Patents by Inventor Sergei A. Kazakov
Sergei A. Kazakov 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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Patent number: 11964997Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.Type: GrantFiled: March 12, 2021Date of Patent: April 23, 2024Assignee: RealSeq Biosciences, Inc.Inventors: Sergei A. Kazakov, Sergio Barberan-Soler, Anne Dallas, Brian H. Johnston
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Publication number: 20210253625Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.Type: ApplicationFiled: March 12, 2021Publication date: August 19, 2021Inventors: Sergei A. KAZAKOV, Sergio BARBERAN-SOLER, Anne DALLAS, Brian H. JOHNSTON
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Patent number: 11072819Abstract: Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.Type: GrantFiled: October 5, 2017Date of Patent: July 27, 2021Assignee: REALSEQ BIOSCIENCES, INC.Inventor: Sergei A. Kazakov
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Patent number: 11014957Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.Type: GrantFiled: December 20, 2016Date of Patent: May 25, 2021Assignee: REALSEQ BIOSCIENCES, INC.Inventors: Sergei A. Kazakov, Sergio Barberan-Soler, Anne Dallas, Brian H. Johnston
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Publication number: 20180371006Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.Type: ApplicationFiled: December 20, 2016Publication date: December 27, 2018Inventors: Sergei A. KAZAKOV, Sergio BARBERAN-SOLER, Anne DALLAS, Brian H. JOHNSTON
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Publication number: 20180362968Abstract: Disclosed herein are methods of constructing a library of target polynucleotides. The present invention finds use in a variety of genomic research and diagnostic applications, including medical, agricultural, food and biodefense fields. Polynucleotides of interest may represent biomarkers of infection (e.g., viral and bacterial), or diseases such as cancer, genetic disorders, and metabolic disorders.Type: ApplicationFiled: June 13, 2018Publication date: December 20, 2018Inventors: Sergei A. KAZAKOV, Sergio BARBERAN-SOLER, Ryan HOGANS, Brian H. JOHNSTON
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Patent number: 10041107Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: GrantFiled: October 6, 2016Date of Patent: August 7, 2018Assignee: SOMAGENICS, INC.Inventors: Sergei A. Kazakov, Pavan Kumar, Brian H. Johnston
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Publication number: 20180066311Abstract: Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.Type: ApplicationFiled: October 5, 2017Publication date: March 8, 2018Inventor: Sergei A. KAZAKOV
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Patent number: 9816130Abstract: Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.Type: GrantFiled: December 21, 2012Date of Patent: November 14, 2017Assignee: SOMAGENICS, INC.Inventor: Sergei A. Kazakov
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Patent number: 9809847Abstract: Disclosed herein are compositions and methods for the processing, amplification and detection of polynucleotides using target-specific oligonucleotides (TSOs). Hybridization of TSOs to target polynucleotides guides target processing into and purification of small target fragments that then can be amplified and detected with high sensitivity and reproducibility. The method is specifically beneficial for highly degraded polynucleotides found in biological samples.Type: GrantFiled: June 19, 2015Date of Patent: November 7, 2017Assignee: SOMAGENICS, INC.Inventors: Sergei A. Kazakov, Catharina Casper-Lindley, Anne Dallas, Heini Ilves, Brian H. Johnston
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Publication number: 20170159106Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: ApplicationFiled: October 6, 2016Publication date: June 8, 2017Inventors: Sergei A. KAZAKOV, Pavan KUMAR, Brian H. JOHNSTON
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Publication number: 20170121762Abstract: Disclosed herein are compositions and methods for the processing, amplification and detection of polynucleotides using target-specific oligonucleotides (TSOs). Hybridization of TSOs to target polynucleotides guides target processing into and purification of small target fragments that then can be amplified and detected with high sensitivity and reproducibility. The method is specifically beneficial for highly degraded polynucleotides found in biological samples.Type: ApplicationFiled: June 19, 2015Publication date: May 4, 2017Applicant: SomaGenics, Inc.Inventors: Sergei A. KAZAKOV, Catharina CASPER-LINDLEY, Anne DALLAS, Heini ILVES, Brian H. JOHNSTON
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Patent number: 9493818Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: GrantFiled: August 25, 2015Date of Patent: November 15, 2016Assignee: SOMAGENICS, INC.Inventors: Sergei A. Kazakov, Pavan Kumar, Brian H. Johnston
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Patent number: 9416402Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: GrantFiled: January 20, 2015Date of Patent: August 16, 2016Assignee: SOMAGENICS, INC.Inventors: Sergei A. Kazakov, Pavan Kumar, Brian H. Johnston
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Publication number: 20160215328Abstract: Methods, systems and compositions are provided for analyzing one or more nucleic acid molecules. The methods, systems and compositions may comprise one or more target specific-oligonucleotide probes (TSPs). The TSPs may hybridize to nucleic acid molecules that are less than or equal to 200 nucleotides in length. The nucleic acid molecules may be small RNA molecules (e.g., miRNA, ncRNA, siRNA, shRNA). The methods, systems and compositions fmd use in a number of applications, for example, isolation of nucleic acid molecules, analysis of low abundance nucleic acid molecules, and/or enrichment of nucleic acid molecules.Type: ApplicationFiled: February 27, 2014Publication date: July 28, 2016Inventors: Sergei A. KAZAKOV, Anne DALLAS, Heini ILVES, Sumedha JAYASENA, Brian H. JOHNSTON
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Publication number: 20160115523Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: ApplicationFiled: August 25, 2015Publication date: April 28, 2016Inventors: Sergei A. KAZAKOV, Pavan KUMAR, Brian H. JOHNSTON
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Publication number: 20150211046Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: ApplicationFiled: January 20, 2015Publication date: July 30, 2015Inventors: Sergei A. KAZAKOV, Pavan KUMAR, Brian H. JOHNSTON
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Patent number: 8962253Abstract: Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5?-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences.Type: GrantFiled: April 13, 2010Date of Patent: February 24, 2015Assignee: Somagenics Inc.Inventors: Sergei A. Kazakov, Pavan Kumar, Brian H. Johnston
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Publication number: 20150051099Abstract: Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.Type: ApplicationFiled: December 21, 2012Publication date: February 19, 2015Applicant: SomaGenics, Inc.Inventor: Sergei A. Kazakov
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Patent number: 8779115Abstract: Methods, compositions, and kits that include small hairpin RNA (shRNA) useful for inhibition of gene expression, such as viral-mediated gene expression, are described.Type: GrantFiled: August 22, 2012Date of Patent: July 15, 2014Assignee: Somagenics Inc.Inventors: Qing Ge, Brian H. Johnston, Sergei A Kazakov, Heini Ilves, Anne Dallas