Patents by Inventor Luis H. Ceze
Luis H. Ceze 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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Publication number: 20240060125Abstract: In some embodiments, a molecular tagging system that uses synthetic DNA-based tags is provided. In some embodiments, a kit for tagging objects with molecular tags is provided that comprises a plurality of molbit reservoirs. Each molbit reservoir is associated with a molbit and includes nucleic acid molecules that represent the molbit. In some embodiments, a method is provided wherein a digital tag value is determined, the digital tag value is converted to a molbit tag value, nucleic acid molecules associated with each molbit value indicated as present in the molbit tag value are combined, and the combined nucleic acid molecules are applied to an object to tag the object. In some embodiments, a system is provided that includes a computing system configured to receive raw nanopore signals from a sequencing device, to identify molbits based on the signals, and to determine a digital tag based on the identified molbits.Type: ApplicationFiled: May 10, 2023Publication date: February 22, 2024Applicant: University of WashingtonInventors: Luis H. Ceze, Kathryn J. Doroschak, Jeffrey M. Nivala
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Publication number: 20220347645Abstract: A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.Type: ApplicationFiled: July 12, 2022Publication date: November 3, 2022Inventors: Bichlien H. NGUYEN, Douglas P. KELLEY, Karin STRAUSS, Robert CARLSON, Hsing-Yeh PARKER, John MULLIGAN, Luis H. CEZE, Yuan-Jyue CHEN, Douglas CARMEAN
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Patent number: 11439970Abstract: A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.Type: GrantFiled: May 22, 2018Date of Patent: September 13, 2022Assignee: MICROSOFT TECHNOLOGY LICENSING, LLCInventors: Bichlien H Nguyen, Douglas P Kelley, Karin Strauss, Robert Carlson, Hsing-Yeh Parker, John Mulligan, Luis H Ceze, Yuan-Jyue Chen, Douglas Carmean
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Publication number: 20200370111Abstract: In some embodiments, a molecular tagging system that uses synthetic DNA-based tags is provided. In some embodiments, a kit for tagging objects with molecular tags is provided that comprises a plurality of molbit reservoirs. Each molbit reservoir is associated with a molbit and includes nucleic acid molecules that represent the molbit. In some embodiments, a method is provided wherein a digital tag value is determined, the digital tag value is converted to a molbit tag value, nucleic acid molecules associated with each molbit value indicated as present in the molbit tag value are combined, and the combined nucleic acid molecules are applied to an object to tag the object. In some embodiments, a system is provided that includes a computing system configured to receive raw nanopore signals from a sequencing device, to identify molbits based on the signals, and to determine a digital tag based on the identified molbits.Type: ApplicationFiled: May 20, 2020Publication date: November 26, 2020Applicant: University of WashingtonInventors: Luis H. Ceze, Kathryn J. Doroschak, Jeffrey M. Nivala
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Patent number: 10793897Abstract: 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: GrantFiled: February 8, 2017Date of Patent: October 6, 2020Assignee: Microsoft Technology Licensing, LLCInventors: Yuan-Jyue Chen, Luis H. Ceze, Sergey Yekhanin, Siena Dumas Ang, Karin Strauss
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Patent number: 10787699Abstract: 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: GrantFiled: February 8, 2017Date of Patent: September 29, 2020Assignee: Microsoft Technology Licensing, LLCInventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Siena Dumas Ang, Sergey Yekhanin
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Patent number: 10774379Abstract: 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: GrantFiled: March 15, 2017Date of Patent: September 15, 2020Assignee: Microsoft Technology Licensing, LLCInventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick
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Patent number: 10689684Abstract: 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: GrantFiled: February 14, 2017Date of Patent: June 23, 2020Assignee: Microsoft Technology Licensing, LLCInventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick, Randolph Lopez, Georg Seelig
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Publication number: 20190358604Abstract: A system includes a synthesizer unit having a fluid input to receive fluids and a communication input to receive commands to synthesize data-encoded DNA sequences and cleave the DNA. A first flexible chemistry reaction chamber module may be fluidically coupled to the synthesizer unit to receive the data-encoded DNA sequences and amplify the sequences. A deposition unit may be fluidically coupled to the first flexible chemistry reaction chamber module to receive the amplified DNA sequences and encapsulate the amplified DNA sequences into one or more wells in a storage plate for storage and retrieval to and from a plate storage unit. Retrieved DNA may be processed and read by further units.Type: ApplicationFiled: May 22, 2018Publication date: November 28, 2019Inventors: Bichlien H. Nguyen, Douglas P. Kelley, Karin Strauss, Robert Carlson, Hsing-Yeh Parker, John Mulligan, Luis H. Ceze, Yuan-Jyue Chen, Douglas Carmean
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Publication number: 20180265921Abstract: 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: ApplicationFiled: March 15, 2017Publication date: September 20, 2018Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick
