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

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US Patent 6,954,722. Methods and systems for data analysis. Inventors: David Parks, Wayne Moore. Assignee: Leland Stanford Junior University.

Covers methods of analyzing and displaying flow cytometry data and other multidimensional data types. In one aspect, the invention provides methods for visualizing or displaying high dynamic range data obtained from flow cytometry analyses. Related systems and computer programs products are also provided. The method includes receiving raw data at the computer, comprising data from a plurality of light detectors of a flow cytometry system. The method also includes scaling the raw data in the computer using a scaling function.


US Patent 6,954,699. System and method for programatic access to biological probe array data. Inventors: Luis Jevons, Derek Bernhart, Nga Yu Cheung, Conrad Sheppy. Assignee: Affymetrix.

Protects an application programming interface that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file. The pixel data and intermediate results data may include data from biological experiments related to probe arrays.


US Patent 6,952,651. Methods and apparatus for nucleic acid sequencing by signal stretching and data integration. Inventor: Xing Su. Assignee: Intel.

Protects methods concerning DNA sequencing. In some embodiments of the invention, the methods comprise measuring the distance between labeled nucleotides, such as nucleotides labeled with bulky groups. The distance maps may be aligned to obtain a nucleic acid sequence. Overlapping data analysis and frequency analysis may be used to construct the distance maps and non-overlapping data analysis may be used to align the distance maps into a sequence.


US Patent 6,950,756. Rearrangement of microarray scan images to form virtual arrays. Inventor: Robert Kincaid. Assignee: Agilent Technologies.

Protects a system and methods for selecting single features from a microarray scan image of genomic data and rearranging the selected single-features of the microarray into a virtual array with a format that is more "relevant or informative to the analyst or user than that of the original microarray scan image," according to the patent abstract. The invention pertains to a software system that divides the microarray scan image into feature cells and then recombines those cells into a new virtual array image that provides only feature cells that are relevant and appropriate to the subject analysis, "thus providing for easier visualization and more meaningful data extraction and management."


US Patent 6,950,755. Genotype pattern recognition and classification. Inventor: Douglas Stahl. Assignee: City of Hope.

Protects a method for interpreting data obtained by analysis of nucleic acids by obtaining nucleic acid data in a spatial domain, transforming the nucleic acid data from the spatial domain into a frequency domain, and obtaining sequence data of the nucleic acid data by executing a data-mining process on the transformed nucleic acid data. The transformation may be performed by a Hadamard transform, a Fourier transform or a wavelet transform to obtain frequency coefficients, with less than all of the frequency coefficients being utilized in the data-mining process. The data mining process may be subjecting the frequency coefficients to a connectionist algorithm or to a classification tree/rule induction algorithm.


US Patent 6,950,754. Apparatus and method for automated protein design. Inventors: Stephen Mayo, Bassil Dahiyat, D. Benjamin Gordon, Arthur Street, Yaoying Su. Assignee: The California Institute of Technology.

Protects computer-based methods for quantitative protein design and optimization. The method comprises the steps of receiving a protein backbone structure with variable residue positions, establishing a group of potential rotamers for each of the variable residue positions, wherein at least one variable residue position has rotamers from at least two different amino acid side chains, and analyzing the interaction of each of the rotamers with all or part of the remainder of the protein backbone structure to generate a set of optimized protein sequences.


US Patent 6,950,753. Methods for extracting information on interactions between biological entities from natural language text data. Inventors: Andrey Rzhetsky, Serey Kalachikov, Michael Krauthammer, Carol Friedman, Pauline Kra, Assignee: The Trustees of the Columbia University in the City of New York.

Protects a method for identifying novel genes that comprises generating one or more specialized databases containing information on gene/protein structure, function and/or regulatory interactions; and searching the specialized databases for homology or for a particular motif and thereby identifying a putative novel gene of interest. The invention also relates to natural language processing and extraction of relational information associated with genes and proteins that are found in genomics journal articles.


US Patent 6,950,752. Methods for removing artifacts from biological profiles. Inventors: Stephen Friend, Roland Stoughton, Yudong He. Assignee: Rosetta Inpharmatics.

Protects methods for removing unwanted response components (artifacts) from a measured biological profile comprising measurements of a plurality of cellular constituents of a cell or organism in response to a perturbation. The methods involve subtracting from the measured biological profile one or more artifact patterns, each of which comprises measurements of changes in cellular constituents as a result of deviation of one or more experimental variables, such as cell culture density and temperature, hybridization temperature, as well as concentrations of total RNA and/or hybridization reagents, from desired values.


US Patent 6,947,849. Method for identifying or characterizing properties of polymeric units. Inventors: Ganesh Venkataraman, Zachary Shriver, Rahul Raman, Ram Sasisekharan, Nishla Keiser. Assignee: Massachusetts Institute of Technology.

Protects methods for identifying and characterizing properties of polymers to provide information about the polymer such as the charge of the polymer, the number and types or characteristics of units of the polymer, and the sequence of the polymers. In one embodiment, the properties are encoded using a binary notation system, and the comparison is accomplished by comparing the binary representations of polymers. For example, a sample polymer is subjected to an experimental constraint to modify the polymer, and the modified polymer is compared to a reference database of polymers to identify a population of polymers having a property that is the same as or similar to a property of the sample polymer.


US Patent 6,947,846. Non-metric tool for predicting gene relationships from expression data. Inventors: Stephen Quake, R. Michael van Dam, James Brody, Rebecca Shafee. Assignee: California Institute of Technology.

Covers techniques for processing gene expression data and predicting gene relationships. The method for processing gene expression ratios may include discretizing a first expression ratio for a first gene and a second expression ratio for a second gene for each of a plurality of experiments into one of three indications, calculating the probability that the combination of the discretized expression ratios for each of the plurality of experiments arises by random chance, and determining whether the first gene and the second gene are related.

 

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The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.