Patents by Inventor Siena Dumas Ang
Siena Dumas Ang 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: 10930370Abstract: 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: GrantFiled: May 26, 2017Date of Patent: February 23, 2021Assignee: Microsoft Technology Licensing, LLCInventors: Karin Strauss, Siena Dumas Ang, Luis Ceze, Yuan-Jyue Chen, Hsing-Yeh Parker, Bichlien Nguyen, Robert Carlson
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Publication number: 20210035657Abstract: 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: ApplicationFiled: September 25, 2017Publication date: February 4, 2021Inventors: Luis CEZE, Sergey YEKHANIN, Siena Dumas ANG, Karin STRAUSS, Cyrus RASHTCHIAN, Ravindran KANNAN, Konstantin MAKARYCHEV
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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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Publication number: 20180253528Abstract: 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: ApplicationFiled: May 26, 2017Publication date: September 6, 2018Inventors: Karin Strauss, Siena Dumas Ang, Luis Ceze, Yuan-Jyue Chen, Hsing-Yeh Parker, Bichlien Nguyen, Robert Carlson
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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: 20180211001Abstract: Polynucleotide sequencing generates multiple reads of a polynucleotide molecule. Many or all of the reads may contain errors. Trace reconstruction takes multiple reads generated by a polynucleotide sequencer and uses those multiple reads to reconstruct accurately the nucleotide sequence. The types of errors are substitutions, deletions, and insertions. The location of an error in a read is identified by comparing the sequence of the read to the other reads. The type of error is determined by comparing both the base call of the read at the error location and base calls of the read and other reads in a look-ahead window that includes base calls adjacent to the error location. A consensus output sequence is developed from the sequences of the multiple reads and identification of the error types for errors in the reads.Type: ApplicationFiled: April 25, 2017Publication date: July 26, 2018Applicant: Microsoft Technology Licensing, LLCInventors: Parikshit S. Gopalan, Sergey Yekhanin, Siena Dumas Ang, Nebojsa Jojic, Miklos Racz, Karen Strauss, Luis Ceze
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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