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IP Update: Affymetrix, Microsoft Among Recent Bioinformatics Patent Winners

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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

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.