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Recent Patents in Bioinformatics, March -- April 2006

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US Patent 7,039,238. Data relationship model. Inventors: Kemal Sonmez, Lawrence Toll, Patrick Lincoln, Peter Karp. Assignee: SRI International.

Protects a model that is used to represent a set of structured data objects that include elements at defined positions. The model includes "distributions of vectors, each distribution corresponding to particular positions in the respective structured data objects, each of the vectors comprising values for the particular positions; and comparing a given set of structured data objects to the model to determine a likelihood that the given set is represented by the model," according to the patent abstract. Distributions of the model can indicate dissimilarity between the structured data objects at defined positions; similarity between the structured data objects at defined positions; or similarity to a reference structure data object at defined positions. According to the patent, "the invention relates to models of data relationships. It is customary to compare different data objects to each other to determine the extent of similarity and to identify differences. One example of data objects for which such comparisons are routine are biopolymer sequences."


US Patent 7,035,740. Artificial intelligence and global normalization methods for genotyping. Inventor: Bahram Ghaffarzadeh Kermani. Assignee: Illumina.

Protects systems and methods for normalizing and analyzing cluster data, such as genotyping data, using an artificial neural network.


US Patent 7,035,739. Computer systems and methods for identifying genes and determining pathways associated with traits. Inventors: Eric Schadt, Stephanie Monks. Assignee: Rosetta Inpharmatics.

Covers a method for "associating a gene with a trait exhibited by one or more organisms in a plurality of organisms from a species," according to the patent abstract. A genetic marker map is constructed from a set of genetic markers associated with the plurality of organisms. For each gene in a plurality of genes, a quantitative trait locus analysis is performed using the genetic marker map and a quantitative trait. "The quantitative trait locus data are clustered from each quantitative trait locus analysis to form a quantitative trait locus interaction map." Clusters of genes in the map are identified as a candidate pathway group. An expression cluster map is used to refine the candidate pathway group and multivariate analysis is used to validate the candidate pathway group as a set of genes that are genetically interacting.


US Patent 7,031,847. Method and apparatus for displaying gene expression patterns. Inventors: Yasuyuki Nozaki, Ryo Nakashige, Tsunehiko Watanabe, Takuro Tamura. Assignee: Hitachi Software Engineering.

Protects a method for displaying gene expression patterns of multiple genes that change according to the experiment cases, where a first axis represents the genes and a second axis represents the experiment cases. The method comprises two steps: designating a segment along the second axis in the expression pattern data of the multiple genes; and clustering the expression pattern data within the designated segment along the second axis based on a predetermined reference value, repeating clustering within the same cluster in a forward or reverse direction along the second axis while changing the reference value, and displaying the results according to a predetermined display format.


US Patent 7,031,846. Method, system, and computer software

Protects a computer program and related systems and methods for processing emission intensity data corresponding to probes of a biological probe array. The program includes a genotype and statistical analysis manager that determines absolute or relative expression values based on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter, the patent abstract states. The analysis manager "may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data," and "may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls."


US Patent 7,031,845. Method for determining biological expression levels by linear programming. Inventors: Ridgeway Scott, Stephen Wright, Stuart Kurtz, Terry Clark, Chris Dyanov, Richard Quigg. Assignee: University of Chicago.

Protects a method for determining a matrix of expression levels corresponding to a set of biological targets, such as genes or gene fragments, and a set of biological samples, including obtaining a matrix of signal values corresponding to the set of biological targets. The method computes a vector of expression levels for a sample in the set of biological samples using the matrix of signal values, stores the vector of computed expression levels in a storage matrix, repeats the computing and storing steps for each sample in the set of biological samples, and outputs the storage matrix as the matrix of expression levels. The method is based on a linear programming formulation of the problem and works for both "promiscuous" probe array data, in which there may be multiple targets indicated by a single probe, and "polygamous" array data, in which there are multiple probes for a single target, according to the patent abstract.


