-
1
-
-
85016104570
-
The BIG Data Center: from deposition to integration to translation
-
BIG Data Center Members, The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res. 45 (2017), D18–D24.
-
(2017)
Nucleic Acids Res.
, vol.45
, pp. D18-D24
-
-
BIG Data Center Members1
-
2
-
-
84905049901
-
Trimmomatic: a flexible trimmer for Illumina sequence data
-
Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
3
-
-
84865147387
-
The rice oligonucleotide array database: an atlas of rice gene expression
-
Cao, P., Jung, K.H., Choi, D., Hwang, D., Zhu, J., Ronald, P.C., The rice oligonucleotide array database: an atlas of rice gene expression. Rice, 5, 2012, 17.
-
(2012)
Rice
, vol.5
, pp. 17
-
-
Cao, P.1
Jung, K.H.2
Choi, D.3
Hwang, D.4
Zhu, J.5
Ronald, P.C.6
-
4
-
-
79951574076
-
OryzaExpress: an integrated database of gene expression networks and omics annotations in rice
-
Hamada, K., Hongo, K., Suwabe, K., Shimizu, A., Nagayama, T., Abe, R., Kikuchi, S., Yamamoto, N., Fujii, T., Yokoyama, K., Tsuchida, H., Sano, K., Mochizuki, T., Oki, N., Horiuchi, Y., Fujita, M., Watanabe, M., Matsuoka, M., Kurata, N., Yano, K., OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol. 52 (2011), 220–229.
-
(2011)
Plant Cell Physiol.
, vol.52
, pp. 220-229
-
-
Hamada, K.1
Hongo, K.2
Suwabe, K.3
Shimizu, A.4
Nagayama, T.5
Abe, R.6
Kikuchi, S.7
Yamamoto, N.8
Fujii, T.9
Yokoyama, K.10
Tsuchida, H.11
Sano, K.12
Mochizuki, T.13
Oki, N.14
Horiuchi, Y.15
Fujita, M.16
Watanabe, M.17
Matsuoka, M.18
Kurata, N.19
Yano, K.20
more..
-
5
-
-
84979641065
-
Information Commons for rice (IC4R)
-
IC4R Project Consortium, Information Commons for rice (IC4R). Nucleic Acids Res. 44 (2016), D1172–D1180.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D1172-D1180
-
-
IC4R Project Consortium1
-
7
-
-
0030039128
-
Identification and characterization of a rice cysteine endopeptidase that digests glutelin
-
Kato, H., Minamikawa, T., Identification and characterization of a rice cysteine endopeptidase that digests glutelin. Eur. J. Biochem. 239 (1996), 310–316.
-
(1996)
Eur. J. Biochem.
, vol.239
, pp. 310-316
-
-
Kato, H.1
Minamikawa, T.2
-
8
-
-
84875134412
-
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
-
Kawahara, Y., de la Bastide, M., Hamilton, J.P., Kanamori, H., McCombie, W.R., Ouyang, S., Schwartz, D.C., Tanaka, T., Wu, J., Zhou, S., Childs, K.L., Davidson, R.M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S.S., Kim, J., Numa, H., Itoh, T., Buell, C.R., Matsumoto, T., Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6, 2013, 4.
-
(2013)
Rice
, vol.6
, pp. 4
-
-
Kawahara, Y.1
de la Bastide, M.2
Hamilton, J.P.3
Kanamori, H.4
McCombie, W.R.5
Ouyang, S.6
Schwartz, D.C.7
Tanaka, T.8
Wu, J.9
Zhou, S.10
Childs, K.L.11
Davidson, R.M.12
Lin, H.13
Quesada-Ocampo, L.14
Vaillancourt, B.15
Sakai, H.16
Lee, S.S.17
Kim, J.18
Numa, H.19
Itoh, T.20
Buell, C.R.21
Matsumoto, T.22
more..
-
9
-
-
84964875379
-
TENOR: database for comprehensive mRNA-Seq experiments in rice
-
Kawahara, Y., Oono, Y., Wakimoto, H., Ogata, J., Kanamori, H., Sasaki, H., Mori, S., Matsumoto, T., Itoh, T., TENOR: database for comprehensive mRNA-Seq experiments in rice. Plant Cell Physiol., 57, 2016, e7.
