Daniel Davis Shoemaker

US Patent:

6518035, Feb 11, 2003

Filed:

Dec 3, 1999

Appl. No.:

09/454889

Inventors:

Matthew Ashby - Mill Valley CA
Daniel D. Shoemaker - Bothell WA

Assignee:

Rosetta Inpharmatics, Inc. - Kirkland WA

International Classification:

C12Q 100

US Classification:

435 18, 435 4, 435 6, 435 771

Abstract:

The present invention provides methods of screening for a molecule that inhibits the expression or activity of a protein encoded by a target gene which affects the fitness of a cell. The methods are based on a co-culture assay, and entail culturing together two cell populations, each of which is a population of identical cells, of the same species that differs substantially only in the expression or activity of the gene to be targeted or its encoded protein and the presence or absence of a reporter gene. The screen can be applied to cultured cells, unicellular and multicellular organisms. Manipulating the expression or activity of the target gene sensitizes the host to a molecule which inhibits the target gene or its encoded protein such that the cell or organism comprising the manipulated target gene grows at a different rate from the cell or organism comprising the unmanipulated gene in response to exposure to the molecule. The methods of the invention can be used for identifying drugs, proteins or any other molecules that inhibit the function of proteins encoded by target genes.

US Patent:

6713257, Mar 30, 2004

Filed:

Feb 12, 2001

Appl. No.:

09/781814

Inventors:

Daniel D. Shoemaker - Bothell WA
Stewart Scherer - Moraga CA
Steven J. Altschuler - Redmond WA
Lani F. Wu - Redmond WA
Christopher D. Armour - Kirkland WA

Assignee:

Rosetta Inpharmatics LLC - Kirkland WA

International Classification:

C12Q 168

US Classification:

435 6, 536 231, 536 243, 702 19, 702 20

Abstract:

The invention relates to methods and systems (e. g. , computer systems and computer program products) for identifying and characterizing genes using microarrays. In particular, the invention provides for improved, robust methods for detecting genes through the use of microarrays to analyze the expression state of the genome. Genes which are expressed can be mapped to their respective positions in the genome, and the structure of such genes can be determined.

US Patent:

6962821, Nov 8, 2005

Filed:

Dec 5, 2002

Appl. No.:

10/309814

Inventors:

John Lewis Danssaert - San Diego CA, US
Robert James Shopes - San Diego CA, US
Daniel Davis Shoemaker - Stanford CA, US

Assignee:

Stratagene California - La Jolla CA

International Classification:

G01N033/566
C12Q001/00
C12M001/34

US Classification:

436501, 435 4, 4352884, 422 63, 422 67, 422 99

Abstract:

A method in which a temperature gradient is generated across a “gradient” block, and an apparatus comprising a block across which a temperature gradient can be generated. By setting up such a gradient, multiple reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures which differ only slightly, thereby permitting an optimum temperature for the reaction to be quickly identified. In a preferred embodiment the gradient block is integrated into a thermal cycler used for nucleic acid amplification reactions.

US Patent:

7432084, Oct 7, 2008

Filed:

Jul 17, 2002

Appl. No.:

10/485008

Inventors:

Daniel D. Shoemaker - San Diego CA, US
Christopher D. Armour - Kirkland WA, US
Philip W. Garrett-Engele - Seattle WA, US

Assignee:

Rosetta Inpharmatics LLC - Seattle WA

International Classification:

C12P 19/34

US Classification:

435 913, 435 9121

Abstract:

In one aspect the present invention provides methods of synthesizing a preparation of nucleic acid molecules, the methods comprising the steps of: (a) utilizing an RNA template to enzymatically synthesize a first DNA molecule that is complementary to at least 50 contiguous bases of the RNA template; (b) utilizing the first DNA molecule as a template to enzymatically synthesize a second DNA molecule, thereby forming a double-stranded DNA molecule wherein the first DNA molecule is hybridized to the second DNA molecule; (c) utilizing the first or second DNA molecule of the double-stranded DNA molecule as a template to enzymatically synthesize a first RNA molecule that is complementary to either the first DNA molecule or to the second DNA molecule; and (d) utilizing the first RNA molecule as a template to enzymatically synthesize a third DNA molecule that is complementary to the first RNA molecule. In another aspect, the present invention provides processed DNA samples prepared by a method of the invention for synthesizing a preparation of nucleic acid molecules. In another aspect, the present invention provides methods for hybridizing a processed DNA sample to a population of immobilized nucleic acid molecules.

