Huu Thanh Tran

6344316, Feb 5, 2002

Jun 25, 1997

08/882649

David J. Lockhart - Santa Clara CA
Mark Chee - Palo Alto CA
Kevin Gunderson - Palo Alto CA
Lisa Wodicka - Santa Clara CA
Maureen T. Cronin - Los Altos CA
Danny Lee - San Jose CA
Huu M. Tran - San Jose CA
Hajime Matsuzaki - Palo Alto CA

Affymetrix, Inc. - Santa Clara CA

C12Q 168

435 6, 536 243

The present invention provides a simplified method for identifying differences in nucleic acid abundances (e. g. , expression levels) between two or more samples. The methods involve providing an array containing a large number (e. g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e. g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase.

6803196, Oct 12, 2004

Oct 13, 2000

09/687932

William A. Lyon - San Jose CA
Huu Minh Tran - San Jose CA

Affymetrix, Inc. - Santa Clara CA

C12Q 168

435 6, 435 911, 435 912, 435183, 4352872, 436501, 436507, 436532, 436 94, 436172, 436800, 436809, 536 231, 536 243, 5303871, 5303911, 530810

Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the presently claimed invention provides a method of labeling a hybridized target wherein the target comprises a binding ligand. In another embodiment, the presently claimed invention provides methods of signal amplification.

6806047, Oct 19, 2004

Feb 6, 2001

09/776770

Martin J. Goldberg - Saratoga CA
Govinda Rao S. Yelagalawadi - San Jose CA
Eugene Yuji Tanimoto - Menlo Park CA
Huu Minh Tran - Milpitas CA
Helin Dong - Palo Alto CA
David Lockhart - Mountain View CA
Thomas B. Ryder - Los Gatos CA
Janet A. Warrington - Los Altos CA
Jody Beecher - San Jose CA

Affymetrix, Inc. - Santa Clara CA

C12Q 168

435 6, 4353201, 4352528, 435174, 435183, 382129, 382133, 382153, 382173, 382286, 382291, 702 19, 702 22, 935 10, 935 24, 935 72, 536 221

Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent. Optionally, the amplification reagent, comprising a plurality of the binding ligands, is contacted with labeled receptor molecules thereby to complex a plurality of labeled receptor molecules to the amplification reagent, and the labeled receptor molecules complexed to the amplification reagent are detected.

6897073, May 24, 2005

Oct 27, 2001

10/046442

Peter Wagner - Belmont CA, US
Peter Kernen - Foster City CA, US
Hongbo Lu - Fremont CA, US
Huu Tran - San Jose CA, US

Zyomyx, Inc. - Hayward CA

G01N033/543

436518, 427 211, 427261, 427287, 427387, 4274072, 427134, 4274872, 4352871, 4352879, 4352883, 4352887, 436524, 436525, 436527, 436528, 436532, 436533, 436535, 436536

Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

7247469, Jul 24, 2007

May 24, 2005

11/137457

Peter Wagner - Belmont CA, US
Peter Kernen - Foster City CA, US
Hongbo Lu - Fremont CA, US
Huu Tran - San Jose CA, US

Zyomyx, Inc. - Hayward CA

C12M 1/34

4352872, 435 6, 4352879, 435810, 435973, 436518, 436524, 436525, 436527, 436809

Arrays of protein-capture agents useful for the simultaneous detection of a plurality of proteins which are the expression products, or fragments thereof, of a cell or population of cells in an organism are provided. A variety of antibody arrays, in particular, are described. Methods of both making and using the arrays of protein-capture agents are also disclosed. The invention arrays are particularly useful for various proteomics applications including assessing patterns of protein expression and modification in cells.

8398839, Mar 19, 2013

Jun 3, 2010

12/793370

Alfredo M. Morales - Livermore CA, US
Josh A. Whaley - Livermore CA, US
Mark D. Zimmerman - Livermore CA, US
Ronald F. Renzi - Tracy CA, US
Huu M. Tran - San Jose CA, US
Scott M. Maurer - Haymarket VA, US
William D. Munslow - Gainesville VA, US

Sandia Corporation - Albuquerque NM

B03C 5/02

204547

A new microfluidic system comprising an automated prototype insulator-based dielectrophoresis (iDEP) triggering microfluidic device for pathogen monitoring that can eventually be run outside the laboratory in a real world environment has been used to demonstrate the feasibility of automated trapping and detection of particles. The system broadly comprised an aerosol collector for collecting air-borne particles, an iDEP chip within which to temporarily trap the collected particles and a laser and fluorescence detector with which to induce a fluorescence signal and detect a change in that signal as particles are trapped within the iDEP chip.

20030064364, Apr 3, 2003

Apr 11, 2002

09/880727

David Lockhart - Santa Clara CA, US
Mark Chee - Palo Alto CA, US
Kevin Gunderson - Palo Alto CA, US
Chaoqiang Lai - Santa Clara CA, US
Lisa Wodicka - Santa Clara CA, US
Maureen Cronin - Los Altos CA, US
Danny Lee - San Jose CA, US
Huu Tran - San Jose CA, US
Hajime Matsuzaki - Palo Alto CA, US
Glenn McGall - Mt. View CA, US
Anthony Barone - San Jose CA, US

C12Q001/68

435/006000

The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by providing a nucleic acid, providing labeled nucleoside triphosphates, and attaching the nucleoside triphosphates to the nucleic acid using a terminal transferase.

20040137493, Jul 15, 2004

Jan 7, 2004

10/752020

Martin Goldberg - Saratoga CA, US
Govinda Rao Yelagalawadi - San Jose CA, US
Eugene Tanimoto - Menlo Park CA, US
Huu Tran - Milpitas CA, US
Helin Dong - Palo Alto CA, US
David Lockhart - Mountain View CA, US
Thomas Ryder - Los Gatos CA, US
Janet Warrington - Los Altos CA, US
Jody Beecher - San Jose CA, US

Affymetrix, Inc.

C12Q001/68
C12P019/34

435/006000, 435/091200

Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising multiple sites capable of binding the binding ligand to complex the receptor to the binding ligand, and the receptor is contacted with an amplification reagent, comprising a plurality of the binding ligands, to complex the amplification reagent to the receptor. The presence of the complexed amplification reagent then is detected, for example, by detecting the presence of a detectable label, such as a fluorescent label, for example, on the receptor or the amplification reagent. Optionally, the amplification reagent, comprising a plurality of the binding ligands, is contacted with labeled receptor molecules thereby to complex a plurality of labeled receptor molecules to the amplification reagent, and the labeled receptor molecules complexed to the amplification reagent are detected. This permits the detectable signal to be enhanced and amplified. In one embodiment, the binding ligand is biotin, the receptor is streptavidin, and the amplification reagent is an antibody or a DNA matrix. In another embodiment, an array of different nucleic acid probes immobilized on a surface, each having a defined sequence and location on the surface, may be used in the assays, thus permitting screening and detection of binding of a large number of nucleic acids.