-
1
-
-
85027940343
-
100 Tomato Genome Sequencing Consortium (2014). Exploring genetic variation in the tomato (Solanum section lycopersicon) clade by whole-genome sequencing
-
Aflitos, S., et al.; 100 Tomato Genome Sequencing Consortium (2014). Exploring genetic variation in the tomato (Solanum section lycopersicon) clade by whole-genome sequencing. Plant J. 80: 136–148.
-
Plant J
, vol.80
, pp. 136-148
-
-
Aflitos, S.1
-
2
-
-
84927717970
-
Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato
-
Alseekh, S., et al. (2015). Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. Plant Cell 27: 485–512.
-
(2015)
Plant Cell
, vol.27
, pp. 485-512
-
-
Alseekh, S.1
-
3
-
-
84930851165
-
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
-
Berlin, K., Koren, S., Chin, C.S., Drake, J.P., Landolin, J.M., and Phillippy, A.M. (2015). Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33: 623–630.
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 623-630
-
-
Berlin, K.1
Koren, S.2
Chin, C.S.3
Drake, J.P.4
Landolin, J.M.5
Phillippy, A.M.6
-
4
-
-
84922395331
-
The genome of the stress-tolerant wild tomato species Solanum pennellii
-
Bolger, A., et al. (2014a). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat. Genet. 46: 1034–1038.
-
(2014)
Nat. Genet
, vol.46
, pp. 1034-1038
-
-
Bolger, A.1
-
5
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., and Usadel, B. (2014b). 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
-
-
85030129427
-
Plant genome and transcriptome annotations: From misconceptions to simple solutions
-
pii: bbw135
-
Bolger, M.E., Arsova, B., and Usadel, B. (2017). Plant genome and transcriptome annotations: from misconceptions to simple solutions. Brief. Bioinform. pii: bbw135.
-
(2017)
Brief. Bioinform
-
-
Bolger, M.E.1
Arsova, B.2
Usadel, B.3
-
7
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
8
-
-
85026906620
-
-
Datema, E., Hulzink, R.J.M., Blommers, L., Espejo Valle-Inclan, J., Van Orsouw, N., Wittenberg, A.H.J., and De Vos, M. (2016). The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only. bioRxiv doi/10.1101/084772.
-
(2016)
The Megabase-Sized Fungal Genome of Rhizoctonia Solani Assembled from Nanopore Reads Only
-
-
Datema, E.1
Hulzink, R.J.M.2
Blommers, L.3
Espejo Valle-Inclan, J.4
Van Orsouw, N.5
Wittenberg, A.H.J.6
De Vos, M.7
-
10
-
-
43349091544
-
Using MUMmer to identify similar regions in large sequence sets
-
Delcher, A.L., Salzberg, S.L., and Phillippy, A.M. (2003). Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinformatics 10: 10.3.1–10.3.18.
-
(2003)
Curr. Protoc. Bioinformatics
, vol.10
, pp. 1-10
-
-
Delcher, A.L.1
Salzberg, S.L.2
Phillippy, A.M.3
-
11
-
-
84976585777
-
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens
-
Deschamps, S., Mudge, J., Cameron, C., Ramaraj, T., Anand, A., Fengler, K., Hayes, K., Llaca, V., Jones, T.J., and May, G. (2016). Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens. Sci. Rep. 6: 28625.
-
(2016)
Sci. Rep.
, vol.6
-
-
Deschamps, S.1
Mudge, J.2
Cameron, C.3
Ramaraj, T.4
Anand, A.5
Fengler, K.6
Hayes, K.7
Llaca, V.8
Jones, T.J.9
May, G.10
-
12
-
-
80055082271
-
Accelerated Profile HMM Searches
-
Eddy, S.R. (2011). Accelerated Profile HMM Searches. PLOS Comput. Biol. 7: e1002195.
-
(2011)
PLOS Comput. Biol.
