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Recent Patents in Bioinformatics Nov. 2005 -- Jan. 2006

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US Patent 6,990,501. Method for organizing laboratory information in a database. Inventor: Thomas Beals. Assignee: Monsanto Technology.

Protects an invention in the field of database information organization that relates to the organization of laboratory procedure information for use in a database. The patent claims a method for organizing information in a database "in order to record information from an RNA transcript profiling laboratory procedure."


US Patent 6,990,221. Automated DNA array image segmentation and analysis. Inventor: Soheil Shams. Assignee: BioDiscovery.

Protects an image segmentation method for DNA microarrays. In one embodiment, the invention provides a method for segmentation of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The method comprises the steps of: transferring the frame of image information into a memory device; selecting a set of image information within the frame including a selected set of the DNA spot images; generating a grid in the memory device that includes a plurality of spaced grid points corresponding to the selected DNA spot images; and modifying a current position of at least one grid point corresponding to a spot image to shift the grid point toward the corresponding spot image.


US Patent 6,989,100. Methods for time-alignment of liquid chromatography-mass spectrometry data. Inventor: Scott Norton. Assignee: PPD Biomarker Discovery Sciences.

Covers a computer-implemented method for time-aligning at least two chromatography-mass spectrometry data sets, each comprising several mass chromatograms. The method includes computing a distance function between the data sets in dependence on at least two mass chromatograms from each data set; and aligning the data sets by minimizing the distance function. The method enables automated comparison of spectra for differential phenotyping and other applications, according to the patent abstract.


US Patent 6,988,109. System, method, software architecture, and business model for an intelligent object-based information technology platform. Inventors: Robert Stanley, Erich Gombocz. Assignee: IO Informatics.

Protects an information technology platform using "intelligent molecular objects" for heterogeneous data environments with high data density and dynamic application needs. The platform "addresses all steps of data processing from data acquisition through diverse sources and instrumentation to final output of diverse data analysis results," according to the abstract.


US Patent 6,988,040. System, method, and computer software for genotyping analysis and identification of allelic imbalance. Inventors: Rui Mei, Teresa Webster. Assignee: Affymetrix.

Covers methods, systems, and software products for determining the genotype of a sample using several probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.


US Patent 6,988,039. Method for determining sequence alignment significance. Inventor: Aleksandar Poleksic. Assignee: Eidogen (now Eidogen-Sertanty).

Covers methods and systems for quickly determining the statistical significance of a raw alignment score produced by aligning a first sequence to a second sequence. The methods determine multiple estimates of the p-value of an alignment score. Each p-value estimate is then compared to a pre-defined threshold p-value. Depending upon whether a particular p-value estimate is less than or greater than the threshold p-value, a raw alignment score may be considered statistically significant or insignificant.


US Patent 6,983,274. Multiple alignment genome sequence matching processor. Inventor: Aaron Patzer. Assignee: None.

Protects a digital hardware system that slides a sequence to be searched, such as a genome, past a query sequence, such as a DNA fragment, via shift registers. In parallel, multiple alignments between search and query sequences are compared. "As each alignment consists of many elements (characters), the parallel matching process is highly accelerated over sequential element-by-element comparison," according to the patent abstract.


US Patent 6,983,237. Method and apparatus for conducting linked simulation operations utilizing a computer-based system model. Inventors: Thomas Paterson, Alex Bangs. Assignee: Entelos.

Protects a method of conducting a sequence of linked simulation operations, utilizing a computer-based simulation model. In an exemplary embodiment, the system model comprises a physiology model that simulates the physiology of diseases (e.g., asthma, obesity, HIV-AIDS, or diabetes). "Nonetheless, it will be appreciated that the system model may model any number of systems, including but not limited to physiological, mechanical, environmental, chemical, biological, electrical, or physical systems," according to the description of the invention.


US Patent 6,980,974. Method for processing expression data of genes. Inventors: Takeshi Kobayashi, Hiroyuki Honda, Taizo Hanai; Tatsuya Ando. Assignee: Nagoya Industrial Science Research Institute (Japan).

Covers a method for processing the expression data of specimen genes using the Sweep operator method and the parameter increasing method. A fuzzy neural network model is constructed by making the expression data of the selected genes as input variables.


US Patent 6,980,674. Reference database. Inventors: Norman Anderson, Leigh Anderson. Assignee: Large Scale Proteomics

Protects a method in which data acquisition and cataloging are used to classify polypeptides into a reference index or database that can be used to identify previously unidentified samples.


US Patent 6,978,244. Computer architecture and process of patient generation, evolution, and simulation for computer based testing system. Inventors: Richard Rovinelli, Walton Sumner, Victor Marek, Miroslaw Truszczynski. Assignee: American Board of Family Practice.

Covers a computer-implemented simulation and evaluation method that simulates interventions to a patient by a user, and evaluates the interventions responsive to predetermined criteria and the interventions. The method includes defining a test area to evaluate the user to at least one of predetermined criteria and a user profile, selecting genetic information of the patient responsive to the test area, and generating a patient history responsive to the test area and the genetic information.


US Patent 6,973,388. Methods of diagnosing disease states using gene expression profiles. Inventors: Stephen Friend, Roland Stoughton. Assignee: Rosetta Inpharmatics.

Protects methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: measuring abundances of cellular constituents in a cell from a subject to obtain a diagnostic profile; measuring abundances of cellular constituents in a cell of one or more analogous subjects to obtain perturbation response profiles that correlate to a particular disease or therapy; and determining the interpolated perturbation response profile or profiles that best fit the diagnostic profile. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, databases comprising perturbation response profiles for one or more diseases and/or therapies, and kits for determining levels of disease states and/or therapeutic effects according to the methods of the invention.

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The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.