-
1
-
-
84883254031
-
-
Andrews S (2010) Fastqc. http://www. bioinformatics. bbsrc. ac. uk/projects/fastqc/.
-
(2010)
Fastqc
-
-
Andrews, S.1
-
2
-
-
84862018035
-
Reference genome sequence of the model plant Setaria
-
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye C-Y, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6): 555-561.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.6
, pp. 555-561
-
-
Bennetzen, J.L.1
Schmutz, J.2
Wang, H.3
Percifield, R.4
Hawkins, J.5
Pontaroli, A.C.6
Estep, M.7
Feng, L.8
Vaughn, J.N.9
Grimwood, J.10
Jenkins, J.11
Barry, K.12
Lindquist, E.13
Hellsten, U.14
Deshpande, S.15
Wang, X.16
Wu, X.17
Mitros, T.18
Triplett, J.19
Yang, X.20
Ye, C.-Y.21
Mauro-Herrera, M.22
Wang, L.23
Li, P.24
Sharma, M.25
Sharma, R.26
Ronald, P.C.27
Panaud, O.28
Kellogg, E.A.29
Brutnell, T.P.30
Doust, A.N.31
Tuskan, G.A.32
Rokhsar, D.33
Devos, K.M.34
more..
-
3
-
-
0000422075
-
Physiology and genetics of interspecific hybrids between photosynthetic types
-
Brown RH, Bouton JH (1993) Physiology and genetics of interspecific hybrids between photosynthetic types. Annu Rev Plant Physiol Plant Mol Biol 44(1): 435-456.
-
(1993)
Annu Rev Plant Physiol Plant Mol Biol
, vol.44
, Issue.1
, pp. 435-456
-
-
Brown, R.H.1
Bouton, J.H.2
-
5
-
-
77957767706
-
4 photosynthesis
-
4 photosynthesis. Plant Cell 22(8): 2537-2544.
-
(2010)
Plant Cell
, vol.22
, Issue.8
, pp. 2537-2544
-
-
Brutnell, T.P.1
Wang, L.2
Swartwood, K.3
Goldschmidt, A.4
Jackson, D.5
Zhu, X.-G.6
Kellogg, E.7
van Eck, J.8
-
6
-
-
33751017957
-
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
-
Cheung F, Haas BJ, Goldberg SMD, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7(1): 272.
-
(2006)
BMC Genomics
, vol.7
, Issue.1
, pp. 272
-
-
Cheung, F.1
Haas, B.J.2
Goldberg, S.M.D.3
May, G.D.4
Xiao, Y.5
Town, C.D.6
-
8
-
-
58449100024
-
Foxtail millet: a sequence-driven grass model system
-
Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149(1): 137-141.
-
(2009)
Plant Physiol
, vol.149
, Issue.1
, pp. 137-141
-
-
Doust, A.N.1
Kellogg, E.A.2
Devos, K.M.3
Bennetzen, J.L.4
-
9
-
-
79958793080
-
4 acid decarboxylation types?
-
4 acid decarboxylation types? J Exp Bot 62(9): 3103-3108.
-
(2011)
J Exp Bot
, vol.62
, Issue.9
, pp. 3103-3108
-
-
Furbank, R.T.1
-
13
-
-
45949125175
-
4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructure
-
4 photosynthesis: a unique blend of modified biochemistry, anatomy and ultrastructure. Biochim Biophys Acta 895: 81-106.
-
(1987)
Biochim Biophys Acta
, vol.895
, pp. 81-106
-
-
Hatch, M.D.1
-
15
-
-
84862576869
-
The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers
-
Huang L, Yang X, Sun P, Tang W, Hu S (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 7(6): e38653.
-
(2012)
PLoS One
, vol.7
, Issue.6
-
-
Huang, L.1
Yang, X.2
Sun, P.3
Tang, W.4
Hu, S.5
-
16
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4): 656-664.
-
(2002)
Genome Res
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
17
-
-
69649109364
-
Circos: an information aesthetic for comparative genomics
-
Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9): 1639-1645.
-
(2009)
Genome Res
, vol.19
, Issue.9
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
18
-
-
84855181935
-
4 photosynthesis
-
4 photosynthesis. Plant Cell 23(11): 3879-3892.
-
(2011)
Plant Cell
, vol.23
, Issue.11
, pp. 3879-3892
-
-
Langdale, J.A.1
-
19
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4): 357-359.
