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Northwestern University, Agilent Technologies, Bacus Laboratories, Gene Logic, University of Nebraska, University of Chicago, Affymetrix

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Northwestern University of Evanston, Ill., has received US Patent No. 7,029,697, "Controlled surface-associated delivery of genes and oligonucleotides." The patent claims a system and methods for controlled gene delivery comprising condensed nucleic acids complexed with polylinkers. According to the patent's abstract, the complexes can be covalently or non-covalently bound to the surface of a substrate capable of supporting cell adhesion. The gene delivery system achieves temporal and spatial control of nucleic acid delivery to a target cell or cells through control of complex density on the surface of the support substrate, and reversibility of the attachment of the polylinker to the support substrate, the abstract states. The abstract claims that the system and methods can be used to create spatial patterns of gene expression, and in tissue engineering, high-throughput screening, and gene therapy applications.


Agilent Technologies of Palo Alto, Calif., has received US Patent No. 7,029,854, "Methods designing multiple mRNA transcript nucleic acid probe sequences for use in nucleic acid arrays." An array that is suitable for use as a surface-immobilized probe for two or more mRNA transcripts encoded by the same gene is claimed. The patent also claims a method where a consensus region for the two or more transcripts is first identified, and then employed to identify the suitable nucleic acid sequence by using a probe design protocol. Algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems are also claimed, as well as nucleic acid arrays produced with probes having sequences identified by the claimed methods.


Bacus Laboratories of Lombard, Ill., has received US Patent No. 7,031,507, "Method and apparatus for processing an image of a tissue sample microarray." The patent claims a method and apparatus for processing an image of a tissue sample microarray where a plurality of tissue samples is placed on an array on a microscope slide. The tissue samples are then simultaneously and uniformly treated and images of the tissue making up the microarray are captured and stored together with identifying information.


Gene Logic of Gaithersburg, Md., has received US Patent No. 7,031,843, "Computer methods and systems for displaying information relating to gene expression data." The patent claims computer and display methods and systems for acquiring, storing, manipulating, analyzing, linking, retrieving and displaying data, particularly data on gene expression. The patent also describes interactive systems for displaying gene expression-related data in three-dimensional molecular topographies where expressed genes and their activity are represented as peaks in the topographies. Additionally, the patent claims methods and systems for generating and displaying delta plots, which show differences in gene expression.


The Board of Regents of the University of Nebraska of Omaha has received US Patent No. 7,031,844, "Cluster analysis of genetic microarray images." The patent describes a method for determining the relative incidence of a binding substance within two biological samples. According to the patent's abstract, the two samples are labeled with luminescent materials having different chromatic properties. An image of the luminescent materials upon a binding site of a microarray is then analyzed as two clusters of data points scattered about representative pairs of chromatic intensity values. The relative incidence of the binding substance is then determined as a ratio of differences between corresponding indices of the representative pairs.


The University of Chicago has received US Patent No. 7,031,845, "Method for determining biological expression levels by linear programming." The patent claims a method for determining a matrix of expression levels corresponding to a set of biological targets and a set of biological samples. Specifically, the method guides the user to obtain a matrix of signal values corresponding to the set of biological targets; compute a vector of expression levels for a sample in the set of biological samples using the matrix of signal values; store the vector of computed expression levels in a storage matrix; repeat the computing and storing steps for each sample in the set of biological samples; and output the storage matrix as the matrix of expression levels. The claimed method works for both promiscuous probe array data where there may be multiple targets indicated by a single probe, and the polygamous case, in which there are multiple probes for a single target.


Affymetrix of Santa Clara, Calif., has received US Patent No. 7,031,846, "Method, system, and computer software for the presentation and storage of analysis results." The patent describes a computer program product, and related systems and methods, that processes emission intensity data corresponding to probes of a biological probe array. The claimed computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based on the emission intensity data, according to the patent's abstract. The analysis manager may further display the absolute or relative expression values based on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls, the abstract states. The measure of normalized change may be based on a comparison of genotype calls and a reference value.

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