Functionalized silicon compounds and methods for their synthesis and use
Granted: October 24, 2006
Patent Number:
7125947
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thiol, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Methods for mixing fluid in a rotating container
Granted: October 24, 2006
Patent Number:
7125161
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…
Identification of new small RNAs and ORFs of as mediators of cell and intercell regulation
Granted: October 10, 2006
Patent Number:
7119193
The invention relates to new small RNAs and ORFs of E. coli as mediators of cell and intercell regulation.
Arrays of nucleic acid probes on biological chips
Granted: October 3, 2006
Patent Number:
7115364
The invention provides chips of immobilized probes, and methods employing the chips, for comparing a reference polynucleotide sequence of known sequence with a target sequence showing substantial similarity with the reference sequence, but differing in the presence of e.g., mutations.
Computer software system, method, and product for scanned image alignment
Granted: October 3, 2006
Patent Number:
7116809
An image alignment tool is described for adjusting the alignment of a grid with an image. An initial grid aligner determines an initial, approximately aligned, position of the grid. An intensity scorer determines, for each of a plurality of test grid elements of the plurality of grid elements, a set of intensity scores. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional…
Methods for selecting nucleic acid probes
Granted: October 3, 2006
Patent Number:
7117095
Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.
Methods, computer software products and systems for correlating gene lists
Granted: October 3, 2006
Patent Number:
7117097
In some embodiment of the invention, methods are provided to compare lists of genes. In one embodiment, the genes are ranked with the lists. The ranks are analyzed using Spearman correlation.
Complexity management of genomic DNA by locus specific amplification
Granted: September 19, 2006
Patent Number:
7108976
The present invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. In one embodiment complexity reduction can be accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers. The locus specific capture probes may be attached to a solid support. Multiple DNA sequences may be amplified simultaneously to produce a reduced…
Methods for detecting and diagnosing oral cancer
Granted: September 19, 2006
Patent Number:
7108969
Methods of monitoring the expression of genes in malignant oral cells is disclosed. Gene expression profiles are used to identify markers associated with malignant oral cells and to diagnose oral cancer.
Mycobacterial rpoB sequences
Granted: September 19, 2006
Patent Number:
7108968
This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.
Cartridge loader and methods
Granted: September 19, 2006
Patent Number:
7108472
A device for transporting cartridges comprises a housing for holding a plurality of cartridges in a temperature controlled environment. A transport system is also provided and has a grasping mechanism for grasping one of the cartridges. The transport system is further used to remove the cartridge from the housing and to place the cartridge into a scanner.
Methods of analysis of allelic imbalance
Granted: August 29, 2006
Patent Number:
7097976
Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for…
Functionalized silicon compounds and methods for their synthesis and use
Granted: August 29, 2006
Patent Number:
7098286
Provided are functionalized silicon compounds and methods for their synthesis and use. The functionalized silicon compounds include at least one activated silicon group and at least one derivatizable functional group. Exemplary derivatizable functional groups include hydroxyl, amino, carboxyl and thiol, as well as modified forms thereof, such as activated or protected forms. The functionalized silicon compounds may be covalently attached to surfaces to form functionalized surfaces which…
Techniques for identifying confirming mapping and categorizing nucleic acids
Granted: August 29, 2006
Patent Number:
7099777
Systems and methods for identifying, confirming, mapping, and categorizing sample polymers, such as nucleic acid sequences, are provided. An estimation of the fraction of first and second polymers in a sample of polymers can be calculated by inputting a first hybridization value indicative of hybridization affinity of the sample of polymers to polymers probes that are complementary to the first polymer and inputting a second hybridization value indicative of hybridization affinity of the…
Capillary array electrophoresis scanner
Granted: August 15, 2006
Patent Number:
7090758
An improved rotary confocal fluorescence scanner capable of detecting analytes separated on over a 1,000 capillaries simultaneously. This system uses a confocal microscope objective and mirror assembly that rotates inside a vertical ring of capillaries to provide rapid and efficient excitation and detection of fluorescently labeled fragments separated within a cylindrical capillary array. Use of automated procedures to load and run all capillaries permits one to read more than 350,000…
Nucleotides and analogs having photoremovable protecting groups
Granted: August 8, 2006
Patent Number:
7087732
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.
Methods for monitoring the expression of alternatively spliced genes
Granted: August 8, 2006
Patent Number:
7089121
Methods, probe arrays and computer software products are provided for determining the arrangement of sequence elements. In one embodiment, methods for making and using exon chips are provided. The exon chips may be used to identify and quantify splice variants.
Method and system for providing a probe array chip design database
Granted: June 27, 2006
Patent Number:
7068830
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…
Methods for testing oligonucleotide arrays
Granted: June 13, 2006
Patent Number:
7060443
Methods for testing oligonucleotide arrays are disclosed including methods for testing the efficiency of nucleotide coupling; methods for testing amounts of deprotected oligonucleotides; methods for determining amounts of depurinated oligonucleotides; and methods of detecting the presence of cleavable structural features, such as double-stranded nucleic acids.
System, method, and computer software product for gain adjustment in biological microarray scanner
Granted: June 13, 2006
Patent Number:
7062092
Systems, methods, and computer program products are described for adjusting the gain of a scanner. The scanner includes one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain. One described method includes receiving a user-selected gain value, adjusting the first gain based on a first portion of the user-selected gain value, and adjusting the second gain based on a second portion of the user-selected gain value. Another…
