Patents by Inventor Igor Nazarenko

Igor Nazarenko 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: 20140188396
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Application
    Filed: December 3, 2013
    Publication date: July 3, 2014
    Applicant: Complete Genomics, Inc.
    Inventors: AARON HALPERN, IGOR NAZARENKO
  • Patent number: 8738296
    Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: May 27, 2014
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Patent number: 8731843
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: May 20, 2014
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Patent number: 8615365
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Grant
    Filed: February 2, 2010
    Date of Patent: December 24, 2013
    Assignee: Complete Genomics, Inc.
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20120197533
    Abstract: Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient.
    Type: Application
    Filed: January 28, 2011
    Publication date: August 2, 2012
    Applicant: Complete Genomics, Inc.
    Inventors: Igor Nazarenko, Aaron L. Halpern, Paolo Carnevali
  • Patent number: 8019751
    Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.
    Type: Grant
    Filed: June 23, 2008
    Date of Patent: September 13, 2011
    Assignee: Oracle International Corporation
    Inventors: Jonathan M. Baccash, Igor Nazarenko, Uri Rodny, Ambuj Shatdal
  • Publication number: 20110015864
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, modifying positions within these keys, and locating the one or more keys in an index configured to map a plurality of candidate and/or validated keys to their respective possible and/or validated locations in a reference.
    Type: Application
    Filed: February 2, 2010
    Publication date: January 20, 2011
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20110004413
    Abstract: Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.
    Type: Application
    Filed: April 29, 2010
    Publication date: January 6, 2011
    Applicant: COMPLETE GENOMICS, INC.
    Inventors: Paolo Carnevali, Jonathan M. Baccash, Igor Nazarenko, Aaron L. Halpern, Geoffrey Nilsen, Bruce Martin, Radoje Drmanac
  • Publication number: 20100286925
    Abstract: Mapping oligomer sequences includes receiving a set of related oligomer sequences, applying one or more key patterns derived from a set of oligomer sequence relationships to obtain one or more keys that are consistent with the set of related oligomer sequences, and locating the one or more keys in an index configured to map a plurality of possible keys to their respective candidate and/or validated locations in a reference.
    Type: Application
    Filed: February 2, 2010
    Publication date: November 11, 2010
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Publication number: 20100287165
    Abstract: Generating an index includes receiving a reference sequence and applying one or more key patterns to the reference sequence to obtain a plurality of keys in the index. Each of the one or more key patterns is derived based on a corresponding set of oligomer sequence relationships of a plurality of oligomer sequences that are expected to be generated from the reference, and the keys correspond to a plurality of candidate and/or validated locations in the reference sequence.
    Type: Application
    Filed: February 2, 2010
    Publication date: November 11, 2010
    Inventors: Aaron L. Halpern, Igor Nazarenko
  • Patent number: 7716172
    Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.
    Type: Grant
    Filed: January 30, 2006
    Date of Patent: May 11, 2010
    Assignee: Hyperion Solutions Corporation
    Inventors: Vaishnavi Anjur, Vijay K. Anjur, Hemanta Banerjee, Maya Binkovich, Srinivas Duvvuri, Mark Goldenshteyn, Arun Kumar, Kevin Kaixuan Liao, Igor Nazarenko
  • Patent number: 7467127
    Abstract: Selection of certain views of a multidimensional database to materialize may be accomplished using an efficient and effective solution. A set of all potential views may be stored in a structure. A path in the structure may then be traversed in an indicated direction through the structure, the path including two or more potential views and beginning at an indicated view. Then two or more immaterialized views in the path may be compared to each other to determine which immaterialized view is the optimum choice for maximizing benefit if selected to be materialized. Then the traversing and comparing may be continually iterated through, each iteration utilizing an indicated direction different than the last, each iteration also utilizing an indicated view set at the optimum choice determined by the last iteration, the iterating continuing until it converges on a single view. That single view may then be selected for materialization.
    Type: Grant
    Filed: June 7, 2004
    Date of Patent: December 16, 2008
    Assignee: Hyperion Solutions Corporation
    Inventors: Jonathan M. Baccash, Igor Nazarenko, Uri Rodny, Ambuj Shatdal
  • Publication number: 20080270365
    Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.
    Type: Application
    Filed: June 23, 2008
    Publication date: October 30, 2008
    Inventors: Jonathan M. Baccash, Igor Nazarenko, Uri Rodny, Ambui Shatdal
  • Patent number: 7392242
    Abstract: The cost of running a query (having a query range) on a multidimensional database may be estimated using a process factors criteria beyond merely the number of affected records. First, a materialized view of the database may be represented as a container of tuples, sorted by key. Then keys may be stepped through, each key representing a mapping of a combination of tuples from the container. At each step, the process may request the next smallest key in the query range greater than or equal to the key of the current step, which results in the tuple in the database whose key is the smallest, greater than or equal to the requested key, and determine if the resulting tuple is in the query range. The cost of the query may then be estimated as the number of tuples upon which the range check was performed.
    Type: Grant
    Filed: June 7, 2004
    Date of Patent: June 24, 2008
    Assignee: Hyperion Solutions Corporation
    Inventors: Jonathan M. Baccash, Igor Nazarenko, Uri Rodny, Ambuj Shatdal
  • Publication number: 20060129598
    Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.
    Type: Application
    Filed: January 30, 2006
    Publication date: June 15, 2006
    Inventors: Vaishnavi Anjur, Vijay Anjur, Hemanta Banerjee, Maya Binkovich, Srinivas Duvvuri, Mark Goldenshteyn, Arun Kumar, Kevin Liao, Igor Nazarenko
  • Patent number: 7028046
    Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.
    Type: Grant
    Filed: March 19, 2002
    Date of Patent: April 11, 2006
    Assignee: Hyperion Solutions Corporation
    Inventors: Vaishnavi Anjur, Vijay K. Anjur, Hemanta Banerjee, Maya Binkovich, Srinivas Duvvuri, Mark Goldenshteyn, Arun Kumar, Kevin Kaixuan Liao, Igor Nazarenko
  • Publication number: 20030182300
    Abstract: A method of operating a multi-dimensional database is disclosed. In this method, a multi-dimensional portion of the data is transferred to a multi-dimensional database. A relational portion of the cube is kept in the relational database. When data from the relational portion needs to be accessed, the system produces the SQL queries to obtain data from the relational database.
    Type: Application
    Filed: March 19, 2002
    Publication date: September 25, 2003
    Inventors: Vaishnavi Anjur, Vijay K. Anjur, Hemanta Banerjee, Maya Binkovich, Srinivas Duvvuri, Mark Goldenshteyn, Arun Kumar, Kevin Kaixuan Liao, Igor Nazarenko