David J Woo

US Patent:

7398171, Jul 8, 2008

Filed:

Jun 30, 2006

Appl. No.:

11/428048

Inventors:

David C. Woo - Foster City CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G06F 19/00
G06F 17/40

US Classification:

702 82, 382100, 382128, 382129, 382133, 702 19, 702 20, 702 81, 702189

Abstract:

Aspects of the present invention describe a method and apparatus for automating quality control for gene expression data. A computer based device receives gene expression data associated with a spectral species and genetic sample in each well of a plate. Gene expression data may be received from a sequence detection instrument performing one or more gene expression related operations for each of the wells of the plate. The computer based device identifies gene expression data determined to have anomalous characteristics according to a set of one or more quality control metrics and may conditionally flag one or more wells of the plate affected by the anomalous characteristics. Filters can then be selectively applied to temporarily or permanently remove the flagged data from subsequent gene expression studies.

US Patent:

7839507, Nov 23, 2010

Filed:

Jun 28, 2007

Appl. No.:

11/770443

Inventors:

Stephen J. Gunstream - San Francisco CA, US
David C. Woo - Foster City CA, US
John P. Bodeau - San Mateo CA, US
Mark A. McCoy - Foster City CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

G01N 21/25

US Classification:

356417

Abstract:

Methods and systems for processing signals to minimize the effects of dye crosstalk. Deconvolution of multiplexed dye signals can include corrections for residual error determined from experimental measurements. Residual error corrections can account for reaction or assay specific factors and modify the subsequent filtering of signals. Correction values can be determined for specific dye-probe conjugates to minimize dye crosstalk and may be combined with residual error correction to further minimize errors in spectral deconvolution. Apparatus, systems, and computer-readable media can process signals and modify filters based on values obtained using the methods.

US Patent:

8649982, Feb 11, 2014

Filed:

Sep 13, 2011

Appl. No.:

13/231618

Inventors:

David Woo - Foster City CA, US
Clinton Lewis - Palo Alto CA, US
Nasser Abbasi - San Mateo CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

G01N 33/48

US Classification:

702 19

Abstract:

The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.

US Patent:

20070011201, Jan 11, 2007

Filed:

Jun 30, 2006

Appl. No.:

11/428293

Inventors:

Madhu Augustine - Foster City CA, US
David Woo - Foster City CA, US
Jacob Burghardt - Seattle WA, US

International Classification:

G06F 17/00

US Classification:

707104100

Abstract:

Aspects of the present invention describe a method and apparatus for viewing and interfacing with gene expression on a computer device. A computer based device interfaces with gene the expression data by representing a plate having one or more wells and their contents with a matrix of elements addressable along at least two-dimensions. Each of the elements in the matrix are processed and then distinguished based upon their passing and failing one or more metrics for gene expression data. The interface displays those values associated with the distinguished elements in the matrix using colors, shapes and symbols. Depending on the results, some of the elements in the matrix may be flagged and then filtered from the data set. Remaining gene expression values not filtered from the matrix of elements are displayed and processed further.

US Patent:

20080201103, Aug 21, 2008

Filed:

Jan 28, 2008

Appl. No.:

12/021032

Inventors:

Chengyong Yang - Foster City CA, US
David C. Woo - Foster City CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G06F 17/18
G01N 33/48
G01D 18/00

US Classification:

702179, 702 19, 702 85

Abstract:

The present teachings comprise systems and methods for calibrating the background or baseline signal in a PCR or other reaction. The background signal derived from detected emissions of sample wells can be subjected to a normalized statistical metric, and be compared to a threshold or other standard to discard outlier cycles or other extraneous data. According to various embodiments, a relative standard deviation (relativeSTD) for the background component can be generated by dividing the standard deviation by the median of differences across all wells, where the difference is defined as the difference between maximum and minimum pixel values of a well. The relativeSTD as a metric is not sensitive to machine-dependent variations in absolute signal output that can be caused by different gain settings, different LED draw currents, different optical paths, or other instrumental variations. More accurate background characterization can be achieved.

US Patent:

60110554, Jan 4, 2000

Filed:

Mar 13, 1998

Appl. No.:

9/039309

Inventors:

David D.L. Woo - Los Angeles CA

Assignee:

The Regents of the University of California - Oakland CA

International Classification:

A01N 4338

US Classification:

514420

Abstract:

A method for treating polycystic kidney disease in an individual in need thereof. This method includes identifying a mammal having a cystic disease and administering to the mammal a pharmacologically effective anti-cystic amount of TNF-. alpha. or an agent which stimulates TNF-. alpha. production in vivo. The agent is administered in a pharmacologically acceptable carrier, excipient or diluent.

US Patent:

20200074624, Mar 5, 2020

Filed:

Aug 30, 2019

Appl. No.:

16/557376

Inventors:

- Carlsbad CA, US
David WOO - Foster City CA, US
Wallace GEORGE - Oakland CA, US

International Classification:

G06T 7/00
H04N 5/372
H04N 5/347
G01N 27/447

Abstract:

A biological analysis system and an associated method are provided. The method is used for recovering off scale data in an image produced by a camera in a capillary electrophoresis instrument. The method comprises the steps of identifying bins of the image where electron counts exceed a maximum number of counts; setting an off-scale flag for the identified bins; and processing the image to obtain a recovered dye signal, based on the flag set for each bin, and using a dye matrix.

US Patent:

20190228053, Jul 25, 2019

Filed:

Jan 28, 2019

Appl. No.:

16/259994

Inventors:

- Carlsbad CA, US
David WOO - Foster City CA, US

International Classification:

G06F 17/18
G01N 21/64
G01D 1/14

Abstract:

The present teachings comprise systems and methods for calibrating the background or baseline signal in a PCR or other reaction. The background signal derived from detected emissions of sample wells can be subjected to a normalized statistical metric, and be compared to a threshold or other standard to discard outlier cycles or other extraneous data. According to various embodiments, a relative standard deviation (relativeSTD) for the background component can be generated by dividing the standard deviation by the median of differences across all wells, where the difference is defined as the difference between maximum and minimum pixel values of a well. The relativeSTD as a metric is not sensitive to machine-dependent variations in absolute signal output that can be caused by different gain settings, different LED draw currents, different optical paths, or other instrumental variations. More accurate background characterization can be achieved.