title: Plant photosynthesis phenomics data quality control.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Software available at www.msu.edu/%7Ejinchen/DynamicFilter .
authors.affiliation: Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Cruz
authors.affiliation: Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA.
authors.forename: Linda J
authors.initials: LJ
authors.lastname: Savage
authors.affiliation: Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Kramer
authors.affiliation: Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA Department of Computer Science and Engineering, Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, MI, East Lansing 48824, USA.
authors.forename: Jin
authors.initials: J
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D008954:Models, Biological; D010641:Phenotype; D010788:Photosynthesis; D010944:Plants / Q000378:metabolism*; D011786:Quality Control