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Recent Patents in Bioinformatics, July — August 2007

US Patent 7,269,517. Computer systems and methods for analyzing experiment design. Inventor: Andrey Bondarenko. Assignee: Rosetta Inpharmatics.
Protects an experiment-definition system that digitally represents an experiment design and “provides the logical structure for data analysis of scans from one or more biological experiments,” the patent abstract states. Experiment definitions are stored as a set of instructions in a database of experiment definitions. A user interface is provided for constructing the experiment definition, and for customizing one or more automated analysis pipelines for processing the experiment definitions.

US Patent 7,266,473. Fast microarray expression data analysis method for network exploration. Inventors: Valery Kanevsky, Aditya Vailaya. Assignee: Agilent Technologies.
Covers a method for feature selection that includes the steps of “selecting a predictor set of features, adding at least one complementary feature to the predictor set based on a quality of prediction, checking to see if all of the features of the predictor set are repeated, and if not, removing at least one feature from the predictor set,” the patent abstract states. The method repeats the steps of adding complements, checking the predictor set, and removing features until the features of the predictor set are repeated “the proper number of times.”

US Patent 7,263,444. System, method and computer program for non-binary sequence comparison. Inventor: Jeffrey Clark. Assignee: BioInformatica LLC.
Protects a method for performing non-binary comparison of biological sequences that uses a new non-binary counting measure that is used in a stand alone module called VaSSA-1. This measure “obtains substantially more information about sequences and comparisons between them than is gathered by conventional bioinformatics techniques,” according to the patent abstract.

US Patent 7,254,489. Systems, methods and apparatus for reconstructing phylogentic trees. Inventor: Elchanan Mossel. Assignee: Microsoft.
Covers a method for reconstructing a tree data structure by reconstructing a local topology from samples of data of known nodes, and estimating the data value of each node in the reconstructed local topology. The reconstructing and estimating are performed iteratively.

US Patent 7,254,488. Probe designing method and information processing apparatus. Inventor: Hiroto Yoshii. Assignee: Canon.
Protects a probe-design method that uses a discrimination tree in which a plurality of partial base sequences obtained from target base sequence data are arranged on nodes and the suitability as a probe of a partial base sequence represented by a desired node is evaluated.

US Patent 7,251,642. Analysis engine and work space manager for use with gene expression data. Inventor: Ernest Szeto. Assignee: Gene Logic.
Protects a platform for managing, integrating, and analyzing gene expression data. The platform includes a run-time engine, “which provides more direct, quicker, and more efficient access to gene expression data through the use of memory mapped files,” according to the patent abstract. The platform also includes a workspace that is “implemented in directories with data objects comprising XML descriptors coupled with binary data objects for storing gene and sample identifiers and input parameters for saved analysis sessions.” The platform provides various application programming interfaces, including two C++ APIs, a Perl API, R API, and CORBA API, to access gene expression data from memory mapped files.

US Patent 7,248,971. Method and apparatus for discovering patterns in a set of sequences. Inventors: Isidore Rigoutsos, Yuan Gao, Aristidis Floratos. Assignee: International Business Machines.
Protects an unsupervised approach to identify additional members for a family that is defined initially through “exemplar sequences,” according to the patent abstract. The method “proceeds without any information related to the exemplar sequences defining the family, without aligning the sequences, without prior knowledge of any patterns in the exemplar sequences, and without knowledge of the cardinality or characteristics of any features that may be present in the exemplar sequences.” In one aspect of the invention, the method is used to take a set of unaligned sequences and discover several or many patterns common to some or all of the sequences. These patterns can then be used to determine if candidate sequences are members of the family.

US Patent 7,247,425. Methods to identify polynucleotide and polypeptide sequences which may be associated with physiological and medical conditions. Inventor: Walter Messier. Assignee: Evolutionary Genomics.
Protects methods for identifying evolutionarily significant polynucleotide and polypeptide sequences in human or non-human primates that may be associated with a physiological condition, such as enhanced resistance to AIDS infection. The methods are based on the comparison of human and non-human primate sequences using statistical methods.

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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.