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IP Update: Boston University, Korea Basic Science Institute among Recent Bioinformatics Patent Winners

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US Patent 8,306,752. Method to determine transcriptional regulation pathways in organisms. Inventors: Timothy Gardner, James Collins, Boris Hayete, Jeremiah Faith. Assignee: Trustees of Boston University

Describes computer-implemented methods and systems for identifying regulatory relationships between polypeptides and the targets of their regulatory activities.


US Patent 8,301,393. Methods and systems for genome-scale kinetic modeling. Inventors: Bernhard Palsson, Neema Jamshidi. Assignee: The Regents of the University of California

Describes a computerized method for constructing, analyzing, and characterizing the dynamic states of biological networks at the cellular level. According to the abstract, the method works by constructing matrices using high-throughput data including fluxomic, metabolomic, and proteomic data.


US Patent 8,301,392. Automated decision support for associating an unknown biological specimen with a family. Inventors: Ranajit Chakraborty, John Douglas Birdwell, Tse-Wei Wang, Dale Stansberry. Assignee: University of Tennessee Research Foundation

Describes a method for predicting the familial origins of unknown biological specimens as well as an automated decision support algorithm that selects a subset of available family members for DNA typing.


US Patent 8,301,391. Identifying components of a network having high importance for network integrity. Inventors: Malcolm Young, Peter Andras, Mark O’Neill. Assignee: E-Therapeutics

Describes a computerized method for identifying target proteins for drug therapies that accepts proteome data in the form of a network as input and then identifies nodes and links between nodes that are important for network integrity.


US Patent 8,301,387. Combinatorial transcription control for programmed genetic response. Inventors: Terence Tai-Li Hwa, Ulrich Gerland, Nicolas Buchler. Assignee: The Regents of the University of California

Describes a method for “combinatorially controlling” the transcription of a target gene in order to produce a programmed response in the cell. The method implements “complex logic functions” where each “logic function combines two or more different inputs to generate an output comprising a unique gene expression in the cell.” The method also includes procedures “for selecting the strengths of the binding sites of different TFs and their relative positioning in order to implement … different logic functions.


US Patent 8,296,300. Method for reconstructing a protein database and a method for screening proteins by using the same method. Inventors: Kyung-Hoon Kwon, Jong Shin Yoo. Assignee: Korea Basic Science Institute

Describes a method for reconstructing a protein database and identifying proteins that is useful for investigating endogenous proteins and their functions and interactions.


US Patent 8,296,116. Bioinformatics system. Inventor: Neal Solomon. Assignee: Not listed

This patent is for a method of developing models of functional proteomics. It has three subsystems, including a system to model protein-protein interactions using an evolvable global proteomic model of functional proteomics; a system to “identify haplotypes customized for specific pathology using dysfunctional protein pathway simulations of the function of combinations of single nucleotide polymorphisms;” and “a pharmacoproteomic modeling system to develop, test, and refine proposed drug solutions based on the molecular structure and topology of mutant proteins. According to the abstract, the system is used to simulate degenerative genetic disease, some kinds of cancer, neurodegenerative diseases, immunodegenerative diseases, and aging.


US Patent 8,296,075. Computer system and computer-facilitated method for nucleic acid sequence alignment and analysis. Inventor: Bobi Den Hartog. Assignee: Mito Tech

Describes computer systems and methods for reliable DNA alignment. Specifically, it “relates to the automation of alignment and naming of mitochondrial DNA sequences for use in forensic analysis,” the abstract states. It provides “consistency of sequence nomenclature by minimizing alignment ambiguities, thus providing a common functional system within and among laboratories.”


US Patent 8,296,070. Method and apparatus for improved simulation of chemical and biochemical reactions. Inventors: Ricardo Paxson, Joseph Hicklin. Assignee: The MathWorks

Describes a computer system for modeling, simulating, and analyzing chemical and biochemical reactions.


US Patent 8,290,715. System and method for multiple-factor selection. Inventors: Dimitris Anastassiou, Vinay Varadan. Assignee: The Trustees of Columbia University in the City of New York.

Describes techniques for multiple-factor selection that can be used to select factors involved in gene expression analysis in disease


US Patent 8,285,489. Multi-stage, regression-based PCR analysis system. Inventor: Jeffrey Lerner. Assignee: Bio-Rad Laboratories

Describes data processing systems and methods for analyzing data from biological and chemical reactions exhibiting amplification, for example, a polymerase chain reaction.


US Patent 8,280,641. Utility of genomic fractals resulting in fractals of organisms. Inventor: Andras Pellionisz. Assignee: Not listed

Describes a method of analyzing repetitive elements in hereditary material as fractal sets for biological research and medical procedures. The abstract explains that the method analyzes fractal genomic information “for correspondences to healthy or pathological structural and functional properties of cells, organelles, or organisms.”


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The Scan

UK Funds to Stay Ahead of Variants

The UK has announced a further £29.3 million to stay on top of SARS-CoV-2 variants, the Guardian reports.

Push for Access

In a letter, researchers in India seek easier access to COVID-19 data, Science reports.

Not as Cold

Late-stage trial results are expected soon for an RNA-based vaccine that could help meet global demand as it does not require very cold storage, the New York Times writes.

Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

In Genome Research this week: influence of microbes on transfer RNA patterns, evolutionary relationships of honeybees, and more.