Timothy B Gardner

US Patent:

6737269, May 18, 2004

Filed:

Jun 1, 2001

Appl. No.:

09/872338

Inventors:

Timothy Gardner - Jamaica Plain MA
James J. Collins - Newton Center MA

Assignee:

Boston University - Boston MA

International Classification:

C12N 1509

US Classification:

435325, 4352351, 4353201, 435 691, 435 6, 435440, 435455, 435471, 536 231, 536 241

Abstract:

Provided are methods and compositions for regulating gene expression in a cell. The invention provides recombinant multi-state genetic oscillators containing an adjustable-threshold genetic switch that is periodically activated by an oscillating amount of an activator agent. The activating agent is a gene product expressed from a promoter regulated by the adjustable-threshold switch and thus forms a feedback loop that causes periodic switching of the adjustable-threshold switch between an âonâ state and an âoffâ state. Multi-state genetic oscillators are useful to express one or more genes of interest in a periodic manner without requiring a periodic application of an external activating agent.

US Patent:

6828140, Dec 7, 2004

Filed:

Jun 1, 2001

Appl. No.:

09/872339

Inventors:

Timothy Gardner - Jamaica Plain MA
James J. Collins - Newton Center MA

Assignee:

Cellicon Technologies, Inc. - Boston MA

International Classification:

C12N 120

US Classification:

4352523, 435 6, 435 691, 4352351, 4353201, 435325, 435440, 435455, 435471, 536 231, 536 241

Abstract:

Provided are methods and compositions for regulating gene expression in a cell. The invention provides recombinant adjustable-threshold switches which contain a first inducible promoter-regulatory gene operon and a second constitutive promoter-regulatory gene operon. A threshold amount of activating agent is required to switch the inducible promoter âonâ and the constitutive promoter âoffâ. An adjustable-threshold switch is useful to reversibly switch the expression of a gene of interest between a stable âonâ state and stable âoffâ state in response to an activating agent at or above a threshold concentration.

US Patent:

6841376, Jan 11, 2005

Filed:

May 1, 2001

Appl. No.:

09/872868

Inventors:

Timothy Gardner - Jamaica Plain MA, US
James J. Collins - Newton Center MA, US

Assignee:

Cellicon Technologies, Inc. - Boston MA

International Classification:

C12N 120
C12N 1500
C12N 1509
C12N 1586
C07H 2104

US Classification:

4352523, 435325, 435 6, 4353201, 4352351, 435455, 435471, 435440, 536 231, 536 241

Abstract:

Provided are methods and compositions for regulating gene expression in a cell. The invention provides recombinant genetic toggle switches which contain a first constitutive promoter-regulatory gene operon and a second constitutive promoter-regulatory gene operon. Expression of the regulatory gene from the first operon inhibits expression from the promoter in the second operon, and expression of the regulatory gene from the second operon inhibits expression from the promoter in the first operon. By use of the toggle switch and various switching agents it is possible to reversibly switch the expression of a gene of interest between a stable “on” state and stable “off” state or vice versa via transient exposure to a switching agent.

US Patent:

8306752, Nov 6, 2012

Filed:

Nov 17, 2008

Appl. No.:

12/271944

Inventors:

Timothy S. Gardner - Needham MA, US
James J. Collins - Newton MA, US
Boris Hayete - Arlington MA, US
Jeremiah Faith - Boston MA, US

Assignee:

Trustees of Boston University - Boston MA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 707700, 435 61

Abstract:

The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.

US Patent:

20060293873, Dec 28, 2006

Filed:

Mar 5, 2003

Appl. No.:

10/506734

Inventors:

Timothy Gardner - Needham MA, US
James Collins - Newton MA, US
Diego di Bernardo - Naples, IT
Jesper Tegner - Stockholm, SE
Man Yeung - Logan UT, US

Assignee:

Trustees of Boston University - Boston MA

International Classification:

G06G 7/48
G06G 7/58

US Classification:

703011000

Abstract:

The present invention provides methods and accompanying computer-based systems and computer-executable code stored on a computer-readable medium for constructing a model of a biological network. The invention further provides methods for performing sensitivity analysis on a biological network and for identifying major regulators of species in the network and of the network as a whole. In addition, the invention provides methods for identifying targets of a perturbation such as that resulting from exposure to a compound or an environmental change. The invention further provides methods for identifying phenotypic mediators that contribute to differences in phenotypes of biological systems.

US Patent:

20070016390, Jan 18, 2007

Filed:

Jul 5, 2005

Appl. No.:

11/174989

Inventors:

Diego Bernardo - Naples, IT
James Collins - Newton MA, US
Timothy Gardner - Needham MA, US
Michael Thompson - San Diego CA, US

International Classification:

G06G 7/48
G06G 7/58

US Classification:

703011000

Abstract:

The present invention provides methods and accompanying computer-based systems and computer-executable code stored on a computer-readable medium for constructing a model of a biological network. The invention further provides methods for performing sensitivity analysis on a biological network and for identifying major regulators of species in the network and of the network as a whole. In addition, the invention provides methods for identifying targets of a perturbation such as that resulting from exposure to a compound or an environmental change. The invention further provides methods for identifying phenotypic mediators that contribute to differences in phenotypes of biological systems.

US Patent:

20100234348, Sep 16, 2010

Filed:

Aug 2, 2007

Appl. No.:

12/376288

Inventors:

Guillaume Cottarel - Mountain View CA, US
Timothy S. Gardner - Needham MA, US
Xiaoguang Lei - Beijing, CN
John Porco - Jamaica Plain MA, US
Scott E. Schaus - Boston MA, US
Jamey Wierzbowski - Stoneham MA, US
Kollol Pal - Needham MA, US

Assignee:

TRUSTEES OF BOSTON UNIVERSITY - Boston MA

International Classification:

A61K 31/4035
C07D 405/08
C07D 487/04
C07D 498/06
C07C 69/00
C07D 231/56
A61K 31/5025
A61K 31/553
A61K 31/22
A61K 31/416
C12Q 1/18
C12Q 1/68
A61P 31/00

US Classification:

51421108, 548454, 544236, 540545, 560257, 5483625, 514414, 514248, 514546, 514403, 435 32, 435 6

Abstract:

The present invention provides compounds that potentiate the activity of antibiotic agents, particularly quinolones such as norflaxin. The invention further provides compositions, e.g., pharmaceutical compositions, comprising the inventive compounds. The invention also provides compositions comprising an antibiotic (e.g., a quinolone) and a compound that potentiates activity of the antibiotic. The invention further provides methods of treating a subject comprising administering any of the inventive compounds or compositions to the subject. The invention also provides screening methods to identify compounds that potentiate the activity of an antibiotic, e.g., a quinolone.

US Patent:

20130060543, Mar 7, 2013

Filed:

Oct 19, 2012

Appl. No.:

13/655737

Inventors:

Diego di Bernardo - Naples, IT
James J. Collins - Newton Centre MA, US
Timothy Gardner - Needham MA, US
Michael J. Thompson - San Diego CA, US

Assignee:

TRUSTEES OF BOSTON UNIVERSITY - Boston MA

International Classification:

G06F 17/10

US Classification:

703 2

Abstract:

The present invention provides methods and accompanying computer-based systems and computer-executable code stored on a computer-readable medium for constructing a model of a biological network. The invention further provides methods for performing sensitivity analysis on a biological network and for identifying major regulators of species in the network and of the network as a whole. In addition, the invention provides methods for identifying targets of a perturbation such as that resulting from exposure to a compound or an environmental change. The invention further provides methods for identifying phenotypic mediators that contribute to differences in phenotypes of biological systems.