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IP Update: University of Washington, Oracle among Recent Bioinformatics Patent Winners


US Patent 8,340,951. Synthetic enzymes derived from computational design. Inventors: David Baker, Alexandre Zanghellini, Lin Jiang, Andrew Wollacott, Daniela Grabs-Rothlisberger, Eric Althoff. Assignee: University of Washington

Describes techniques for computationally designing enzymes that can be used to create variations of naturally occurring enzymes as well as new enzymes that have “no natural counterparts.” The abstract states that the method first identifies functional reactive sites that are needed to produce a desired reaction, and then uses hashing algorithms to identify potential protein backbone structures that are “capable of supporting the required functional sites.”

US Patent 8,340,917. Sequence matching allowing for errors. Inventors: Jayanta Banerjee, Seema Sundara. Assignee: Oracle

Describes a method of sequence matching in the context of genomic research. The method is based on a test fragment located within a target sequence "with at most a number E errors," according to the patent. The test fragment "is broken into E+1 test sub-fragments. If one test sub-fragment is located within the target sequence with no errors; a determination is made as to whether the other test sub-fragments are located within the target sequence adjacent to the one test sub-fragment with a total of at most E errors." According to the inventors, the approach provides an “effective way to locate a test fragment within a target sequence.”

US Patent 8,340,915. Systems and method for analyzing microarrays. Inventors: Lei Li, Chao Cheng, Huanying Ge. Assignee: University of Southern California.

This patent describes a computer-implemented method for analyzing microarray data that includes a standard data normalization step as well as a method for “improving measurement accuracy and salvaging array data from arrays containing minor defects.” It also includes a probe-treatment-reference model that streamlines normalization and summarizes microarray data by allowing multiple references.

US Patent 8,340,914. Methods and systems for compressing and comparing genomic data. Inventors: Joe Gatewood, Valerio Aimale, Callum Bell. Assignee: Not listed.

Describes a method of compressing and comparing genomic sequences that is based on a technique called delta compression.

US Patent 8,335,652. Self-improving identification method. Inventors: Orhan Soykan, Daisy Phan Cross. Assignee: Yougene.

Describes a self-improving identification method that uses a set of class identifiers to categorize specimens in a database and then improves these initial classifications as new data becomes available.

US Patent 8,332,160. System and methods for engineering nucleic acid constructs using scoring techniques. Inventors: Darren Platt, Michael Bissell, Sunil Chandran, Brian Hawthorne, Erik Jedediah Dean, Christopher Dolan. Assignee: Amyris Biotechnologies.

Describes a method for “defining a nucleic acid construct for integration into a genomic locus L of a target organism or a host cell.”

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