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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Nov 24, 2003

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US Patent 6,651,008. Database system including computer code for predictive cellular bioinformatics. Inventors: Eugeni Vaisberg, Cynthia Adams, James Sabry, Anne Crompton. Assignee: Cytokinetics.

Protects computer-based techniques for determining information about the properties of substances based upon information about the structure of living or non-living cells exposed to substances.


US Patent 6,647,358. Pharmacokinetic-based drug design tool and method. Inventors: George Grass, Glen Leesman, Daniel Norris, Patrick Sinko, John Wehrli. Assignee: Lion Bioscience.

Covers a pharmacokinetic-based design and selection tool that includes as computer-readable components: an input/output system; a physiological simulation model of a mammalian system of interest having one or more physiological barriers to absorption; and a simulation engine having a differential equation solver.


US Patent 6,647,341. Methods for classifying samples and ascertaining previously unknown classes. Inventors: Todd Golub, Eric Lander, Jill Mesirov, Donna Slonim, Pablo Tamayo. Assignees: Whitehead Institute for Biomedical Research, Dana-Farber Cancer Institute.

Protects methods and apparatus for classifying or predicting the classes for samples based on gene expression and for ascertaining or discovering new, previously unknown classes based on gene expression. In one embodiment, the invention includes a method of determining a treatment plan for an individual having a disease in which a sample is obtained from the individual and is assessed for the level of gene expression for at least one gene. Next, a computer model built with a weighted voting scheme is used to classify the sample into a disease class, as a function of relative gene expression level of the sample with respect to that of the model. Finally, a treatment plan is determined using the disease class.


US Patent 6,643,634. Graphical viewer for biomolecular sequence data. Inventors: Alex Koleszar, Frank Russo, Joe Heath, Stephanie Berry, Rachel Wright, Peter Covitz, Yvonne Boldt, Lee Crawford. Assignee: Incyte Genomics (now Incyte).

Protects methods, media, and systems for graphically displaying computer-based biomolecular sequence information in a variety of different forms. The sequence information may be composed of nucleotide or amino acid sequence information or both.


US Patent 6,640,231. Ontology for database design and application development. Inventors: William Andersen, Paul Brinkley, Joshua Engel, Brian Peterson. Assignee: Ontology Works.

Protects a system and method to create or import ontologies and create databases and related application software. The invention relates to a process for creating and maintaining ontologies and processes for semi-automatically generating deductive databases, especially for biological information systems.


US Patent 6,640,227. Unsupervised automated hierarchical data clustering based on simulation of a similarity matrix evolution. Inventor: Leonid Andreev.

Protects methods for automated computerized hierarchical clustering of data in any field of science and technology based on similarity matrix evolution. Hierarchical clustering of matrix components is carried out by iterative transformation and division followed by transformation and division of each level of cluster, or by monitoring the changes in individual binary similarities throughout transformation of the entire matrix.

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The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.