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
-
Wu, T.D. & Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.D.1
Watanabe, C.K.2
-
70
-
-
85008499664
-
TRNAscan-SE On-line: Integrating search and context for analysis of transfer RNA genes
-
Lowe, T.M. & Chan, P.P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44, W54-W57 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. W54-W57
-
-
Lowe, T.M.1
Chan, P.P.2
-
71
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
-
72
-
-
84946094179
-
Rfam 12.0: Updates to the RNA families database
-
Nawrocki, E.P. et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43 (W1), D130-D137 (2015).
-
(2015)
Nucleic Acids Res.
, vol.43
, Issue.W1
, pp. D130-D137
-
-
Nawrocki, E.P.1
-
73
-
-
84899518211
-
InterProScan 5: Genome-scale protein function classification
-
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1236-1240
-
-
Jones, P.1
-
74
-
-
34248531753
-
Locating proteins in the cell using TargetP, SignalP and related tools
-
Emanuelsson, O., Brunak, S., von Heijne, G. & Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2, 953-971 (2007).
-
(2007)
Nat. Protoc.
, vol.2
, pp. 953-971
-
-
Emanuelsson, O.1
Brunak, S.2
Von Heijne, G.3
Nielsen, H.4
-
75
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
76
-
-
84893676156
-
Bio++: Efficient extensible libraries and tools for computational molecular evolution
-
Guéguen, L. et al. Bio++: efficient extensible libraries and tools for computational molecular evolution. Mol. Biol. Evol. 30, 1745-1750 (2013).
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1745-1750
-
-
Guéguen, L.1
-
77
-
-
84900421805
-
PASTEC: An automatic transposable element classification tool
-
Hoede, C. et al. PASTEC: an automatic transposable element classification tool. PLoS One 9, e91929 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e91929
-
-
Hoede, C.1
-
78
-
-
84860640144
-
The predominantly selfng plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
-
de la Chaux, N., Tsuchimatsu, T., Shimizu, K.K. & Wagner, A. The predominantly selfng plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mob. DNA 3, 2 (2012).
-
(2012)
Mob. DNA
, vol.3
, pp. 2
-
-
De La Chaux, N.1
Tsuchimatsu, T.2
Shimizu, K.K.3
Wagner, A.4
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