selected publications
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article
- From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives. Crop Science. 61:1-1566. 2021
- Phenotypic response of farmer‐selected CWR‐derived rice lines to salt stress in the Mekong Delta. Crop Science. 61:201-218. 2021
- Machine Learning Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication. bioRxiv. 829168. 2020
- A platinum standard pan-genome resource that represents the population structure of Asian rice. Scientific Data. 7:113. 2020
- Genetic erosion in traditional rice agro-ecosystems in Southern Philippines: drivers and consequences. PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION. 18:1-10. 2020
- Multiple streams of genetic diversity in Japonica rice. bioRxiv. 2020
- Advanced Strategic Research to Promote the Use of Rice Genetic Resources. AGRONOMY-BASEL. 10. 2020
- Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0.. Plant Biotechnology Journal. 18:14-16. 2020
- Upland Rice: Cultural Keystone Species in a Philippine Traditions Agroecosystem. ASIAN JOURNAL OF AGRICULTURE AND DEVELOPMENT. 17:93-104. 2020
- Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice. bioRxiv. 2019
- Variation in seed longevity among diverse Indica rice varieties.. Annals of Botany. 124:447-460. 2019
- Predicting agronomic traits and associated genomic regions in diverse rice landraces using marker stability. bioRxiv. 805002. 2019
- Fine Scale Genomic Signals of Admixture and Alien Introgression Among Asian Rice Landraces. Genome Biology and Evolution. 11:1358-1373. 2019
- Leaf morphology, rather than plant water status, underlies genetic variation of rice leaf rolling under drought.. Plant Cell and Environment. 42:1532-1544. 2019
- Structural variants in 3000 rice genomes.. Genome Research. 29:870-880. 2019
- Genetic diversity, linkage disequilibrium, and population structure in a panel of Brazilian rice accessions.. Journal of Applied Genetics. 60:27-31. 2019
- Traditional agro-ecosystems in Southern Philippines Vulnerabilities, threats and interventions. INTERNATIONAL JOURNAL OF DISASTER RESILIENCE IN THE BUILT ENVIRONMENT. 10:289-300. 2019
- Genome Wide Association mapping of grain and straw biomass traits in the rice Bengal and Assam Aus Panel (BAAP) grown under alternate wetting and drying and permanently flooded irrigation. Frontiers in Plant Science. 9:1223. 2018
- An imputation platform to enhance integration of rice genetic resources.. Nature Communications. 9:3519. 2018
- Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 557:43-+. 2018
- Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.. Nature Genetics. 50:1618-1618. 2018
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.. Nature Genetics. 50:285-+. 2018
- Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions.. Frontiers in Plant Science. 8:1763-1763. 2017
- Genetic diversity patterns in ex situ collections of Oryza officinalis Wall. ex G. Watt revealed by morphological and microsatellite markers. Genetic Resources and Crop Evolution. 64:733-744. 2017
- Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice.. Scientific Reports. 7:42839-42839. 2017
- Rice SNP-seek database update: new SNPs, indels, and queries.. Nucleic Acids Research. 45:D1075-D1081. 2017
- SNP-Seek II: A resource for allele mining and analysis of big genomic data in Oryza sativa ☆. Current Plant Biology. 7:16-25. 2016
- Nucleotide diversity analysis highlights functionally important genomic regions.. Scientific Reports. 6:35730-35730. 2016
- Open access resources for genome-wide association mapping in rice.. Nature Communications. 7:10532-10532. 2016
- Identification of stable QTLs causing chalk in rice grains in nine environments. Theoretical and Applied Genetics. 129:141-153. 2016
- Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal.. Rice. 8:35-35. 2015
- Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems. PLOS ONE. 10:124127. 2015
- Rice functional genomics and breeding database (RFGB)-3K-rice SNP and InDel sub-database. Chinese Science Bulletin. 60:367-371. 2015
- SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Research. 43:1023-1027. 2015
- Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment, Tissue Type, and Genotype. Bioenergy Research. 8:1165-1182. 2015
- Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon.. Ecology and Evolution. 3:3047-3062. 2013
- Screening of rice Genebank germplasm for yield and selection of new drought tolerance donors. Field Crops Research. 147:12-22. 2013