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Publication number: 20180230509Abstract: 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: ApplicationFiled: February 14, 2017Publication date: August 16, 2018Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Lee Organick, Randolph Lopez, Georg Seelig
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Publication number: 20180223340Abstract: 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: ApplicationFiled: February 8, 2017Publication date: August 9, 2018Inventors: Yuan-Jyue Chen, Luis H. Ceze, Sergey Yekhanin, Siena Dumas Ang, Karin Strauss
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Publication number: 20180223341Abstract: 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: ApplicationFiled: February 8, 2017Publication date: August 9, 2018Inventors: Yuan-Jyue Chen, Karin Strauss, Luis H. Ceze, Siena Dumas Ang, Sergey Yekhanin
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Publication number: 20170141793Abstract: This disclosure provides techniques for adding error correction to information in a data store that encodes information as a sequence of bases in polynucleotides. Errors may be introduced through creation of the database (e.g., oligonucleotide synthesis) and/or reading information from the database (e.g., polynucleotide sequencing). Additional polynucleotides added to the database can provide error correction through redundancy. The sequence of polynucleotides that provide error correction may be designed by performing an invertible summary operation on information to be stored in the database. One example of an invertible summary operation is the exclusive or operation (XOR). This disclosure also provides techniques for storing metadata related to organization of a database and structure of information on polynucleotides within the database. Metadata may be encoded in polynucleotides and added to the data store.Type: ApplicationFiled: January 22, 2016Publication date: May 18, 2017Inventors: Karin Strauss, Siena Dumas Ang, Luis H. Ceze, James Bornholt
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Patent number: 9507647Abstract: In a multiprocessor system, a conflict checking mechanism is implemented in the L2 cache memory. Different versions of speculative writes are maintained in different ways of the cache. A record of speculative writes is maintained in the cache directory. Conflict checking occurs as part of directory lookup. Speculative versions that do not conflict are aggregated into an aggregated version in a different way of the cache. Speculative memory access requests do not go to main memory.Type: GrantFiled: January 18, 2011Date of Patent: November 29, 2016Assignee: GLOBALFOUNDRIES INC.Inventors: Matthias A. Blumrich, Luis H. Ceze, Dong Chen, Alan Gara, Phlip Heidelberger, Martin Ohmacht, Burkhard Steinmacher-Burow, Xiaotong Zhuang
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Patent number: 9501333Abstract: A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.Type: GrantFiled: December 30, 2013Date of Patent: November 22, 2016Assignee: International Business Machines CorporationInventors: Daniel Ahn, Luis H. Ceze, Dong Chen Chen, Alan Gara, Philip Heidelberger, Martin Ohmacht
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Publication number: 20140207987Abstract: A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.Type: ApplicationFiled: December 30, 2013Publication date: July 24, 2014Applicant: INTERNATIONAL BUSINESS MACHINES CORPORATIONInventors: Daniel Ahn, Luis H. Ceze, Dong Chen Chen, Alan Gara, Philip Heidelberger, Martin Ohmacht
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Patent number: 8751748Abstract: In a parallel processing system with speculative execution, conflict checking occurs in a directory lookup of a cache memory that is shared by all processors. In each case, the same physical memory address will map to the same set of that cache, no matter which processor originated that access. The directory includes a dynamic reader set encoding, indicating what speculative threads have read a particular line. This reader set encoding is used in conflict checking. A bitset encoding is used to specify particular threads that have read the line.Type: GrantFiled: January 18, 2011Date of Patent: June 10, 2014Assignee: International Business Machines CorporationInventors: Daniel Ahn, Luis H. Ceze, Alan Gara, Martin Ohmacht, Zhuang Xiaotong
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Patent number: 8694997Abstract: A hardware and/or software facility for controlling the order of operations performed by threads of a multithreaded application on a multiprocessing system is provided. The facility may serialize or selectively-serialize execution of the multithreaded application such that, given the same input to the multithreaded application, the multiprocessing system deterministically interleaves operations, thereby producing the same output each time the multithreaded application is executed. The facility divides the execution of the multithreaded application code into two or more quantum specifying a deterministic number of operations, and the facility specifies a deterministic order in which the threads execute the two or more quantum. The facility may operate together with a transactional memory system.Type: GrantFiled: December 12, 2008Date of Patent: April 8, 2014Assignee: University of WashingtonInventors: Luis H. Ceze, Mark H. Oskin
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Patent number: 8621478Abstract: A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.Type: GrantFiled: January 18, 2011Date of Patent: December 31, 2013Assignee: International Business Machines CorporationInventors: Daniel Ahn, Luis H. Ceze, Dong Chen, Alan Gara, Philip Heidelberger, Martin Ohmacht