-
(2016)
Plant Cell Physiol.
, vol.57
, pp. e7
-
-
Kawahara, Y.1
Oono, Y.2
Wakimoto, H.3
Ogata, J.4
Kanamori, H.5
Sasaki, H.6
Mori, S.7
Matsumoto, T.8
Itoh, T.9
-
10
-
-
84926519013
-
HISAT: a fast spliced aligner with low memory requirements
-
Kim, D., Langmead, B., Salzberg, S.L., HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12 (2015), 357–360.
-
(2015)
Nat. Methods
, vol.12
, pp. 357-360
-
-
Kim, D.1
Langmead, B.2
Salzberg, S.L.3
-
11
-
-
33846101405
-
The TIGR rice genome annotation resource: improvements and new features
-
Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J., Buell, C.R., The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 35 (2007), D883–D887.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D883-D887
-
-
Ouyang, S.1
Zhu, W.2
Hamilton, J.3
Lin, H.4
Campbell, M.5
Childs, K.6
Thibaud-Nissen, F.7
Malek, R.L.8
Lee, Y.9
Zheng, L.10
Orvis, J.11
Haas, B.12
Wortman, J.13
Buell, C.R.14
-
12
-
-
84924377038
-
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
-
Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T., Salzberg, S.L., StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33 (2015), 290–295.
-
(2015)
Nat. Biotechnol.
, vol.33
, pp. 290-295
-
-
Pertea, M.1
Pertea, G.M.2
Antonescu, C.M.3
Chang, T.C.4
Mendell, J.T.5
Salzberg, S.L.6
-
13
-
-
84976878197
-
Expression Atlas update – an integrated database of gene and protein expression in humans, animals and plants
-
Petryszak, R., Keays, M., Tang, Y.A., Fonseca, N.A., Barrera, E., Burdett, T., Fullgrabe, A., Fuentes, A.M., Jupp, S., Koskinen, S., Mannion, O., Huerta, L., Megy, K., Snow, C., Williams, E., Barzine, M., Hastings, E., Weisser, H., Wright, J., Jaiswal, P., Huber, W., Choudhary, J., Parkinson, H.E., Brazma, A., Expression Atlas update – an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44 (2016), D746–D752.
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. D746-D752
-
-
Petryszak, R.1
Keays, M.2
Tang, Y.A.3
Fonseca, N.A.4
Barrera, E.5
Burdett, T.6
Fullgrabe, A.7
Fuentes, A.M.8
Jupp, S.9
Koskinen, S.10
Mannion, O.11
Huerta, L.12
Megy, K.13
Snow, C.14
Williams, E.15
Barzine, M.16
Hastings, E.17
Weisser, H.18
Wright, J.19
Jaiswal, P.20
Huber, W.21
Choudhary, J.22
Parkinson, H.E.23
Brazma, A.24
more..
-
14
-
-
84874236029
-
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics
-
Sakai, H., Lee, S.S., Tanaka, T., Numa, H., Kim, J., Kawahara, Y., Wakimoto, H., Yang, C.C., Iwamoto, M., Abe, T., Yamada, Y., Muto, A., Inokuchi, H., Ikemura, T., Matsumoto, T., Sasaki, T., Itoh, T., Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol., 54, 2013, e6.
-
(2013)
Plant Cell Physiol.
, vol.54
, pp. e6
-
-
Sakai, H.1
Lee, S.S.2
Tanaka, T.3
Numa, H.4
Kim, J.5
Kawahara, Y.6
Wakimoto, H.7
Yang, C.C.8
Iwamoto, M.9
Abe, T.10
Yamada, Y.11
Muto, A.12
Inokuchi, H.13
Ikemura, T.14
Matsumoto, T.15
Sasaki, T.16
Itoh, T.17
-
15
-
-
78651302194
-
RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions
-
Sato, Y., Antonio, B.A., Namiki, N., Takehisa, H., Minami, H., Kamatsuki, K., Sugimoto, K., Shimizu, Y., Hirochika, H., Nagamura, Y., RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res. 39 (2011), D1141–D1148.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D1141-D1148
-
-
Sato, Y.1
Antonio, B.A.2
Namiki, N.3
Takehisa, H.4
Minami, H.5
Kamatsuki, K.6
Sugimoto, K.7
Shimizu, Y.8
Hirochika, H.9
Nagamura, Y.10
-
16
-
-
69749083447
-
JBrowse: a next-generation genome browser
-
Skinner, M.E., Uzilov, A.V., Stein, L.D., Mungall, C.J., Holmes, I.H., JBrowse: a next-generation genome browser. Genome Res. 19 (2009), 1630–1638.
