Patent application number | Description | Published |
20090062129 | REAGENTS, METHODS, AND LIBRARIES FOR GEL-FREE BEAD-BASED SEQUENCING - The present disclosure provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles typically comprise steps of extension, ligation, and cleavage. In certain embodiments, the methods make use of extension probes containing phosphorothiolate linkages and agents capable of cleaving such linkages. Methods of determining information about a sequence using at least two distinguishably labeled probe families are provided, as are methods of performing multiple sequencing reactions on a single template. Automated sequencing systems, flow cells, image processing methods, and computer-readable media that store computer-executable instructions and/or sequence information that can be used in accordance with such methods are also provided. In certain embodiments, blocking oligonucleotides are provided to facilitate sequencing using disclosed methods. | 03-05-2009 |
20090181385 | Reagents, methods, and libraries for bead-based sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. | 07-16-2009 |
20090280540 | DIRECTED ENRICHMENT OF GENOMIC DNA FOR HIGH-THROUGHPUT SEQUENCING - The present invention provides microarrays of oligonucleotide primer pairs, and in particular, microarrays of primers that comprise at least one cleavable linkage. Also provided are methods to capture oligonucleotide primer pairs from one or more microarrays, and methods to use the captured oligonucleotide primer pairs, such as for amplification of a target polynucleotide sequence. In addition, methods of using a microarray to isolate, purify and/or amplify a target polynucleotide are provided. | 11-12-2009 |
20100297626 | Reagents, Methods, and Libraries for Bead-Based Sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. In certain embodiments the methods make use of extension probes containing an abasic residue or a damaged base and employ agents appropriate to cleave linkages between a nucleoside and an abasic residue and/or agents appropriate to remove a damaged base from a nucleic acid. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads, which are immobilized in or on a semi-solid support. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages or trigger residues that are suitable for use in the method. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. The invention further provides efficient methods for preparing templates, particularly for performing sequencing multiple different templates in parallel. The invention also provides methods for performing ligation and cleavage. The invention also provides new libraries of nucleic acid fragments containing paired tags, and methods of preparing microparticles having multiple different templates (e.g., containing paired tags) attached thereto and of sequencing the templates individually. The invention also provides automated sequencing systems, flow cells, image processing methods, and computer-readable media that store computer-executable instructions (e.g., to perform the image-processing methods) and/or sequence information. In certain embodiments the sequence information is stored in a database. | 11-25-2010 |
20110077169 | Reagents, Methods, and Libraries for Bead-Based Sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. In certain embodiments the methods make use of extension probes containing an abasic residue or a damaged base and employ agents appropriate to cleave linkages between a nucleoside and an abasic residue and/or agents appropriate to remove a damaged base from a nucleic acid. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads, which are immobilized in or on a semi-solid support. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages or trigger residues that are suitable for use in the method. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. The invention further provides efficient methods for preparing templates, particularly for performing sequencing multiple different templates in parallel. The invention also provides methods for performing ligation and cleavage. The invention also provides new libraries of nucleic acid fragments containing paired tags, and methods of preparing microparticles having multiple different templates (e.g., containing paired tags) attached thereto and of sequencing the templates individually. The invention also provides automated sequencing systems, flow cells, image processing methods, and computer-readable media that store computer-executable instructions (e.g., to perform the image-processing methods) and/or sequence information. In certain embodiments the sequence information is stored in a database. | 03-31-2011 |
20110202280 | SYSTEMS AND METHODS FOR ERROR CORRECTION IN DNA SEQUENCING - Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided. | 08-18-2011 |
20110257019 | Directed Enrichment of Genomic DNA for High-Throughput Sequencing - The present invention provides microarrays of oligonucleotide primer pairs, and in particular, microarrays of primers that comprise at least one cleavable linkage. Also provided are methods to capture oligonucleotide primer pairs from one or more microarrays, and methods to use the captured oligonucleotide primer pairs, such as for amplification of a target polynucleotide sequence. In addition, methods of using a microarray to isolate, purify and/or amplify a target polynucleotide are provided. | 10-20-2011 |
20110257385 | METHODS FOR FLIP-STRAND IMMOBILIZING AND SEQUENCING NUCLEIC ACIDS - Provided herein are compositions, materials, methods and kits for immobilizing a template polynucleotide in a first orientation, and immobilizing a complementary sequence of the template polynucleotide in an orientation that is flipped compared to the orientation of the template polynucleotide. Provided herein are adaptive oligonucleotides that can be used in various nucleic acid manipulations to generate immobilized complement polynucleotides that are flipped in orientation compared to the orientation of the immobilized template polynucleotides. | 10-20-2011 |
20120191363 | Reagents, Methods, and Libraries for Bead-Based Sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. | 07-26-2012 |
20130211006 | Conjugated Polymeric Particle and Method of Making Same - A method of conjugating a substrate includes exchanging a counter ion associated with a biomolecule with a lipophilic counter ion to form a biomolecule complex, dispersing the biomolecule complex in a nonaqueous solvent, and coupling the biomolecule complex to a substrate in the presence of the nonaqueous solvent. | 08-15-2013 |
20140248610 | Reagents, Methods, and Libraries for Bead-Based Sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. | 09-04-2014 |
