Patents by Inventor David Lockhart
David Lockhart has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20050158772Abstract: 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.Type: ApplicationFiled: December 23, 2004Publication date: July 21, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Mark Chee, Kevin Gunderson, Lai Chaoqiang, Lisa Wodicka, Maureen Cronin, Danny Lee, Huu Tran, Hajime Matsuzaki, Glenn McGall, Anthony Barone
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Publication number: 20050158744Abstract: Libraries of unimolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA. In a related aspect, the present invention provides libraries of conformationally restricted probes on a solid support. The probes are restricted in their movement and flexibility using double-stranded oligonucleotides as scaffolding. The probes are also useful in various screening procedures associated with drug discovery and diagnosis. The present invention further provides methods for the preparation and screening of the above libraries.Type: ApplicationFiled: November 19, 2004Publication date: July 21, 2005Applicants: Affymetrix, Inc., Affymax Technologies, N.V., a Netherlands Antilles corporationInventors: David Lockhart, Dirk Vetter, Martin Diggelmann
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Publication number: 20050153371Abstract: Provided herein are linker compounds and conjugates that include the linker compounds. In one embodiment, the linker compounds comprise 2 or 3 residues of 6-aminohexanoic acid and optionally 7-10 residues of polyethyleneglycol (PEG). The linker compounds are useful in forming conjugates with one or more components useful in biopharmaceutical or bioanalytical applications. In particular, the biopharmaceutically useful compounds are kinase inhibitors. The conjugates described herein have utility in a variety of diagnostic, separation, and therapeutic applications.Type: ApplicationFiled: January 7, 2005Publication date: July 14, 2005Inventors: Robert Grotzfeld, Zdravko Milanov, Hitesh Patel, Andiliy Lai, Shamal Mehta, David Lockhart
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Publication number: 20050153989Abstract: Described herein are compounds and compositions for modulating kinase activity, and methods for modulating kinase activity using the compounds and compositions. Also described herein are methods of using the compounds and/or compositions in the treatment and prevention of a variety of diseases and unwanted conditions in subjects.Type: ApplicationFiled: January 13, 2005Publication date: July 14, 2005Inventors: Robert Grotzfeld, Hitesh Patel, Shamal Mehta, Zdravko Milanov, Andiliy Lai, David Lockhart
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Publication number: 20050148605Abstract: The invention provides methods and compositions for treating conditions mediated by abl wherein derivatives of amide compounds are employed. The invention also provides methods of using the compounds and/or compositions in the treatment of a variety of diseases and unwanted conditions in subjects.Type: ApplicationFiled: November 15, 2004Publication date: July 7, 2005Inventors: Robert Grotzfeld, Hitesh Patel, Shamal Mehta, Zdravko Milanov, Andiliy Lai, David Lockhart
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Publication number: 20050074787Abstract: An array of oligonucleotides on a solid substrate is disclosed, which can be used for multiple purposes. Methods and reagents are provided for performing genotyping to determine the identity or ratio of allelic forms of a gene in a sample. A single base extension primer is coupled to a sequence identity code. During the primer extension reaction a distinctive label is incorporated which identifies the allelic form present in the sample. This permits multiple simultaneous analyses to be performed easily and efficiently.Type: ApplicationFiled: December 8, 2003Publication date: April 7, 2005Applicants: Whitehead Institute for Biomedical Research, The General Hospital Corporation, Affymetrix, IncInventors: Jian-Bing Fan, Joel Hirschhorn, Xiaohua Huang, Paul Kaplan, Eric Lander, David Lockhart, Thomas Ryder, Pamela Sklar
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Publication number: 20050069927Abstract: Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.Type: ApplicationFiled: August 4, 2004Publication date: March 31, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Gordon Wong, Pennina Langer-Safer
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Publication number: 20050048531Abstract: The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of murine genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. As such, the invention related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.Type: ApplicationFiled: March 25, 2004Publication date: March 3, 2005Applicant: Affymetrix, INC.Inventors: Michael Mittman, David Mack, David Lockhart
