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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Jul 12, 2004


US Patent 6,760,715. Enhancing biological knowledge discovery using multiple support vector machines. Inventors: Stephan Barnhill, Isabelle Guyon, Jason Weston. Assignee: Barnhill Technologies.

Covers multiple support vector machines that are used to extract useful information from vast quantities of biological data. The method includes pre-processing of training data and test data to add dimensionality or to identify missing or erroneous data points. After the training has been confirmed, live biological data can be pre-processed and then input into the identified support vector machine that provides the optimal solution for extraction of useful information.

US Patent 6,760,668. Method for alignment of DNA sequences with enhanced accuracy and read length. Inventors: Alexandre Izmailov, Henryk Zaleski, Stephen Darasch. Assignee: Bayer HealthCare.

Protects a method for aligning DNA sequence data traces using an experimental data trace that represents the positions of a first species of base within a target polynucleotide and a reference data trace representing the positions of a second species of base within a reference polynucleotide. A base number is assigned to each of the selected peaks in the reference data trace, and a numerical “peak file” is created with information about the peak number and migration time (or distance). This peak file is analyzed to determine a set of polynomial coefficients that will allow substantial linearization of a plot of peak number versus separation between adjacent peaks and alignment of the traces with respect to each other. These coefficients are used to create a corrected time scale identifying where peaks should be located on a given experimental gel, which is used to guide the sampling of the experimental data, and for assignment of peaks within the data.

US Patent 6,753,142. Methods and compositions for elucidating relative protein expression levels in cells. Inventors: Charles Link, Tatiana Seregina, Nicholas Vahanian, James Higginbotham, Jay Ramsey, Bradley Powers, Sachet Shukla, Won Bin Young. Assignee: NewLink Genetics.

Protects a method for identifying a particular protein profile for a cell that can be used for diagnosis or as a target site for a drug. Activity at specific genetic loci is correlated with the functional state and/or concentration of product proteins in a test cell and is then compared to a reference cell for elucidation of differential and quantitative protein expression profiles. The method can be used to identify gene or gene products associated with a biological process or state of interest, to identify proteins including entire pathways of expression associated with a particular state, to screen cells for the identification of a particular protein profile for diagnosis, to identify novel proteins associated with particular cell types or states, or to identify polymorphisms in genes causing differential proteins between genes.

US Patent 6,750,011. Method and system for genotyping. Inventor: Mark Perlin.

Covers a method of genotyping that includes the steps of obtaining nucleic acid material; amplifying a short tandem repeat polymorphism of the material to produce a signal; and analyzing the signal using a computing device with a memory.

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The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.