Patents by Inventor Karin Strauss

Karin Strauss 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: 20210106967
    Abstract: High surface area coatings are applied to solid substrates to increase the surface area available for solid-phase synthesis of polymers. The high surface area coatings use three-dimensional space to provide more area for functional groups to bind polymers than an untreated solid substrate. The polymers may be oligonucleotides, polypeptides, or another type of polymer. The solid substrate is a rigid supportive layer made from a material such as glass, a silicon material, a metal material, and plastic. The coating may be thin films, hydrogels, microparticles. The coating may be made from a metal oxide, a high-? dielectric, a low-? dielectric, an etched metal, a carbon material, or an organic polymer. The functional groups may be hydroxyl groups, amine groups, thiolate groups, alkenes, n-alkenes, alkalines, N-Hydroxysuccinimide (NHS)-activated esters, polyaniline, aminosilane groups, silanized oxides, oligothiophenes, and diazonium compounds.
    Type: Application
    Filed: October 9, 2019
    Publication date: April 15, 2021
    Inventors: Bichlien Hoang Nguyen, Karin Strauss, Hsing-Yeh Parker
  • Publication number: 20210074380
    Abstract: Redundancy information can be included in nucleotide symbol strings encoding underlying data. To avoid propagation of errors during the decoding process, during encoding, a constrained encoding can be performed before the redundancy information is computed. The redundancy information can be an outer encoding across multiple nucleotide symbol strings. An inner coding within nucleotide symbol strings can also be supported. Such redundancy information can be interleaved into the underlying nucleotide symbol strings to which the constrained encoding has been applied, resulting in a relaxed constraint. Insertion/deletion redundancy information can also be included in the resulting strings, and an insertion/deletion-sensitive sequence can be included to assist in recovering accurate sequences during decoding operations.
    Type: Application
    Filed: September 5, 2019
    Publication date: March 11, 2021
    Applicant: Microsoft Technology Licensing, LLC
    Inventors: Sergey Yekhanin, Sivakanth Gopi, Henry Pfister, Karin Strauss
  • Publication number: 20210071170
    Abstract: Array-based enzymatic oligonucleotide synthesis creates a large number of polynucleotides using an uncontrolled and template independent polymerase such as terminal deoxynucleotidyl transferase (TdT). Spatial control of reaction conditions on the surface of the array allows creation of polynucleotides with a variety of arbitrary sequences. Spatial control may be implemented by removing protecting groups attached to nucleotides only at a selected location on the array or by other techniques such as location-specific regulation of enzymatic activity. The ratio of polynucleotides with protecting groups to unprotected polynucleotides used during a cycle of synthesis is adjusted to control the length of homopolymers created by the polymerase. Digital information may be encoded in the enzymatically synthesized polynucleotides.
    Type: Application
    Filed: September 6, 2019
    Publication date: March 11, 2021
    Inventors: Bichlien NGUYEN, Sergey YEKHANIN, Karin STRAUSS
  • Patent number: 10930370
    Abstract: Artificial polynucleotides may have different characteristics than natural polynucleotides so conventional base-calling algorithms may make incorrect base calls. However, because artificial polynucleotides are typically designed to have certain characteristics, the known characteristics of the artificial polynucleotide can be used to modify the base-calling algorithm. This disclosure describes polynucleotide sequencers adapted to sequence artificial polynucleotides by modifying a base-calling algorithm of the polynucleotide sequencer according to known characteristics of the artificial polynucleotides. The base-calling algorithm analyzes raw data generated by a polynucleotide sequencer and identifies which nucleotide base occupies a given position on a polynucleotide strand.
    Type: Grant
    Filed: May 26, 2017
    Date of Patent: February 23, 2021
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Karin Strauss, Siena Dumas Ang, Luis Ceze, Yuan-Jyue Chen, Hsing-Yeh Parker, Bichlien Nguyen, Robert Carlson
  • Publication number: 20210050073
    Abstract: Multiplex similarity search can be performed in a DNA data storage context. The described technologies can support a plurality of different DNA data storage queries in a single query run. A linking strand can be used to connect a query to its matching data element. After the query finds a matching data element, a result strand can be sequenced to the reveal the matching data element as well as which of the queries resulted in the match. Thus, in a multiplex similarity search scenario, a plurality of result strands from a single query run can be correlated to a plurality of different queries. Also, the result strand can be of significantly longer length than both the unmatched data strands and the unmatched query strands. Therefore, filtering based on length can provide more accurate results.
