Patents by Inventor Thomas Gingeras
Thomas Gingeras 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).
-
Publication number: 20110250602Abstract: Methods and computer software products are provided for transcriptional annotation. In one embodiment of the invention, a region of the genome where the intensity of hybridization of all the probes are above a threshold value (usually the level of non-specific hybridization) is identified. The region may be identified by aligning the probes against the genome; walking through the genome to find regions where all consecutive probes have intensities above the threshold value.Type: ApplicationFiled: June 23, 2011Publication date: October 13, 2011Applicant: Affymetrix, Inc.Inventors: Carsten Rosenow, Thomas Gingeras
-
Publication number: 20070122838Abstract: Methods and computer software products are provided for transcriptional annotation. In one embodiment of the invention, a region of the genome where the intensity of hybridization of all the probes are above a threshold value (usually the level of non-specific hybridization) is identified. The region may be identified by aligning the probes against the genome; walking through the genome to find regions where all consecutive probes have intensities above the threshold value.Type: ApplicationFiled: January 31, 2007Publication date: May 31, 2007Applicant: Affymetrix, INC.Inventors: Carsten Rosenow, Thomas Gingeras
-
Publication number: 20070009939Abstract: The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence In a further embodiment the invention can be used to reproducibly label and detect extremely small amounts of nucleic acidsType: ApplicationFiled: May 30, 2006Publication date: January 11, 2007Applicant: Affymetrix, INC.Inventors: Fred Christians, Duc Do, Thomas Gingeras, Kevin Gunderson, Charles Miyada, Carsten Rosenow, Kai Wu, Qing Yang
-
Publication number: 20060223097Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic napping, screening and manipulation.Type: ApplicationFiled: June 12, 2006Publication date: October 5, 2006Applicant: Affymetrix, INC.Inventors: Ronald Sapolsky, Robert Lipshutz, Thomas Gingeras
-
Publication number: 20060204991Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample Methods of producing such affinity matrices are also provided In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of said different oligonucleotides have an identical terminal 3? nucleic acid sequence and an identical terminal 5? nucleic acid sequence b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids, and c) attaching the pool of nucleic acids to a solid supportType: ApplicationFiled: February 22, 2006Publication date: September 14, 2006Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, MacDonald Morris, Mark Chee, Thomas Gingeras
-
Publication number: 20060204970Abstract: This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.Type: ApplicationFiled: February 4, 2005Publication date: September 14, 2006Inventors: Thomas Gingeras, David Mack, Mark Chee, Anthony Berno, Lubert Stryer, Ghassan Ghandour, Ching Wang
-
Publication number: 20060177843Abstract: This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.Type: ApplicationFiled: October 20, 2005Publication date: August 10, 2006Applicant: Affymetrix, INC.Inventors: Thomas Gingeras, David Mack, Mark Chee, Anthony Berno, Lubert Stryer, Ghassan Ghandour, Ching Wang
-
Publication number: 20060147964Abstract: This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.Type: ApplicationFiled: December 22, 2005Publication date: July 6, 2006Applicant: AFFYMETRIX, INC.Inventors: Thomas Gingeras, Jorg Drenkow
-
Publication number: 20060134665Abstract: In one aspect of the invention, high density arrays are used with 5? and 3? RACE (rapid amplification of cDNA ends) or RAGE (rapid amplification of Genomic DNA) in tandem to detect and characterize transcripts or genomic structures.Type: ApplicationFiled: November 8, 2005Publication date: June 22, 2006Applicant: Affymetrix, INC.Inventors: Thomas Gingeras, Philipp Kapranov
-
Publication number: 20060105363Abstract: In some embodiments of the invention, methods are provided to interrogate the transcriptional activity. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs in a cellular compartment.Type: ApplicationFiled: September 23, 2005Publication date: May 18, 2006Applicant: Affymetrix, INC.Inventors: Thomas Gingeras, Philipp Kapranov
-