, vol.7
-
-
Eddy, S.R.1
-
13
-
-
84938582898
-
OrthoFinder: Solving fundamental biases in whole genome comparisons dramatically improves or-thogroup inference accuracy
-
Emms, D.M., and Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves or-thogroup inference accuracy. Genome Biol. 16: 157.
-
(2015)
Genome Biol
, vol.16
, pp. 157
-
-
Emms, D.M.1
Kelly, S.2
-
14
-
-
0028846653
-
An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL
-
Eshed, Y., and Zamir, D. (1995). An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141: 1147–1162.
-
(1995)
Genetics
, vol.141
, pp. 1147-1162
-
-
Eshed, Y.1
Zamir, D.2
-
15
-
-
85024479345
-
Uncovering tomato quantitative trait loci and candidate genes for fruit cuticular lipid composition using the Solanum pennellii introgression line population
-
Fernandez-Moreno, J.P., Levy-Samoha, D., Malitsky, S., Monforte, A.J., Orzaez, D., Aharoni, A., and Granell, A. (2017). Uncovering tomato quantitative trait loci and candidate genes for fruit cuticular lipid composition using the Solanum pennellii introgression line population. J. Exp. Bot. 68: 2703–2716.
-
(2017)
J. Exp. Bot.
, vol.68
, pp. 2703-2716
-
-
Fernandez-Moreno, J.P.1
Levy-Samoha, D.2
Malitsky, S.3
Monforte, A.J.4
Orzaez, D.5
Aharoni, A.6
Granell, A.7
-
16
-
-
80051688000
-
Field guide to next-generation DNA sequencers
-
Glenn, T.C. (2011). Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11: 759–769.
-
(2011)
Mol. Ecol. Resour.
, vol.11
, pp. 759-769
-
-
Glenn, T.C.1
-
17
-
-
84876266928
-
QUAST: Quality assessment tool for genome assemblies
-
Gurevich, A., Saveliev, V., Vyahhi, N., and Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072–1075.
-
(2013)
Bioinformatics
, vol.29
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
18
-
-
85006263051
-
Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
-
Hirsch, C.N., et al. (2016). Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell 28: 2700–2714.
-
(2016)
Plant Cell
, vol.28
, pp. 2700-2714
-
-
Hirsch, C.N.1
-
19
-
-
84970952281
-
MinION Analysis and Reference Consortium (2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis
-
Ip, C.L.C., et al.; MinION Analysis and Reference Consortium (2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000 Res. 4: 1075.
-
F1000 Res
, vol.4
, pp. 1075
-
-
Ip, C.L.C.1
-
20
-
-
85021859981
-
De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
-
Istace, B., et al. (2017). de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Gigascience 6: 1–13.
-
(2017)
Gigascience
, vol.6
, pp. 1-13
-
-
Istace, B.1
-
21
-
-
84998996876
-
The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community
-
Jain, M., Olsen, H.E., Paten, B., and Akeson, M. (2016). The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17: 239.
-
(2016)
Genome Biol
, vol.17
, pp. 239
-
-
Jain, M.1
Olsen, H.E.2
Paten, B.3
Akeson, M.4
-
22
-
-
85014835664
-
The genome of Chenopodium quinoa
-
Jarvis, D.E., et al. (2017). The genome of Chenopodium quinoa. Nature 542: 307–312.
-
(2017)
Nature
, vol.542
, pp. 307-312
-
-
Jarvis, D.E.1
-
23
-
-
85013287793
-
The impact of third generation genomic technologies on plant genome assembly
-
Jiao, W.-B., and Schneeberger, K. (2017). The impact of third generation genomic technologies on plant genome assembly. Curr. Opin. Plant Biol. 36: 64–70.
-
(2017)
Curr. Opin. Plant Biol.
, vol.36
, pp. 64-70
-
-
Jiao, W.-B.1
Schneeberger, K.2
-
24
-
-
85013348722
-
Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
-
Jiao, W.-B., et al. (2017). Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Res. 27: 778–786.