    Type: Application
    Filed: August 14, 2019
    Publication date: February 18, 2021
    Applicant: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss
  • Publication number: 20210035657
    Abstract: A technique for clustering DNA reads from polynucleotide sequencing is described. DNA reads with a level of difference that is likely caused by errors in sequencing are grouped together in the same cluster. DNA reads that represent reads of different DNA molecules are placed in different clusters. The clusters are based on edit distance, which is the number of changes necessary to convert a given DNA read into another. The process of forming clusters may be performed iteratively and may use other types of distance that serve as an approximation for edit distance. Well clustered DNA reads provide a starting point for further analysis.
    Type: Application
    Filed: September 25, 2017
    Publication date: February 4, 2021
    Inventors: Luis CEZE, Sergey YEKHANIN, Siena Dumas ANG, Karin STRAUSS, Cyrus RASHTCHIAN, Ravindran KANNAN, Konstantin MAKARYCHEV
  • Publication number: 20200391175
    Abstract: Reagents and solvents used for polymer synthesis are reused or recycled rather than discarded. The outflow from each step of polymer synthesis may be collected separately in one of multiple dedicated containers. Reuse returns the outflow from a step of polymer synthesis back to an input of a polymer synthesizer for subsequent use in that same step. Recycling processes the outflow from one or more steps of polymer synthesis to restore original concentrations or purity levels for use in a later synthesis run. Quality control analysis may determine if outflow collected from a polymer synthesizer is reused or recycled. These techniques reduce reagent cost and waste quantity. These techniques may be used with phosphoramidite or enzyme-based synthesis of deoxyribonucleic acid (DNA).
    Type: Application
    Filed: June 17, 2019
    Publication date: December 17, 2020
    Inventors: Bichlien Hoang NGUYEN, Karin Strauss, Douglas P. Kelley
  • Publication number: 20200384434
    Abstract: Polymers synthesized by solid-phase synthesis are selectively released from a solid support by reversing the bias of spatially addressable electrodes. Change in the current and voltage direction at one or more of the spatially addressable electrodes changes the ionic environment which triggers cleavage of linkers that leads to release of the attached polymers. The spatially addressable electrodes may be implemented as CMOS inverters embedded in an integrated circuit (IC). The IC may contain an array of many thousands of spatially addressable electrodes. Control circuity may independently reverse the bias on any of the individual electrodes in the array. This provides fine-grained control of which polymers are released from the solid support. Examples of polymers that may be synthesized on this type of array include oligonucleotides and peptides.
    Type: Application
    Filed: June 7, 2019
    Publication date: December 10, 2020
    Inventors: Bichlien NGUYEN, Karin STRAUSS, Gagan GUPTA, Richard ROUSE
  • Publication number: 20200388351
    Abstract: The efficiency of polymer synthesis is increased by reducing the number of monomer addition cycles needed to create a set of polymer strands. The number of cycles depends on the sequences of the polymer strands and the order in which each type of monomer is made available for addition to the growing strands. Efficiencies are created by grouping the polymer strands into batches such that all the strands in a batch require a similar number of cycles to synthesize. Efficiencies are also created by selecting an order in which the monomers are made available for addition to the growing polymer strands in a batch. Both techniques can be used together. With these techniques, the number of cycles of monomer addition and commensurate reagent use may be reduced by over 10% as compared to naïve synthesis techniques.
    Type: Application
    Filed: June 7, 2019
    Publication date: December 10, 2020
    Inventors: Sergey YEKHANIN, Miklos RACZ, Konstantin MAKARYCHEV, Cyrus A. RASHTCHIAN, Karin STRAUSS, Bichlien Hoang NGUYEN
  • Patent number: 10793852
    Abstract: A data storage medium is disclosed comprising a dried product formed by drying a salt solution dried together with artificially synthesized DNA molecules encoding digital information. The cation in the salt may be calcium, magnesium, lanthanum, or another cation. The anion in the salt may be chloride, phosphate, or another anion. The DNA is protected from degradation by drying with the salt. Stored DNA may be freed from the salt for sequencing or other analysis by mixing the dried product with a chelator. The dry product formed from DNA and a salt may contain more than 30% DNA by weight and degrade at rates that are less than a third of rate at which untreated DNA degrades.
