Christophe Heinz Schilling

US Patent:

7803589, Sep 28, 2010

Filed:

Jan 22, 2009

Appl. No.:

12/358217

Inventors:

Mark J. Burk - San Diego CA, US
Christophe H. Schilling - San Diego CA, US
Anthony P. Burgard - Bellefonte PA, US
John D. Trawick - La Mesa CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

C12N 9/00
C12N 1/20

US Classification:

435183, 43525233

Abstract:

The invention provides a non-naturally occurring microbial organism having an acetyl-CoA pathway and the capability of utilizing syngas or syngas and methanol. In one embodiment, the invention provides a non-naturally occurring microorganism, comprising one or more exogenous proteins conferring to the microorganism a pathway to convert CO, COand/or Hto acetyl-coenzyme A (acetyl-CoA), methyl tetrahydrofolate (methyl-THF) or other desired products, wherein the microorganism lacks the ability to convert CO or COand Hto acetyl-CoA or methyl-THF in the absence of the one or more exogenous proteins. For example, the microbial organism can contain at least one exogenous nucleic acid encoding an enzyme or protein in an acetyl-CoA pathway. The microbial organism is capable of utilizing synthesis gases comprising CO, COand/or H, alone or in combination with methanol, to produce acetyl-CoA. The invention additionally provides a method for producing acetyl-CoA, for example, by culturing an acetyl-CoA producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an acetyl-CoA pathway enzyme or protein in a sufficient amount to produce acetyl-CoA, under conditions and for a sufficient period of time to produce acetyl-CoA.

US Patent:

7856317, Dec 21, 2010

Filed:

Jun 14, 2002

Appl. No.:

10/173547

Inventors:

Christophe H. Schilling - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

G01N 33/48

US Classification:

702 19

Abstract:

The invention provides a computer implemented process for constructing a scalable output network model of a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.

US Patent:

8026386, Sep 27, 2011

Filed:

Aug 8, 2008

Appl. No.:

12/188582

Inventors:

Mark J. Burk - San Diego CA, US
Priti Pharkya - San Diego CA, US
Stephen J. Van Dien - Encinitas CA, US
Anthony P. Burgard - Bellefonte PA, US
Christophe H. Schilling - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

C07C 67/00
C07C 69/52
C12P 7/40

US Classification:

560204, 562598, 435136

Abstract:

The invention provides a method of producing acrylic acid. The method includes contacting fumaric acid with a sufficient amount of ethylene in the presence of a cross-metathesis transformation catalyst to produce about two moles of acrylic acid per mole of fumaric acid. Also provided is an acrylate ester. The method includes contacting fumarate diester with a sufficient amount of ethylene in the presence of a cross-metathesis transformation catalyst to produce about two moles of acrylate ester per mole of fumarate diester. An integrated process for process for producing acrylic acid or acrylate ester is provided which couples bioproduction of fumaric acid with metathesis transformation. An acrylic acid and an acrylate ester production also is provided.

US Patent:

8229673, Jul 24, 2012

Filed:

Mar 27, 2003

Appl. No.:

10/402854

Inventors:

Imandokht Famili - San Diego CA, US
Markus W. Covert - San Diego CA, US
Christophe H. Schilling - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

G01N 33/50
G01N 33/48

US Classification:

702 19, 702 20

Abstract:

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 of reactants to a plurality of reactions, a constraint set for the plurality of reactions, and commands for determining a distribution of flux through the reactions that is predictive of a physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. A regulated reaction 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 silico model and methods for determining a physiological function using a model of the invention.

US Patent:

8301430, Oct 30, 2012

Filed:

Nov 16, 2010

Appl. No.:

12/947814

Inventors:

Christophe H. Schilling - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

G06G 7/58

US Classification:

703 11

Abstract:

The invention provides a computer implemented process for constructing a scalable output network model of a bioparticle. The process includes computer implemented steps of: (a) accessing a database of network gene components including an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) forming a data structure associating the network gene components with network reaction components, the data structure establishing a data set specifying a network model of connectivity and flow of the network reaction components, and (c) transforming the data set into a mathematical description of reactant fluxes defining the network model of connectivity and flow, wherein the mathematical description defines a scalable output network model of a bioparticle.

