Toward the automated generation of genome-scale metabolic networks in the SEED. - Matthew DeJongh; Kevin Formsma; Paul Boillot; John Gould; Matthew Rycenga; Aaron A. Best (BMC Bioinform., 2007)

Gene set analyses for interpreting microarray experiments on prokaryotic organisms. - Nathan L. Tintle; Aaron A. Best; Matthew DeJongh; Dirk Van Bruggen; Fred Heffron; Steffen Porwollik; Ronald C. Taylor (BMC Bioinform., 2008)

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data. - Nathan L. Tintle; Alexandra Sitarik; Benjamin Boerema; Kylie Young; Aaron A. Best; Matthew DeJongh (BMC Bioinform., 2012)

Identification and Analysis of Bacterial Genomic Metabolic Signatures. - Nathan Bowerman; Nathan L. Tintle; Matthew DeJongh; Aaron A. Best (PSB, 2017)

Implementing and Evaluating A Gaussian Mixture Framework for Identifying Gene Function from TnSeq Data. - Kevin Li; Rachel Chen; William Lindsey; Aaron A. Best; Matthew DeJongh; Christopher S. Henry; Nathan L. Tintle (PSB, 2019)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)