Patents by Inventor Alex Nemiroski
Alex Nemiroski 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: 12044624Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: GrantFiled: May 16, 2022Date of Patent: July 23, 2024Assignee: Illumina, Inc.Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Patent number: 11938475Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: GrantFiled: December 7, 2020Date of Patent: March 26, 2024Assignees: Ilumina, Inc., Illumina Cambridge LimitedInventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Patent number: 11896944Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.Type: GrantFiled: January 31, 2018Date of Patent: February 13, 2024Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Publication number: 20240011086Abstract: A sensor having a first electrode and a second electrode operably connected by a conduction channel, wherein a polymerase, primed template nucleic acid and nucleotide form a stabilized ternary complex that is immobilized in or on the conduction channel, whereby association and dissociation of the ternary complex is detected due to changes in electrical properties of the sensor. Identification of the nucleotide type that participates in the complex indicates the identity of the next template base in the template. Repeated cycles of extending the primer and detecting stabilized ternary complexes can allow determination of the sequence of nucleotides for the template.Type: ApplicationFiled: September 10, 2019Publication date: January 11, 2024Applicant: OMNIOME, INC.Inventors: Maxim ABASHIN, Pinar IYIDOGAN, John T. MURPHY, Alex NEMIROSKI, Min-Jui Richard SHEN, Michele Elizabeth WISNIEWSKI
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Patent number: 11835460Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include offset layouts that may be useful in detecting the fiducials in different types and approaches in imaging, and that may help to distinguish regions of the array from one another in image data.Type: GrantFiled: January 31, 2018Date of Patent: December 5, 2023Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Patent number: 11680950Abstract: A scanning apparatus that can include (a) a scan actuator including a linear actuator and a mount for a removeable vessel, wherein the mount has a mechanical fastener that is configured to engage a complementary mechanical fastener on the removeable vessel, and wherein the linear actuator is configured to translate the mount while the mechanical fastener engages the complementary mechanical fastener on the removeable vessel; (b) a reference surface; and (c) a preload configured to urge the vessel to contact the reference surface, wherein the linear actuator is configured to slide the vessel along the reference surface while the preload urges the vessel to contact the reference surface.Type: GrantFiled: February 20, 2020Date of Patent: June 20, 2023Assignee: Pacific Biosciences of California, Inc.Inventors: Matias Negatu, Alex Nemiroski, Drew Ival Frerichs, Dale Buermann, Michael John Erickstad, Rebecca McGinley, Harry Scott Rapoport, Arnold Oliphant, Eugene Pogrebinsky
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Publication number: 20230054204Abstract: A flow cell that includes (a) a gasket interposed between a first substrate and a second substrate, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive, wherein the gasket has a footprint on the first substrate that delineates a channel for containing the aqueous liquid; (b) a via in the gasket, the via containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the via is separated from the channel by the gasket; and (c) a channel port connecting the channel to the exterior of the flow cell, wherein the channel port is permeable to the aqueous liquid.Type: ApplicationFiled: February 2, 2021Publication date: February 23, 2023Inventors: Alex NEMIROSKI, Drew Ival FRERICHS, Julian Sean ALBERNI, Luke DAENITZ, Edgar GUTIERREZ, Arnold OLIPHANT
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Publication number: 20220298568Abstract: Disclosed herein include methods of specifying sites (e.g., sites for colony formation) on a surface (e.g., a planar surface) and generating a flow cell having the sites specified on a surface. Also disclosed are methods of performing sequencing (e.g., sequencing-by-synthesis and sequencing-by-binding) using the flow cell generated and processing (e.g., aligning, orienting, sorting, and assessing quality) images of the flow cell captured during sequencing.Type: ApplicationFiled: January 13, 2022Publication date: September 22, 2022Inventors: Alex Nemiroski, Gary R. Abel, Hamed Hosseini Bay, Joshua Garretson, Richard D. LeCoultre, Kurt Patterson, Tejas Gulati, Fabian Block
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Publication number: 20220276169Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: ApplicationFiled: May 16, 2022Publication date: September 1, 2022Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Patent number: 11427868Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include a non-closed shape that may encode information, allow for bubbles to escape during manufacture, and provide additional advantages over closed shape fiducials.Type: GrantFiled: January 31, 2018Date of Patent: August 30, 2022Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Patent number: 11360027Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: GrantFiled: March 12, 2019Date of Patent: June 14, 2022Assignee: Illumina, Inc.Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Patent number: 11262307Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.Type: GrantFiled: January 31, 2018Date of Patent: March 1, 2022Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Patent number: 11249025Abstract: Fiducial markers are provided on a patterned array of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include non-rectilinear layouts that may provide for more robust location of both the fiducial markers and sites of the patterned array.Type: GrantFiled: January 31, 2018Date of Patent: February 15, 2022Assignee: Illumina, Inc.Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
