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Recent Patents in Bioinformatics Oct. 2005 -- Nov. 2005

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US Patent 6,970,790. Method and apparatus for analysis of molecular combination based on computational estimation of electrostatic affinity using basis expansions. Inventors: David Kita, Somalee Datta, Adityo Prakash, Eniko Fodor. Assignee: Verseon.

Protects a method for computer-aided drug design, which estimates the electrostatic affinity of a molecular system using a basis expansion that represents charge density and electrostatic potential functions associated with the first and second molecular subsets in a coordinate system. An electrostatic affinity is computed by translating and rotating operators to the basis expansion coefficients over a sequence of different sampled configurations for the molecular combination. The method may also be combined with other methods for computation of shape complementarity in determining a composite or augmented score that reflects both electrostatic affinity and shape complementarity for configurations of a molecular combination.


US Patent 6,969,589. Methods for genomic analysis. Inventors: Nila Patil, David Cox, Anthony Berno, David Hinds. Assignee: Perlegen Sciences.

Covers methods for identifying variations that occur in the human genome and relating these variations to the genetic basis of disease and drug response. In particular, the invention relates to identifying individual SNPs, determining SNP haplotype blocks and patterns, and using the SNP haplotype blocks and patterns to dissect the genetic bases of disease and drug response.


US Patent 6,968,301. Method for analysis of biological systems. Inventors: David Smith, Roger Smith. Assignee: None.

Protects a method for analyzing the evolution of a biological system that comprises the steps of determining a series of variables upon which a state of the biological system depends, and mapping the variables to an n-dimensional space. The evolution of the biological system is monitored using a trajectory formed from sets of the variables that define the states of the biological system at different times, "thereby using time as a parameter in the n-dimensional space in a manner such that every point on the trajectory corresponds to at least one value of time," according to the patent abstract.


US Patent 6,965,831. Coupled two-way clustering analysis of data. Inventors: Eytan Domany, Gad Getz, Erel Levine. Assignee: Yeda Research and Development Co. Ltd.

Covers a coupled two-way iterative clustering approach for gene microarray data analysis, which identifies subsets of genes and samples, "such that when one of these items is used to cluster the other, stable and significant partitions emerge," according to the patent abstract. The method was applied to two gene microarray data sets, on colon cancer and leukemia. "By identifying relevant subsets of the data and focusing on these subsets, partitions and correlations were found that were masked and hidden when the full data set was used in the analysis," the abstract states.


US Patent 6,965,704. System, method, and computer software product for grid alignment of multiple scanned images. Inventors: Shantanu Kaushikkar, Sangita Patil. Assignee: Affymetrix.

Protects systems, methods, and computer programs for aligning multiple images of arrays of biological materials. One method includes aligning a grid with a first image, generating grid alignment data based on the alignment of the grid with the first image, storing the grid alignment data in memory, retrieving the grid alignment data responsive to an indication to align a second image, and analyzing the second image based on the retrieved grid alignment data.


US Patents 6,964,850 and 6,960,439. Identification, monitoring and treatment of disease and characterization of biological condition using gene expression profiles. Inventors: Michael Bevilacqua, John Cheronis, Victor Tryon, Danute Bankaitis-Davis. Assignee: Source Precision Medicine.

Protects methods for using gene expression profiles to identify, monitor, and treat disease and to characterize biological conditions. Profile data sets are derived from subject samples and include quantitative, repeatable measures of a distinct amount of RNA or protein constituent in a panel selected to enable evaluation of a biological condition. Such profile data sets may be used to provide an "index indicative of the biological state of a subject, which may be compared to a normative value of the index determined with respect to a relevant population of subjects," according to the patent abstract.


US Patent 6,963,807. Automated identification of peptides. Inventors: Robert Reid Townsend, Andrew William Robinson. Assignee: Oxford Glycosciences (now Oxford Genome Sciences).

Protects a computer-mediated method for interpreting data derived by mass spectrometry to identify and characterize a corresponding peptide sequence in a peptide database. The method automatically identifies the corresponding sequence if it is present in the database, eliminating the need for a user to choose from among a list of possible matches. The method uses an automated back-read process to uniquely identify a corresponding peptide sequence in a database based on a single matching peptide sequence. The method also permits mapping of mass spectral data to sequences in peptide or nucleotide databases for unambiguous identification of exons; determining a correct reading frame; identifying artefacts and errors in sequences; identifying mutations and polymorphisms; identifying post-translational modifications; and identifying exon-intron boundaries, according to the patent abstract.


US Patent 6,961,664. Methods of populating data structures for use in evolutionary simulations. Inventors: Sergey Selifonov, Willem Stemmer. Assignee: Maxygen.

Covers methods of populating data structures for use in evolutionary modeling. The invention involves encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.


US Patent 6,957,149. Computer-aided probability base calling for arrays of nucleic acid probes on chips. Inventors: Robert Lipshutz, Michael Walker. Assignee: Affymetrix.

Protects a computer system for analyzing nucleic acid sequences that calculates probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips.


US Patent 6,956,961. Extracting shape information contained in cell images. Inventors: Ge Cong, Eugeni Vaisberg. Assignee: Cytokinetics.

Protects methods for analyzing images of cells and extracting biologically significant shape-related features from the cell images. The invention provides methods for segmentation of cells in an image using a combination of a reference component image data and cell shape-indicative marker image data in a watershed technique, according to the patent abstract. The invention also provides a skeletonization and skeleton analysis technique for extracting biologically relevant features from cell shapes.

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