Adam’s research expertise is in the technologies of adaptive laboratory evolution and constraint-based reconstruction and modeling and has focused his current research towards the fields of metabolic engineering, antimicrobial resistance, and discovery of unknown genetic content in microorganisms.
Adam’s current efforts are focused on generating a full technology platform (laboratory automation, bioinformatics, workflows, and databasing) around the use and application of adaptive laboratory evolution for strain development and discovery. This technology platform is being applied for Joint BioEnergy Institute projects to provide a unique and efficient tool for various strain design issues (e.g., strain tolerance, substrate utilization, and strain robustness).
- Application of an Adaptive Laboratory Evolution for strain construction and discovery
- “Enzyme promiscuity shapes adaptation to novel growth substrates,” Molecular Systems Biology (2019)
- “Reframing gene essentiality in terms of adaptive flexibility,” BMC Systems Biology (2018)
- “ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation,” Nucleic Acids Research (2018)
- “Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System,” Metabolic Engineering (2018)
- “Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies,” Applied & Environmental Microbiology (2017)
- “A Model for Designing Adaptive Laboratory Evolution Experiments,” Applied & Environmental Microbiology (2017)
- “Model-driven discovery of underground metabolic functions in Escherichia coli,” Proceedings of the National Academy of Sciences U S A (2015)
- “Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution,” Applied and Environmental Biology (2015)
- “Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path,” Metabolic Engineering (2014)