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Publication number: 20210204833Abstract: A system and method for monitoring a physical parameter of a subject is provided. The system may include a casing with a sensor coupled to the casing. The sensor may be configured to detect a physical parameter of the subject. The physical parameter may include a chemical parameter of the subject. The system includes an endoscopic clip coupled to the casing and may include a wireless transmitter for transmitting a signal via a wireless medium. The signal encodes the physical parameter of the subject detected by the sensor and the wireless transmitter is electronically connected to the endoscopic clip. The system may further include a monitor configured to communicate with the wireless transmitter for receiving the signal encoding the physical parameter of the subject.Type: ApplicationFiled: March 4, 2021Publication date: July 8, 2021Inventors: Christopher C. Thompson, Robert Westervelt, Alex Nemiroski, Keith L. Obstein
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Publication number: 20210187469Abstract: Provided is a nanoparticle including a scaffold, a single template site for bonding a template polynucleotide to the scaffold, and a plurality of accessory sites for bonding accessory oligonucleotides to the scaffold, wherein the scaffold is selected from one or more scaffold DNA molecules and one or more scaffold polypeptides, the single template site for bonding a template polynucleotide to the scaffold is selected from a covalent template bonding site and a noncovalent template bonding site and the plurality of accessory sites for bonding accessory oligonucleotides to the scaffold are selected from covalent accessory oligonucleotide bonding sites and noncovalent accessory oligonucleotide bonding sites. Also provided are methods of using the nanoparticle.Type: ApplicationFiled: December 22, 2020Publication date: June 24, 2021Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED, ILLUMINA SINGAPORE PTE. LTD.Inventors: Wayne N. GEORGE, Jonathan Mark BOUTELL, Mathieu LESSARD-VIGER, Saurabh NIRANTAR, Pietro GATTI LAFRANCONI, Seth MCDONALD, Yin Nah TEO, Maria Rogert BACIGALUPO, Sergio PEISAJOVICH, Eric BRUSTAD, Michael HOWARD, Xiangyuan YANG, M. Shane Bowen, Alex NEMIROSKI, Jeffrey BRODIN, Ludovic VINCENT, Lorenzo BERTI, Andrew A. BROWN, Fei SHEN, Lena STORMS, Olivia BENICE
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Publication number: 20210086174Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: ApplicationFiled: December 7, 2020Publication date: March 25, 2021Inventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Publication number: 20210054453Abstract: An apparatus can include a vessel, a reference surface, a preload, a scan actuator, and a transmitter. The reference surface can form a structural loop with a detector. The preload can be configured to urge the vessel to contact an area on the reference surface. The scan actuator can be configured to slide the vessel along the reference surface in a scan dimension. The transmitter can be configured to direct signal from the vessel to a detector and/or direct energy from an energy source to the vessel, when the vessel is urged by the preload to contact the reference surface.Type: ApplicationFiled: November 4, 2020Publication date: February 25, 2021Inventors: Dale Buermann, Michael John Erickstad, Rebecca McGinley, Alex Nemiroski, Harry Scott Rapoport, Arnold Oliphant
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Patent number: 10919033Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.Type: GrantFiled: December 17, 2018Date of Patent: February 16, 2021Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
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Patent number: 10858701Abstract: An apparatus can include a vessel, a reference surface, a preload, a scan actuator, and a transmitter. The reference surface can form a structural loop with a detector. The preload can be configured to urge the vessel to contact an area on the reference surface. The scan actuator can be configured to slide the vessel along the reference surface in a scan dimension. The transmitter can be configured to direct signal from the vessel to a detector and/or direct energy from an energy source to the vessel, when the vessel is urged by the preload to contact the reference surface.Type: GrantFiled: August 15, 2018Date of Patent: December 8, 2020Assignee: Omniome, Inc.Inventors: Dale Buermann, Michael John Erickstad, Rebecca McGinley, Alex Nemiroski, Harry Scott Rapoport, Arnold Oliphant
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Patent number: 10858703Abstract: An apparatus can include a vessel, a reference surface, a preload, a scan actuator, and a transmitter. The reference surface can form a structural loop with a detector. The preload can be configured to urge the vessel to contact an area on the reference surface. The scan actuator can be configured to slide the vessel along the reference surface in a scan dimension. The transmitter can be configured to direct signal from the vessel to a detector and/or direct energy from an energy source to the vessel, when the vessel is urged by the preload to contact the reference surface.Type: GrantFiled: October 31, 2019Date of Patent: December 8, 2020Assignee: Omniome, Inc.Inventors: Dale Buermann, Michael John Erickstad, Rebecca McGinley, Alex Nemiroski, Harry Scott Rapoport, Arnold Oliphant