US Patent:

8323950, Dec 4, 2012

Filed:

May 12, 2011

Appl. No.:

13/106764

Inventors:

Mark J. Burk - San Diego CA, US
Christophe H. Schilling - San Diego CA, US
Anthony P. Burgard - Bellefonte PA, US
John D. Trawick - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

C12N 1/20
C12N 1/00
C12P 19/60
C12P 19/32
C12P 11/00
C12P 7/26
C12P 5/02
C07H 21/04

US Classification:

4352523, 435 75, 435 92, 435130, 435148, 435167, 435243, 536 232

Abstract:

The invention provides a non-naturally occurring microbial organism having an acetyl-CoA pathway and the capability of utilizing syngas or syngas and methanol. In one embodiment, the invention provides a non-naturally occurring microorganism, comprising one or more exogenous proteins conferring to the microorganism a pathway to convert CO, COand/or Hto acetyl-coenzyme A (acetyl-CoA), methyl tetrahydrofolate (methyl-THF) or other desired products, wherein the microorganism lacks the ability to convert CO or COand Hto acetyl-CoA or methyl-THF in the absence of the one or more exogenous proteins. For example, the microbial organism can contain at least one exogenous nucleic acid encoding an enzyme or protein in an acetyl-CoA pathway. The microbial organism is capable of utilizing synthesis gases comprising CO, COand/or H, alone or in combination with methanol, to produce acetyl-CoA. The invention additionally provides a method for producing acetyl-CoA, for example, by culturing an acetyl-CoA producing microbial organism, where the microbial organism expresses at least one exogenous nucleic acid encoding an acetyl-CoA pathway enzyme or protein in a sufficient amount to produce acetyl-CoA, under conditions and for a sufficient period of time to produce acetyl-CoA.

US Patent:

8455683, Jun 4, 2013

Filed:

Aug 26, 2011

Appl. No.:

13/219423

Inventors:

Mark J. Burk - San Diego CA, US
Priti Pharkya - San Diego CA, US
Stephen J. Van Dien - Encinitas CA, US
Anthony P. Burgard - Bellenfonte PA, US
Christophe H. Schilling - San Diego CA, US

Assignee:

Genomatica, Inc. - San Diego CA

International Classification:

C07C 57/04
C12P 7/40

US Classification:

562598, 435136

Abstract:

The invention provides a method of producing acrylic acid. The method includes contacting fumaric acid with a sufficient amount of ethylene in the presence of a cross-metathesis transformation catalyst to produce about two moles of acrylic acid per mole of fumaric acid. Also provided is an acrylate ester. The method includes contacting fumarate diester with a sufficient amount of ethylene in the presence of a cross-metathesis transformation catalyst to produce about two moles of acrylate ester per mole of fumarate diester. An integrated process for process for producing acrylic acid or acrylate ester is provided which couples bioproduction of fumaric acid with metathesis transformation. An acrylic acid and an acrylate ester production also is provided.

US Patent:

20030059792, Mar 27, 2003

Filed:

Mar 1, 2002

Appl. No.:

10/087441

Inventors:

Bernhard Palsson - La Jolla CA, US
Markus Covert - San Diego CA, US
Christophe Schilling - San Diego CA, US

International Classification:

C12Q001/68
G01N033/53
G06G007/48
G06G007/58
G06F019/00

US Classification:

435/006000, 435/007100, 702/019000, 702/020000, 703/011000

Abstract:

The invention provides a model of a reaction network integrated with regulatory controls related to the reactions. A method is provided for determining a systemic property of a reaction network using a model of the invention. Also provided is a method for modeling changes that occur in a reaction network at various time points due to regulatory events.