Patents by Inventor Willem P.C. Stemmer

Willem P.C. Stemmer 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).

  • Publication number: 20170016042
    Abstract: The present invention relates to binding fusion protein compositions comprising targeting moieties linked to extended recombinant polypeptide (XTEN), binding fusion protein-drug conjugate compositions, and XTEN-drug conjugate compositions, isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of using such compositions in treatment of diseases, disorders, and conditions.
    Type: Application
    Filed: December 21, 2015
    Publication date: January 19, 2017
    Inventors: Volker Schellenberger, Joshua Silverman, Chia-wei Wang, Benjamin Spink, Willem P.C. Stemmer, Nathan C. Geething
  • Patent number: 8589085
    Abstract: In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.
    Type: Grant
    Filed: March 29, 2012
    Date of Patent: November 19, 2013
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Sergey A. Selifonov, Willem P. C. Stemmer
  • Patent number: 8377681
    Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.
    Type: Grant
    Filed: December 2, 2011
    Date of Patent: February 19, 2013
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Stephen DelCardayre, Matthew B. Tobin, Willem P. C. Stemmer, Jon E. Ness, Jeremy S. Minshull, Phillip A. Patten, Venkiteswatan Mani Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Anthony R. Cox, Gjalt W. Huisman, Ling Yuan, Joseph A. Affholter
  • Publication number: 20120252701
    Abstract: A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins.
    Type: Application
    Filed: August 18, 2011
    Publication date: October 4, 2012
    Applicant: CODEXIS, INC.
    Inventors: Willem P.C. Stemmer, Andreas Crameri
  • Publication number: 20120252684
    Abstract: In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.
    Type: Application
    Filed: March 29, 2012
    Publication date: October 4, 2012
    Applicant: CODEXIS MAYFLOWER HOLDINGS, LLC
    Inventors: Sergey A. Selifonov, Willem P.C. Stemmer
  • Publication number: 20120252681
    Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.
    Type: Application
    Filed: December 2, 2011
    Publication date: October 4, 2012
    Applicant: CODEXIS MAYFLOWER HOLDINGS, LLC
    Inventors: Stephen del Cardayre, Matthew Tobin, Willem P.C. Stemmer, Jon E. Ness, Jeremy Minshull, Phillip Patten, Venkiteswaran Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Tony Cox, Gjalt Huisman, Ling Yuan, Joseph A. Affholter
  • Patent number: 8170806
    Abstract: In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.
    Type: Grant
    Filed: September 11, 2009
    Date of Patent: May 1, 2012
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Sergey A. Selifonov, Willem P. C. Stemmer
  • Publication number: 20120015820
    Abstract: Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed.
    Type: Application
    Filed: September 1, 2011
    Publication date: January 19, 2012
    Applicant: CODEXIS MAYFLOWER HOLDINGS, LLC
    Inventors: Phillip A. Patten, Willem P.C. Stemmer
  • Patent number: 8076138
    Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.
    Type: Grant
    Filed: October 15, 2009
    Date of Patent: December 13, 2011
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Stephen DelCardayre, Matthew B. Tobin, Willem P. C. Stemmer, Jon E. Ness, Jeremy S. Minshull, Phillip A. Patten, Venkiteswatan Mani Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Anthony R. Cox, Gjalt W. Huisman, Ling Yuan, Joseph A. Affholter
  • Patent number: 8058001
    Abstract: 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: Grant
    Filed: September 11, 2009
    Date of Patent: November 15, 2011
    Assignee: Codexis Mayflower Holdings LLC
    Inventors: Andreas Crameri, Willem P. C. Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, John E. Ness, Claes Gustafsson, Phillip A. Patten
  • Patent number: 8048674
    Abstract: The present invention is generally directed to the evolution of new metabolic pathways and the enhancement of bioprocessing through a process herein termed recursive sequence recombination. Recursive sequence recombination entails performing iterative cycles of recombination and screening or selection to “evolve” individual genes, whole plasmids or viruses, multigene clusters, or even whole genomes. Such techniques do not require the extensive analysis and computation required by conventional methods for metabolic engineering.
    Type: Grant
    Filed: September 11, 2009
    Date of Patent: November 1, 2011
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Jeremy Minshull, Willem P. C. Stemmer
  • Publication number: 20110257892
    Abstract: In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.
    Type: Application
    Filed: April 27, 2011
    Publication date: October 20, 2011
    Applicant: CODEXIS MAYFLOWER HOLDINGS, LLC
    Inventors: Sergey A. Selifonov, Willem P.C. Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip A. Patten, Jeremy Minshull, Lorraine J. Giver
  • Patent number: 8029988
    Abstract: 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: Grant
    Filed: November 30, 2007
    Date of Patent: October 4, 2011
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Andreas Crameri, Willem P. C. Stemmer, Jeremy Minshull, Steven H. Bass, Mark Welch, Jon E. Ness, Claes Gustafsson, Phillip A. Patten
  • Patent number: 8014961
    Abstract: Integrated systems and methods for diversity generation and screening are provided. The systems use common fluid and array handling components to provide nucleic acid diversification, transcription, translation, product screening and subsequent diversification reactions.