-
(2017)
Genome Res
, vol.27
, pp. 778-786
-
-
Jiao, W.-B.1
-
25
-
-
84943806095
-
Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes
-
Judge, K., Harris, S.R., Reuter, S., Parkhill, J., and Peacock, S.J. (2015). Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J. Antimicrob. Chemother. 70: 2775–2778.
-
(2015)
J. Antimicrob. Chemother.
, vol.70
, pp. 2775-2778
-
-
Judge, K.1
Harris, S.R.2
Reuter, S.3
Parkhill, J.4
Peacock, S.J.5
-
26
-
-
84879984347
-
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
-
Koenig, D., et al. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc. Natl. Acad. Sci. USA 110: E2655–E2662.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. E2655-E2662
-
-
Koenig, D.1
-
27
-
-
85019066712
-
Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
-
Koren, S., Walenz, B.P., Berlin, K., Miller, J.R., Bergman, N.H., and Phillippy, A.M. (2017). Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27: 722–736.
-
(2017)
Genome Res
, vol.27
, pp. 722-736
-
-
Koren, S.1
Walenz, B.P.2
Berlin, K.3
Miller, J.R.4
Bergman, N.H.5
Phillippy, A.M.6
-
28
-
-
85018968487
-
High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads
-
Kranz, A., Vogel, A., Degner, U., Kiefler, I., Bott, M., Usadel, B., and Polen, T. (2017). High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads. J. Biotechnol. 258: 197–205.
-
(2017)
J. Biotechnol.
, vol.258
, pp. 197-205
-
-
Kranz, A.1
Vogel, A.2
Degner, U.3
Kiefler, I.4
Bott, M.5
Usadel, B.6
Polen, T.7
-
30
-
-
84992371738
-
Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences
-
Li, H. (2016). Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32: 2103–2110.
-
(2016)
Bioinformatics
, vol.32
, pp. 2103-2110
-
-
Li, H.1
-
31
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R, 1000 Genome Project Data Processing Subgroup (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
32
-
-
84908689021
-
Genomic analyses provide insights into the history of tomato breeding
-
Lin, T., et al. (2014). Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46: 1220–1226.
-
(2014)
Nat. Genet.
, vol.46
, pp. 1220-1226
-
-
Lin, T.1
-
33
-
-
36549080467
-
An integrated view of quantitative trait variation using tomato interspecific introgression lines
-
Lippman, Z.B., Semel, Y., and Zamir, D. (2007). An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr. Opin. Genet. Dev. 17: 545–552.
-
(2007)
Curr. Opin. Genet. Dev.
, vol.17
, pp. 545-552
-
-
Lippman, Z.B.1
Semel, Y.2
Zamir, D.3
-
34
-
-
34248580879
-
Gas chromatography mass spectrometry-based metabolite profiling in plants
-
Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., and Fernie, A.R. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat. Protoc. 1: 387–396.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 387-396
-
-
Lisec, J.1
Schauer, N.2
Kopka, J.3
Willmitzer, L.4
Fernie, A.R.5
-
35
-
-
84898056944
-
Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data
-
Lohse, M., Nagel, A., Herter, T., May, P., Schroda, M., Zrenner, R., Tohge, T., Fernie, A.R., Stitt, M., and Usadel, B. (2014). Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ. 37: 1250–1258.
-
(2014)
Plant Cell Environ
, vol.37
, pp. 1250-1258
-
-
Lohse, M.1
Nagel, A.2
Herter, T.3
May, P.4
Schroda, M.5
Zrenner, R.6
Tohge, T.7
Fernie, A.R.8
Stitt, M.9
Usadel, B.10
-
36
-
-
84938421951
-
A complete bacterial genome assembled de novo using only nanopore sequencing data
-
Loman, N.J., Quick, J., and Simpson, J.T. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12: 733–735.
-
(2015)
Nat. Methods
, vol.12
, pp. 733-735
-
-
Loman, N.J.1
Quick, J.2
Simpson, J.T.3
-
37
-
-
84994515712
-
Oxford Nanopore MinION Sequencing and Genome Assembly
-
Lu, H., Giordano, F., and Ning, Z. (2016). Oxford Nanopore MinION Sequencing and Genome Assembly. Genomics Proteomics Bioinformatics 14: 265–279.