    Type: Grant
    Filed: June 25, 2018
    Date of Patent: October 6, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Karin Strauss, Weida Chen, Robert Grass, Alexander Xavier Christof Kohll, Bichlien Hoang Nguyen
  • Patent number: 10793897
    Abstract: This disclosure describes techniques to improve the accuracy of random access of data stored in polynucleotide sequence data storage systems. Primers used in polynucleotide sequence replication and amplification can be scored against a number of criteria that indicate the fitness of sequences of nucleotides to function as primers. Primers having scores that indicate a particular fitness to function as primers can be added to a specific group of primers. The primers from the group of primers can be used in amplification and replication of polynucleotide sequences that encode digital data. Additionally, an amount of overlap between primer targets and payloads encoding digital data can be determined. Minimizing the amount of overlap between primer targets and payloads can improve the efficiency of polynucleotide replication and amplification. The bits of the digital data can be randomized to minimize the amount of overlap between payloads encoding the digital data and primer targets.
    Type: Grant
    Filed: February 8, 2017
    Date of Patent: October 6, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Luis H. Ceze, Sergey Yekhanin, Siena Dumas Ang, Karin Strauss
  • Patent number: 10787699
    Abstract: This disclosure describes techniques to improve the accuracy of random access of data stored in polynucleotide sequence data storage systems. Primers used in polynucleotide sequence replication and amplification can be scored against a number of criteria that indicate the fitness of sequences of nucleotides to function as primers. Primers having scores that indicate a particular fitness to function as primers can be added to a specific group of primers. The primers from the group of primers can be used in amplification and replication of polynucleotide sequences that encode digital data. Additionally, an amount of overlap between primer targets and payloads encoding digital data can be determined. Minimizing the amount of overlap between primer targets and payloads can improve the efficiency of polynucleotide replication and amplification. The bits of the digital data can be randomized to minimize the amount of overlap between payloads encoding the digital data and primer targets.
    Type: Grant
    Filed: February 8, 2017
    Date of Patent: September 29, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Siena Dumas Ang, Sergey Yekhanin
  • Patent number: 10774379
    Abstract: This disclosure describes frameworks and techniques related to the random access of digital data encoded by polynucleotides. Digital data of a data file can be encoded as a series of nucleotides and one or more polynucleotide sequences can be generated that encode the digital data for the data file. The bits of the digital data can be segmented to produce multiple polynucleotide sequences that encode the bits of the digital data with each polynucleotide sequence encoding an individual segment of the digital data. The individual segments can be grouped together and associated with a group identifier. Each data file can be associated with a number of group identifiers and the number of segments in each group can be within a specified range. Primers corresponding to the group identifiers can be used to selectively access the polynucleotides that encode the digital data of a data file.
    Type: Grant
    Filed: March 15, 2017
    Date of Patent: September 15, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick
  • Publication number: 20200199662
    Abstract: Selectively controllable cleavable linkers include electrochemically-cleavable linkers, photolabile linkers, thermolabile linkers, chemically-labile linkers, and enzymatically-cleavable linkers. Selective cleavage of individual linkers may be controlled by changing local conditions. Local conditions may be changed by activating electrodes in proximity to the linkers, exposing the linkers to light, heating the linkers, or applying chemicals. Selective cleaving of enzymatically-cleavable linkers may be controlled by designing the sequences of different sets of the individual linkers to respond to different enzymes. Cleavable linkers may be used to attach polymers to a solid substrate. Selective cleavage of the linkers enables release of specific polymers from the solid substrate. Cleavable linkers may also be used to attach protecting groups to the ends of growing polymers. The protecting groups may be selectively removed by cleavage of the linkers to enable growth of specific polymers.
    Type: Application
    Filed: December 21, 2018
    Publication date: June 25, 2020
    Inventors: Karin STRAUSS, Bichlien Hoang NGUYEN
  • Publication number: 20200202223
    Abstract: Neural networks can be implemented with DNA strand displacement (DSD) circuits. The neural networks are designed and trained in silico taking into account the behavior of DSD circuits. Oligonucleotides comprising DSD circuits are synthesized and combined to form a neural network. In an implementation, the neural network may be a binary neural network in which the output from each neuron is a binary value and the weight of each neuron either maintains the incoming binary value or flips the binary value. Inputs to the neural network are one more oligonucleotides such as synthetic oligonucleotides containing digital data or natural oligonucleotides such as mRNA. Outputs from the neural networks may be oligonucleotides that are read by directly sequencing or oligonucleotides that generate signals such as by release of fluorescent reporters.
