Patents by Inventor Claes Gustafsson
Claes Gustafsson 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: 10883137Abstract: The present invention relates to methods for detection of nucleotide polymerase activity and methods of detecting compounds that modulate nucleotide polymerase activity, by detecting product formation of the nucleotide polymerase to be tested based on determination of close proximity of two labeled nucleotide probes able to bind the product of the nucleotide polymerase. It is preferred that proximity dependent energy transfer, such as forster resonance energy transfer, between said labeled nucleotide probes is determined. The invention further provides kits comprising components for carrying out the inventive methods for detection of nucleotide polymerase activity.Type: GrantFiled: May 30, 2016Date of Patent: January 5, 2021Assignees: MAX-PLANCK-GESELLSCHAFT ZUR FÖRDERUNG DER WISSENSCHAFTEN E.V., LEAD DISCOVERY CENTER GMBHInventors: Tim Bergbrede, Nils-Göran Larsson, Claes Gustafsson, Maria Falkenberg-Gustafsson
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Patent number: 9996661Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.Type: GrantFiled: December 28, 2010Date of Patent: June 12, 2018Assignee: Codexis Mayflower Holdings, LLCInventors: Claes Gustafsson, Sridhar Govindarajan, Robin A. Emig, Richard John Fox, Ajoy K. Roy, Jeremy S. Minshull, S. Christopher Davis, Anthony R. Cox, Phillip A. Patten, Linda A. Castle, Daniel L. Siehl, Rebecca Lynne Gorton, Teddy Chen
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Publication number: 20180142285Abstract: The present invention relates to methods for detection of nucleotide polymerase activity and methods of detecting compounds that modulate nucleotide polymerase activity, by detecting product formation of the nucleotide polymerase to be tested based on determination of close proximity of two labeled nucleotide probes able to bind the product of the nucleotide polymerase. It is preferred that proximity dependent energy transfer, such as forster resonance energy transfer, between said labeled nucleotide probes is determined. The invention further provides kits comprising components for carrying out the inventive methods for detection of nucleotide polymerase activity.Type: ApplicationFiled: May 30, 2016Publication date: May 24, 2018Inventors: Tim Bergbrede, Nils-Göran Larsson, Claes Gustafsson, Maria Falkenberg-Gustafsson
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Patent number: 8849575Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.Type: GrantFiled: May 5, 2006Date of Patent: September 30, 2014Assignee: Codexis Mayflower Holdings, LLCInventors: Claes Gustafsson, Sridhar Govindarajan, Robin A. Emig, Richard John Fox, Ajoy K. Roy, Jeremy S. Minshull, S. Christopher Davis, Anthony R. Cox, Phillip A. Patten, Linda A. Castle, Daniel L. Siehl, Rebecca Lynne Gorton, Teddy Chen
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Publication number: 20140032186Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions, and the substitutions for each respective position in the plurality of positions collectively defined a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-actively relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.Type: ApplicationFiled: March 29, 2013Publication date: January 30, 2014Applicant: DNA Twopointo, Inc.Inventors: Claes GUSTAFSSON, Sridhar GOVINDARAJAN, Jeremy Minshull
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Patent number: 8635029Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.Type: GrantFiled: September 25, 2008Date of Patent: January 21, 2014Assignee: DNA Twopointo, Inc.Inventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy Minshull
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Patent number: 8457903Abstract: Computer processing methods and/or systems for minimizing and/or optimizing data strings in accordance with rules and options. Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses. In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions. In specific embodiments, a server can use proprietary methods or data at the server side while protecting those proprietary methods and data from access by the client system.Type: GrantFiled: September 9, 2011Date of Patent: June 4, 2013Assignee: Codexis Mayflower Holdings, LLCInventors: Robin A. Emig, Richard John Fox, Claes Gustafsson, Sridhar Govindarajan, Jeremy S. Minshull, Guy Cavet
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Patent number: 8412461Abstract: Methods, computer systems, and computer program products for antibody engineering. A variant set for an antibody of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the antibody of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of position collectively define an antibody sequence space. A variant set comprising a plurality of variants of the antibody is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the antibody of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.Type: GrantFiled: March 18, 2010Date of Patent: April 2, 2013Assignee: DNA Twopointo, Inc.Inventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy Stephen Minshull
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Patent number: 8401798Abstract: Methods for determining a property that affects expression of polynucleotides are provided. A plurality of polynucleotides each encoding a polypeptide sequence is constructed. A frequency that a sequence element is used in a first polynucleotide is different than in a second polynucleotide. Each polynucleotide is expressed in an expression system to obtain an expression property value thereby constructing a dataset that contains, for each respective polynucleotide, sequence element occurrence in the respective polynucleotide and the measured expression property value of the respective polynucleotide. A model is computed that describes variation in the measured expression property values as a function of a plurality of variables and weights.Type: GrantFiled: July 31, 2008Date of Patent: March 19, 2013Assignee: DNA Twopointo, Inc.Inventors: Mark Welch, Claes Gustafsson