US Patent 7,031,844. Cluster analysis of genetic microarray images. Inventors: Daniel Bozinov, Jörg Rahnenf hrer. Assignee: The Board of Regents of the University of Nebraska.

Covers a method for determining the relative incidence of a binding substance within two biological samples. The two samples are labeled with luminescent materials having different chromatic properties. An image of the luminescent materials upon a binding site of a microarray is analyzed as two clusters of data points scattered about respective representative pairs of chromatic intensity values. The relative incidence of the binding substance is determined as a ratio of differences between corresponding indices of the representative pairs.


US Patent 7,031,843. Computer methods and systems for displaying information relating to gene expression data. Inventors: Brian Bullard, Sean Mullins. Assignee: Gene Logic.

Covers computer and display methods and systems for acquiring, storing, manipulating, analyzing, linking, retrieving, and displaying gene expression data in "three-dimensional molecular topographies" in which expressed genes and their activity are represented as peaks in the topographies, according to the patent abstract. The abstract also describes methods and systems for generating and displaying delta plots, which show differences in gene expression, and to methods and systems for generating "molecular movies" that show changes in gene expression.


US Patent 7,027,933. Method for analyzing mass spectra. Inventors: Chris Paulse, Edward Gavin, Leonid Braginsky, William Rich, Eric Fung. Assignee: Ciphergen Biosystems.

Protects a computer-based method that analyzes mass spectra that includes entering into a computer a dataset obtained from mass spectra from a plurality of samples. Each sample is assigned to a class within a class set and each class is characterized by a different biological status. A classification model then discriminates between the classes in the class set, according to the patent abstract.


US Patent 7,027,930. Reading chemical arrays. Inventor: Herbert Cattell. Assignee: Agilent Technologies.

Covers methods of using an addressable array of biopolymers that has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established and a definition of the shapes of the established regions of each set is saved in a memory.


US Patent 7,024,312. Methods for making character strings, polynucleotides and polypeptides having desired characteristics. Inventors: Sergey Selifonov, Willem Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip Patten, Jeremy Minshull, Lorraine Giver. Assignee: Maxygen.

Covers "in silico" nucleic acid recombination methods, related integrated systems utilizing genetic operators, and libraries made by in silico shuffling methods, according to the patent abstract. Claims describe a method of identifying a set of oligonucleotides for use in an in vitro recombination procedure that includes providing the sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides; computationally selecting one or more cross-over sites on the sequences based on structural information about the parental polypeptides or polypeptides encoded by the parental nucleic acids; selecting at least one of the recombinant polypeptides or recombinant nucleic acids by computationally assessing structural stability of at least some of the recombinant polypeptides or polypeptides encoded by the recombinant nucleic acids; and computationally identifying one or more oligonucleotides for in vitro recombination.


US Patent 7,024,311. Computer-aided method for the provision, identification, and description of molecules capable of exhibiting a desired behavior, more particularly in the pharmaceutical sector, and molecules obtained by said method. Inventors: Gérard Grassy, Michel Kaczorek, Roger Lahana, Abdelaziz Yasri. Assignee: Synt:EM (France).

Protects a computer-aided method for the provision, identification, and description of molecules exhibiting a desired behavior, particularly in the pharmaceutical sector. The methods employ a molecular modeling step, a combinatorial library building step, and a step of selecting potentially useful molecules in which the candidate molecules are filtered using a dynamic filter representing constraints of conformational variations that the molecules must satisfy in order to exhibit a particular activity.


US Patent 7,010,760. Batch-based method and tool for graphical manipulation of workflows. Inventors: Larry Arnstein, Zheng Li, John Hill, Michael Kellen, Christophe Poulain, Neil Fanger, Kuang Chen. Assignee: Teranode.

Protects an "autofill algorithm" that provides tools for defining and automatically executing batch-based procedures in an adaptive hierarchical workflow environment, according to the patent abstract. The method is suitable for laboratory procedure planning, execution, documentation, as well as driving robotic apparatus.

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