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IP Update: Affymetrix, Microsoft Among Recent Bioinformatics Patent Winners


US Patent 8,467,974. System, method, and computer software for the presentation and storage of analysis results. Inventors: Shantanu Kaushikkar, Teresa Webster, Rui Mei, Linda McAllister. Assignee: Affymetrix

This patent is for a system and methods of processing "emission intensity data" from biological array probes. According to the abstract, the system includes a genotype and statistical analysis manager that "determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter." The manager may also "determine genotype calls for one or more probes" as well as "display the absolute or relative expression values."

US Patent 8,467,971. Structure based alignment and clustering of proteins (STRALCP). Inventors: Adam Zemla, Carol Zhou, Jason Smith, Marisa Lam. Assignee: Lawrence Livermore National Security

Describes computational methods of clustering protein structures based on local and pair-wise global similarity values and "identifying spans of conserved residues within the clustered proteins," the abstract states.

US Patent 8,463,555. System and methods for indel identification using short read sequencing. Inventors: 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 8,457,903. Method and/or apparatus for determining codons. Inventors: Robin Emig, Richard John Fox, Claes Gustafsson, Sridhar Govindarajan, Jeremy Minshull, Guy Cavet. Assignee: Codexis Mayflower Holdings

This patent application describes methods and systems for "minimizing and/or optimizing data strings in accordance with rules and options." These strings, the abstract states, can "represent data sequences important in certain biologic analyses/or syntheses."

US Patent 8,452,542. Structure-sequence based analysis for identification of conserved regions in proteins. Inventors: Adam Zemla, Carol Zhou, Jason Smith, Marisa Lam, Jason Smith, Elizabeth Pardes. Assignee: Lawrence Livermore National Security

Describes computational methods for scoring conservation in a protein structure based on "a computationally identified family or cluster of protein structures," the abstract states.

US Patent 8,447,526. Methods and computer systems for analyzing high-throughput assays. Inventors: Lee Weng, Hongyue Dai, Steven Bartz. Assignee: Microsoft

Describes methods of detecting variations in measurements of biological variables, for example, variations in cell viability with or without treatment.

US Patent 8,442,771. Methods and apparatus for term normalization. Inventor: Xinglong Wang. Assignee: ITI Scotland

Describes a natural language processing-based method for "normalizing … mentions of subcellular entities, such as proteins and/or genes" in biomedical texts.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.