Improvements to the GDB Human Genome Data Base. - Kenneth H. Fasman; Stanley Letovsky; Robert W. Cottingham; David T. Kingsbury (Nucleic Acids Res., 1996)

The GDB Human Genome Database Anno 1997. - Kenneth H. Fasman; Stanley Letovsky; Peter W. D. Li; Robert W. Cottingham; David T. Kingsbury (Nucleic Acids Res., 1997)

GDB: the Human Genome Database. - Stanley Letovsky; Robert W. Cottingham; Christopher J. Porter; Peter W. D. Li (Nucleic Acids Res., 1998)

Mouse-human Comparative Map Resources on the Web. - Beth K. Gatewood; Robert W. Cottingham (Briefings Bioinform., 2000)

Next generation models for storage and representation of microbial biological annotation. - Daniel Quest; Miriam L. Land; Thomas S. Brettin; Robert W. Cottingham (BMC Bioinform., 2010)

Scenario driven data modelling: a method for integrating diverse sources of data and data streams. - Shelton D. Griffith; Daniel Quest; Thomas S. Brettin; Robert W. Cottingham (BMC Bioinform., 2011)

The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function. - Robert W. Cottingham (BCB, 2014)

Navigating the maze: the impact of configurability in bioinformatics software. - Mikaela Cashman; Myra B. Cohen; Priya Ranjan; Robert W. Cottingham (ASE, 2018)

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)

CORE: Comparable, Open, Reliable, Extensible Software: An Experience Report of Four Flux Balance Analysis Tools. - Alexis L. Marsh; Myra B. Cohen; Robert W. Cottingham (BCB, 2023)

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software. - Alexis L. Marsh; Myra B. Cohen; Robert W. Cottingham (ICST, 2025)