Arrays for detecting nucleic acids
Granted: April 8, 2004
Application Number:
20040067521
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Methods, systems and software for biological analysis
Granted: April 1, 2004
Application Number:
20040063099
Methods, computer software and systems are provided for biological data analysis. In one embodiment, significantly changed measurements are mapped to a biological function, such as a GO (Gene Ontology) annotation, category or biological pathway.
Expression monitoring for gene function identification
Granted: March 25, 2004
Application Number:
20040058376
This invention provides methods, compositions and apparatus for mapping the regulatory relationship among genes by massive parallel monitoring gene expression. In some embodiments, mutations in the up-stream regulatory genes are detected by monitoring the change in down-stream gene expression. Similarly, the function of a specific mutation in a up-stream gene is determined by monitoring the down-stream gene expression. In addition, regulatory function of a target gene can be determined…
Method, system and computer software providing a genomic web portal for functional analysis of alternative splice variants
Granted: March 11, 2004
Application Number:
20040049354
A system for analyzing alternative splice variant sequences is described, comprising an input manager for receiving alternative splice variant sequences that are identified by one or more probe sets, a correlator that correlates functional domains with each of the alternative splice variant sequences and an associater that associates putative functions with the alternative splice variant sequences based upon a combination of the functional domains. A method for analyzing alternative…
Support bound probes and methods of analysis using the same
Granted: February 26, 2004
Application Number:
20040038268
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Manufacturing process for array plate assembly
Granted: February 26, 2004
Application Number:
20040038388
In one embodiment, a method is provided for manufacturing an array plate consisting of several different arrays.
Molecular genetic profiling of gleason grades 3 and 4/5 prostate cancer
Granted: February 12, 2004
Application Number:
20040029151
Many genes are affected in prostate cancers which have not been previously identified. This includes genes that have been up-regulated or down-regulated. Monitoring the expression levels of these genes is useful to identify the existence of prostate cancer. Also, monitoring the expression levels of these genes is useful to predict the effectiveness of treatment, outcome, use of therapeutics, and screening drugs useful for the treatment of prostate cancer.
System, method, and computer program product for the representation of biological sequence data
Granted: February 12, 2004
Application Number:
20040030504
A method is described that includes the acts of receiving related biological sequences; and representing each of the related biological sequences as objects of a data model, where at least one of the objects is enabled to map at least one of the related biological sequences with at least one other of the related biological sequences.
Polymorphism detection utilizing clustering analysis
Granted: February 5, 2004
Application Number:
20040024537
Systems and methods for detecting differences in sample polymers, such as nucleic acid sequences, are provided. Hybridization affinity information for the sample polymers is clustered so that the differences, if any, between or among the sample polymers can be readily identified. By clustering the hybridization affinity information of the sample polymers, differences in the sample polymers can be accurately achieved even in the presence of random and systematic errors.
Method of photolithographic production of polymer arrays
Granted: February 5, 2004
Application Number:
20040023367
In one embodiment of the invention, methods for synthesizing polymers on a substrate are provided. The method includes the steps of coupling a monomer into exposed areas of a substrate in positive-tone application of a photoresist, or coupling a monomer into unexposed areas of a substrate in negative-tone application of a photoresist, where at least one area of the substrate is coated with the photoresist.
Quality control methods for microarray production
Granted: February 5, 2004
Application Number:
20040023247
In one embodiment of the invention, surface properties of a microarray are examined to detect manufacturing failure. The surface properties may be determined using FTIR.
System, method, and computer program product for dynamic display, and analysis of biological sequence data
Granted: January 22, 2004
Application Number:
20040012633
A system for providing an interactive interface for biological sequence information is described that includes a GUI manager to manage and display graphical elements, each associated with a user selection of one or more biological sequences, in the panes of a graphical user interface, where the one or more biological sequences includes a chromosome sequence; and one or more biological sequence tools that provide one or more tools to process information based upon a user selection of at…
System, method, and product for scanning of biological materials
Granted: January 22, 2004
Application Number:
20040012676
An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon…
Compositions and methods involving direct write optical lithography
Granted: January 15, 2004
Application Number:
20040008811
In one embodiment, fiber optic arrays or bundles are used as a light guide to transmit ultraviolet light to the substrate surface for photo-directed polymer synthesis. Digital Micromirror Array (DMA) is used as a switching device to reflect light onto the entry side of the fiber optic array.
System, method and computer software product for grid placement, alignment and analysis of images of biological probe arrays
Granted: January 8, 2004
Application Number:
20040006431
A system is described that associates grids with a probe array image based upon a positional placement of one or more control features, aligns the grids with one or more pixels based upon a metric value determined by one or more characteristics of the one or more pixels, and generates cell intensity values. The system may also associate grids with a probe array image based upon a positional placement of one or more control features, determine a ratio of pixel intensity values associated…
Nucleic acid labeling compounds
Granted: January 1, 2004
Application Number:
20040002595
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
Computer software products for nucleic acid hybridization analysis
Granted: January 1, 2004
Application Number:
20040002817
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.
Method, system and computer software for providing microarray probe data
Granted: January 1, 2004
Application Number:
20040002818
A genomic web portal system provides correlations between probes of probe arrays, such as probes of microarrays, and biological sequences. The system receives a user selection of probe identifiers, associates the probe identifiers with probe sequences, correlates the probe sequences with the biological sequences; and displays a graphical user interface including graphical elements representing probe sequences associated with the probe identifiers and graphical elements representing the…
Computer-aided probability base calling for arrays of nucleic acid probes on chips
Granted: January 1, 2004
Application Number:
20040002819
A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.
Antireflective coatings for high-resolution photolithographic synthesis of DNA array
Granted: December 25, 2003
Application Number:
20030235824
The present invention provides an array of polymers and methods of forming arrays of polymers by providing a substrate having a first layer including one or more dielectric coatings on a solid support and a second layer including a plurality of polymers disposed on the first layer. The invention also provides methods for forming an array of polymers on a substrate using light-directed synthesis by providing a substrate having a first layer including one or more dielectric coatings on a…