- Crossability patterns within and among Oryza series Sativae species from Asia and Australia. Genetic Resources and Crop Evolution. 60:1899-1914. 2013
- ECOGEOGRAPHIC VARIATION IN THE MORPHOLOGY OF TWO ASIAN WILD RICE SPECIES, ORYZA NIVARA AND ORYZA RUFIPOGON. International Journal of Plant Sciences. 174:896-909. 2013
- New allelic variants found in key rice salt-tolerance genes: an association study.. Plant Biotechnology Journal. 11:87-100. 2013
- Developmental Dynamics and Early Growth Vigour in Rice. I. Relationship Between Development Rate (1/Phyllochron) and Growth. Journal of Agronomy and Crop Science. 198:374-384. 2012
- High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875-886. 2012
- Genomics of gene banks: A case study in rice. American Journal of Botany. 99:407-423. 2012
- Omics Technologies to Tap Genetic Variation for Rice Improvement. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL. 48:4-4. 2012
- Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields. Field Crops Research. 120:205-214. 2011
- Identification of SUB1A alleles from wild rice Oryza rufipogon Griff.. Genetic Resources and Crop Evolution. 58:1237-1242. 2011
- Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties. Plant Physiology. 155:157-168. 2011
- Use of EcoTILLING to identify natural allelic variants of rice candidate genes involved in salinity tolerance. PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION. 9:300-304. 2011
- Migration, isolation and hybridization in island crop populations: the case of Madagascar rice.. Molecular Ecology. 19:4892-4905. 2010
- Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery. Nature Precedings. 1-1. 2010
- Development of a Research Platform for Dissecting Phenotype–Genotype Associations in Rice ( Oryza spp.). Rice. 3:205-217. 2010
- Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives. Theoretical and Applied Genetics. 121:769-787. 2010
- Development of a Core Set from a Large Rice Collection using a Modified Heuristic Algorithm to Retain Maximum Diversity. Journal of Integrative Plant Biology. 51:1116-1125. 2009
- Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species. Plant Science. 177:460-467. 2009
- Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America. 106:12273-12278. 2009
- Revealing sequence variation patterns in rice with machine learning methods. BMC Bioinformatics. 9:1-3. 2008
- Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations. International Journal of Plant Genomics. 2008:524847-524847. 2008
- Rapid method for detecting SNPs on agarose gels and its application in candidate gene mapping.. Molecular Breeding. 19:87-101. 2007
- Chemical- and Irradiation-Induced Mutants and TILLING 2007
- A High-throughput Genomic Tool: Diversity Array Technology Complementary for Rice Genotyping. Journal of Integrative Plant Biology. 48:1069-1076. 2006
- Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes. Plant Physiology. 141:26-31. 2006
- Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display.. Genes & Genetic Systems. 81:93-101. 2006
- Fertility in an interspecific rice population and its effect on selection for rhizome length. Field Crops Research. 95:30-38. 2006
- A Model Crop Species: Molecular Markers in Rice 2004
- Linking genotype to phenotype: the International Rice Information System (IRIS).. Bioinformatics. 19:63-65. 2003
- Convergent evolution of perenniality in rice and sorghum.. Proceedings of the National Academy of Sciences of the United States of America. 100:4050-4054. 2003
- Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theoretical and Applied Genetics. 103:75-83. 2001
- Genetic composition and complexity of virus populations at tungro-endemic and outbreak rice sites.. Archives of Virology. 145:2643-2657. 2000
- Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia.. Archives of Virology. 145:1183-1197. 2000
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dataset
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document
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review
- Progress in single-access information systems for wheat and rice crop improvement.. Briefings in Bioinformatics. 565-571. 2019
- Allele mining and enhanced genetic recombination for rice breeding.. Rice. 1-11. 2015
- Alternate wetting and drying irrigation for rice in Bangladesh: Is it sustainable and has plant breeding something to offer?. Food and Energy Security. 120-129. 2013
- Drought Resistance Improvement in Rice: An Integrated Genetic and Resource Management Strategy. Plant Production Science. 1-14. 2011
- Improvement of drought resistance in rice.. Advances in Agronomy. 41-99. 2009