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IP Update: U North Carolina, Fujitsu, MathWorks among Recent Bioinformatics Patent Winners

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US Patent 8,244,504. Computer implemented system for quantifying stability and flexibility relationships in macromolecules. Inventor: Donald Jacobs. Assignee: The University of North Carolina, Charlotte

Describes a method that analyzes the thermodynamic and mechanical properties of molecules, such as proteins, within chemical environments under given conditions.


US Patent 8,244,483. Shape recognition methods and systems for searching molecular databases. Inventor: Pedro Ballester. Assignee: Isis Innovation

Describes a computer-implemented method for determining shape similarity between a query and a target molecule, and methods for screening one or more molecules in a database based on shape similarity to a query molecule.


US Patent 8,244,480. Computer product, analysis support apparatus, and analysis support method. Inventor: Kentarou Doi. Assignee: Fujitsu

Describes a method for analyzing biological phenomena.


US Patent 8,244,474. Feature pattern recognition system, method, and program. Inventors: Yasuo Matsuyama, Ryo Kawamura, Keita Shimoda. Assignee: Waseda University

Describes a method and program that is capable of recognizing patterns. According to the investigators, it can be used to recognize promoters in DNA sequences and motifs in amino acid sequences.


US Patent 8,239,142. System, method, device, and computer program product for extraction, gathering, manipulation, and analysis of peak data from an automated sequencer. Inventors: Alexis Collette, Adrien Six, Sylviane Bernadette Pied, Pierre-Andre Cazenave. Assignees: Pierre-and-Marie-Curie University, National Center for Scientific Research

Describes a bioinformatics tool that extracts and stores data from DNA sequencers as well as methods of analyzing information within a database.


US Patent 8,239,140. System, method, and computer program product for DNA sequence alignment using symmetric phase only matched filters. Inventor: Andrzej Brodzik. Assignee: Mitre

Describes a method of local and global alignment of DNA sequences that uses a symmetric phase only matched filter.


US Patent 8,239,137. Analytical method and instrument. Inventor: Rolf Knobel. Assignee: Roche Molecular Systems

Describes a method and an instrument for determining an analyte, such as a nucleic acid, using an algorithm based on a mathematical model for “transforming measurement data into a growth curve.”


US Patent 8,234,098. Method and apparatus for integrated modeling, simulation, and analysis of chemical and biochemical reactions. Inventors: Ricardo Paxson, Joseph Hicklin, Ramamurthy Mani. Assignee: The MathWorks

Describes a system for modeling, simulating, and analyzing chemical and biochemical reactions.


US Patent 8,234,075. Apparatus and method for processing information concerning biological condition, system, program, and recording medium for managing information concerning biological condition. Inventors: Takeshi Kimura, Yasushi Noguchi. Assignee: Ajinomoto

Describes a method for processing and managing information concerning a biological condition that offers an analytical approach for determining a combination of metabolites that are closely related to an index associated with the condition. According to the patent description, the method is based on correlations between phenomics data — defined as phenomena defining biological conditions — and metabolomics data.


US Patent 8,234,074. Methods, systems, and computer program products for simulating biomembrances using coarse grain models. Inventors: Carlos Lopez, Steven Nielsen, Preston Moore, Michael Klein. Assignee: University of Pennsylvania

Describes a method that uses a coarse grain model, which is designed to mimic lipid molecules, to “simulate self-assembly of a lamellar bilayer starting from a disordered configuration.”


US Patent 8,229,721. Apparatus and method for structure-based prediction of amino acid sequences. Inventors: Johan Desmet, Ignace Lasters, Dominique Vlieghe, Carlo Boutton, Philippe Stas. Assignee: Lonza Biologics

Describes a method to “determine the amino acid sequence space accessible to a given protein structure” and to use this information to align amino acid sequences with a protein structure in order to identify potential structural relationships and to generate new amino acid sequences that are compatible with protein structures.


US Patent 8,229,675. Patient information bar and method for tracking and displaying blood products. Inventors: Miklos Csore, Gerald Willman, Noah Bentley. Assignee: Global Med Technologies

Describes a system for managing and tracking blood products that includes a database for storing information and a toolbar for selectively displaying patients’ information including each patient's special needs, prior transfusion reaction history, directed blood components, and blood type.


US Patent 8,229,673. Human metabolic models and methods. Inventors: Bornhard Palsson, Imandokht Famili, Markus Covert, Christophe Schilling. Assignee: Genomatica

Describes in silico methods for simulating and predicting the activity of human reaction networks including core metabolic reaction networks and those in specialized cell types. According to the patent description, these can be used to simulate different aspects of cellular behavior under physiological, pathological, and therapeutic conditions.


US Patent 8,224,586. System, method, and computer product for exon array analysis. Inventors: Alan Williams, Charles Sugnet, James Gorrell. Assignee: Affymetrix

Describes a method for analyzing data generated by biological probe arrays.


US Patent 8,224,585. Documenting and presenting mutation observations. Inventor: Mark Hoffman. Assignee: Cerner

Describes software for documenting and presenting genomic mutations so that they can be presented using published or user-preferred standards.


US Patent 8,224,584. Parametric system for quantifying analyte polynucleotides. Inventor: James Carrick, Mark Kennedy, Jeffrey Chismar. Assignee: Gen-Probe

According to the abstract, this patent is for a system that quantifies analyte polynucleotides using “computer-implemented analysis of real-time amplification data using a calibration curve defined by parametric equations.”


US Patent 8,224,584. Parametric system for quantifying analyte polynucleotides. Inventor: James Carrick, Mark Kennedy, Jeffrey Chismar. Assignee: Gen-Probe

According to the description, this patent is for a system that applies structure-activity analyses to recombinant protein and nucleic acid design.


US Patent 8,219,323. System and method for quantifying the sequence specificity of nucelotide binding factors. Inventor: Harmen Bussemaker, Barrett Foat, Ronald Tepper. Assignee: The Trustees of Columbia University, New York

Describes a technique for “determining free energy parameters for predicting binding affinities of nucleotide sequences.”


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The Scan

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Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

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Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

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The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.