-
(2016)
Genomics Proteomics Bioinformatics
, vol.14
, pp. 265-279
-
-
Lu, H.1
Giordano, F.2
Ning, Z.3
-
38
-
-
38949151064
-
How to usefully compare homologous plant genes and chromosomes as DNA sequences
-
Lyons, E., and Freeling, M. (2008). How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53: 661–673.
-
(2008)
Plant J
, vol.53
, pp. 661-673
-
-
Lyons, E.1
Freeling, M.2
-
39
-
-
79952592810
-
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-
Marçais, G., and Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27: 764–770.
-
(2011)
Bioinformatics
, vol.27
, pp. 764-770
-
-
Marçais, G.1
Kingsford, C.2
-
40
-
-
85039801698
-
-
Michael, T. P., Jupe, F., Bemm, F., Motley, S.T., Sandoval, J.P, Loudet, O. Weigel, D., Ecker, J.R. (2017). High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. bioRxiv doi/10.1101/149997.
-
(2017)
High Contiguity Arabidopsis Thaliana Genome Assembly with a Single Nanopore Flow Cell
-
-
Michael, T.P.1
Jupe, F.2
Bemm, F.3
Motley, S.T.4
Sandovalloudet, J.P.5
Weigel, O.D.6
Ecker, J.R.7
-
41
-
-
8844263835
-
SNM-dependent recombinational repair of oxidatively induced DNA damage in Arabidopsis thaliana
-
Molinier, J., Stamm, M.E., and Hohn, B. (2004). SNM-dependent recombinational repair of oxidatively induced DNA damage in Arabidopsis thaliana. EMBO Rep. 5: 994–999.
-
(2004)
EMBO Rep
, vol.5
, pp. 994-999
-
-
Molinier, J.1
Stamm, M.E.2
Hohn, B.3
-
42
-
-
85027958176
-
Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits
-
Ofner, I., Lashbrooke, J., Pleban, T., Aharoni, A., and Zamir, D. (2016). Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits. Plant J. 87: 151–160.
-
(2016)
Plant J
, vol.87
, pp. 151-160
-
-
Ofner, I.1
Lashbrooke, J.2
Pleban, T.3
Aharoni, A.4
Zamir, D.5
-
43
-
-
84959932296
-
Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data
-
Okonechnikov, K., Conesa, A., and García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32: 292–294.
-
(2016)
Bioinformatics
, vol.32
, pp. 292-294
-
-
Okonechnikov, K.1
Conesa, A.2
García-Alcalde, F.3
-
44
-
-
84955703917
-
Phylogenomics reveals three sources of adaptive variation during a rapid radiation
-
Pease, J.B., Haak, D.C., Hahn, M.W., and Moyle, L.C. (2016a). Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biol. 14: e1002379.
-
(2016)
Plos Biol
, vol.14
-
-
Pease, J.B.1
Haak, D.C.2
Hahn, M.W.3
Moyle, L.C.4
-
45
-
-
85027924537
-
Molecular mechanisms of postmating pre-zygotic reproductive isolation uncovered by transcriptome analysis
-
Pease, J.B., Guerrero, R.F., Sherman, N.A., Hahn, M.W., and Moyle, L.C. (2016b). Molecular mechanisms of postmating pre-zygotic reproductive isolation uncovered by transcriptome analysis. Mol. Ecol. 25: 2592–2608.
-
(2016)
Mol. Ecol.
, vol.25
, pp. 2592-2608
-
-
Pease, J.B.1
Guerrero, R.F.2
Sherman, N.A.3
Hahn, M.W.4
Moyle, L.C.5
-
46
-
-
34250663833
-
Arabidopsis irregular xylem8 and irregular xylem9: Implications for the complexity of glucuronoxylan biosynthesis
-
Peña, M.J., Zhong, R., Zhou, G.K., Richardson, E.A., O’Neill, M.A., Darvill, A.G., York, W.S., and Ye, Z.H. (2007). Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19: 549–563.