-
(2012)
Nat Methods
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
20
-
-
84864465389
-
From bench to bountiful harvests: a road map for the next decade of Arabidopsis research
-
Lavagi I, Estelle M, Weckwerth W, Beynon J, Bastow RM (2012) From bench to bountiful harvests: a road map for the next decade of Arabidopsis research. Plant Cell 24: 2240-2247.
-
(2012)
Plant Cell
, vol.24
, pp. 2240-2247
-
-
Lavagi, I.1
Estelle, M.2
Weckwerth, W.3
Beynon, J.4
Bastow, R.M.5
-
21
-
-
79958774172
-
Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses
-
Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J Exp Bot 62(9): 3031-3037.
-
(2011)
J Exp Bot
, vol.62
, Issue.9
, pp. 3031-3037
-
-
Li, P.1
Brutnell, T.P.2
-
22
-
-
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(14): 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
2442701496
-
Microsatellites within genes: structure, function, and evolution
-
Li Y-C, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21(6): 991-1007.
-
(2004)
Mol Biol Evol
, vol.21
, Issue.6
, pp. 991-1007
-
-
Li, Y.-C.1
Korol, A.B.2
Fahima, T.3
Nevo, E.4
-
24
-
-
84862786822
-
RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus
-
Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 32(5): 816-827.
-
(2012)
Fish Shellfish Immunol
, vol.32
, Issue.5
, pp. 816-827
-
-
Li, C.1
Zhang, Y.2
Wang, R.3
Lu, J.4
Nandi, S.5
Mohanty, S.6
Terhune, J.7
Liu, Z.8
Peatman, E.9
-
25
-
-
80052960863
-
Next-generation transcriptome assembly
-
Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10): 671-682.
-
(2011)
Nat Rev Genet
, vol.12
, Issue.10
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
27
-
-
79953164140
-
-
Mayer C (2006-2010) Phobos 3. 3. 11. http://www. rub. de/spezzoo/cm/cm_phobos. htm.
-
(2006)
Phobos 3. 3. 11
-
-
Mayer, C.1
-
28
-
-
72849144434
-
Sequencing technologies-the next generation
-
Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11(1): 31-46.
-
(2010)
Nat Rev Genet
, vol.11
, Issue.1
, pp. 31-46
-
-
Metzker, M.L.1
-
29
-
-
84861529088
-
Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research
-
Meyer E, Logan TL, Juenger TE (2012) Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. Plant J 70(5): 879-890.
-
(2012)
Plant J
, vol.70
, Issue.5
, pp. 879-890
-
-
Meyer, E.1
Logan, T.L.2
Juenger, T.E.3
-
30
-
-
0036478903
-
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes
-
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30(2): 194-200.
-
(2002)
Nat Genet
, vol.30
, Issue.2
, pp. 194-200
-
-
Morgante, M.1
Hanafey, M.2
Powell, W.3
-
31
-
-
0032919364
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27(1): 29-34.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.1
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
33
-
-
79958842311
-
3 plants
-
3 plants. J Exp Bot 62(9): 3011-3019.
-
(2011)
J Exp Bot
, vol.62
, Issue.9
, pp. 3011-3019
-
-
Peterhansel, C.1
-
34
-
-
0030183057
-
Polymorphism revealed by simple sequence repeats
-
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1(7): 215-222.
-
(1996)
Trends Plant Sci
, vol.1
, Issue.7
, pp. 215-222
-
-
Powell, W.1
Machray, G.C.2
Provan, J.3
-
36
-
-
84859768479
-
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
-
Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8): 1086-1092.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
Birney, E.4
-
38
-
-
0033858199
-
Microsatellites in different eukaryotic genomes: survey and analysis
-
Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7): 967-981.
-
(2000)
Genome Res
, vol.10
, Issue.7
, pp. 967-981
-
-
Tóth, G.1
Gáspári, Z.2
Jurka, J.3
-
39
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9): 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, Issue.9
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
40
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5): 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.5
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
41
-
-
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 DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3): 562-578.
-
(2012)
Nat Protoc
, vol.7
, Issue.3
, 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
-
42
-
-
11344276529
-
Genic microsatellite markers in plants: features and applications
-
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1): 48-55.
