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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

Unwrapping Mummies' Faces

LiveScience reports that Parabon NanoLabs researchers have reconstructed how three Egyptian mummies may have looked.

Study on Hold

The Spectrum 10K study has been put on hold due to a backlash, leading the researchers to conduct consultations with the autism community, Nature News reports.

Others Out There Already

Reuters reports that Sanofi is no longer developing an mRNA-based vaccine for SARS-CoV-2.

PNAS Papers on GWAS False Discovery, PRAMEF2 Role in Tumorigenesis, RNA Virus Reverse Genetics

In PNAS this week: strategy to account for GWAS false-discovery rates, role of PRAMEF2 in cancer development, and more.