20140342353 | Reagents, Methods, and Libraries for Bead-Based Sequencing - The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. | 11-20-2014 |
Patent application number | Description | Published |
20090286294 | Methods and Compositions for Improving the Production of Fuels in Microorganisms - The invention relates to compositions, systems, and methods for producing fuels, such as ethanol and hydrogen, and related compounds. More specifically, compositions and methods are provided for making recombinant microorganisms for the production of fuels using genes from the | 11-19-2009 |
20100028966 | Methods and Compositions for Improving The production Of Products In Microorganisms - Methods and compositions are provided for improving the production of products, such as fuel products like ethanol, in microorganisms. In particular, methods and compositions are described for improving ethanol production utilizing genes identified in | 02-04-2010 |
20100035320 | METHODS AND COMPOSITIONS FOR IMPROVING THE PRODUCTION OF PRODUCTS IN MICROORGANISMS - Methods and compositions are provided for improving the production of products, such as fuel products like ethanol, in microorganisms. In particular, methods and compositions are described for improving ethanol production utilizing genes identified in | 02-11-2010 |
20100105114 | Methods and Compositions for Regulating Sporulation - Methods and compositions are provided for producing fuel utilizing various strains of | 04-29-2010 |
20120196338 | METHODS AND COMPOSITIONS FOR IMPROVING THE PRODUCTION OF PRODUCTS IN MICROORGANISMS - Methods and compositions are provided for improving the production of products, such as fuel products like ethanol, in microorganisms. In particular, methods and compositions are described for improving ethanol production utilizing genes identified in | 08-02-2012 |
Patent application number | Description | Published |
20120229500 | SYSTEM AND METHOD FOR CONCEPT DEVELOPMENT - A framework is provided for building a visual representation of a product concept including a textual component and/or a graphical component. A designation is received of a first element within at least one of the textual component and the graphical components as a dynamic element. The dynamic element is associated with a variant list including one or more element variants. A second element corresponding to the first element is identified. The second element is linked with the first element. A selection of a first element variant from the variant list is received. A first instantiation of the visual representation is generated including the first element variant as the dynamic element and including the first element variant as the second element. | 09-13-2012 |
20120232850 | SYSTEM AND METHOD FOR CONCEPT DEVELOPMENT - A computer implemented method, system, and computer program product include one or more processors providing a framework for building a visual representation of a product concept, the visual representation including one or more of a textual component and a graphical component; one or more processors receiving a designation of an element within at least one of the textual component and the graphical components as a dynamic element; one or more processors associating the dynamic element with a variant list including one or more element variants; one or more processors receiving a selection of a first element variant from the variant list; and one or more processors generating a first instantiation of the visual representation including the first element variant as the dynamic element. | 09-13-2012 |
20120232851 | SYSTEM AND METHOD FOR CONCEPT DEVELOPMENT - A computer implemented method, system, and computer program product include one or more processors providing a framework for building a visual representation of a product concept, the visual representation including one or more of a textual component and a graphical component; one or more processors receiving a designation of an element within at least one of the textual component and the graphical components as a dynamic element; one or more processors associating the dynamic element with a variant list including a plurality of element variants; one or more processors receiving a selection of a subset of the plurality of element variants from the variant list; and one or more processors generating a first instantiation of the visual representation including a combination of the subset of the plurality of element variants as the dynamic element. | 09-13-2012 |
20120232852 | SYSTEM AND METHOD FOR CONCEPT DEVELOPMENT - A computer implemented method, system, and computer program product include one or more processors identifying a dynamic element within framework for building a visual representation of a product concept, the visual representation including one or more of a textual component and a graphical component, the dynamic element associated with a variant list including one or more variant elements; one or more processors identifying one of a longest variant element and a shortest variant element from within the variant list; and one or more processors generating a first instantiation of a visual representation of a product concept including the one of the longest variant element and the shortest variant element as the dynamic element. | 09-13-2012 |
20120233037 | SYSTEM AND METHOD FOR CONCEPT DEVELOPMENT - A framework is provided for building a visual representation of a product concept including a textual component and/or a graphical component. A first element within one of the textual component and the graphical components is designated as a first dynamic element. A second element within one of the textual component and the graphical component is designated as a second dynamic element. The first dynamic element is associated with a first variant list. The second dynamic element is associated with a second variant list. A constraint is associated between at least a first element variant and at least a second element variant. A selection of a first element variant from the first variant list and a second element variant from the second variant list are received. A first instantiation of the visual representation is generated including the first element variant and the second element variant based upon the constraint. | 09-13-2012 |
Patent application number | Description | Published |
