Patents by Inventor Wouter Meuleman
Wouter Meuleman 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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Patent number: 11900600Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.Type: GrantFiled: October 10, 2022Date of Patent: February 13, 2024Assignee: Altius Institute for Biomedical SciencesInventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
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Patent number: 11873480Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: GrantFiled: October 16, 2015Date of Patent: January 16, 2024Assignee: ILLUMINA CAMBRIDGE LIMITEDInventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20230274423Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.Type: ApplicationFiled: October 10, 2022Publication date: August 31, 2023Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
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Patent number: 11501429Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.Type: GrantFiled: July 19, 2018Date of Patent: November 15, 2022Assignee: Altius Institute for Biomedical SciencesInventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
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Publication number: 20220282242Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: April 12, 2022Publication date: September 8, 2022Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20220177960Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: ApplicationFiled: February 22, 2022Publication date: June 9, 2022Inventor: Wouter Meuleman
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Patent number: 11286521Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: GrantFiled: October 18, 2019Date of Patent: March 29, 2022Assignee: Illumina Cambridge LimitedInventor: Wouter Meuleman
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Patent number: 11195596Abstract: Embodiments of techniques for analyzing one or more genomic regions of a genome of an organism. Data about a genomic region may be analyzed to determine an information content of the genomic region, which may indicate an amount of information provided by the genomic region. The data about the genomic region may be or include data identifying a chromatin state for the genomic region. A chromatin state may be one of a set of chromatin states that each define a different set of one or more chromatin characteristics. Chromatin characteristics may be structural and/or functional features of genomic regions. A chromatin state of a genomic region may be determined from, and describe, the genomic region such that when a genomic region has a set of one or more chromatin characteristics, a chromatin state associated with that combination of one or more chromatin characteristics is identified for the genomic region.Type: GrantFiled: January 29, 2016Date of Patent: December 7, 2021Assignee: Massachusetts Institute of TechnologyInventor: Wouter Meuleman
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Publication number: 20200167914Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.Type: ApplicationFiled: July 19, 2018Publication date: May 28, 2020Inventors: John A. STAMATOYANNOPOULOS, Shreeram AKILESH, Alexander MURATOV, Wouter MEULEMAN, William KERWIN
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Publication number: 20200157619Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: ApplicationFiled: October 18, 2019Publication date: May 21, 2020Inventor: Wouter Meuleman
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Patent number: 10450605Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: GrantFiled: December 19, 2017Date of Patent: October 22, 2019Assignee: ILLUMINA CAMBRIDGE LIMITEDInventor: Wouter Meuleman
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Patent number: 10378051Abstract: A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety.Type: GrantFiled: September 26, 2012Date of Patent: August 13, 2019Assignee: Illumina Cambridge LimitedInventors: Wouter Meuleman, Elena Cressina, Geoffrey Paul Smith, Rosamond Jackson, Xiaohai Liu
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Publication number: 20190048332Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: October 29, 2018Publication date: February 14, 2019Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20190040382Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.Type: ApplicationFiled: October 16, 2015Publication date: February 7, 2019Applicant: ILLUMINA CAMBRIDGE LIMITEDInventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
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Publication number: 20180105874Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: ApplicationFiled: December 19, 2017Publication date: April 19, 2018Inventor: Wouter Meuleman
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Publication number: 20180025110Abstract: Embodiments of techniques for analyzing one or more genomic regions of a genome of an organism. Data about a genomic region may be analyzed to determine an information content of the genomic region, which may indicate an amount of information provided by the genomic region. The data about the genomic region may be or include data identifying a chromatin state for the genomic region. A chromatin state may be one of a set of chromatin states that each define a different set of one or more chromatin characteristics. Chromatin characteristics may be structural and/or functional features of genomic regions. A chromatin state of a genomic region may be determined from, and describe, the genomic region such that when a genomic region has a set of one or more chromatin characteristics, a chromatin state associated with that combination of one or more chromatin characteristics is identified for the genomic region.Type: ApplicationFiled: January 29, 2016Publication date: January 25, 2018Applicant: Massachusetts Institute of TechnologyInventor: Wouter Meuleman
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Publication number: 20140349300Abstract: A method for determining the sequence of a target nucleic acid, including steps of contacting a target nucleic acid with a polymerase to sequentially remove nucleotide triphosphates from the target nucleic acid, wherein the nucleotide triphosphates that are removed have a variety of different base moieties; and distinguishing the different base moieties for the nucleotide triphosphates that are removed. Also provided is a apparatus including a nanopore positioned in a fluid impermeable barrier to form a passage through which a nucleotide triphosphate can pass from a first fluid reservoir to a second fluid reservoir, and a reaction mix in the first fluid reservoir that includes a polymerase, target nucleic acid having two strands, and pyrophosphorolytic concentration of pyrophosphate.Type: ApplicationFiled: May 23, 2014Publication date: November 27, 2014Applicant: Illumina Cambridge LimitedInventor: Wouter MEULEMAN
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Patent number: 8372629Abstract: A device for individually analysing cells of interest, comprising (a) a channel for receiving the contents of a cell of interest, wherein the channel has an input end and an output end, and (b) a cell trapping site in proximity to the input end of the channel, wherein (i) the input end of the channel is adapted such that an intact cell of interest cannot enter the channel; and (ii) the channel contains one or more analytical components for analysing the contents of the cell of interest. In use, a cell is applied to the device, where it is trapped by the cell trapping means. The cell cannot enter the channel intact, but its contents can be released in situ to enter the channel's input end. The contents can then move down the channel, towards the output end, and they encounter the immobilised reagents, thereby permitting analysis of the cell contents.Type: GrantFiled: May 3, 2006Date of Patent: February 12, 2013Assignee: Oxford Gene Technology IP LimitedInventors: Edwin Southern, Wouter Meuleman, Dietrich Wilhelm Karl Lueerssen, Natalie Milner
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Publication number: 20090098541Abstract: A device for individually analysing cells of interest, comprising (a) a channel for receiving the contents of a cell of interest, wherein the channel has an input end and an output end, and (b) a cell trapping site in proximity to the input end of the channel, wherein (i) the input end of the channel is adapted such that an intact cell of interest cannot enter the channel; and (ii) the channel contains one or more analytical components for analysing the contents of the cell of interest. In use, a cell is applied to the device, where it is trapped by the cell trapping means. The cell cannot enter the channel intact, but its contents can be released in situ to enter the channel's input end. The contents can then move down the channel, towards the output end, and they encounter the immobilised reagents, thereby permitting analysis of the cell contents.Type: ApplicationFiled: May 3, 2006Publication date: April 16, 2009Inventors: Edwin Southern, Wouter Meuleman, Dietrich Wilhelm Karl Lueerssen, Natalie Milner