Intrexon Ceu, Inc.

University of California

Genomatica, Inc.

Imandokht Famili

Christophe H Schilling

Bernhard O Palsson

Jochen Förster

Jens Bredal Nielsen

Pengcheng Patrick Fu

Renata Usaite Black

Markus W Covert

Bornhard O Palsson

Jochen Forster

Pengcheng Fu

The invention relates to newly identified selectable marker systems, cells for use in a selectable marker system, and methods for using the selectable marker systems.

Methods of expressing products in mammalian cells

The invention provides models and methods useful for optimizing cell lines. The invention provides methods and computer readable medium or media containing such methods. Such a computer readable medium or media can comprise commands for carrying out a method of the invention. The methods of the invention can be utilized to model improved characteristics of a cell line, for example, improved product production, improved growth, improved culture characteristics, and the like.

Mammalian cell line models and related methods

Selectable markers and related methods

The invention provides a computer readable medium or media, having: (a) a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) a constraint set for said plurality of reactions for said first, second and third data structures, and (e) commands for determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells. The first, second and third data structures also can include a plurality of data structures. Additionally provided is a method for predicting a physiological function of a multicellular organism. The method includes: (a) providing a first data structure relating a plurality of reactants to a plurality of reactions from a first cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (b) providing a second data structure relating a plurality of reactants to a plurality of reactions from a second cell, each of said reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (c) providing a third data structure relating a plurality of intra-system reactants to a plurality of intra-system reactions between said first and second cells, each of said intra-system reactions comprising a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product; (d) providing a constraint set for said plurality of reactions for said first, second and third data structures; (e) providing an objective function, and (f) determining at least one flux distribution that minimizes or maximizes an objective function when said constraint set is applied to said first and second data structures, wherein said at least one flux distribution is predictive of a physiological function of said first and second cells.

Multicellular metabolic models and methods

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 invention provides an in silico model for determining aphysiological function. The model includes 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. The invention further provides methods for making an in silicomodel and methods for determining aphysiological function using a model of the invention.

[object Object]

Growing community of inventors

San Diego, CA, United States of America

Imandokht Famili