Patents by Inventor Snezana Drmanac
Snezana Drmanac 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: 20160237488Abstract: This application discloses methods of producing a DNA strand for sequencing, as well as genetic constructs, libraries, and arrays using DNA strands produced according to these methods. The application also discloses methods of sequencing using the DNA strands, genetic constructs, libraries, and arrays produced. In certain aspects, DNA being sequenced includes a target sequence and at least one adaptor sequence.Type: ApplicationFiled: February 10, 2016Publication date: August 18, 2016Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
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Publication number: 20160130647Abstract: Novel fluorescent nucleotide analogues are provided herein. Also provided herein are methods of using the nucleotide analogues in sequencing-by-synthesis and signal confinement methods.Type: ApplicationFiled: October 23, 2015Publication date: May 12, 2016Inventors: Snezana Drmanac, Handong Li, Radoje Drmanac, Eric Harness, Chongjun Xu
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Publication number: 20160017414Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: May 15, 2015Publication date: January 21, 2016Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20150159204Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: December 24, 2014Publication date: June 11, 2015Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8951731Abstract: The present invention provides a sequence interrogation chemistry that combines the accuracy and haplotype integrity of long-read sequencing with improved methods of preparing genomic nucleic acids and analyzing sequence information generated from those nucleic acids. The present invention encompasses compositions comprising decorated nucleic acids stretched on substrates. The present invention further encompasses methods of making stretched decorated nucleic acids and methods of using decorated nucleic acids to obtain sequence information.Type: GrantFiled: October 15, 2008Date of Patent: February 10, 2015Assignee: Complete Genomics, Inc.Inventors: Radoje Drmanac, Snezana Drmanac
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Patent number: 8722326Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: GrantFiled: October 31, 2007Date of Patent: May 13, 2014Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Patent number: 8445196Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: October 31, 2007Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8445194Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: June 13, 2006Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8445197Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: October 31, 2007Date of Patent: May 21, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8440397Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: GrantFiled: October 31, 2007Date of Patent: May 14, 2013Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Publication number: 20130071821Abstract: Exemplary embodiments of the present invention beneficially provide systems, computer-implemented methods, and computer-readable program products to facilitate a plurality of user-driven virtual sponsoring sessions for a plurality of users through one or more user-designed virtual sponsors where the topic of the virtual sponsoring session, the type of virtual sponsoring session, and the form of each virtual sponsoring statement is controlled by each of the plurality of users. The virtual sponsoring sessions can be for any subject matter domain through user-designed virtual sponsors that have no domain-specific knowledge, such that users are provided with real-time, on-demand access to virtual sponsoring services via a user-designed virtual sponsor designed and constructed responsive to the personality, preferences, and specifications of each individual user.Type: ApplicationFiled: April 30, 2010Publication date: March 21, 2013Inventors: Radoje T. Drmanac, Snezana Drmanac
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Publication number: 20120135893Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: May 31, 2012Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac
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Patent number: 8133719Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: GrantFiled: October 31, 2007Date of Patent: March 13, 2012Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Patent number: 8034566Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: GrantFiled: October 30, 2007Date of Patent: October 11, 2011Assignee: Callida Genomics, Inc.Inventors: Radoje T. Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Publication number: 20110071053Abstract: Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 ?m2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.Type: ApplicationFiled: September 15, 2010Publication date: March 24, 2011Applicant: Callida Genomics, Inc.Inventors: Radoje DRMANAC, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
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Publication number: 20110039731Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and set of pools of probes, as well as method of generating pools of probes.Type: ApplicationFiled: December 22, 2009Publication date: February 17, 2011Applicant: CALLIDA GENOMICS, INC.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Publication number: 20090280481Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: ApplicationFiled: October 30, 2007Publication date: November 12, 2009Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Publication number: 20090264299Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: February 26, 2007Publication date: October 22, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Matthew J. Callow, Snezana Drmanac
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Patent number: 7582431Abstract: The invention provides methods for sequencing by hybridization (SBH) using pools of probes that allow greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence. The invention also provides pools and sets of pools of probes, as well as methods of generating pools of probes.Type: GrantFiled: November 12, 2004Date of Patent: September 1, 2009Assignee: Callida Genomics, Inc.Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
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Publication number: 20090155781Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.Type: ApplicationFiled: October 31, 2007Publication date: June 18, 2009Applicant: Complete Genomics, Inc.Inventors: Radoje T. Drmanac, Matthew Callow, Snezana Drmanac