Publication number: 20060003321Abstract: Certain human genes have been found to be induced or repressed in host cells infected with HCMV. A large set of such genes has been identified. These have diagnostic use in determining the extent of tissue damage caused by the infection as well as in determining the stage of disease progression of the HCMV infection. Such genes are likely those involved in mediating the pathology of the infected tissues. Thus by identifying agents which are able to reverse the induction or repression of such genes, one can find candidate therapeutic agents for use in treating and or preventing HCMV-caused disease pathologies.Type: ApplicationFiled: August 29, 2005Publication date: January 5, 2006Applicants: Affymetrix, Inc., Princeton UniversityInventors: Hua Zhu, Thomas Gingeras, Thomas Shenk
-
Publication number: 20050202500Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample.Type: ApplicationFiled: April 28, 2005Publication date: September 15, 2005Applicant: Affymetrix, INC.Inventors: David Lockhart, Eugene Brown, Gordon Wong, Mark Chee, Thomas Gingeras
-
Publication number: 20050158746Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample.Type: ApplicationFiled: November 23, 2004Publication date: July 21, 2005Applicant: Affymetrix Inc.Inventors: David Lockhart, Eugene Brown, Gordon Wong, Mark Chee, Thomas Gingeras
-
Publication number: 20050136412Abstract: In one aspect of the invention, single biological molecules are detected and manipulated using light tweezers. In some embodiments, the biological molecules are selectively moved to detection features for characterization.Type: ApplicationFiled: December 22, 2003Publication date: June 23, 2005Applicant: Affymetrix, INC.Inventor: Thomas Gingeras
-
Publication number: 20050136420Abstract: Methods and computer software products are provided for transcriptional annotation. In one embodiment of the invention, a region of the genome where the intensity of hybridization of all the probes are above a threshold value (usually the level of non-specific hybridization) is identified. The region may be identified by aligning the probes against the genome; walking through the genome to find regions where all consecutive probes have intensities above the threshold value.Type: ApplicationFiled: March 31, 2004Publication date: June 23, 2005Applicant: Affymetrix, INC.Inventors: Carsten Rosenow, Thomas Gingeras
-
Publication number: 20050118633Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided.Type: ApplicationFiled: November 8, 2004Publication date: June 2, 2005Applicant: Affymetrix, INC.Inventors: Robert Lipshutz, MacDonald Morris, Mark Chee, Thomas Gingeras
-
Publication number: 20050059009Abstract: The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids. Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids. In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence. In a further embodiment, the invention can be used to reproducibly label and detect extremely small amounts of nucleic acids.Type: ApplicationFiled: July 3, 2003Publication date: March 17, 2005Applicant: Affymetrix, INC.Inventors: Fred Christians, Duc Do, Thomas Gingeras, Kevin Gunderson, Charles Miyada, Carsten Rosenow, Kai Wu, Qing Yang
-
Publication number: 20050026212Abstract: The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.Type: ApplicationFiled: September 16, 2004Publication date: February 3, 2005Applicants: Affymetrix, INC., Affymax Technologies N.V.Inventors: Ronald Sapolsky, Robert Lipshutz, Thomas Gingeras
-
Publication number: 20050003381Abstract: In one aspect of the invention, high density arrays are used with 5? and 3? RACE (rapid amplification of cDNA ends) or RAGE (rapid amplification of Genomic DNA) in tandem to detect and characterize transcripts or genomic structures.Type: ApplicationFiled: December 19, 2003Publication date: January 6, 2005Applicant: Affymetrix, INC.Inventors: Thomas Gingeras, Philipp Kapranov
-
Patent number: 6613516Abstract: The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids. Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids. In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence. In a further embodiment, the invention can be used to reproducibly label and detect extremely small amounts of nucleic acids.Type: GrantFiled: October 11, 2000Date of Patent: September 2, 2003Assignee: Affymetrix, Inc.Inventors: Fred C. Christians, Duc Do, Thomas Gingeras, Kevin Gunderson, Charles G. Miyada, Carsten Rosenow, Kai Wu, Qing Yang