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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Feb 2, 2004

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US Patent 6,681,186. System and method for improving the accuracy of DNA sequencing and error probability estimation through application of a mathematical model to the analysis of electropherograms. Inventors: Gennady Denisov, Alan Arehart, Michael Curtin. Assignee: Paracel.

Protects a method that uses a mathematical model to improve the accuracy of DNA sequencing by analyzing electropherograms. The method assigns a quality value to base calls by detecting a plurality of peaks, expanding the plurality of peaks, and resolving the plurality of expanded peaks by fitting the plurality of expanded peaks using a model of a peak shape. A peak resolution parameter is calculated and used in processing.


US Patent 6,678,619. Method, system, and computer program product for encoding and building products of a virtual combinatorial library. Inventors: Victor Lobanov, Dimitris Agrafiotis, Francis Salemme.

Covers a method, system, and computer program product for encoding and building products of a virtual combinatorial library. Chemical reaction and reagent data for forming products of the virtual combinatorial library are encoded in a computer-readable form, and a compiler then operates on the encoded information and generates reagent-mapping data.


US Patent 6,678,618. Neural network methods to predict enzyme inhibitor or receptor ligand potency. Inventors: Steven Schwartz, Vern Schramm, Benjamin Braunheim. Assignee: Albert Einstein College of Medicine of Yeshiva University.

Protects a method to analyze and predict the binding energy for enzyme-transition state inhibitor interactions using computational neural networks. According to the inventors, experimental results show that the neural networks can predict with quantitative accuracy the binding strength of new inhibitors. The method is also applicable to prediction of the binding free energy of a ligand to a receptor.


US Patent 6,677,114. Polypeptide fingerprinting methods and bioinformatics database system. Inventors: Luke Schneider, Michael Hall, Robert Petesch, Jeffrey Peterson. Assignee: Target Discovery.

Covers methods and devices for determining the sequence of polypeptides using electrophoretic methods and mass spectroscopy, including methods to generate protein expression fingerprint datasets and a computer-based database query and retrieval system for the protein expression fingerprint datasets.


US Patent 6,675,166. Integrated multidimensional database. Inventor: Steven Bova. Assignee: John Hopkins University.

Describes a method of distributing research data from a common database to a user of the common database. The method stores research results in a local database, which can be selectively extracted from the local database to the common database.


US Patent 6,675,104. Method for analyzing mass spectra. Inventors: Chris Paulse, Edward Gavin, Leonid Braginsky, William Rich, Eric Fung. Assignee: Ciphergen Biosystems.

Covers a method for analyzing mass spectra using a digital computer, in which a classification model is used to assign sample data obtained from mass spectra to different biological classes.


US Patent 6,675,103. Visualizing high dimensional descriptors of molecular structures. Inventor: David Patterson. Assignee: Tripos.

Covers a projection method for visualizing chemical compounds in high-dimensional molecular descriptor space in two dimensions.


US Patent 6,674,882. Automated DNA array image segmentation and analysis. Inventor: Soheil Shams. Assignee: BioDiscovery.

Describes a method for segmenting spaced DNA spot images. For each DNA spot image, the method extracts background and signal intensity levels, and determines difference values between the background intensity levels and signal intensity levels.


US Patent 6,671,627. Method and computer program product for designing combinatorial arrays. Inventors: Dimitris Agrafiotis, Victor Lobanov. Francis Salemme. Assignee: 3-D Pharmaceuticals.

Describes a computerized method for designing combinatorial arrays in which reagents are initially selected from a list of candidates in a combinatorial library. The reagents that maximize a design objective are determined in an iterative manner, by examining each variation site in the combinatorial library in an alternating sequence.


US Patent 6,671,625. Method and system for signal detection in arrayed instrumentation based on quantum resonance interferometry. Inventor: Sandeep Gulati. Assignee: ViaLogy.

Protects a signal processing technique for detecting hybridization expression patterns in digitized images of biological samples in arrayed platforms. The method uses quantum resonance interferometry to amplify those signals having an intensity lower than the intensity of signals associated with background noise so that they may be clearly distinguished.


US Patent 6,671,624. Machine readable storage media for detecting distribution of macromolecules between nucleus and cytoplasm in cells. Inventors: Terry Dunlay. Lansing Taylor, Albert Gough, Kenneth Giuliano. Assignee: Cellomics.

Protects systems, methods, and screens for an optical system to rapidly determine the distribution, environment, or activity of fluorescently labeled reporter molecules in cells for the purpose of screening large numbers of compounds for those that specifically affect particular biological functions. The invention includes a computerized method for processing, displaying, and storing the experimental data.


US Patent 6,670,127. Method for assembly of a polynucleotide encoding a target polypeptide. Inventors: Glen Evan. Assignee: Egea Biosciences.

Protects a method for computer-directed polynucleotide assembly based upon information available in public genomic databases. The method can be used to select, synthesize, and assemble a novel, synthetic target polynucleotide sequence encoding a target polypeptide, according to the inventors.

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The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.