Patents by Inventor Monib Zirvi
Monib Zirvi 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: 20110177975Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: March 25, 2011Publication date: July 21, 2011Applicant: CORNELL RESEARCH FOUNDATION, INC.Inventors: Francis BARANY, George BARANY, Robert P. HAMMER, Maria KEMPE, Herman BLOK, Monib ZIRVI
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Patent number: 7914981Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: May 25, 2004Date of Patent: March 29, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Patent number: 7893233Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: March 16, 2010Date of Patent: February 22, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Patent number: 7892746Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: March 16, 2010Date of Patent: February 22, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Patent number: 7892747Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: March 16, 2010Date of Patent: February 22, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Patent number: 7888009Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: May 25, 2004Date of Patent: February 15, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Patent number: 7879579Abstract: The present invention relates to a method of forming arrays of oligonucleotides on a solid support. This method involves providing a solid support having an array of positions each suitable for attachment of an oligonucleotide. Linkers, suitable for coupling oligonucleotides to the solid support, are attached to the solid support surface at each of the array positions. An array of a plurality of capture oligonucleotides are formed on the solid support by a series of cycles of activating selected array positions for attachment of multimer nucleotides and attaching multimer nucleotides at activated array positions. The multimer nucleotides are selected for attachment so that the capture oligonucleotides formed on the array hybridize with complementary oligonucleotide target sequences under uniform hybridization conditions.Type: GrantFiled: September 26, 2001Date of Patent: February 1, 2011Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20100173790Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: March 16, 2010Publication date: July 8, 2010Applicant: CORNELL RESEARCH FOUNDATION, INC.Inventors: Francis BARANY, George BARANY, Robert P. HAMMER, Maria KEMPE, Herman BLOK, Monib ZIRVI
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Publication number: 20100173787Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: March 16, 2010Publication date: July 8, 2010Applicant: CORNELL RESEARCH FOUNDATION, INC.Inventors: Francis BARANY, George BARANY, Robert P. HAMMER, Maria KEMPE, Herman BLOK, Monib ZIRVI
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Publication number: 20100173802Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: March 16, 2010Publication date: July 8, 2010Applicant: CORNELL RESEARCH FOUNDATION, INC.Inventors: Francis BARANY, George BARANY, Robert P. HAMMER, Maria KEMPE, Herman BLOK, Monib ZIRVI
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Patent number: 7455965Abstract: The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The first step of the method involves providing a first set of a plurality of tetramers of four nucleotides linked together, where (1) each tetramer within the first set differs from all other tetramers in the first set by at least two nucleotide bases, (2) no two tetramers within the first set are complementary to one another, (3) no tetramers within the first set are palindromic or dinucleotide repeats, and (4) no tetramer within the first set has one or less or three or more G or C nucleotides. Groups of 2 to 4 of the tetramers from the first set are linked together to form a collection of multimer units.Type: GrantFiled: April 4, 2001Date of Patent: November 25, 2008Assignee: Cornell Research Foundation, Inc.Inventors: Francis Barany, Monib Zirvi, Norman P. Gerry, Reyna Favis, Richard Kliman
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Patent number: 7083917Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: September 26, 2001Date of Patent: August 1, 2006Assignees: Cornell Research Foundation, Inc., Board of Supervisors of Louisiana State University and Agricultural and Mechanical College, Regents of the University of MinnesotaInventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20050233320Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: September 26, 2001Publication date: October 20, 2005Inventors: Francis Barany, George Barany, Robert Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20050142543Abstract: The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The first step of the method involves providing a first set of a plurality of tetramers of four nucleotides linked together, where (1) each tetramer within the set differs from all other tetramers in the set by at least two nucleotide bases, (2) no two tetramers within a set are complementary to one another, (3) no tetramers within a set are palindromic or dinucleotide repeats, and (4) no tetramer within a set has one or less or three or more G or C nucleotides. Groups of 2 to 4 of the tetramers from the first set are linked together to form a collection of multimer units.Type: ApplicationFiled: April 4, 2001Publication date: June 30, 2005Inventors: Francis Barany, Monib Zirvi, Norman Gerry, Reyna Favis, Richard Kliman
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Patent number: 6852487Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: GrantFiled: February 4, 1997Date of Patent: February 8, 2005Assignees: Cornell Research Foundation, Inc., Board of Supervisors of Louisiana State University and Agricultural and Mechanical College, Regents of the University of MinnesotaInventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20040259141Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: May 25, 2004Publication date: December 23, 2004Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20040253625Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: May 25, 2004Publication date: December 16, 2004Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi
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Publication number: 20030190634Abstract: The present invention is directed to a method of assembling genomic maps of an organism's DNA or portions thereof. A library of an organism's DNA is provided where the individual genomic segments or sequences are found on more than one clone in the library. Representations of the genome are created, and nucleic acid sequence information is generated from the representations. The sequence information is analyzed to determine clone overlap from a representation. The clone overlap and sequence information from different representations is combined to assemble a genomic map of the organism. Once the genomic map is obtained, genomic sequence information from multiple individuals can be applied to the map and compared with one another to identify single nucleotide polymorphisms.Type: ApplicationFiled: July 17, 2002Publication date: October 9, 2003Inventors: Francis Barany, Jianzhao Liu, Brian W. Kirk, Monib Zirvi, Norman P. Gerry, Philip B. Paty
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Patent number: 6534293Abstract: The present invention is directed to a method of assembling genomic maps of an organism's DNA or portions thereof. A library of an organism's DNA is provided where the individual genomic segments or sequences are found on more than one clone in the library. Representations of the genome are created, and nucleic acid sequence information is generated from the representations. The sequence information is analyzed to determine clone overlap from a representation. The clone overlap and sequence information from different representations is combined to assemble a genomic map of the organism. Once the genomic map is obtained, genomic sequence information from multiple individuals can be applied to the map and compared with one another to identify single nucleotide polymorphisms.Type: GrantFiled: January 5, 2000Date of Patent: March 18, 2003Assignees: Cornell Research Foundation, Inc., Sloan-Kettering Institute for Cancer ResearchInventors: Francis Barany, Jianzhao Liu, Brian W. Kirk, Monib Zirvi, Norman P. Gerry, Philip B. Paty
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Publication number: 20030022182Abstract: The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.Type: ApplicationFiled: September 26, 2001Publication date: January 30, 2003Inventors: Francis Barany, George Barany, Robert P. Hammer, Maria Kempe, Herman Blok, Monib Zirvi