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Recent Patents in Bioinformatics, Dec. 2007 — Jan. 2008

US Patent 7,317,820. System and method for automatically identifying sub-grids in a microarray. Inventor: James Darrell Park. Assignee: BioDiscovery.
Covers a digital image processing-based method for quantitatively processing nucleic acid species expressed in a microarray. According to the patent abstract, the computational method identifies the position of each of the sub-grids in a microarray by first identifying regions in the digital image that each contains one of the sub-grids, then identifying rows and columns in each region where nucleic acid species are expressed to form a set of candidate sub-grids in each region, then selecting for each region a “probable sub-grid” from the set of candidate sub-grids in each region, and finally comparing the positions of the probable sub-grids from each region to finalize the sub-grid positions.

US Patent 7,315,786. Protein design automation for protein libraries. Inventors: Bassil Dahiyat, Jo Bentzien, Klaus Fiebig, Robert Hayes. Assignee: Xencor.
Protects a protein design automation method that generates “computationally prescreened secondary libraries of proteins,” according to the patent abstract. The patent also covers methods and compositions that use the libraries.

US Patent 7,308,363. Modeling and evaluation metabolic reaction pathways and culturing cells. Inventors: Steven Mark Eker, Patrick Denis Lincoln, Peter Karp, Pedro Romero. Assignee: SRI International.
Protects a method for representing biological and chemical systems as symbolic models. “Minimal sets of elements of the system are identified from the model, for example, by automatic inference,” according to the patent abstract. The model can be constructed from “Boolean propositions that are mapped to a binary decision diagram” and can be probed using a branch and bound algorithm, the abstract states.

US Patent 7,305,331. System and method for simulating cellular biochemical pathways. Inventors: Eric Allen, Gilberto Fragoso, John Armstrong, Sandra Allen. Assignee: New World Science & Technology.
Covers a computer-implemented method for dynamically displaying biological pathways, specifically signal transduction pathways. One aspect of the invention relates to predicting the functional properties of a protein, the potential interaction partners of the protein, and/or the potential target biochemical pathways in which the protein may interact. Thus, the abstract states, “the influence of a given stimulus on a biochemical pathway can be assessed.”

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The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.