    Type: Grant
    Filed: February 21, 2007
    Date of Patent: September 6, 2011
    Assignee: Codexis Mayflower Holdings, LLC
    Inventors: Steven H. Bass, Simon Christopher Davis, Phillip A. Patten, Matthew Tobin, Jeremy S. Minshull, Mark Welch, Claus Gustafsson, Brian Carr, Stephan J. Jenne, Sun Ai Raillard, Andreas Crameri, Willem P. C. Stemmer, Robin Emig, Pascal Longchamp, Stanley Goldman, Lorraine J. Giver, Joseph A. Affholter
  • Publication number: 20110190140
    Abstract: The invention provides methods employing iterative cycles of recombination and selection/screening for evolution of whole cells and organisms toward acquisition of desired properties. Examples of such properties include enhanced recombinogenicity, genome copy number, and capacity for expression and/or secretion of proteins and secondary metabolites.
    Type: Application
    Filed: October 15, 2009
    Publication date: August 4, 2011
    Applicant: Maxygen, Inc.
    Inventors: Stephen del Cardayre, Matthew Tobin, Willem P.C. Stemmer, Jon E. Ness, Jeremy Minshull, Phillip Patten, Venkiteswatan Subramanian, Linda A. Castle, Claus M. Krebber, Steven H. Bass, Ying-Xin Zhang, Tony Cox, Gjalt Huisman, Ling Yuan, Joseph A. Affholter
  • Patent number: 7981614
    Abstract: A method for DNA reassembly after random fragmentation, and its application to mutagenesis of nucleic acid sequences by in vitro or in vivo recombination is described. In particular, a method for the production of nucleic acid fragments or polynucleotides encoding mutant proteins is described. The present invention also relates to a method of repeated cycles of mutagenesis, shuffling and selection which allow for the directed molecular evolution in vitro or in vivo of proteins.
    Type: Grant
    Filed: September 11, 2009
    Date of Patent: July 19, 2011
    Assignee: Codexis Mayflower Holdings LLC
    Inventors: Willem P. C. Stemmer, Andreas Crameri
  • Patent number: 7968681
    Abstract: Polypeptides comprising monomer domains that bind to c-MET, or portions thereof, are provided.
    Type: Grant
    Filed: April 15, 2010
    Date of Patent: June 28, 2011
    Assignee: Amgen Mountain View, Inc.
    Inventors: Willem P. C. Stemmer, D. Victor Perlroth, Sanjeev Satyal, Benjamin M. Alba, Alice Bakker, Amy N. Duguay, Qiang Lui, Joshua Silverman, Richard Smith, Candace Swimmer
  • Patent number: 7957912
    Abstract: In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided. One disclosed method involves identifying and producing a polypeptide. The method may involve (a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides; (b) selecting one or more cross-over sites on the sequences thereby defining one or more recombinant polypeptides or recombinant nucleic acids; (c) selecting at least one of the recombinant polypeptides or recombinant nucleic acids; (d) recombining one or more oligonucleotides, at least one of which has a sequence matching some or all of that of the recombinant polypeptides or recombinant nucleic acids selected in (c); (e) selecting at least some of the recombined oligonucleotides produced in (d); and (f) producing a polypeptide encoded by the selected nucleic acid.
    Type: Grant
    Filed: September 10, 2009
    Date of Patent: June 7, 2011
    Assignee: Codexis Mayflower Holdings LLC
    Inventors: Sergey A. Selifonov, Willem P. C. Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip A. Patten, Jeremy Minshull, Lorraine J. Giver
  • Patent number: 7904249
    Abstract: In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators are used to identify sets of oligonucleotides for in vitro recombination. In certain embodiments, the methods involve inputting amino acid sequence character strings into a digital system and back-translating the amino acid character strings into a plurality of nucleic acid character strings. The nucleic acid character strings are then processed to define and select at least one recombinant nucleic acid for use in identifying one or more oligonucleotides for in vitro recombination.
    Type: Grant
    Filed: October 31, 2007
    Date of Patent: March 8, 2011
    Assignee: Codexis Mayflower Holding, LLC
    Inventors: Sergey A. Selifonov, Willem P. C. Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip A. Patten, Jeremy Minshull, Lorraine J. Giver
  • Publication number: 20110053781
    Abstract: Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed.
    Type: Application
    Filed: September 11, 2009
    Publication date: March 3, 2011
    Applicant: Maxygen, Inc.
    Inventors: Phillip A. Patten, Willem P.C. Stemmer