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Qiaoping Yuan
J. Craig Venter Institute
12Publications
10H-index
4,087Citations
Publications 12
Newest
Published on Aug 31, 2009in International Rice Research Notes
Shu Ouyang26
Estimated H-index: 26
,
Wei Zhu11
Estimated H-index: 11
+ 9 AuthorsBrian J. Haas62
Estimated H-index: 62
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Published on Oct 6, 2008in PLOS ONE 2.77
Ki-Hong Jung31
Estimated H-index: 31
(University of California, Davis),
Christopher Dardick15
Estimated H-index: 15
(West Virginia University)
+ 20 AuthorsQiaoping Yuan10
Estimated H-index: 10
(J. Craig Venter Institute)
Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the bio...
101 Citations Source Cite
Published on Jun 1, 2007
Shu Ouyang26
Estimated H-index: 26
,
Wei Zhu11
Estimated H-index: 11
+ 9 AuthorsBrian J. Haas62
Estimated H-index: 62
A high-quality finished sequence of the rice genome was completed in 2005. However, to maximally use the sequences, quality annotation of the genes and genome features is necessary. The process of annotation is iterative in nature and requires the application and refinement of computational tools coupled with manual curation and evalutation. We are funded by the U.S. National Science Foundation to annotate the rice genome and have constructed pseudomolecules for the 12 Oryza sativa subspecies ja...
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Published on Sep 27, 2005in BMC Biology 5.77
Nathalie Choisne16
Estimated H-index: 16
,
Nadia Demange2
Estimated H-index: 2
+ 96 AuthorsPatrick Wincker81
Estimated H-index: 81
Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. ...
136 Citations Source Cite
Published on Sep 1, 2005in Genome Research 10.10
C. Robin Buell66
Estimated H-index: 66
(J. Craig Venter Institute),
W. Richard McCombie58
Estimated H-index: 58
(Cold Spring Harbor Laboratory)
+ 69 AuthorsBrian J. Haas62
Estimated H-index: 62
(J. Craig Venter Institute)
Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (∼97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be as...
62 Citations Source Cite
Published on Aug 1, 2005in Nature 41.58
Takashi Matsumoto47
Estimated H-index: 47
,
Jianzhong Wu33
Estimated H-index: 33
+ 260 AuthorsTomoya Baba26
Estimated H-index: 26
Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of ...
2,568 Citations Source Cite
Published on May 1, 2005in Plant Physiology 5.95
Qiaoping Yuan10
Estimated H-index: 10
,
Shu Ouyang26
Estimated H-index: 26
+ 9 AuthorsFoo Cheung31
Estimated H-index: 31
We have developed a rice ( Oryza sativa ) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were id...
184 Citations Source Cite
C. Robin Buell66
Estimated H-index: 66
(J. Craig Venter Institute),
Vinita Joardar17
Estimated H-index: 17
(J. Craig Venter Institute)
+ 41 AuthorsJames F. Kolonay24
Estimated H-index: 24
(J. Craig Venter Institute)
We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virule...
689 Citations Source Cite
Published on Feb 1, 2003in Genetics 4.08
Kiyotaka Nagaki17
Estimated H-index: 17
(University of Wisconsin-Madison),
Junqi Song20
Estimated H-index: 20
(University of Wisconsin-Madison)
+ 9 AuthorsR. Kelly Dawe38
Estimated H-index: 38
(University of Georgia)
We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of ∼200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that w...
140 Citations
Published on Jan 1, 2003in Nucleic Acids Research 11.56
Qiaoping Yuan10
Estimated H-index: 10
,
Shu Ouyang26
Estimated H-index: 26
+ 6 AuthorsC. Robin Buell66
Estimated H-index: 66
Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two subspecies of rice, Oryza sativa spp. japonica and indica ssp. are publicly available. To provide the community with a resource to data-mine the rice genome, we have constructed an annotation resource for rice (http://www.tigr.org/tdb/e2k1/osa1/). In this resource, we have annotated the rice genome for gen...
130 Citations Source Cite
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