Patents by Inventor Stepan Tymoshenko

Stepan Tymoshenko 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: 20230399647
    Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of ectoine and provides novel engineered microbial cells and cultures, as well as related ectoine production methods.
    Type: Application
    Filed: February 11, 2021
    Publication date: December 14, 2023
    Inventors: Stepan Tymoshenko, Anupam Chowdhury, Zhihao Wang, Jeffrey Mellin, Michael Shareef Siddiqui, Cara Ann Tracewell, Alexander Glennon Shearer, Hannah Edstrom, Michael Blaisse
  • Publication number: 20230323406
    Abstract: Provided herein are compositions, systems, and methods comprising effector proteins and uses thereof. These effector proteins are shown to be active with guide RNAs and may be characterized as CRISPR-associated (Cas) proteins. Various compositions, systems, and methods of the present disclosure leverage the activities of these effector proteins for the modification, detection, and engineering of nucleic acids.
    Type: Application
    Filed: June 12, 2023
    Publication date: October 12, 2023
    Inventors: Aaron DELOUGHERY, Matan DRORY RETWITZER, Lucas Benjamin HARRINGTON, Wiputra Jaya HARTONO, Alexander Richard NECKELMANN, David PAEZ-ESPINO, Benjamin Julius RAUCH, Clarissa Oriel RHINES, Stepan TYMOSHENKO, Fnu YUNANDA, William Douglass WRIGHT
  • Publication number: 20230257739
    Abstract: Provided herein are compositions, systems, and methods comprising effector proteins and uses thereof. These effector proteins are shown to be active with guide RNAs and may be characterized as CRISPR-associated (Cas) proteins. Various compositions, systems, and methods of the present disclosure leverage the activities of these effector proteins for the modification, detection, and engineering of nucleic acids.
    Type: Application
    Filed: September 23, 2022
    Publication date: August 17, 2023
    Inventors: Aaron DELOUGHERY, David PAEZ-ESPINO, Benjamin Julius RAUCH, Clarissa Oriel RHINES, Stepan TYMOSHENKO, Fnu YUNANDA, Matan DRORY RETWITZER, Lucas Benjamin HARRINGTON, Wiputra Jaya HARTONO, William Douglass WRIGHT, Alexander Richard NECKELMANN
  • Publication number: 20230073351
    Abstract: Systems, methods, and non-transitory computer-readable media are described for identifying candidate biological sequences for screening to determine whether the candidate biological sequences enable a biological function. Identification may be based upon (a) degrees of similarity between test sequences and reference sequences that are known to enable the function, and (b) comparisons of regions in the test sequences to reference regions that are known to bind to a molecule. Identification may also be based upon determining sequence similarities between reference sequences, grouping the reference sequences into clusters that each correspond to a molecule that is indicated as capable of being bound by a reference sequence in the cluster, and identifying matching test sequences based upon a comparison of the test sequences with reference sequences in the clusters.
    Type: Application
    Filed: February 12, 2021
    Publication date: March 9, 2023
    Applicant: Zymergen Inc.
    Inventors: Eyal Akiva, Rebecca Davidson, Stepan Tymoshenko
  • Publication number: 20220033862
    Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of 2-oxoadipate and provides novel engineered microbial cells and cultures, as well as related 2-oxoadipate production methods.
    Type: Application
    Filed: November 25, 2019
    Publication date: February 3, 2022
    Applicant: Zymergen Inc.
    Inventors: Anupam Chowdhury, Steven M. Edgar, Alexander Glennon Shearer, Cara Ann Tracewell, Stepan Tymoshenko, Zhihao Wang
  • Publication number: 20210256394
    Abstract: The present disclosure provides methods and systems for identifying variants of a given target protein or target gene that perform the same function and/or improve the phenotypic performance of a host cell transformed with such a variant. To enhance the diversity of identified candidate sequences, the methods may implement the use of a metagenomic database and/or machine learning methods. The methods and systems may be implemented in optimizing a biosynthetic pathway, e.g., to improve the production of a target molecule of interest.
    Type: Application
    Filed: February 12, 2021
    Publication date: August 19, 2021
    Inventors: Stepan TYMOSHENKO, Oliver LIU
  • Publication number: 20210225455
    Abstract: Systems, methods and non-transitory computer-readable media identify a candidate biological sequence for enabling a function in a host cell. Embodiments access a predictive model that associates a plurality of biological sequences, such as enzymes, with one or more functions, such as reaction catalysis; predict, using the predictive model, that one or more candidate sequences of the plurality of biological sequences enable a desired function; and classify using a processor, candidate sequences that satisfy a confidence threshold as filtered candidate sequences.
    Type: Application
    Filed: August 14, 2019
    Publication date: July 22, 2021
    Applicant: Zymergen Inc.
    Inventors: Anupam Chowdhury, Alexander Glennon Shearer, Stepan Tymoshenko, Michelle L. Wynn, Erik Jedediah Dean
  • Patent number: 10662415
    Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of (6E)-8-hydroxygeraniol and provides novel engineered microbial cells and cultures, as well as related (6E)-8-hydroxygeraniol production method.
    Type: Grant
    Filed: June 24, 2019
    Date of Patent: May 26, 2020
    Assignee: Zymergen Inc.
    Inventors: Cara Ann Tracewell, Steven M. Edgar, Stepan Tymoshenko, Alexander Glennon Shearer
  • Publication number: 20190338259
    Abstract: The present disclosure describes the engineering of microbial cells for fermentative production of (6E)-8-hydroxygeraniol and provides novel engineered microbial cells and cultures, as well as related (6E)-8-hydroxygeraniol production method.
    Type: Application
    Filed: June 24, 2019
    Publication date: November 7, 2019
    Inventors: Cara Ann Tracewell, Steven M. Edgar, Stepan Tymoshenko, Alexander Glennon Shearer