20090033336 | WIRELESS REMOTE DETECTOR SYSTEMS AND METHODS - A device for associating a circuit breaker with a circuit may have one or more sensors for remotely sensing that a circuit is active. When a sensor senses that a circuit is active, a transmitter may transmit a signal to a receiver that alerts a user. In this manner, the user may determine which of a plurality of different circuit breakers is associated with a particular circuit. This device mitigates the contemporary need to repeatedly turn off circuit breakers, go to the room in which the circuit is being monitored, and check to see if the circuit is active. | 02-05-2009 |
20100185406 | WIRELESS REMOTE DETECTOR SYSTEMS AND METHODS - A system for an embodiment includes a sensor device having at least one sensor adapted to monitor at least one parameter associated with a circuit and selectively provide measurement information on the at least one parameter. The at least one sensor may include an electrical sensor adapted to monitor an electrical parameter of the circuit for the sensor device to selectively provide as the measurement information, and wherein the sensor device includes a wireless transceiver within the sensor device and is adapted to transmit the measurement information and receive control information. The system may further include a receiver indicator device having a wireless transceiver and adapted to wirelessly receive the measurement information from the sensor device, provide the control information to the sensor device, and provide an indication based on the measurement information to a user operating the receiver indicator device | 07-22-2010 |
20120154140 | WIRELESS REMOTE DETECTOR SYSTEMS AND METHODS - A system is provided that includes: a sensor device adapted to selectively monitor a plurality of sensors including an electrical sensor adapted to monitor at least one electrical parameter associated with a circuit and a heat sensor adapted to monitor heat, wherein the sensor device includes a wireless transceiver within the sensor device adapted to transmit measurement information from the selected sensor; and a receiver indicator device adapted to wirelessly receive the measurement information from the sensor device, and provide an indication based on the measurement information to a user operating the receiver indicator device. | 06-21-2012 |
20130147460 | WIRELESS REMOTE DETECTORS SYSTEMS AND METHODS - A system is provided that includes: a sensor device adapted to selectively monitor a plurality of sensors, wherein the sensor device includes a wireless transceiver within the sensor device adapted to transmit measurement information from the selected sensor; and a receiver indicator device adapted to wirelessly receive the measurement information from the sensor device, and provide an indication based on the measurement information to a user operating the receiver indicator device. | 06-13-2013 |
Patent application number | Description | Published |
20110315898 | Plasmonic Polarizer - A radiation-emitting device (e.g., a laser) includes an active region configured to generate a radiation emission linearly polarized along a first polarization direction and a device facet covered by an insulating layer and a metal layer on the insulating layer. The metal layer defines an aperture through which the radiation emission from the active region can be transmitted and coupled into surface plasmons on the outer side of the metal layer. The long axis of the aperture is non-orthogonal to the first polarization direction, and a sequential series of features are defined in or on the device facet or in the metal layer and spaced apart from the aperture, wherein the series of features are configured to manipulate the surface plasmons and to scatter surface plasmons into the far field with a second polarization direction distinct from the first polarization direction. | 12-29-2011 |
20130148678 | QUANTUM CASCADE LASER SOURCE WITH ULTRABROADBAND SPECTRAL COVERAGE - A broadband quantum cascade laser includes multiple gain regions and a spacer layer disposed between at least two of the gain regions. The arrangement and characteristics of the gain regions and the spacer layer may be configured to reduce cross absorption between the gain regions. For example, one gain region may be configured to produce gain in an energy range in which another gain region produces absorptive effects. The thickness of the spacer layer may be selected to separate optical modes produced by adjacent gain regions while still producing a single broadband output from the quantum cascade laser. Gain competition between gain stages within a gain region may be mitigated by dividing gain stages with overlapping gain curves among multiple gain regions. | 06-13-2013 |
20130208743 | BROADBAND QUANTUM CASCADE LASER SOURCE - A broadband quantum cascade laser (QCL) source includes one or more QCLs having an active region designed based on a diagonal laser transition. The QCL source may include multiple QCLs formed in an array or the QCL source may comprise a single QCL device. Although each QCL provides an emission spectrum comprising a small range of wavelengths at a given applied voltage, changes in the applied operating voltage result in changes in the emission spectrum of the QCL due to the Stark shift. When the QCL source comprises a plurality of QCLs formed in an array, at least some of the elements in the array may receive different applied operating voltages such that the combined output spectrum of the array is broader than that achievable by a single QCL. When the QCL source comprises a single QCL device, an applied operating voltage may be swept through a range of applied voltages such that that combined output spectrum over one sweep cycle is broader than the output spectrum of the QCL device when a static operating voltage is applied. Alternatively, the single QCL device may comprise multiple independent gain sections, wherein each of the independent gain sections is configured to operate at a different voltages to provide a broadband output spectrum. | 08-15-2013 |
20140016895 | Plasmonic Polarizer - A radiation-emitting device (e.g., a laser) includes an active region configured to generate a radiation emission linearly polarized along a first polarization direction and a device facet covered by an insulating layer and a metal layer on the insulating layer. The metal layer defines an aperture through which the radiation emission from the active region can be transmitted and coupled into surface plasmons on the outer side of the metal layer. The long axis of the aperture is non-orthogonal to the first polarization direction, and a sequential series of features are defined in or on the device facet or in the metal layer and spaced apart from the aperture, wherein the series of features are configured to manipulate the surface plasmons and to scatter surface plasmons into the far field with a second polarization direction distinct from the first polarization direction. | 01-16-2014 |