System, method, and product for dynamic noise reduction in scanning of biological materials
Granted: October 31, 2002
Application Number:
20020161529
Systems and methods are described for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam, such as a laser beam. As one example, a scanning system is described that includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization…
System, method, and product for symmetrical filtering in scanning of biological materials
Granted: October 31, 2002
Application Number:
20020159058
An apparatus is described that includes an emission signal detector and an emission signal filter. An excitation beam scans an array of biological materials, and the emission signal detector detects an emission signal indicative of an emission beam responsive to the excitation beam. The emission signal filter is a linear-phase filter that provides a filtered emission signal having substantially symmetrical rise and fall edges. A linear-phase excitation signal filter may also be provided…
Arrays for detecting nucleic acids
Granted: October 24, 2002
Application Number:
20020155491
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.
Arrays for detecting nucleic acids
Granted: October 24, 2002
Application Number:
20020155492
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.
Very large scale immobilized polymer synthesis
Granted: October 24, 2002
Application Number:
20020155588
A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
Computer-aided visualization of expression comparison
Granted: October 17, 2002
Application Number:
20020150932
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…
Printing oligonucleotide arrays
Granted: October 10, 2002
Application Number:
20020147319
A method and apparatus for selectively applying a print material onto a substrate for the synthesis of an array of oligonucleotides at selected regions of a substrate. The print material includes a barrier material, a monomer sequence, a nucleoside, a deprotection agent, a carrier material, among other materials. The method and apparatus also relies upon standard DMT based chemistry, and a vapor phase deprotection agent such as solid TCA and the like.
System and method for management of microarray and laboratory information
Granted: October 10, 2002
Application Number:
20020147512
Systems, methods, and computer program products are described that provide an applications programming interface (API) for enabling a user-provided software application to access a data structure of a laboratory information management system application. The API includes one or more code libraries that enable transfer of user data from the user-provided software application directly or indirectly to the data structure. The user data includes data from a number of biological experiments.…
Complexity management and analysis of genomic data
Granted: October 3, 2002
Application Number:
20020142314
The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to…
Apparatus comprising polymers
Granted: September 26, 2002
Application Number:
20020137096
A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protecting groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
System, method, and user interfaces for managing genomic data
Granted: September 12, 2002
Application Number:
20020128993
A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may…
System, method, and user interfaces for mining of genomic data
Granted: September 12, 2002
Application Number:
20020129009
A data mining tool is described that includes a data structure populator that stores one or more first sets of data selected for querying into a first data structure. The tool also has a query builder that builds at least a first query based, at least in part, on one or more query parameters. Also included in the tool is a query manager that interrogates the first data structure with the first query. The one or more first sets of data are based, at least in part, on experiments using…
Nucleic acid endocing growth factor protein
Granted: September 5, 2002
Application Number:
20020123083
The present invention provides a novel growth factor polynucleotide, growth factor polypeptide, gene delivery vehicles comprising and/or expressing the growth factor polynucleotide, antibodies and fragments capable of specifically binding to the growth factor polypeptide, receptors of the growth factor polypeptide, modulators of the growth factor activity, and modulators of growth factor expression. Also provided by the invention are host cells and transgenic organisms comprising the…
Methods for gene expression analysis
Granted: August 29, 2002
Application Number:
20020120409
The present invention relates to the detection of nucleic acids, preferably RNA. Primers of random sequence hybridize to the template at regions where complementarity exists between a given random primer and the template. The hybridized primers are used to prime cDNA synthesis. The resulting cDNA product is not biased toward representation of the 3′ ends of the RNAs in the starting sample.
Blocker-aided target amplification of nucleic acids
Granted: July 25, 2002
Application Number:
20020098510
The present invention describes a method for blocking an unwanted sequence from been amplified, duplicated or reverse transcribed by using a blocking molecule. Preferred embodiments of the blocking molecule have sequences complimentary at least partially to the unwanted sequence. The preferred blocking molecule can be made of nucleic acids and analogues, for example, peptide nucleic acid and locked nucleic acid.
Determining signal transduction pathways
Granted: July 18, 2002
Application Number:
20020094518
Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
System and method for addressable light-directed microarray printing
Granted: June 20, 2002
Application Number:
20020075490
Systems and methods are described for synthesizing probe arrays of polymers. In one such system, a network server processes customer orders to provide data indicative of at least one probe array sequence desired by the customer to be included in a synthesized probe array. A probe array design and control computer executes a probe array design application that processes the probe and array configuration data to provide probe array design data that is then processed by a manufacturing…
Device and methods for mixing fluids
Granted: June 13, 2002
Application Number:
20020071339
The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the…
Very large scale immobilized polymer synthesis
Granted: May 30, 2002
Application Number:
20020064796
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Integrated microvolume device
Granted: May 23, 2002
Application Number:
20020060156
A fully integrated monolithic small volume PCR-CE device in glass, or the like materials, is fabricated using thin film metal heaters and thermocouples to thermally cycle sub-microliter PCR volumes. Successful amplification of a PCR fragment is demonstrated on a PCR-CE chip. The process utilizes a linear polyacrylamide surface coating coupled with addition of BSA to the amplification buffer was necessary to obtain amplification efficiencies comparable to a positive control. The…