    Type: Application
    Filed: December 21, 2018
    Publication date: June 25, 2020
    Inventors: Karin STRAUSS, Luis CEZE, Johannes Staffan Anders LINDER
  • Patent number: 10689684
    Abstract: This disclosure describes techniques to improve the sequencing of polynucleotides by decreasing the likelihood of errors occurring during a sequencing calibration process. In implementations, regions of polynucleotides that are used for the calibration process can be modified to reduce a number of polynucleotides that have a same nucleotide at one or more positions of the calibration regions. In some cases, the calibration regions can be modified by adding a sequence to the polynucleotides that replaces the original calibration regions. Also, the calibration regions can be modified by rearranging the nucleotides at the different positions of the calibration regions. Additionally, the calibration regions can be modified by adding sequences of varying length to the polynucleotides being sequenced to produce polynucleotides having varying length with different calibration regions.
    Type: Grant
    Filed: February 14, 2017
    Date of Patent: June 23, 2020
    Assignee: Microsoft Technology Licensing, LLC
    Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick, Randolph Lopez, Georg Seelig
  • Publication number: 20200140849
    Abstract: A data storage medium is disclosed comprising a two-dimensional (2D) support structure onto which artificially synthesized DNA molecules encoding digital information are placed and then covered with a protective layer. The 2D support structure is formed from a material such as metal foil, glass, or plastic. The 2D support structure may be functionalized with positively charged molecules to improve DNA adhesion. The DNA is protected from degradation by encapsulation in a protective layer of a non-reactive material such as silica or a thin layer of metal. A process for storing DNA on 2D support structures is also disclosed. Correlation of specific DNA molecules with a physical storage location on a 2D support structure provides geometric addressability for selective access to specific digital information.
    Type: Application
    Filed: November 2, 2018
    Publication date: May 7, 2020
    Inventors: Karin STRAUSS, Bichlien Hoang NGUYEN, Robert N. GRASS, Alexander Xavier Christof KOHLL, Weida CHEN
  • Publication number: 20200129432
    Abstract: Polynucleotides such as DNA are stored inside vesicles formed from self-assembling membranes. The vesicles may be protocells, liposome, micelles, colloidosomes, proteinosomes, or coacervates. The vesicles may include surface functionalization to improve polynucleotide encapsulation and/or to bind polynucleotides having specific sequences. Encapsulation in vesicles provides protection for the polynucleotides. Additional protection is provided by addition of one or more stabilizers. The stabilizer may be nucleic-acid stabilizers that stabilize the polynucleotides or may be a protective structural layer around the vesicles such as a layer of silica. A process for stably storing polynucleotides in vesicles and a process for recovering stored polynucleotides from vesicles are both disclosed. The polynucleotides may be used for storage of digital information.
    Type: Application
    Filed: October 31, 2018
    Publication date: April 30, 2020
    Inventors: Karin STRAUSS, Bichlien Hoang NGUYEN
  • Publication number: 20200004926
    Abstract: This disclosure describes an efficient method to copy all polynucleotides encoding digital data of digital files in a polynucleotide storage container while maintaining random access capabilities over a collection of files or data items in the container. The disclosure further describes a process whereby random-access and sequencing of the polynucleotides are combined in a single step.
    Type: Application
    Filed: June 29, 2018
    Publication date: January 2, 2020
    Inventors: Karin Strauss, Yuan Jyue Chen
  • Publication number: 20190388862
    Abstract: A data storage medium is disclosed comprising a substrate covered with alternating layers of a polycationic molecule and artificially synthesized DNA molecules encoding digital information. The magnetic substrate may be a metallic nanoparticle formed from a metal such as iron or cobalt. The polycationic molecule may be polyethyleneimine (PEI). The DNA is protected from degradation by encapsulation in silica. A process for stably storing DNA is also disclosed. Stored DNA may be freed from the silica for sequencing or other analysis by washing the silica-coated DNA with a buffered hydrogen fluoride solution. Storage densities of more than 7% DNA by weight are achieved on nanoparticles.
    Type: Application
    Filed: June 25, 2018
    Publication date: December 26, 2019
    Inventors: Karin STRAUSS, Weida CHEN, Robert GRASS, Alexander Xavier Christof KOHLL, Bichlien Hoang NGUYEN