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IP Update: Bioinformatics Systems, Applied Biosystems, Pharnext, among Recent Bioinformatics Patent Winners

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US Patent 8,571,809. Apparatus for calculating scores of chains for sequence alignments. Inventor: Gregory Knowles. Assignee: Bioinformatics Systems

This patent is for a system of calculating "scores of chains of sequence alignments of biological sequences." According to the abstract, "each of a plurality of substantially co-linear alignments has a score. Each alignment may comprise a starting alignment that has been diagonally extended to meet a length requirement. Dynamic programming is performed in interalignment regions between the extended alignments to generate a corresponding set of interalignment scores [and then] alignment scores and interalignment scores are summed to generate a score for the entire chain of alignments. This process is repeated for multiple chains. Chains of alignments are ranked by chain score and are displayed to a user."


US Patent 8,571,807. Computer algorithm for automatic allele determination from fluorometer genotyping device. Inventors: Stephen Glanowski, Jeremy Heil, Emily Winn-Deen, Ivy McMullen. Assignee: Applied Biosystems

This patent is for an automated method of identifying allele values from fluorophore emission data obtained "during the observation of fluorophore labeled nucleotide probes, [which are] used in analyzing polymorphic DNA."


US Patent 8,571,806. Method for generating information related to the molecular structure of a biomolecule. Inventors: Johan Desmet, Ignace Lasters, Dominique Vlieghe, Carlo Boutton, Philippe Stas, Jan Spriet. Assignee: Lonza Biologies

This patent is for methods of generating information about the molecular structure of biomolecules.


US Patent 8,571,804. Disease treatment by predicting drug association. Inventors: Daniel Cohen, Ilya Chumakov. Assignee: Pharnext

This patent is for an in silico-based drug repositioning approach that involves generating "dynamic models" of disease using "multivariate genetic, proteomic, and metabolomics statistical analysis of groups of genes; and establishing disease-associated pathways involved in disease genesis and progression" that could serve as drug targets. It also includes in silico drug screening capabilities.


US Patent 8,571,803. Systems and methods for modeling and analyzing networks. Inventors: Colin Hill, Bruce Church, Paul McDonagh, Iya Khalil, Thomas Neyarapally, Zachary Pitluk. Assignee: Gene Network Sciences

According to the abstract, this patent is for "a probabilistic modeling framework for reverse engineering an ensemble of causal models, from data and then forward simulating the ensemble of models to analyze and predict the behavior of the network." The abstract explains that "causal network models include computational representations of the causal relationships between independent variables such as a compound of interest and dependent variables such as measured DNA alterations, changes in mRNA, protein, and metabolites to phenotypic readouts of efficacy and toxicity."


US Patent 8,566,039. Methods and system to characterize transcriptionally active regions and quantify sequence abundance for large scale sequencing data. Inventors: Xitong Li, Kenneth Stineman. Assignee: Genomic Health

This patent covers a quantitative analysis method for identifying "transcriptionally active regions and quantify[ing] sequence abundance from large scale sequencing data" in RNA expression profiling.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.