Patents by Inventor John W. Simpson
John W. Simpson has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20030100102Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (>10,000) of different oligonucleotides.Type: ApplicationFiled: August 15, 2002Publication date: May 29, 2003Inventors: Jonathan M. Rothberg, Joel S. Bader, Scott B. Dewell, Keith McDade, John W. Simpson, Jan Berka, Christopher M. Colangelo, Michael P. Weiner
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Patent number: 6554985Abstract: This invention relates to methods and formulations for the separation of biological macromolecules according to their size using capillary electrophoresis with improved polyacrylamide matrixes under denaturing conditions.Type: GrantFiled: August 13, 1999Date of Patent: April 29, 2003Assignee: CuraGen CorporationInventors: Marie C. Ruiz-Martinez, Jan Berka, John W. Simpson
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Publication number: 20030068629Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (>10,000) of different oligonucleotides.Type: ApplicationFiled: March 21, 2002Publication date: April 10, 2003Inventors: Jonathan M. Rothberg, Joel S. Bader, Scott B. Dewell, Keith McDade, John W. Simpson, Jan Berka, Christopher M. Colangelo, Michael P. Weiner
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Patent number: 6485625Abstract: This invention is an integrated instrument for the high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: GrantFiled: June 21, 1999Date of Patent: November 26, 2002Assignee: CuraGen CorporationInventors: John W. Simpson, Jonathan M. Rothberg, Gregory T. Went, Marie Carmen Ruiz-Martinez, Gregory T. Mulhern
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Publication number: 20020130659Abstract: A giant magnetoresistive flux focusing eddy current device effectively detects deep flaws in thick multilayer conductive materials. The probe uses an excitation coil to induce eddy currents in conducting material perpendicularly oriented to the coil's longitudinal axis. A giant magnetoresistive (GMR) sensor, surrounded by the excitation coil, is used to detect generated fields. Between the excitation coil and GMR sensor is a highly permeable flux focusing lens which magnetically separates the GMR sensor and excitation coil and produces high flux density at the outer edge of the GMR sensor. The use of feedback inside the flux focusing lens enables complete cancellation of the leakage fields at the GMR sensor location and biasing of the GMR sensor to a location of high magnetic field sensitivity. In an alternate embodiment, a permanent magnet is positioned adjacent to the GMR sensor to accomplish the biasing.Type: ApplicationFiled: November 28, 2001Publication date: September 19, 2002Applicant: National Aeronautics and Space AdministrationInventors: Russell A. Wincheski, Min Namkung, John W. Simpson
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Patent number: 6453245Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: GrantFiled: January 10, 2001Date of Patent: September 17, 2002Assignee: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6432361Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: GrantFiled: November 28, 2000Date of Patent: August 13, 2002Assignee: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6418382Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: GrantFiled: December 29, 2000Date of Patent: July 9, 2002Assignee: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Publication number: 20020058256Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: ApplicationFiled: January 10, 2001Publication date: May 16, 2002Applicant: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Publication number: 20020012930Abstract: Disclosed herein are methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (>10,000) of different oligonucleotides.Type: ApplicationFiled: March 21, 2001Publication date: January 31, 2002Inventors: Jonathan M. Rothberg, Joel S. Bader, Scott B. Dewell, Keith McDade, John W. Simpson, Jan Berka, Christopher M. Colangelo
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Publication number: 20020009741Abstract: This invention is an integrated instrument for the high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: ApplicationFiled: April 17, 2001Publication date: January 24, 2002Applicant: CuraGen CorporationInventors: John W. Simpson, Jonathan Marc Rothberg, Gregory T. Went
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Publication number: 20020009721Abstract: This invention relates to methods and formulations for the separation of biological macromolecules according to their size using capillary electrophoresis with improved polyacrylamide matrixes under denaturing conditions.Type: ApplicationFiled: August 13, 1999Publication date: January 24, 2002Inventors: MARIE C. RUIZ-MARTINEZ, JAN BERKA, JOHN W. SIMPSON
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Publication number: 20010007985Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: ApplicationFiled: December 29, 2000Publication date: July 12, 2001Applicant: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6236945Abstract: This invention is an integrated instrument for the high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: GrantFiled: April 26, 1999Date of Patent: May 22, 2001Assignee: CuraGen CorporationInventors: John W. Simpson, Jonathan Marc Rothberg, Gregory T. Went
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Patent number: 6231812Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: GrantFiled: May 28, 1999Date of Patent: May 15, 2001Assignee: CuraGen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6218121Abstract: This invention is an integrated instrument for the high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: GrantFiled: April 26, 1999Date of Patent: April 17, 2001Assignee: CuraGen CorporationInventors: John W. Simpson, Jonathan Marc Rothberg, Gregory T. Went
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Patent number: 6190868Abstract: The present invention discloses a methodology which is directed to providing positive confirmation that nucleic acids, possessing putatively identified sequence predicted to generate observed GeneCalling™ signals, are actually present within the sample from which the signal was originally derived.Type: GrantFiled: September 23, 1999Date of Patent: February 20, 2001Assignee: CuraGen CorporationInventors: Jonathan M. Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6141657Abstract: This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification.Type: GrantFiled: October 1, 1997Date of Patent: October 31, 2000Assignee: Curagen CorporationInventors: Jonathan Marc Rothberg, Michael W. Deem, John W. Simpson
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Patent number: 6017434Abstract: This invention is an integrated instrument for the high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: GrantFiled: May 9, 1995Date of Patent: January 25, 2000Assignee: CuraGen CorporationInventors: John W. Simpson, Jonathan Marc Rothberg, Gregory T. Went
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Patent number: 5993634Abstract: This invention is an integrated instrument for high-capacity electrophoretic analysis of biopolymer samples. It comprises a specialized high-voltage, electrophoretic module in which the migration lanes are formed between a bottom plate and a plurality of etched grooves in a top plate, the module permitting concurrent separation of 80 or more separate samples. In thermal contact with the bottom plate is a thermal control module incorporating a plurality of Peltier heat transfer devices for the control of temperature and gradients in the electrophoretic medium. Fragments are detected by a transmission imaging spectrograph which simultaneously spatially focuses and spectrally resolves the detection region of all the migration lanes. The spectrograph comprises a transmission dispersion element and a CCD array to detect signals. Signal analysis comprises the steps of noise filtering, comparison in a configuration space with signal prototypes, and selection of the best prototype.Type: GrantFiled: May 9, 1996Date of Patent: November 30, 1999Assignee: CuraGen CorporationInventors: John W. Simpson, Jonathan M. Rothberg, Gregory T. Went