US Patent:

7501254, Mar 10, 2009

Filed:

Jul 19, 2007

Appl. No.:

11/879966

Inventors:

Daniel D. Shoemaker - San Diego CA, US

Assignee:

GHC Technologies, Inc. - La Jolla CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 6, 435 911, 435 912

Abstract:

Methods for amplification and capture of nucleic acid sequences include annealing a forward primer to a DNA or RNA template in a first reaction vessel including fewer than four different dNTPs; forming an extended primer that terminates when an omitted dNTP is required for further extension; releasing the extended primer; exponentially amplifying the extended primer in a second reaction vessel that includes a reverse primer, four different dNTPs and a capture probe that includes n oligonucleotides having fewer than n locking nucleic acids; and concurrently capturing one of the extended primers with the capture probe while amplifying the extended primer. The steps of annealing, extending and releasing can occur at a first reaction temperature that is substantially isothermal and in the absence of a helicase. The steps of exponentially amplifying and capturing can occur at a second reaction temperature that is substantially isothermal.

US Patent:

7794985, Sep 14, 2010

Filed:

Mar 27, 2008

Appl. No.:

12/079851

Inventors:

Daniel D. Shoemaker - San Diego CA, US

Assignee:

GHC Technologies, Inc. - La Jolla CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 912, 435 6, 435 911

Abstract:

A method for detecting the presence of a nucleic acid template () in a sample includes the steps of combining the sample in a reaction vessel with a first primer (F) and a second primer (R) having a first section (), a second section () and a spacer (). The method also includes one or more of the steps of extending the first section () with additional nucleotides, binding the first primer (F) to the extended first section, extending the first primer (F) with additional nucleotides and terminating extension of the first primer (F) with the spacer (). The first section () includes a plurality of nucleotides that bind with a portion of the nucleic acid template (). The second section () is spaced-apart from the first section () and includes a plurality of nucleotides that do not bind with the nucleic acid template (). The spacer () couples the first section () to the second section (). The invention is also directed toward the second primer (R).

US Patent:

7807447, Oct 5, 2010

Filed:

Nov 28, 2000

Appl. No.:

09/724538

Inventors:

Daniel D. Shoemaker - Bothell WA, US
Stewart Scherer - Moraga CA, US
Stephen H. Friend - Seattle WA, US

Assignee:

Merck Sharp & Dohme Corp. - Rahway NJ

International Classification:

C12M 1/34
C12M 3/00
C12Q 1/68
C12P 1/34
C07H 21/02
C07H 21/04

US Classification:

4352872, 435 6, 435 911, 435 9151, 4352871, 536 231, 536 243, 536 2433

Abstract:

The present invention provides methods for analyzing exon expression profiles of a cell or type of cell. In the invention, the expression levels of a plurality of individual exons or multiexons for each of a plurality of genes in the genome of an organism are measured and analyzed to determine the biological state, such as the exon expression state or transcriptional state, of the cell or type of cell. The methods of the invention are useful for determination of alternative RNA splicing in a plurality of genes. The invention also provides nucleic acid probe arrays for determining in parallel the expression levels of a plurality of exons or multiexons for each of a plurality of genes in the genome of an organism. The invention further provides methods for determining the effects of perturbations, such as perturbations by drugs, on exon expression and alternative RNA splicing pathways.

US Patent:

7930406, Apr 19, 2011

Filed:

Oct 31, 2007

Appl. No.:

11/981425

Inventors:

Daniel D. Shoemaker - San Diego CA, US
Lee Thomas O'Donnell - Tarzana CA, US
James P. Broder - San Diego CA, US
Scott D. Shoemaker - San Diego CA, US

Assignee:

BOSS Logic, LLC - San Diego CA

International Classification:

G06F 17/30

US Classification:

709227, 709228, 709229

Abstract:

A system for transmission of mode of access information between a first device operated by a first user and a second device operated by a second user includes a database that is in network communication with the first device and the second device. The database stores a plurality of different modes of access for contacting the first user that are devoid of alpha-numeric identifiers specific to the first user. The database allows the first user to select one of the modes of access as a current mode of access of the first user. The current mode of access of the first user can be communicated to the second device once the second device queries the database. The current mode of access of the first user can be selected from the group consisting of mobile phone, text message and electronic mail. The current mode of access of the first user can change automatically over time according to a schedule input into the database by the first user. In some embodiments, at least one of the first device and the second device is a web-based mobile phone.