University of California

Genomatica, Inc.

Markus W Covert

Bernhard O Palsson

Markus Herrgard

Christophe H Schilling

Imandokht Famili

Bornhard O Palsson

The invention provides in silico models for determining the physiological function of human cells, including human skeletal muscle cells. The models include a data structure relating a plurality ofreactants to a plurality ofreactions, a constraint set for the plurality ofreactions, and commands for determining a distribution of flux through the reactions that is predictive of aphysiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulatedreaction can be represented in a model of the invention by including a variable constraint for the regulated reaction. The invention further provides methods for making an in silicomodel and methods for determining aphysiological function using a model of the invention.

Human metabolic models and methods

The present invention provides a method of refining a biosystem reaction network. The method consists of: (a) providing a mathematical representation of a biosystem; (b) reconciling said mathematical representation of said biosystem; (c) determining differences between observed behavior of a biosystem and in silico behavior of said mathematical representation of said biosystem under similar conditions; (d) modifying a structure of said mathematical representation of said biosystem, and (e) determining differences between said observed behavior of said biosystem and in silico behavior of said modified mathematical representation of said biosystem under similar conditions.

Methods and systems to identify operational reaction pathways

The present invention provides a method for identifying an operational reaction pathway of a biosystem. The method includes (a) providing a set of systemic reaction pathways through a reaction network representing said biosystem; (b) providing a set of phenomenological reaction pathways of said biosystem, and (c) comparing said set of systemic reaction pathways with said set of phenomenological reaction pathways, wherein a pathway common to said sets is an perational reaction pathway of said biosystem. Also described is a method of refining a biosystem reaction network; a method of reconciling biosystem data sets; a method of determining the effect of a genetic polymorphism on whole cell function; and a method of diagnosing a genetic polymorphism-mediated pathology.

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San Diego, CA, United States of America

Markus W Covert