John G Sheehan

US Patent:

6898531, May 24, 2005

Filed:

Jan 9, 2002

Appl. No.:

10/042406

Inventors:

John B. Sheehan - Mountain View CA, US
Daryl J. Thomas - Menlo Park CA, US
Wade A. Barrett - Santa Clara CA, US

Assignee:

Perlegen Sciences, Inc. - Mountain View CA

International Classification:

G01N033/48
G06F019/00
C12Q001/68

US Classification:

702 19, 702 20, 435 6

Abstract:

The presently claimed invention provides methods for amplifying a DNA target sequence. One embodiment of the present invention provides robust methods for amplification of target sequences. In a first aspect of the invention, a method for designing primer pairs for the amplification reaction is provided. In a further aspect of the invention, reagents and cycling parameters for the amplification reaction are provided.

US Patent:

6963805, Nov 8, 2005

Filed:

Oct 5, 2001

Appl. No.:

09/972595

Inventors:

Kelly A. Frazer - San Mateo CA, US
Nila Patil - Woodside CA, US
John Sheehan - Mountain View CA, US

Assignee:

Perlegen Sciences, Inc. - Mountain View CA

International Classification:

G01N033/48
G01N033/50
G06F019/00

US Classification:

702 20, 702 19, 435 6

Abstract:

The present invention provides methods for determining sequence similarity (conserved sequences) between nucleic acids from a first organism and nucleic acids from a second, different organism without having to know a priori the nucleic acid sequence from the second, different organism. The first nucleic acid can be from any organism where the sequence of the nucleic acid is known and the second nucleic acid can be from any organism. The method involves determining which bases from the second nucleic acid are identical to the first nucleic acid, and allows one to determine the sequence of portions of the second nucleic acid. The invention is useful for identifying putative functional regions or putative organism-sequences in a genome.

US Patent:

D537137, Feb 20, 2007

Filed:

Jun 20, 2005

Appl. No.:

29/232479

Inventors:

John Sheehan - Westmont NJ, US

International Classification:

2102

US Classification:

D21746

US Patent:

7334672, Feb 26, 2008

Filed:

Aug 14, 2006

Appl. No.:

11/503743

Inventors:

John R. Sheehan - Jamison PA, US
Paul J. Gandolfo - Doylestown PA, US
Lou Filo - Hatfield PA, US

Assignee:

Motor Drives & Controls, Inc. - Hatfiled PA

International Classification:

B66B 25/00

US Classification:

198323, 198325

Abstract:

A combplate closes the terminal ends of a continuous belt transport system having grooved carrier plates. The combplate has a plurality of protrusions and a communications board. The plurality of spaced apart projections are located along the one lateral edge with a portion thereof extending forward of the one lateral edge, shaped to align with and pass between the carrier plate grooves, and provided with a detector that senses a break in its integrity and a circuit for communicating its status externally. The communications board is in electrical contact with each of the projections for repeatedly monitoring the status of each projection to detect a break in a projection's integrity.

US Patent:

20030108919, Jun 12, 2003

Filed:

Sep 5, 2002

Appl. No.:

10/236480

Inventors:

Curtis Kautzer - San Jose CA, US
Nila Patil - Woodside CA, US
Coleen Hacker - San Carlos CA, US
David McDonough - Cupertino CA, US
Daryl Thomas - Menlo park CA, US
Wade Barrett - Santa Clara CA, US
John Sheehan - Mountain View CA, US

Assignee:

Perlegen Sciences, Inc.

International Classification:

C12Q001/68
G06G007/48
G06G007/58
G06F019/00
G01N033/48
G01N033/50
C12P019/34

US Classification:

435/006000, 435/091200, 702/020000, 703/011000

Abstract:

The presently claimed invention provides methods for amplifying a DNA target sequence. One embodiment of the present invention provides robust methods for amplification of target sequences. In a first aspect of the invention, a method for selecting primer pairs for the amplification reaction is provided. In a further aspect of the invention, reagents and cycling parameters for the amplification reaction are provided.

US Patent:

20030119015, Jun 26, 2003

Filed:

May 8, 2002

Appl. No.:

10/142364

Inventors:

Kelly Frazer - San Mateo CA, US
Nila Patil - Woodside CA, US
John Sheehan - Mountain View CA, US

Assignee:

Perlegen Sciences, Inc.

International Classification:

C12Q001/68
G06F019/00
G01N033/48
G01N033/50
C12P019/34

US Classification:

435/006000, 702/020000, 435/091200

Abstract:

The present invention provides methods for determining sequence similarity (conserved sequences) between nucleic acids from a first organism and nucleic acids from a second, different organism without having to know a priori the nucleic acid sequence from the second, different organism. The first nucleic acid can be from any organism where the sequence of the nucleic acid is known and the second nucleic acid can be from any organism. The method involves determining which bases from the second nucleic acid are identical to the first nucleic acid, and allows one to determine the sequence of portions of the second nucleic acid. The invention is useful for identifying putative functional regions or putative organism-sequences in a genome.

US Patent:

20050019787, Jan 27, 2005

Filed:

Jan 30, 2004

Appl. No.:

10/768788

Inventors:

Anthony Berno - San Jose CA, US
Karel Konvicka - Palo Alto CA, US
David Hinds - Mountain View CA, US
Nila Patil - Woodside CA, US
Naiping Shen - Saratoga CA, US
David Stern - Mountain View CA, US
John Sheehan - Mountain View CA, US

Assignee:

Perlegen Sciences, Inc., a Delaware Corporation - Mountain View CA

International Classification:

C12Q001/68
G06F019/00
G01N033/48
G01N033/50

US Classification:

435006000, 702020000

Abstract:

Computer-implemented methods, data processing apparatus and computer program codes for characterizing an interrogation position, such as a SNP position, in a nucleic acid sequence are provided herein. Computer-implemented methods involving various statistical analyses are provided for characterizing an interrogation position as being associated with a phenotypic trait of interest.

US Patent:

20060183132, Aug 17, 2006

Filed:

Feb 14, 2005

Appl. No.:

11/058432

Inventors:

Glenn Fu - Dublin CA, US
Laura Stuve - San Jose CA, US
John Sheehan - Mountain View CA, US
Amy Ollmann - Redwood City CA, US
Naiping Shen - Saratoga CA, US
Andrew Sparks - Saratoga CA, US
Dennis Ballinger - Menlo Park CA, US

Assignee:

Perlegen Sciences, Inc. - Mountain View CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435006000, 435091200

Abstract:

Multiple unique selection probes are provided in a single medium. Each selection probe has a sequence that is complementary to a unique target sequence that may be present in a sample under consideration. For example, each selection probe may be complementary to a sequence that includes one of the SNPs used to genotype an organism. Single-stranded selection probes anneal or hybridize with sample sequences having the unique target sequences specified by the selection probe sequences. Sequences from the sample that do not anneal or hybridize with the selection probes are separated from the bound sequences by an appropriate technique. The bound sequences can then be freed to provide a mixture of isolated target sequences, which can be used as needed for the application at hand.