Patents by Inventor Eric Bruening
Eric Bruening 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: 11661628Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: August 10, 2017Date of Patent: May 30, 2023Assignee: Takara Bio USA, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Patent number: 11628215Abstract: Provided herein are HIV-1 vaccines comprising a carrier and a population episensus antigen determined using the EpiGraph approach. Also provided are HIV-1 vaccines comprising a carrier, a population episensus antigen, and a tailored antigen. Also provided are methods of designing and producing an HIV-1 vaccine for a subject comprising designing vaccine antigens to optimally cover the diversity within a geographic area using an antigen amino acid sequence generated using the EpiGraph approach, and producing said designed vaccine antigen. Also provided are methods of inducing an effector memory T cell response comprising designing the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to a subject. Further provided are methods of treating HIV-1 in a subject comprising administering an effective amount of the described HIV-1 vaccines to the subject in need thereof.Type: GrantFiled: August 31, 2020Date of Patent: April 18, 2023Assignees: Vir Biotechnology, Inc., Triad National Security, LLC, Oregon Health & Science UniversityInventors: Eric Bruening, Klaus Frueh, Louis Picker, Bette T. M. Korber, James Theiler, Emily Marshall
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Patent number: 11554168Abstract: Provided herein are HIV-1 vaccines comprising a carrier and a population episensus antigen determined using the EpiGraph approach. Also provided are HIV-1 vaccines comprising a carrier, a population episensus antigen, and a tailored antigen. Also provided are methods of designing and producing an HIV-1 vaccine for a subject comprising designing vaccine antigens to optimally cover the diversity within a geographic area using an antigen amino acid sequence generated using the EpiGraph approach, and producing said designed vaccine antigen. Also provided are methods of inducing an effector memory T cell response comprising designing the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to a subject. Further provided are methods of treating HIV-1 in a subject comprising administering an effective amount of the described HIV-1 vaccines to the subject in need thereof.Type: GrantFiled: August 31, 2020Date of Patent: January 17, 2023Assignees: Vir Biotechnology, Inc., Triad National Security, LLC, Oregon Health & Science UniversityInventors: Eric Bruening, Klaus Frueh, Louis Picker, Bette T. M. Korber, James Theiler, Emily Marshall
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Patent number: 11492663Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: February 15, 2019Date of Patent: November 8, 2022Assignee: Takara Bio USA, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Publication number: 20220288195Abstract: The present disclosure relates to isolated polynucleotides and polypeptides, and related hepatitis B virus (HBV)vaccines. The present disclosure also relates to viral vectors for expressing such polypeptides, and which may be used in HBV vaccines, as well as methods of protecting a subject from HBV infection and methods of treating HBV in a subject comprising administering the polypeptides, vectors, or vaccines described herein. Methods of designing and producing an HBV vaccine comprising designing vaccine antigens to cover the diversity within a geographic area using an antigen amino acid sequence that efficiently covers the epitopes in the HBV genotypes present in the geographic area are also provided herein.Type: ApplicationFiled: August 28, 2020Publication date: September 15, 2022Inventors: Eric BRUENING, Janet DOUGLAS, Emily MARSHALL, Karina YUSIM, Bette KORBER, James THEILER
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Publication number: 20210046174Abstract: Provided herein are HIV-1 vaccines comprising a carrier and a population episensus antigen determined using the EpiGraph approach. Also provided are HIV-1 vaccines comprising a carrier, a population episensus antigen, and a tailored antigen. Also provided are methods of designing and producing an HIV-1 vaccine for a subject comprising designing vaccine antigens to optimally cover the diversity within a geographic area using an antigen amino acid sequence generated using the EpiGraph approach, and producing said designed vaccine antigen. Also provided are methods of inducing an effector memory T cell response comprising designing the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to a subject. Further provided are methods of treating HIV-1 in a subject comprising administering an effective amount of the described HIV-1 vaccines to the subject in need thereof.Type: ApplicationFiled: August 31, 2020Publication date: February 18, 2021Inventors: Eric Bruening, Klaus Frueh, Louis Picker, Bette T.M. Korber, James Theiler, Emily Marshall
