Patents by Inventor Jeremy Lackey
Jeremy Lackey 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: 20180231465Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: ApplicationFiled: January 29, 2018Publication date: August 16, 2018Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Paul E. Glenn, Lawrence C. West, Benjamin Cipriany, Keith G. Fife
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Patent number: 10048208Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well.Type: GrantFiled: November 17, 2014Date of Patent: August 14, 2018Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence West, Michael Ferrigno, Paul E. Glenn, Anthony Bellofiore
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Publication number: 20180223353Abstract: Methods of loading a molecule of interest into a sample well are provided. In some aspects, methods of loading a molecule of interest into a sample well involve loading a molecule of interest into a sample well in the presence of a crowding agent and/or a condensing agent. In some aspects, methods of loading a sequencing template into a sample well are provided.Type: ApplicationFiled: December 19, 2017Publication date: August 9, 2018Applicant: Quantum-Si IncorporatedInventors: James A. Ball, Jeremy Lackey, Brian Reed, Alexander Goryaynov, Jonathan M. Rothberg
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Publication number: 20180208911Abstract: Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.Type: ApplicationFiled: December 19, 2017Publication date: July 26, 2018Applicant: Quantum-Si IncorporatedInventors: Brian Reed, Mohammad Wadud Bhuiya, Manjula Pandey, Jeremy Lackey, Jonathan M. Rothberg
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Patent number: 9983135Abstract: An active-source-pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule.Type: GrantFiled: November 17, 2014Date of Patent: May 29, 2018Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid
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Publication number: 20180120229Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: December 18, 2017Publication date: May 3, 2018Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Publication number: 20180088052Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: ApplicationFiled: November 10, 2017Publication date: March 29, 2018Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence C. West, Michael Ferrigno, Paul E. Glenn, Adam Ezra Cohen, Anthony Bellofiore
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Patent number: 9921157Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: GrantFiled: August 7, 2015Date of Patent: March 20, 2018Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Paul E. Glenn, Lawrence C. West, Benjamin Cipriany, Keith G. Fife
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Patent number: 9885657Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: August 7, 2015Date of Patent: February 6, 2018Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Patent number: 9863880Abstract: Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.Type: GrantFiled: November 17, 2014Date of Patent: January 9, 2018Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Benjamin Cipriany, Jack Jewell, Lawrence West, Michael Ferrigno, Paul E. Glenn, Adam E. Cohen, Anthony Bellofiore
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Publication number: 20170362651Abstract: Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction. In some aspects, the disclosure provides compositions comprising luminescently labeled nucleotides.Type: ApplicationFiled: May 22, 2017Publication date: December 21, 2017Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Jeremy Lackey, Brian Reed, Xinghua Shi, Haidong Huang, David Dodd
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Publication number: 20170350818Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device may include multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region. The integrated device also includes a waveguide configured to couple excitation energy to at least one sample well in the array and positioned at a first distance from a surface of the trench region and at a second distance from the surface in a region separate from the trench region. The first distance is smaller than the second distance. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: June 1, 2017Publication date: December 7, 2017Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Gerard Schmid, Keith G. Fife, James Beach, Jason W. Sickler, Lawrence C. West, Paul E. Glenn, Kyle Preston, Farshid Ghasemi, Benjamin Cipriany, Jeremy Lackey
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Publication number: 20170299518Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: July 5, 2017Publication date: October 19, 2017Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Patent number: 9784679Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: September 2, 2016Date of Patent: October 10, 2017Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Patent number: 9732113Abstract: The invention provides novel oligonucleotide probes that have dendrimeric dyes useful for detecting and analyzing biological samples, and compositions and methods thereof. The dendrimeric dye-containing oligonucleotide probes are useful for high sensitivity fluorescence in situ hybridization (FISH) of nucleic acids such as DNA and RNA.Type: GrantFiled: January 12, 2014Date of Patent: August 15, 2017Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Jeremy Lackey, Siyuan Chen, Maithreyan Srinivasan
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Patent number: 9678012Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: GrantFiled: September 2, 2016Date of Patent: June 13, 2017Assignee: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Publication number: 20170107562Abstract: Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction.Type: ApplicationFiled: May 20, 2016Publication date: April 20, 2017Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Jeremy Lackey, Brian Reed, Xinghua Shi, Haidong Huang
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Publication number: 20160370292Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: September 2, 2016Publication date: December 22, 2016Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Publication number: 20160370291Abstract: System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device.Type: ApplicationFiled: September 2, 2016Publication date: December 22, 2016Applicant: Quantum-Si IncorporatedInventors: Jonathan M. Rothberg, Ali Kabiri, Jason W. Sickler, Brett J. Gyarfas, Jeremy Lackey, Gerard Schmid, Lawrence C. West, Keith G. Fife, Benjamin Cipriany, Farshid Ghasemi
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Publication number: 20160340382Abstract: The present invention is directed to RNA monomers comprising O-acetal levulinyl protecting groups at the 2? and/or the 5?-hydroxy functionalities of the ribose moiety. Said monomers may be incorporated into oligoribonucleotides or RNA polynucleotides. Furthermore, the invention is directed to methods for the synthesis of said RNA monomers, oligoribonucleotides and RNA polynucleotides, as well as methods for their deprotection and methods for the use of said compounds and compositions comprising said compounds. In particular, such compounds and compositions comprising them are used in methods for light-directed synthesis of RNA microarrays.Type: ApplicationFiled: December 29, 2015Publication date: November 24, 2016Applicants: THE ROYAL INSTITUTION FOR THE ADVANCEMENT OF LEARNING/MCGILL UNIVERSITY, WISCONSIN ALUMNI RESEARCH FOUNDATIONInventors: Masad Damha, Jeremy Lackey, Debbie Mitra, Marvin Wickens, Franco Cerrina, Mark Somoza