The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
SNP-Seek database of SNPs derived from 3000 rice genomes
Open accessAbstract
We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
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Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
Yield trends are insufficient to double global crop production by 2050
Ray, D. K., Mueller, N. D., West, P. C., & Foley, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066428 · Cited by 3,415
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., et al. (2013) · Rice · doi:10.1186/1939-8433-6-4 · Cited by 2,251
The genes of the Green Revolution
Hedden, P. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(02)00009-4 · Cited by 1,330
Genetic Engineering and Breeding of Drought-Resistant Crops
Hu, H., & Xiong, L. (2014) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-050213-040000 · Cited by 783
JBrowse: A next-generation genome browser
Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C. J., & Holmes, I. H. (2009) · Genome Research · doi:10.1101/gr.094607.109 · Cited by 717
Threat to future global food security from climate change and ozone air pollution
Tai, A. P. K., Martin, M. V., & Heald, C. L. (2014) · Nature Climate Change · doi:10.1038/nclimate2317 · Cited by 633
The 3,000 rice genomes project
The 3, 0. R. G. P. (2014) · Gigascience · doi:10.1186/2047-217x-3-7 · Cited by 480
BioJava: an open-source framework for bioinformatics
Holland, R. C. G., Down, T. A., Pocock, M., Prlić, A., Huen, D., James, K., Foisy, S., Dräger, A., Yates, A., Heuer, M., et al. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn397 · Cited by 273
Cited by
Genomic variation in 3,010 diverse accessions of Asian cultivated rice
Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., et al. (2018) · Nature · doi:10.1038/s41586-018-0063-9 · Cited by 1,748
Self-citationJBrowse: a dynamic web platform for genome visualization and analysis
Buels, R., Yao, E., Diesh, C. M., Hayes, R. D., Munoz-Torres, M., Helt, G., Goodstein, D. M., Elsik, C. G., Lewis, S. E., Stein, L., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0924-1 · Cited by 758
Past and Future Use of Wild Relatives in Crop Breeding
Dempewolf, H., Baute, G., Anderson, J., Kilian, B., Smith, C., & Guarino, L. (2017) · Crop Science · doi:10.2135/cropsci2016.10.0885 · Cited by 620
Caine, R. S., Yin, X., Sloan, J., Harrison, E. L., Mohammed, U., Fulton, T., Biswal, A. K., Dionora, J., Chater, C. C., Coe, R. A., et al. (2019) · New Phytologist · doi:10.1111/nph.15344 · Cited by 561
Genomic basis of geographical adaptation to soil nitrogen in rice
Liu, Y., Wang, H., Jiang, Z., Wang, W., Xu, R., Wang, Q., Zhang, Z., Li, A., Liang, Y., Ou, S., et al. (2021) · Nature · doi:10.1038/s41586-020-03091-w · Cited by 468
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Metadata
- Authors
- Alexandrov, N., Tai, S., Wang, W., Mansueto, L., Palis, K., Fuentes, R. R., Ulat, V. J., Chebotarov, D., Zhang, G., Li, Z., Mauleon, R., Hamilton, R. S., & McNally, K. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-11-27
- Volume
- 43
- Issue
- D1
- Pages
- D1023-D1027
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2043116503
- Cited by
- 364
- References
- 13
- FWCI
- 15.85
- Type
- journal article
- Language
- en
- Open access
- gold
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- Alexandrov, N., Tai, S., Wang, W., Mansueto, L., Palis, K., Fuentes, R. R., Ulat, V. J., Chebotarov, D., Zhang, G., Li, Z., Mauleon, R., Hamilton, R. S., & McNally, K. L. (2015). SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research. https://doi.org/10.1093/nar/gku1039
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