Affymetrix, Inc.

Mds Sciex

Affymatrix, Inc

David J Balaban

Arun Aggarwal

Josie Dai

Earl A Hubbell

Gloria Cheung

Elina Khurgin

Michael P Mittmann

Andrew Paul May

Kurt C Gish

David H Mack

Igor A Shmulevich

Anthony J Berno

Robert G Chapman

Michael Mittman

Pejman Ghanouni

Joseph A Heanue

Joyti Baid

Jim Snyder

James Snyder

Nikolai Sharkov

System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.

Method and apparatus for providing a bioinformatics database

Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.

Method and system for providing a probe array chip design database

Disclosed are methods for analyzing molecular binding events in which the formation of ligand/antiligand complexes can be directly detected in a mixture without requiring separation of the components of the mixture from each other by measuring bulk properties of the mixture (i.e., properties that have contributions from several or all of the components present in the mixture). Using these techniques, it is possible to screen libraries without labeling either the target antiligand or ligand. The invention also provides a method for determining the strength of ligand/antiligand binding by further analysis of the same signals.

Detection of ligand-antiligand complex formation by electromagnetically detectable bulk property measurement

Methods and computer software products are provided for analyzing gene expression data. In one embodiment, multiple probes are used to detect a single transcript. The hybridization intensities of each probe is adjusted by dividing the intensities by the affinities of the probes. The minimal adjusted hybridization intensity may be used as the measurement of the gene expression.

Computer software products for nucleic acid hybridization analysis

According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression or concentration information collected from large numbers of samples.

Method and apparatus for providing an expression data mining database

A filter table provides a framework in which queries are efficiently and easily developed to access a gene expression database. The filter table is used to filter a plurality of expression levels to return a reduced set of expression levels, which may be further queried to provide more specific results. Using the filtering and querying provided one can easily identify genes or expressed sequence tags whose expression correlates to particular tissue types. Various tissue types may correspond to different diseases, states of disease progression, different organs, different species, etc. Researchers may now use large-scale gene expression databases to full advantage.

Gene expression and evaluation system using a filter table with a gene expression database

Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of subjects, samples, experiments, chips, etc.

Method and system for providing a polymorphism database

Innovative systems and methods for visualizing information collected from analyzing samples are provided. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is significant to a characteristic such as disease or resistance to disease. Additionally, the computer system may facilitate display of further information about relevant genes once they are identified.

Computer-aided display for comparative gene expression

Described is a novel relational database architecture that is adapted to storing information regarding the terms of one or more contracts, and the actions required to be performed under it. The database resides on a computer-readable storage medium as part of a multi-user computer network. By using simple subroutines readily apparent to one skilled in the computer arts, one can automatically generate alerts whenever an action needs to be performed. These alerts are then transmitted to users along the multi-computer network, appearing in an e-mail message that specifies the action, the individuals performing it, and the duties of each of these individuals. In this manner, one can ensure timely execution of the actions required under a contract.

Method and system for providing a contract management system using an action-item table

An efficient and easy to use query system for a gene expression database. Using such a system, one can easily identify genes or expressed sequence tags whose expression correlates to particular tissue types. Various tissue types may correspond to different diseases, states of disease progression, different organs, different species, etc. Researchers may now use large scale gene expression databases to full advantage.

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San Jose, CA, United States of America

David J Balaban