-
(2009)
Genome Res.
, vol.19
, pp. 1630-1638
-
-
Skinner, M.E.1
Uzilov, A.V.2
Stein, L.D.3
Mungall, C.J.4
Holmes, I.H.5
-
17
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart, J.M., Segal, E., Koller, D., Kim, S.K., A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (2003), 249–255.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
18
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D., Shmueli, O., Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21 (2005), 650–659.
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
Benjamin, H.2
Shmoish, M.3
Chalifa-Caspi, V.4
Shklar, M.5
Ophir, R.6
Bar-Even, A.7
Horn-Saban, S.8
Safran, M.9
Domany, E.10
Lancet, D.11
Shmueli, O.12
-
19
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia, H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L., Yang, H., A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296 (2002), 79–92.
-
(2002)
Science
, vol.296
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.4
Li, S.5
Liu, B.6
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
Cao, M.11
Liu, J.12
Sun, J.13
Tang, J.14
Chen, Y.15
Huang, X.16
Lin, W.17
Ye, C.18
Tong, W.19
Cong, L.20
Geng, J.21
Han, Y.22
Li, L.23
Li, W.24
Hu, G.25
Huang, X.26
Li, W.27
Li, J.28
Liu, Z.29
Li, L.30
Liu, J.31
Qi, Q.32
Liu, J.33
Li, L.34
Li, T.35
Wang, X.36
Lu, H.37
Wu, T.38
Zhu, M.39
Ni, P.40
Han, H.41
Dong, W.42
Ren, X.43
Feng, X.44
Cui, P.45
Li, X.46
Wang, H.47
Xu, X.48
Zhai, W.49
Xu, Z.50
Zhang, J.51
He, S.52
Zhang, J.53
Xu, J.54
Zhang, K.55
Zheng, X.56
Dong, J.57
Zeng, W.58
Tao, L.59
Ye, J.60
Tan, J.61
Ren, X.62
Chen, X.63
He, J.64
Liu, D.65
Tian, W.66
Tian, C.67
Xia, H.68
Bao, Q.69
Li, G.70
Gao, H.71
Cao, T.72
Wang, J.73
Zhao, W.74
Li, P.75
Chen, W.76
Wang, X.77
Zhang, Y.78
Hu, J.79
Wang, J.80
Liu, S.81
Yang, J.82
Zhang, G.83
Xiong, Y.84
Li, Z.85
Mao, L.86
Zhou, C.87
Zhu, Z.88
Chen, R.89
Hao, B.90
Zheng, W.91
Chen, S.92
Guo, W.93
Li, G.94
Liu, S.95
Tao, M.96
Wang, J.97
Zhu, L.98
Yuan, L.99
Yang, H.100
more..
-
20
-
-
52949138674
-
On the nature of human housekeeping genes
-
Zhu, J., He, F., Hu, S., Yu, J., On the nature of human housekeeping genes. Trends Genet. 24 (2008), 481–484.
-
(2008)
Trends Genet.
, vol.24
, pp. 481-484
-
-
Zhu, J.1
He, F.2
Hu, S.3
Yu, J.4
-
21
-
-
84943196407
-
MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data
-
Zou, D., Sun, S., Li, R., Liu, J., Zhang, J., Zhang, Z., MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. Nucleic Acids Res. 43 (2015), D54–D58.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D54-D58
-
-
Zou, D.1
Sun, S.2
Li, R.3
Liu, J.4
Zhang, J.5
Zhang, Z.6
|