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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2020)

Independent Component Analysis (ICA) is an unsupervised machine learning algorithm which models a complex multivariate dataset as a linear combination of statistically independent hidden factors. Applied to high-quality gene expression data from E. coli, it effectively reveals these hidden factors of the transcriptional regulatory network as sets of co-regulated genes and their corresponding activities across diverse growth conditions. The two main variables affecting the output of ICA are the data itself and the user-defined number of components to compute. In this study, a new method for effectively setting dimensionality is proposed which aims to maximize the number of biologically relevant components revealed while minimizing the potential for over-decomposition.

    Cover page: Independent Component Analysis in Alternate Dimensions – Parameter-free dimensionality selection for ICA of transcriptomic data
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2020)
    The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.
      Cover page: BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic treeCreative Commons 'BY' version 4.0 license
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