Patents by Inventor Michael Previte
Michael Previte 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: 20240117428Abstract: The present disclosure provides nucleotide conjugates each configured to include a core attached to multiple nucleotide-arms, where the nucleotide-arms are modular and comprise (i) a core attachment moiety, (ii) a spacer, (iii) a linker, and (iv) a nucleotide unit. The nucleotide unit of each nucleotide-arm can bind a polymerase which is complexed with a nucleic acid template and nucleic acid primer. The nucleotide unit can bind the 3? end of the primer at a position that is opposite a complementary nucleotide in the template strand. Under suitable conditions, the nucleotide unit of the nucleotide conjugates binds the primer strand but does not undergo polymerase-catalyzed incorporation. The binding event can be detected, and the specific base of the nucleotide unit can be identified. The nucleotide conjugates described herein are useful for nucleic acid sequencing methods, particularly for massively parallel sequencing methods employed for next gen sequencing platforms.Type: ApplicationFiled: August 2, 2023Publication date: April 11, 2024Inventors: MICHAEL PREVITE, MARK AMBROSO, TYLER LOPEZ, MICHAEL KLEIN, VIRGINIA SAADE, MATTHEW KELLINGER
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Publication number: 20240052398Abstract: The present disclosure provides compositions, apparatuses and methods for capturing on a support nucleic acids from cellular samples, preparing library molecules on the support, amplifying the library molecules on the support to generate nucleic acid template molecules, and analyzing the immobilized nucleic acid template molecules including detecting and/or sequencing the immobilized nucleic acid template molecules. The immobilized nucleic acid template molecules correspond to the nucleic acids from the cellular samples. The immobilized nucleic acid template molecules are spatially located on the support at positions that correspond to the spatial location of the nucleic acids from the cellular sample.Type: ApplicationFiled: August 15, 2023Publication date: February 15, 2024Inventors: Michael PREVITE, Shawn LEVY
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Patent number: 11891651Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: November 8, 2021Date of Patent: February 6, 2024Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker
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Publication number: 20240003057Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.Type: ApplicationFiled: September 14, 2023Publication date: January 4, 2024Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
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Patent number: 11859241Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: GrantFiled: February 8, 2023Date of Patent: January 2, 2024Assignee: Element Biosciences, Inc.Inventors: Sinan Arslan, Junhua Zhao, Molly He, Samantha Snow, William Light, Matthew Kellinger, Michael Previte, Michael Kim, Hua Yu, Yu-Hsien Hwang-Fu, Marco Tjioe, Andrew Boddicker, Mark Ambroso, Tyler Lopez, Michael Klein, Virginia Saade
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Publication number: 20230392201Abstract: The disclosure relates to methods for obtaining nucleic acid sequence information by constructing a nucleic acid library and reconstructing longer nucleic acid sequences by assembling a series of shorter nucleic acid sequences.Type: ApplicationFiled: June 6, 2023Publication date: December 7, 2023Inventors: James A. STAPLETON, Timothy WHITEHEAD, Michael PREVITE, Molly HE, Tuval BEN-YEHEZKEL, Matthew KELLINGER, Kyle METCALFE
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Patent number: 11795581Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.Type: GrantFiled: October 11, 2018Date of Patent: October 24, 2023Assignee: Illumina, Inc.Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
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Patent number: 11795504Abstract: Fluorescence imaging system designs are described that provide larger fields-of-view, increased spatial resolution, improved modulation transfer and image quality, higher spatial sampling frequency, faster transitions between image capture when repositioning the sample plane to capture a series of images (e.g., of different fields-of-view), and improved imaging system duty cycle, and thus enable higher throughput image acquisition and analysis for genomics and other imaging applications.Type: GrantFiled: January 12, 2022Date of Patent: October 24, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Steve Xiangling Chen, Minghao Guo, Michael Previte, Chunhong Zhou, Derek Fuller
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Publication number: 20230323450Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: March 9, 2023Publication date: October 12, 2023Inventors: Sinan Arslan, Molly Min HE, Matthew KELLINGER, Jake LEVIEUX, Michael PREVITE, Junhua ZHAO, Su ZHANG, Tyler LOPEZ