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Patent number: 8224580Abstract: Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination.Type: GrantFiled: June 12, 2007Date of Patent: July 17, 2012Assignee: Codexis Mayflower Holdings LLCInventors: Emily C. Mundorff, Sridhar Govindarajan, Claes Gustafsson, Jeremy S. Minshull
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Patent number: 8126653Abstract: A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.Type: GrantFiled: July 31, 2008Date of Patent: February 28, 2012Assignee: DNA Twopointo, Inc.Inventors: Mark Welch, Claes Gustafsson
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Publication number: 20120040871Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.Type: ApplicationFiled: September 23, 2011Publication date: February 16, 2012Applicant: CODEXIS MAYFLOWER HOLDINGS, LLCInventors: Andreas Crameri, Willem PC Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, Jon E. Ness, Claes Gustafsson, Phillip A Patten
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Patent number: 8108150Abstract: Methods and devices for more efficiently engineering diversity into recombinant polypeptides and/or nucleic acids are provided herein. For example, a variety of methods of selecting and/or assessing potential crossover sites in an amino acid sequence or a nucleotide sequence are provided, as well as the resulting chimeric product sequences. These methods include, e.g., consideration of structural, functional and/or statistical data in the selection and assessment of sequences and crossover sites for use in recombination.Type: GrantFiled: September 10, 2009Date of Patent: January 31, 2012Assignee: Codexis Mayflower Holdings, LLCInventors: Emily C. Mundorff, Sridhar Govindarajan, Claes Gustafsson, Jeremy S. Minshull
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Patent number: 8058001Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.Type: GrantFiled: September 11, 2009Date of Patent: November 15, 2011Assignee: Codexis Mayflower Holdings LLCInventors: Andreas Crameri, Willem P. C. Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, John E. Ness, Claes Gustafsson, Phillip A. Patten
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Publication number: 20110257892Abstract: In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.Type: ApplicationFiled: April 27, 2011Publication date: October 20, 2011Applicant: CODEXIS MAYFLOWER HOLDINGS, LLCInventors: Sergey A. Selifonov, Willem P.C. Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip A. Patten, Jeremy Minshull, Lorraine J. Giver
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Publication number: 20110257023Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.Type: ApplicationFiled: June 24, 2011Publication date: October 20, 2011Applicant: CODEXIS MAYFLOWER HOLDINGS, LLCInventors: Claes Gustafsson, Sridhar Govindarajan, Robin A. Emig, Richard John Fox, Ajoy K. Roy, Jeremy S. Minshull, S. Christopher Davis, Anthony R. Cox, Phillip A. Patten, Linda A. Castle, Daniel L. Siehl, Rebecca Lynne Gorton, Teddy Chen
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Patent number: 8029988Abstract: Methods of recombining nucleic acids, including homologous nucleic acids, are provided. Families of gene shuffling oligonucleotides and their use in recombination procedures, as well as polymerase and ligase mediated recombination methods are also provided.Type: GrantFiled: November 30, 2007Date of Patent: October 4, 2011Assignee: Codexis Mayflower Holdings, LLCInventors: Andreas Crameri, Willem P. C. Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, Jon E. Ness, Claes Gustafsson, Phillip A. Patten
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Patent number: 8008078Abstract: The present invention relates to polynucleotide molecules comprising nucleotide sequences encoding an aveC gene product, which polynucleotide molecules can be used to alter the ratio or amount of class 2:1 avermectins produced in fermentation cultures of S. avermitilis. The present invention further relates to vectors, host cells, and mutant strains of S. avermitilis in which the aveC gene has been inactivated, or mutated so as to change the ratio or amount of class 2:1 avermectins produced.Type: GrantFiled: April 23, 2008Date of Patent: August 30, 2011Assignees: Pfizer Inc., Pfizer Products Inc.Inventors: Kim J. Stutzman-Engwall, Anke Krebber, Claes Gustafsson, Jeremy S. Minshull, Sun Ai Raillard, Seran Kim, Yan Chen
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Patent number: 8005620Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.Type: GrantFiled: July 30, 2004Date of Patent: August 23, 2011Assignee: DNA Twopointo Inc.Inventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy Stephen Minshull
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Publication number: 20110166844Abstract: Methods, computer systems, and computer program products for antibody engineering. A variant set for an antibody of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the antibody of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of position collectively define an antibody sequence space. A variant set comprising a plurality of variants of the antibody is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the antibody of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.Type: ApplicationFiled: March 18, 2010Publication date: July 7, 2011Applicant: DNA TWOPOINTO, INCInventors: Claes Gustafsson, Sridhar Govindarajan, Jeremy Stephen Minshull