期刊
BIOINFORMATICS
卷 31, 期 11, 页码 1796-1804出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu854
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资金
- Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy [DE-FG02-91ER20021]
- Center For Advanced Camelina Oils, Advanced Research Projects Agency - Energy, U.S. Department of Energy [DE-AR0000202, sub 21018-MI]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1458556] Funding Source: National Science Foundation
Motivation: Plant phenomics, the collection of large-scale plant phenotype data, is growing exponentially. The resources have become essential component of modern plant science. Such complex datasets are critical for understanding the mechanisms governing energy intake and storage in plants, and this is essential for improving crop productivity. However, a major issue facing these efforts is the determination of the quality of phenotypic data. Automated methods are needed to identify and characterize alterations caused by system errors, all of which are difficult to remove in the data collection step and distinguish them from more interesting cases of altered biological responses. Results: As a step towards solving this problem, we have developed a coarse-to-refined model called dynamic filter to identify abnormalities in plant photosynthesis phenotype data by comparing light responses of photosynthesis using a simplified kinetic model of photosynthesis. Dynamic filter employs an expectation-maximization process to adjust the kinetic model in coarse and refined regions to identify both abnormalities and biological outliers. The experimental results show that our algorithm can effectively identify most of the abnormalities in both real and synthetic datasets.
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