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Patent number: 11781185Abstract: Provided herein are fluorescently-labeled nucleotide conjugates for nucleic acid analysis. Also provided are reagents used for forming binding complexes between a fluorescently-labeled nucleotide conjugate and a target nucleic acid sequence in the presence of one or more reagents disclosed herein. Binding complexes can be detected in the presence of the one or more reagents. For example, the one or more reagents may contain a photobleaching reducing agent configured to reduce photobleaching resulting from use of the fluorescently-labeled nucleotide conjugate to form the binding complex in a nucleic acid analysis. Such nucleic acid analysis may be used to identify sites of nucleobase binding or incorporation between the target nucleic acid sequence and one or more nucleotide moieties of the fluorescently-labeled nucleotide conjugate in a nucleic acid sequence reaction.Type: GrantFiled: September 19, 2022Date of Patent: October 10, 2023Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Sinan Arslan, Molly He, Michael Previte, Ramreddy Tippana, Hua Yu, William Light, Junhua Zhao
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Publication number: 20230295692Abstract: Methods and systems for detecting the presence of a target nucleic acid sequence in one or more samples of a plurality of samples are described. The methods may comprise the use of linear barcoded nucleic acid probes that, upon hybridization to a target nucleic acid sequence, may be ligated to circularize the probe molecule, amplified, and sequenced. The use of a probe-specific barcode integrated into the nucleic acid probe molecule, and sample-specific barcodes that may be incorporated into the nucleic acid probe molecule or added during the amplification step, enable large-scale multiplexed assay and sample processing.Type: ApplicationFiled: January 30, 2023Publication date: September 21, 2023Inventors: Lorenzo BERTI, Semyon KRUGLYAK, Matthew KELLINGER, Molly HE, Sinan ARSLAN, Junhua ZHAO, Michael PREVITE
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Publication number: 20230296593Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: May 25, 2023Publication date: September 21, 2023Inventors: Michael PREVITE, Molly HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Publication number: 20230296592Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: May 25, 2023Publication date: September 21, 2023Inventors: Michael PREVITE, Molly HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Publication number: 20230235395Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: ApplicationFiled: March 31, 2023Publication date: July 27, 2023Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
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Publication number: 20230235392Abstract: Provided herein are methods for generating circular nucleic acid molecules and circular nucleic acid libraries. The methods can be used to generate clonal populations of target nucleic acid molecules for downstream applications such as sequencing. Nucleic acid sequence methods, systems and kits are also provided for sequencing circular nucleic acid molecules.Type: ApplicationFiled: May 19, 2021Publication date: July 27, 2023Inventors: Sinan ARSLAN, Junhua ZHAO, Molly HE, William LIGHT, Matthew KELLINGER, Michael PREVITE
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Publication number: 20230212534Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.Type: ApplicationFiled: December 21, 2022Publication date: July 6, 2023Applicants: ILLUMINA, INC., ILLUMINA SINGAPORE PTE LTDInventors: Misha Golynskiy, Seth McDonald, Saurabh Nirantar, Matthew Kellinger, Michael Previte, Sergio Peisajovich, Molly He
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Publication number: 20230203564Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: ApplicationFiled: February 8, 2023Publication date: June 29, 2023Inventors: Sinan ARSLAN, Junhua ZHAO, Molly HE, Samantha SNOW, William LIGHT, Matthew KELLINGER, Michael PREVITE, Michael KIM, Hua YU, Yu-Hsien HWANG-FU, Marco TJIOE, Andrew BODDICKER, Mark AMBROSO, Tyler LOPEZ, Michael KLEIN, Virginia SAADE
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Publication number: 20230193354Abstract: The disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.Type: ApplicationFiled: November 22, 2022Publication date: June 22, 2023Inventors: Sinan ARSLAN, Junhua ZHAO, Molly HE, Samantha SNOW, William LIGHT, Matthew KELLINGER, Michael PREVITE, Michael KIM, Hua YU, Yu-Hsien HWANG-FU, Marco TJIOE, Andrew BODDICKER
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Publication number: 20230193223Abstract: Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.Type: ApplicationFiled: September 16, 2022Publication date: June 22, 2023Inventors: Peter VANDER HORN, Cheng-Yao CHEN, Guobin LUO, Michael PREVITE, Jamshid TEMIROV, Theo NIKIFOROV, Zhaohui ZHOU, Hongye SUN, Yufang WANG, Stefanie Yukiko NISHIMURA, Hongyi WANG, Marian PERIS, Barnett ROSENBLUM, Michael PHELAN
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Publication number: 20230167434Abstract: Provided herein are methods for generating circular nucleic acid molecules and circular nucleic acid libraries. The methods can be used to generate clonal populations of target nucleic acid molecules for downstream applications such as sequencing.Type: ApplicationFiled: January 11, 2023Publication date: June 1, 2023Inventors: Matthew KELLINGER, Sinan ARSLAN, Michael PREVITE, Junhua ZHAO