3 documents found, page 1 of 1
Improving automated model reconstruction across phylogenetically diverse genome...
Faria, José P.; Edirisinghe, Janaka N.; Seaver, Samuel M. D.; Liu, Filipe Alexandre Wang; Weisenhorn, Pamela; Jeffryes, James G.; Gu, Tian; Zhang, Qizh
Automated pathway curation and improving metabolic model reconstruction based o...
Edirisinghe, Janaka N.; Faria, J.; Liu, Filipe Alexandre Wang; Xavier, Joana Rute Calça; Seaver, Samuel; Weisenhorn, Pamela; Jeffryes, James; Gu, TianMetabolic models generated by automated reconstruction pipelines are widely used for high-throughput prediction of microbial phenotypes. However, the generation of accurate in-silico phenotype predictions based solely on genomic data continues to be a challenge as metabolic models often require extensive gapfilling in order to produce biomass. As a result, the true physiological profile of an organism can be al...
Computing and applying atomic regulons to understand gene expression and regula...
Faria, J.; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela; Olson, Robert D.; Stevens, Rick L.; Rocha, MiguelUnderstanding gene function and regulation is essential for the interpretation prediction and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets Atomic Regulons ARs represent fundamental units of function within a cell and...