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Publication number: 20210046175Abstract: Provided herein are HIV-1 vaccines comprising a carrier and a population episensus antigen determined using the EpiGraph approach. Also provided are HIV-1 vaccines comprising a carrier, a population episensus antigen, and a tailored antigen. Also provided are methods of designing and producing an HIV-1 vaccine for a subject comprising designing vaccine antigens to optimally cover the diversity within a geographic area using an antigen amino acid sequence generated using the EpiGraph approach, and producing said designed vaccine antigen. Also provided are methods of inducing an effector memory T cell response comprising designing the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to a subject. Further provided are methods of treating HIV-1 in a subject comprising administering an effective amount of the described HIV-1 vaccines to the subject in need thereof.Type: ApplicationFiled: August 31, 2020Publication date: February 18, 2021Inventors: Eric Bruening, Klaus Frueh, Louis Picker, Bette T.M. Korber, James Theiler, Emily Marshall
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Patent number: 10894078Abstract: Provided herein are HIV-1 vaccines comprising a carrier and a population episensus antigen determined using the EpiGraph approach. Also provided are HIV-1 vaccines comprising a carrier, a population episensus antigen, and a tailored antigen. Also provided are methods of designing and producing an HIV-1 vaccine for a subject comprising designing vaccine antigens to optimally cover the diversity within a geographic area using an antigen amino acid sequence generated using the EpiGraph approach, and producing said designed vaccine antigen. Also provided are methods of inducing an effector memory T cell response comprising designing the one or more EpiGraph amino acid sequences, producing a vaccine comprising the one or more EpiGraph amino acid sequences and a vector, and administering the vaccine to a subject. Further provided are methods of treating HIV-1 in a subject comprising administering an effective amount of the described HIV-1 vaccines to the subject in need thereof.Type: GrantFiled: October 5, 2015Date of Patent: January 19, 2021Assignees: Vir Biotechnology, Inc., Triad National Security, LLC, Oregon Health & Science UniversityInventors: Eric Bruening, Klaus Frueh, Louis Picker, Bette T. M. Korber, James Theiler, Emily Marshall
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Patent number: 10837049Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: July 22, 2016Date of Patent: November 17, 2020Assignee: Takara Bio USA, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Publication number: 20190271033Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: ApplicationFiled: February 15, 2019Publication date: September 5, 2019Inventors: Emmanuel KAMBEROV, Tong SUN, Eric BRUENING, Jonathon H. PINTER, Irina SLEPTSOVA, Takao KURIHARA, Vladimir L. MAKAROV
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Patent number: 10214771Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: GrantFiled: August 5, 2016Date of Patent: February 26, 2019Assignee: Takara Bio USA, Inc.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
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Publication number: 20180030522Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: ApplicationFiled: August 10, 2017Publication date: February 1, 2018Inventors: Emmanuel KAMBEROV, Tong SUN, Eric BRUENING, Jonathon H. PINTER, Irina SLEPTSOVA, Takao KURIHARA, Vladimir L. MAKAROV
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Publication number: 20170037460Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: August 5, 2016Publication date: February 9, 2017Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
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Publication number: 20160355879Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: ApplicationFiled: July 22, 2016Publication date: December 8, 2016Applicant: Rubicon Genomics, Inc.Inventors: Emmanuel KAMBEROV, Tong SUN, Eric BRUENING, Jonathon H. PINTER, Irina SLEPTSOVA, Takao KURIHARA, Vladimir L. MAKAROV
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Patent number: 9410193Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: GrantFiled: August 4, 2014Date of Patent: August 9, 2016Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
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Publication number: 20150087528Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: August 4, 2014Publication date: March 26, 2015Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. MAKAROV, Irina SLEPTSOVA, Emmanuel KAMBEROV, Eric BRUENING
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Patent number: 8815504Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: GrantFiled: February 1, 2010Date of Patent: August 26, 2014Assignee: Rubicon Genomics, Inc.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening
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Publication number: 20130085083Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: ApplicationFiled: June 4, 2012Publication date: April 4, 2013Applicant: Rubicon GenomicsInventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Patent number: 8206913Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.Type: GrantFiled: March 3, 2010Date of Patent: June 26, 2012Assignee: Rubicon Genomics, Inc.Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
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Publication number: 20100145037Abstract: The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3? end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.Type: ApplicationFiled: February 1, 2010Publication date: June 10, 2010Applicant: RUBICON GENOMICS, INC.Inventors: Vladimir L. Makarov, Irina Sleptsova, Emmanuel Kamberov, Eric Bruening