selected publications
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article
- Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis. bioRxiv. 163097. 2017
- Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.. PLOS ONE. 7. 2012
- Light-regulated and cell-specific methylation of the maize PEPC promoter. Journal of Experimental Botany. 63:1381-1390. 2012
- Physiological and Proteomic Responses of Rice Peduncles to Drought Stress. Molecular Biotechnology. 48:173-182. 2011
- Characterization of statistical features for plant microRNA prediction. BMC Genomics. 12:108-108. 2011
- Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery. Nature Precedings. 1-1. 2010
- Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.. BMC Plant Biology. 10:16-16. 2010
- Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. Aob Plants. 2010. 2010
- 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
- Development of GCP Ontology for Sharing Crop Information. Nature Precedings. 4:1-1. 2009
- RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. Nucleic Acids Research. 37:996-1000. 2009
- The crop ontology. A referenced controlled vocabulary on crop trait information for maize, wheat, chickpea, sorghum, Musa, potato and rice 2009
- The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network. Rice. 1:177-187. 2008
- Revealing sequence variation patterns in rice with machine learning methods. BMC Bioinformatics. 9:1-3. 2008
- The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science. International Journal of Plant Genomics. 2008:369601-369601. 2008
- Development of a novel data mining tool to find cis -elements in rice gene promoter regions. BMC Plant Biology. 8:20-20. 2008
- The Generation Challenge Programme comparative plant stress-responsive gene catalogue. Nucleic Acids Research. 36:943-946. 2008
- The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research. 36:1028-1033. 2008
- Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research. 17:175-183. 2007
- Informatics Resources for Rice Functional Genomics 2007
- International crop information system for germplasm data management.. Methods of Molecular Biology. 406:459-471. 2007
- Generation Challenge Programme (GCP): standards for crop data.. Omics A Journal of Integrative Biology. 10:215-219. 2006
- Gene expression microarrays and their application in drought stress research.. Field Crops Research. 97:101-110. 2006
- Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes. Plant Physiology. 141:26-31. 2006
- Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering.. Plant Molecular Biology. 59:945-964. 2005
- The International Rice Information System. A Platform for Meta-Analysis of Rice Crop Data. Plant Physiology. 139:637-642. 2005
- Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics.. Plant Molecular Biology. 59:85-97. 2005
- The map-based sequence of the rice genome. Nature. 436:793-800. 2005
- Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map.. Journal of Zhejiang University-science B. 6:382-388. 2005
- Transposable element annotation of the rice genome. Bioinformatics. 20:155-160. 2004
- Linking genotype to phenotype: the International Rice Information System (IRIS).. Bioinformatics. 19:63-65. 2003
- Meeting review: plant bioinformatics at the NSF and NPGI (PAMGX satellite) meetings.. Comparative and Functional Genomics. 3:176-176. 2002
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document
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hide from search
- Guest Editor Preface. Bioinformatics. 139-139. 2004
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review
- Chapter 4 Informatics in Agricultural Research for Development. Advances in Agronomy. 135-157. 2009
- Improvement of drought resistance in rice.. Advances in Agronomy. 41-99. 2009