Publications

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

Integrative research about multiple biochemical subsystems has significant potential to help advance biology, bioengineering and medicine. However, it is difficult to obtain the diverse data needed for integrative research. To facilitate biochemical research, we developed Datanator, an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments. Currently, Datanator includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction rate constants about a broad range of organisms. Going forward, we aim to launch a community initiative to curate additional data. Datanator also provides tools for filtering, visualizing and exporting these data clouds. We believe that Datanator can facilitate a wide range of research from integrative mechanistic models, such as whole-cell models, to comparative data-driven analyses of multiple organisms.

BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
Salts and energy balance: A special role for dietary salts in metabolic syndrome