-
(2005)
Trends Biotechnol
, vol.23
, Issue.1
, pp. 48-55
-
-
Varshney, R.K.1
Graner, A.2
Sorrells, M.E.3
-
44
-
-
84859061827
-
Exploring the switchgrass transcriptome using second-generation sequencing technology
-
Wang Y, Zeng X, Iyer NJ, Bryant DW, Mockler TC, Mahalingam R (2012) Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS One 7(3): e34225.
-
(2012)
PLoS One
, vol.7
, Issue.3
-
-
Wang, Y.1
Zeng, X.2
Iyer, N.J.3
Bryant, D.W.4
Mockler, T.C.5
Mahalingam, R.6
-
46
-
-
84862868321
-
De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome
-
Xie F, Burklew CE, Yang Y, Liu M, Xiao P, Zhang B, Qiu D (2012) De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. Planta 236(1): 101-113.
-
(2012)
Planta
, vol.236
, Issue.1
, pp. 101-113
-
-
Xie, F.1
Burklew, C.E.2
Yang, Y.3
Liu, M.4
Xiao, P.5
Zhang, B.6
Qiu, D.7
-
47
-
-
79955877212
-
RAPSearch: a fast protein similarity search tool for short reads
-
Ye Y, Choi J-H, Tang H (2011) RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinform 12(1): 159.
-
(2011)
BMC Bioinform
, vol.12
, Issue.1
, pp. 159
-
-
Ye, Y.1
Choi, J.-H.2
Tang, H.3
-
48
-
-
84863393816
-
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
-
Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2): 193-208.
-
(2012)
Am J Bot
, vol.99
, Issue.2
, pp. 193-208
-
-
Zalapa, J.E.1
Cuevas, H.2
Zhu, H.3
Steffan, S.4
Senalik, D.5
Zeldin, E.6
McCown, B.7
Harbut, R.8
Simon, P.9
-
49
-
-
84862023110
-
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
-
Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, Huang P, Chen Q, Li Y, Wang J, Zhao Z, Wang J (2012a) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30(6): 549-554.
-
(2012)
Nat Biotechnol
, vol.30
, Issue.6
, pp. 549-554
-
-
Zhang, G.1
Liu, X.2
Quan, Z.3
Cheng, S.4
Xu, X.5
Pan, S.6
Xie, M.7
Zeng, P.8
Yue, Z.9
Wang, W.10
Tao, Y.11
Bian, C.12
Han, C.13
Xia, Q.14
Peng, X.15
Cao, R.16
Yang, X.17
Zhan, D.18
Hu, J.19
Zhang, Y.20
Li, H.21
Li, H.22
Li, N.23
Wang, J.24
Wang, C.25
Wang, R.26
Guo, T.27
Cai, Y.28
Liu, C.29
Xiang, H.30
Shi, Q.31
Huang, P.32
Chen, Q.33
Li, Y.34
Wang, J.35
Zhao, Z.36
Wang, J.37
more..
-
50
-
-
84862768926
-
Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirds
-
Zhang Y, Jiang R, Wu H, Liu P, Xie J, He Y, Pang H (2012b) Next-generation sequencing-based transcriptome analysis of Cryptolaemus montrouzieri under insecticide stress reveals resistance-relevant genes in ladybirds. Genomics 100(1): 35-41.
-
(2012)
Genomics
, vol.100
, Issue.1
, pp. 35-41
-
-
Zhang, Y.1
Jiang, R.2
Wu, H.3
Liu, P.4
Xie, J.5
He, Y.6
Pang, H.7
-
51
-
-
42249085227
-
What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?
-
Zhu X-G, Long SP, Ort DR (2008) What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Curr Opin Biotechnol 19(2): 153-159.
-
(2008)
Curr Opin Biotechnol
, vol.19
, Issue.2
, pp. 153-159
-
-
Zhu, X.-G.1
Long, S.P.2
Ort, D.R.3
-
52
-
-
77955169277
-
C4 rice-an ideal arena for systems biology research
-
Zhu X-G, Shan LL, Wang Y, Quick WP (2010) C4 rice-an ideal arena for systems biology research. J Integr Plant Biol 52(8): 762-770.
-
(2010)
J Integr Plant Biol
, vol.52
, Issue.8
, pp. 762-770
-
-
Zhu, X.-G.1
Shan, L.L.2
Wang, Y.3
Quick, W.P.4
|