-
(2007)
Plant Cell
, vol.19
, pp. 549-563
-
-
Peña, M.J.1
Zhong, R.2
Zhou, G.K.3
Richardson, E.A.4
O’Neill, M.A.5
Darvill, A.G.6
York, W.S.7
Ye, Z.H.8
-
47
-
-
84903641120
-
Natural occurring epialleles determine vitamin E accumulation in tomato fruits
-
Quadrana, L., et al. (2014). Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat. Commun. 5: 3027.
-
(2014)
Nat. Commun.
, vol.5
, pp. 3027
-
-
Quadrana, L.1
-
48
-
-
84934284959
-
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
-
Quick, J., et al. (2015). Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16: 114.
-
(2015)
Genome Biol
, vol.16
, pp. 114
-
-
Quick, J.1
-
49
-
-
84984893138
-
EQTL regulating transcript levels associated with diverse biological processes in tomato
-
Ranjan, A., Budke, J.M., Rowland, S.D., Chitwood, D.H., Kumar, R., Carriedo, L., Ichihashi, Y., Zumstein, K., Maloof, J.N., and Sinha, N.R. (2016). eQTL regulating transcript levels associated with diverse biological processes in tomato. Plant Physiol. 172: 328–340.
-
(2016)
Plant Physiol
, vol.172
, pp. 328-340
-
-
Ranjan, A.1
Budke, J.M.2
Rowland, S.D.3
Chitwood, D.H.4
Kumar, R.5
Carriedo, L.6
Ichihashi, Y.7
Zumstein, K.8
Maloof, J.N.9
Sinha, N.R.10
-
50
-
-
85017430250
-
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
-
Reyes-Chin-Wo, S., et al. (2017). Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8: 14953.
-
(2017)
Nat. Commun.
, vol.8
-
-
Reyes-Chin-Wo, S.1
-
51
-
-
0003136233
-
Genetic variation in Solanum pennellii: Comparisons with two other sympatric tomato species
-
Rick, C.M., and Tanksley, S.D. (1981). Genetic variation in Solanum pennellii: Comparisons with two other sympatric tomato species. Plant Syst. Evol. 139: 11–45.
-
(1981)
Plant Syst. Evol
, vol.139
, pp. 11-45
-
-
Rick, C.M.1
Tanksley, S.D.2
-
52
-
-
84940907209
-
BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
-
Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., and Zdobnov, E.M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210–3212.
-
(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
-
53
-
-
85013175291
-
Detecting DNA cytosine methylation using nanopore sequencing
-
Simpson, J.T., Workman, R.E., Zuzarte, P.C., David, M., Dursi, L.J., and Timp, W. (2017). Detecting DNA cytosine methylation using nanopore sequencing. Nat. Methods 14: 407–410.
-
(2017)
Nat. Methods
, vol.14
, pp. 407-410
-
-
Simpson, J.T.1
Workman, R.E.2
Zuzarte, P.C.3
David, M.4
Dursi, L.J.5
Timp, W.6
-
54
-
-
57649114783
-
Phylogenetic and transcriptional analysis of a strictosidine synthase-like gene family in Arabidopsis thaliana reveals involvement in plant defence responses
-
Sohani, M.M., Schenk, P.M., Schultz, C.J., and Schmidt, O. (2009). Phylogenetic and transcriptional analysis of a strictosidine synthase-like gene family in Arabidopsis thaliana reveals involvement in plant defence responses. Plant Biol (Stuttg.) 11: 105– 117.
-
(2009)
Plant Biol (Stuttg.)
, vol.11
, pp. 105-117
-
-
Sohani, M.M.1
Schenk, P.M.2
Schultz, C.J.3
Schmidt, O.4
-
55
-
-
2942527473
-
Gene prediction with a hidden Markov model and a new intron submodel
-
Stanke, M., and Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (Suppl. 2): ii215–ii225.
