David Timothy Ruff

US Patent:

8012685, Sep 6, 2011

Filed:

Jul 31, 2007

Appl. No.:

11/888656

Inventors:

Mark E. Shannon - San Francisco CA, US
David W. Ruff - San Francisco CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

C12Q 1/68
G01N 33/53
C07H 21/02
C07H 21/04

US Classification:

435 6, 435 71, 536 231, 536 243

Abstract:

Methods of detecting at least one analyte and at least one nucleic acid in a sample are provided. Reagents for carrying out the methods are also provided.

US Patent:

8323897, Dec 4, 2012

Filed:

Nov 26, 2003

Appl. No.:

10/723520

Inventors:

Mark R. Andersen - San Mateo CA, US
David W. Ruff - San Francisco CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 612, 435 912

Abstract:

The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.

US Patent:

8535878, Sep 17, 2013

Filed:

May 2, 2007

Appl. No.:

11/743517

Inventors:

David W. Ruff - San Francisco CA, US
Mark E. Shannon - San Francisco CA, US
Kenneth J. Livak - San Jose CA, US
Karl J. Guegler - Menlo Park CA, US
Kevin M. Hennessy - San Mateo CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

C12Q 1/68

US Classification:

435 61, 435 611, 435 612, 435 615

Abstract:

The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.

US Patent:

8568580, Oct 29, 2013

Filed:

Jul 24, 2008

Appl. No.:

12/179455

Inventors:

Charles S. Vann - El Granada CA, US
Maxim G. Brevnov - Union City CA, US
David W. Ruff - San Francisco CA, US
Kenneth J. Livak - San Jose CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

G01N 27/453
B01D 61/42

US Classification:

204627, 204518, 204606, 204614

Abstract:

A system for collecting target nucleic acids from a sample can include at least one sample chamber configured to receive a sample containing target nucleic acids and other material, at least one collection chamber removably mountable relative to the at least one sample chamber and configured to collect target nucleic acids separated from the other material, a filter removably mountable relative to the at least one sample chamber and configured to be disposed between the at least one sample chamber and the at least one collection chamber when the at least one collection chamber is mounted relative to the at least one sample chamber. The system may further include a pair of electrodes configured to generate an electric field sufficient to cause target nucleic acids in the at least one sample chamber to migrate via electrophoresis from the at least one sample chamber through the filter into the at least one collection chamber, wherein the filter may be configured to permit passage of target nucleic acids and to block passage of material of a size larger than the target nucleic acids.

US Patent:

20040245163, Dec 9, 2004

Filed:

Jan 15, 2004

Appl. No.:

10/757865

Inventors:

Gary Lim - San Francisco CA, US
David Ruff - San Francisco CA, US
Michael Tanner - Brentwood CA, US
Somaya Bit - Fremont CA, US

International Classification:

B01D029/00

US Classification:

210/323100, 210/406000, 210/489000, 422/101000, 435/287100

Abstract:

A device, system, kit, and method are provided for filtering relatively large volumes of whole blood to recover purified RNA for analysis. The device can include: a filter including a body having an interior, a first filter connector in communication with the interior of the body, a ribonucleic acid-capturing (RNA-capturing) membrane disposed within the interior, and an optional filter frit disposed within the interior adjacent the RNA-capturing membrane. The system can include a vacuum adapter plate including a substrate having a first surface, a second surface, and one or more through-holes each extending at least from the first surface to the second surface. The first filter connector can connect to a respective through-hole to form a fluid communication between the filter and the vacuum adapter plate. The system can include a collection vessel in fluid communication with the filter.

US Patent:

20070020667, Jan 25, 2007

Filed:

Jun 29, 2006

Appl. No.:

11/478840

Inventors:

David Ruff - San Francisco CA, US
Mark Shannon - San Francisco CA, US

International Classification:

C12Q 1/68
C07H 21/04
C12P 19/34

US Classification:

435006000, 435091200, 536024300

Abstract:

Methods and compositions for amplifying nucleic acids are provided.

US Patent:

20100036616, Feb 11, 2010

Filed:

Sep 11, 2009

Appl. No.:

12/558428

Inventors:

Mark E. Shannon - San Francisco CA, US
Mark F. Oldham - Los Gatos CA, US
David W. Ruff - San Francisco CA, US

Assignee:

Life Technologies Corporation - Carlsbad CA

International Classification:

G06F 19/00

US Classification:

702 19

Abstract:

A method for determining bias across two domains comprising gene expression data. The method can comprise (a) providing a first domain and a second domain; (b) obtaining information indicative of a bias within the first domain; (c) obtaining information indicative of a bias within the second domain; and (d) using the information indicative of the bias within the first domain and the information indicative of the bias within the second domain to produce an indication of bias across the two domains.

US Patent:

20110208441, Aug 25, 2011

Filed:

Aug 5, 2010

Appl. No.:

12/851532

Inventors:

Shiaw-Min Chen - Fremont CA, US
David W. Ruff - San Francisco CA, US
Harrison M. Leong - San Francisco CA, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

G06F 19/00

US Classification:

702 32

Abstract:

Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.