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Publication number: 20050009099Abstract: The invention provides methods for determining the interactions between phage-displayed proteins and test molecules. The phage-displayed proteins are contacted with a reference moiety in the presence and absence of a test molecule; the behavior of the phage-displayed proteins as a function of concentration of the test molecule permits calculation of the binding affinity of the phage-displayed protein for the test molecule.Type: ApplicationFiled: June 21, 2004Publication date: January 13, 2005Applicant: Ambit Biosciences CorporationInventors: David Lockhart, Patrick Zarrinkar, Daniel Treiber
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Patent number: 6806047Abstract: 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.Type: GrantFiled: February 6, 2001Date of Patent: October 19, 2004Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Publication number: 20040137493Abstract: 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.Type: ApplicationFiled: January 7, 2004Publication date: July 15, 2004Applicant: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Publication number: 20040114456Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: ApplicationFiled: December 3, 2003Publication date: June 17, 2004Applicant: Affymetrix, Inc.Inventors: James L. Winkler, Mark Chee, David Lockhart
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Patent number: 6705754Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: GrantFiled: January 30, 2002Date of Patent: March 16, 2004Assignee: Affymetrix, Inc.Inventors: James L. Winkler, Mark Chee, David Lockhart
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Publication number: 20030194711Abstract: A system and methods for identifying sequence diversity in a gene or expressed sequence is disclosed wherein hybridization differences arising from polymorphic bases in analogous expressed sequences are identified between two or more nucleotide populations. By scaling the hybridization data to account for differences in abundance and observed intensity, sequence diversity can be identified in a highly specific and sensitive manner. Data confidence levels are also accounted for to increase the accuracy of the sequence diversity determination. The invention can be applied to both newly collected gene expression data and archived data to generate valuable insight into polymorphic behavior within complex nucleotide populations.Type: ApplicationFiled: April 10, 2002Publication date: October 16, 2003Inventors: Matthew Zapala, David Lockhart, Carrolee Barlow, Jennifer A. Greenhall
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Publication number: 20020071339Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: ApplicationFiled: January 30, 2002Publication date: June 13, 2002Applicant: AFFYMETRIX, INC.Inventors: James L. Winkler, Mark Chee, David Lockhart
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Publication number: 20010041335Abstract: 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.Type: ApplicationFiled: February 6, 2001Publication date: November 15, 2001Applicant: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Patent number: 6203989Abstract: 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.Type: GrantFiled: March 25, 1999Date of Patent: March 20, 2001Assignee: Affymetrix, Inc.Inventors: Martin J. Goldberg, Govinda Rao S. Yelagalawadi, Eugene Yuji Tanimoto, Huu Minh Tran, Helin Dong, David Lockhart, Thomas B. Ryder, Janet A. Warrington, Jody Beecher
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Patent number: 6050719Abstract: The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.Type: GrantFiled: February 27, 1998Date of Patent: April 18, 2000Assignee: Affymetrix, Inc.Inventors: James L. Winkler, Mark Chee, David Lockhart
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Patent number: 4303362Abstract: Spacers are used where added bolt length is advantageous. Such spacers are usually one piece and are formed from tubing having a solid cylindrical wall which often splits or yields when stressed by highly torqued bolts. An improved spacer (10) is formed from wound coil (12) to form a spiral walled cylindrical body (20) having advantageous over prior spacers. Each spiral (14) includes a portion (26) which abuts each adjacent spiral (14) and a portion (30) which is free of such abutment.Type: GrantFiled: April 23, 1979Date of Patent: December 1, 1981Assignee: Caterpillar Tractor Co.Inventor: David A. Lockhart
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Patent number: 4300273Abstract: A laminated spacer plate (10) for engines, pumps and the like comprises a plurality of metallic sheets (11-14), each having openings (15,16,17,24,40) preformed therethrough and secured together. The preforming of the openings through the individual sheets facilitates intercommunication of certain of the openings with passages formed within the spacer plate and eliminates the need for costly machining and related manufacturing operations normally required for the fabrication of a one-piece spacer plate.Type: GrantFiled: November 19, 1979Date of Patent: November 17, 1981Assignee: Caterpillar Tractor Co.Inventor: David A. Lockhart