Stephen Merrill Friend

US Patent:

6673536, Jan 6, 2004

Filed:

Sep 29, 1999

Appl. No.:

09/408582

Inventors:

Roland Stoughton - San Diego CA
Julja Burchard - Kirkland WA
Stephen H. Friend - Seattle WA

Assignee:

Rosetta Inpharmatics LLC. - Kirkland WA

International Classification:

C12Q 168

US Classification:

435 6, 435 911, 435 912, 536 231, 536 243

Abstract:

The present invention provides methods and systems, particularly computer systems, for determining the relative specificity with which a particular polynucleotide molecule hybridizes to a polynucleotide probe. For example, the methods and systems of the invention enable a user to compare the specificity with which different polynucleotides hybridize to a given probe and/or rank these polynucleotides according to their specificity to that probe. The methods and systems of the invention also enable a user to compare the specificity with which a particular polynucleotide hybridizes to different probes, and/or rank those different probes according to their specificity for that particular polynucleotide.

US Patent:

6859735, Feb 22, 2005

Filed:

Aug 13, 1999

Appl. No.:

09/374565

Inventors:

Roland Stoughton - San Diego CA, US
Stephen H. Friend - Seattle WA, US

Assignee:

Rosetta Inpharmatics LLC - Seattle WA

International Classification:

G01N033/48
G01N033/53
C12Q001/68
C12P021/06
G06G007/48

US Classification:

702 19, 435 6, 435 71, 435 691, 703 11

Abstract:

The present invention provides methods and computer systems for identifying and representing the biological pathways of drug action on a cell The present invention also provides methods and computer systems for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. The present invention also provides methods and computer systems for drug development based on the methods for identifying biological pathways of drug action, and methods and computer systems for representing the biological pathways involved in the effect of an environmental change upon a cell.

US Patent:

59653523, Oct 12, 1999

Filed:

May 8, 1998

Appl. No.:

9/074983

Inventors:

Roland Stoughton - San Diego CA
Stephen H. Friend - Seattle WA

Assignee:

Rosetta Inpharmatics, Inc. - Kirkland WA

International Classification:

C12Q 100
G01N 3353
G06F 1714
C12N 1500

US Classification:

435 4

Abstract:

The present invention provides methods for identifying and representing the biological pathways of drug action on a cell by: (i) measuring responses of cellular constituents to graded exposures of the cell to a drug of interest; (ii) measuring the responses of cellular constituents to perturbations in one or more biological pathways of the cell; and (iii) scaling a combination of the measured pathway responses to fit the measured drug responses best according to an objective measure. In alternative embodiments, the present invention also provides for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. In various embodiments, the effects on the cell can be determined by measuring gene expression, protein abundances, protein activities, or a combination of such measurements. In various embodiments, perturbation to a biological pathway in the cell can be made by use of titratable expression systems, use of transfection systems, modification to abundances of pathway RNAs, modifications to abundances of pathway proteins, or modifications to activities of the pathway proteins.

US Patent:

20190032139, Jan 31, 2019

Filed:

Sep 25, 2018

Appl. No.:

16/141076

Inventors:

- Oakland CA, US
- Seattle WA, US
Trey Ideker - La Jolla CA, US
Stephen H. Friend - Seattle WA, US
Justin Guinney - Seattle WA, US

International Classification:

C12Q 1/6883
C12Q 1/6881
G01N 33/53
G01N 33/574

Abstract:

The invention provides for methods for predicting age of a subject based on the epigenome of the subject.

US Patent:

20150259742, Sep 17, 2015

Filed:

Nov 12, 2013

Appl. No.:

14/442089

Inventors:

- Oakland CA, US
- Seattle WA, US
Trey Ideker - La Jolla CA, US
Stephen H. Friend - Seattle WA, US
Justin Guinney - Seattle WA, US

International Classification:

C12Q 1/68

Abstract:

The invention provides for methods for predicting age of a subject based on the epigenome of the subject.