Vikas Upadhyay

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

The paper introduces iCloudBiofoundry, a cloud platform that autonomously designs, executes, and iteratively improves biological experiments using AI-driven workflows.

MechFind predicts enzyme mechanisms from reaction stoichiometry, achieving 72% accuracy on a training set and generating 18,000 novel hypotheses across 28,412 reactions.

novoSstoic2.0 streamlines pathway design by integrating stoichiometry, thermodynamics, and enzyme selection to identify efficient bioproduct synthesis routes.

dGPredictor improves thermodynamic analysis of metabolic reactions by incorporating stereochemistry and enables accurate prediction of free energy changes for novel reactions and pathway design.