-
(2003)
Bioinformatics
, vol.19
, pp. ii215-ii225
-
-
Stanke, M.1
Waack, S.2
-
56
-
-
40049091292
-
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
-
Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637–644.
-
(2008)
Bioinformatics
, vol.24
, pp. 637-644
-
-
Stanke, M.1
Diekhans, M.2
Baertsch, R.3
Haussler, D.4
-
57
-
-
85020935229
-
A chemical genetic roadmap to improved tomato flavor
-
Tieman, D., et al. (2017). A chemical genetic roadmap to improved tomato flavor. Science 355: 391–394.
-
(2017)
Science
, vol.355
, pp. 391-394
-
-
Tieman, D.1
-
58
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635–641.
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
-
59
-
-
84948440327
-
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
-
VanBuren, R., et al. (2015). Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527: 508–511.
-
(2015)
Nature
, vol.527
, pp. 508-511
-
-
Vanburen, R.1
-
60
-
-
85019121900
-
Fast and accurate de novo genome assembly from long uncorrected reads
-
Vaser, R., Sović, I., Nagarajan, N., and Sikić, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27: 737–746.
-
(2017)
Genome Res
, vol.27
, pp. 737-746
-
-
Vaser, R.1
Sović, I.2
Nagarajan, N.3
Sikić, M.4
-
61
-
-
84914689868
-
Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
-
Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., Young, S.K., and Earl, A.M. (2014). Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9: e112963.
-
(2014)
Plos One
, vol.9
-
-
Walker, B.J.1
Abeel, T.2
Shea, T.3
Priest, M.4
Abouelliel, A.5
Sakthikumar, S.6
Cuomo, C.A.7
Zeng, Q.8
Wortman, J.9
Young, S.K.10
Earl, A.M.11
-
62
-
-
84860137835
-
MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity
-
Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T.H., Jin, H., Marler, B., Guo, H., Kissinger, J.C., and Paterson, A.H. (2012). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40: e49.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Wang, Y.1
Tang, H.2
Debarry, J.D.3
Tan, X.4
Li, J.5
Wang, X.6
Lee, T.H.7
Jin, H.8
Marler, B.9
Guo, H.10
Kissinger, J.C.11
Paterson, A.H.12
-
63
-
-
85017198613
-
Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
-
Wang, X., et al. (2017). Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat. Genet. 49: 765–772.
-
(2017)
Nat. Genet.
, vol.49
, pp. 765-772
-
-
Wang, X.1
-
64
-
-
85026895692
-
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
-
Weirather, J., de Cesare, M., Wang, Y., Piazza, P., Sebastiano, V., Wang, X., Buck, D., and Au, K. (2017). Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Research 6: 100.
-
(2017)
F1000research
, vol.6
, pp. 100
-
-
Weirather, J.1
De Cesare, M.2
Wang, Y.3
Piazza, P.4
Sebastiano, V.5
Wang, X.6
Buck, D.7
Au, K.8
-
65
-
-
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., and Ma, Z.S. (2016). DBG2OLC: Efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci. Rep. 6: 31900.
-
(2016)
Sci. Rep.
, vol.6
-
-
Ye, C.1
Hill, C.M.2
Wu, S.3
Ruan, J.4
Ma, Z.S.5
-
66
-
-
84873587727
-
Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
-
Zhong, S., Fei, Z., Chen, Y.R., Zheng, Y., Huang, M., Vrebalov, J., McQuinn, R., Gapper, N., Liu, B., Xiang, J., Shao, Y., and Giovannoni, J.J. (2013). Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat. Biotechnol. 31: 154–159.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 154-159
-
-
Zhong, S.1
Fei, Z.2
Chen, Y.R.3
Zheng, Y.4
Huang, M.5
Vrebalov, J.6
McQuinn, R.7
Gapper, N.8
Liu, B.9
Xiang, J.10
Shao, Y.11
Giovannoni, J.J.12
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