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IP Update: Yale University, Boehringer Ingelheim among Recent Bioinformatics Patent Winners

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US Patent 8,185,321. Method for predicting interaction between protein and chemical. Inventors: Yasubumi Sakakibara, Nobuyoshi Nagamine. Assignee: Keio University

Describes an approach for predicting unknown interactions between proteins and chemicals


US Patent 8,185,320. Systems and methods for automated analysis of cells and tissues. Inventors: David Rimm, Robert Camp. Assignee: Yale University

Describes a computer-implemented approach for analyzing cell samples to identify morphology or to localize and quantitate biomarkers.


US Patent 8,175,843. Computer-implemented methods for evaluating, summarizing, and present[ing] data on stability of drug substances and drug products and software-modified computers for such methods. Inventors: Kubiak Rene, James Schwenke, Volker Krzykalla, Hans-Juergen Lomp, Cornelia Schepers. Assignee: Boehringer Ingelheim

Describes a computerized method for statistical analysis of a pharmaceutical product in stability studies. It includes capabilities for inputting and summarizing the data observed, statistically analyzing the data, and providing standardized output data and graphical presentations of the observed stability response data.


US Patent 8,175,813. Computational methods for synthetic gene design. Inventor: Daniel Tomso. Assignee: Athenix

Describes a computerized method for designing synthetic genes in heterologous organisms such as plants. According to the abstract, the method involves "organizing a database of sequences as a set of N-length oligomer sequences and compiling a list of probability scores for each N-length sequence." These scores are then used to substitute "one or more higher-scoring sequences into the parent nucleotide sequence to generate an optimized sequence" that can then be further optimized by removing unintended open reading frames or undesired short DNA elements; and/or substituting oligomer sequences to achieve a specific GC content.


US Patent 8,170,852. Data structures and methods for modeling Saccharomyces cerevisiae metabolism. Inventors: Imandokht Famili, Jochen Forster, Pengcheng Fu, Jens Nielsen, Bernhard Palsson. Assignee: The Regents of the University of California

Describes an in silico model for determining a S. cerevisiae physiological function. According to the abstract, the model includes a data structure that relates S. cerevisiae reactants and reactions; a constraint set for these reactions; and commands for determining a distribution of flux through the reactions that predicts the physiological function of the organism. The model can also include a gene database containing information that characterizes the associated gene or genes.


US Patent 8,170,808. Methods and computer software for detecting splice variants. Inventors: Alan Williams, Simon Cawley, John Blume, Hui Wang, Tyson Clark. Assignee: Affymetrix

Describes methods and software products for analyzing microarray data to identify differentially spliced exons.


US Patent 8,170,806. Methods of populating data structures for use in evolutionary simulations. Inventors: Sergey Selifonov, Willem Stemmer. Assignee: Codexis Mayflower Holdings

Describes methods of populating data structures for use in evolutionary modeling that uses multiple character strings to encode biological molecules.


US Patent 8,170,805. Methods for selecting statistically validated candidate genes. Inventors: Venkata Krishna Kishore, Zhigang Guo, Min Li, Daolong Wang, Libardo Andres Gutierrez Rojas, Joseph Dallas Clarke, Joseph Byrum. Assignee: Syngenta Participations

Describes methods for evaluating associations between candidate genes and traits of interest in populations. The methods use a combination of genome-wide association analysis, nested association mapping, expression QTL analysis, and allele epistastic analysis.


US Patent 8,165,821. Systems and methods for indel identification using short read sequencing. Inventor: Zheng Zhang. Assignee: Applied Biosystems

Describes systems, methods, and analytical approaches for short read sequence assembly and for detecting insertions and deletions in a reference genome.


US Patent 8,165,818. Methods and apparatus for searching molecular structure databases. Inventor: Anthony Nicholls. Assignee: OpenEye Scientific Software

Describes several methods for organizing and searching databases of molecular structures. Also described are methods for characterizing molecules based on the shapes of their fields. The technique could be applied in drug discovery and design studies.


US Patent 8,155,889. Methods for assessing degree of reliability of nucleic acid base sequence. Inventors: Shinichi Utsunomiya, Makoto Hazama. Assignee: Shimadzu

Describes a mathematical approach for assessing the degree of reliability of nucleic acid base sequences


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The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.