Patents by Inventor Sean M. Ramirez
Sean M. Ramirez 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: 11975325Abstract: An example of a kit includes a flow cell assembly. The flow cell assembly includes a reaction chamber, a temperature controlled flow channel in selective fluid communication with an inlet of the reaction chamber, and a filter positioned in the temperature controlled flow channel. The reaction chamber includes depressions separated by interstitial regions and capture primers attached within each of the depressions. The filter is i) to block concentrated biological sample-polymer complexes generated in the temperature controlled flow channel at a first temperature, and ii) to allow passage of concentrated biological sample and polymer released from the complexes in the temperature controlled flow channel at a second temperature.Type: GrantFiled: June 25, 2021Date of Patent: May 7, 2024Assignee: Illumina, Inc.Inventors: Sean M. Ramirez, Anmiv Prabhu, Rigo Pantoja, Michelle Higgins
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Patent number: 11846580Abstract: A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.Type: GrantFiled: March 3, 2021Date of Patent: December 19, 2023Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: James Tsay, Anmiv Prabhu, David Heiner, Edwin Li, Alexandre Richez, John M. Beierle, Kevan Samiee, Kristina Munoz, Leonid Malevanchik, Ludovic Vincent, Naiqian Zhan, Peyton Shieh, Robert Yang, Samantha Schmitt, Sang Park, Scott Bailey, Sean M. Ramirez, Sunmin Ahn, Valerie Uzzell, Wei Wei, Yuxiang Huang, Tyler Jamison Dill
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Publication number: 20230295455Abstract: A flow cell includes a substrate and a copolymer coating. The copolymer coating includes copolymer chains, each having recurring units of formula (I): and formula (II):. In formula (I), R1 is —H, a halogen, an alkyl, an alkoxy, an alkenyl, an alkynyl, a cycloalkyl, an aryl, a heteroaryl, a heterocycle, or optionally substituted variants thereof; R2 is an azido; each (CH2)p can be optionally substituted; and p is an integer from 1 to 50. In formula (II), each of R3, R3?, R4, R4? is —H, R5, —OR5, —C(O)OR5, —C(O)R5, —OC(O)R5, —C(O)NR6R7, or —NR6R7; R5 is —H, —OH, an alkyl, a cycloalkyl, a hydroxyalkyl, an aryl, a heteroaryl, a heterocycle, or optionally substituted variants thereof; and each of R6 and R7 is —H or an alkyl. Some copolymer chains include at least one alkoxyamine end group.Type: ApplicationFiled: October 19, 2021Publication date: September 21, 2023Inventors: Raymond Campos, Brian D. Mather, Sean M. Ramirez
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Publication number: 20230272469Abstract: An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.Type: ApplicationFiled: May 9, 2023Publication date: August 31, 2023Inventors: Sean M. Ramirez, Brian D. Mather, Edwin Li, Sojeong Moon, Innsu Daniel Kim, Alexandre Richez, Ludovic Vincent, Xavier von Hatten, Hai Quang Tran, Maxwell Zimmerley, Julia Morrison, Gianluca Andrea Artioli, Krystal Sly, Hayden Black, Lewis J. Kraft, Hong Xie, Wei Wei, Ryan Sanford
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Patent number: 11667969Abstract: An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.Type: GrantFiled: May 2, 2018Date of Patent: June 6, 2023Assignees: Illumina, Inc., Illumina Cambridge Limited, Illumina Singapore Pte. Ltd.Inventors: Sean M. Ramirez, Brian D. Mather, Edwin Li, Sojeong Moon, Innsu Daniel Kim, Alexandre Richez, Ludovic Vincent, Xavier von Hatten, Hai Quang Tran, Maxwell Zimmerley, Julia Morrison, Gianluca Andrea Artioli, Krystal Sly, Hayden Black, Lewis J. Kraft, Hong Xie, Wei Wei, Ryan Sanford
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Publication number: 20230109614Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: ApplicationFiled: October 25, 2022Publication date: April 6, 2023Inventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Patent number: 11512339Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: GrantFiled: December 20, 2017Date of Patent: November 29, 2022Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Publication number: 20220001384Abstract: An example of a kit includes a flow cell assembly. The flow cell assembly includes a reaction chamber, a temperature controlled flow channel in selective fluid communication with an inlet of the reaction chamber, and a filter positioned in the temperature controlled flow channel. The reaction chamber includes depressions separated by interstitial regions and capture primers attached within each of the depressions. The filter is i) to block concentrated biological sample-polymer complexes generated in the temperature controlled flow channel at a first temperature, and ii) to allow passage of concentrated biological sample and polymer released from the complexes in the temperature controlled flow channel at a second temperature.Type: ApplicationFiled: June 25, 2021Publication date: January 6, 2022Inventors: Sean M. Ramirez, Anmiv Prabhu, Rigo Pantoja, Michelle Higgins
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Publication number: 20210208055Abstract: A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.Type: ApplicationFiled: March 3, 2021Publication date: July 8, 2021Inventors: James Tsay, Anmiv Prabhu, David Heiner, Edwin Li, Alexandre Richez, John M. Beierle, Kevan Samiee, Kristina Munoz, Leonid Malevanchik, Ludovic Vincent, Naiqian Zhan, Peyton Shieh, Robert Yang, Samantha Schmitt, Sang Park, Scott Bailey, Sean M. Ramirez, Sunmin Ahn, Valerie Uzzell, Wei Wei, Yuxiang Huang, Tyler Jamison Dill
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Publication number: 20210130885Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: ApplicationFiled: January 11, 2021Publication date: May 6, 2021Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Patent number: 10955332Abstract: A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.Type: GrantFiled: December 20, 2017Date of Patent: March 23, 2021Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: James Tsay, Anmiv Prabhu, David Heiner, Edwin Li, Alexandre Richez, John M. Beierle, Kevan Samiee, Kristina Munoz, Leonid Malevanchik, Ludovic Vincent, Naiqian Zhan, Peyton Shieh, Robert Yang, Samantha Schmitt, Sang Park, Scott Bailey, Sean M. Ramirez, Sunmin Ahn, Valerie Uzzell, Wei Wei, Yuxiang Huang, Tyler Jamison Dill
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Patent number: 10913975Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: GrantFiled: July 21, 2016Date of Patent: February 9, 2021Assignee: Illumina, Inc.Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Patent number: 10589273Abstract: Embodiments of present application are directed to microfluidic devices and particularly digital micro-plastic fluidic devices that are specifically designed to prevent sample contamination during sample processing, methods of manufacturing the same, and methods to improve sample analysis process by preventing sample contamination.Type: GrantFiled: May 4, 2016Date of Patent: March 17, 2020Assignee: ILLUMINA, INC.Inventors: Allen E Eckhardt, Rigo Pantoja, Sean M Ramirez, Petr Capek, Edwin Li
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Publication number: 20190151850Abstract: Embodiments of present application are directed to microfluidic devices and particularly digital micro-plastic fluidic devices that are specifically designed to prevent sample contamination during sample processing, methods of manufacturing the same, and methods to improve sample analysis process by preventing sample contamination.Type: ApplicationFiled: May 4, 2016Publication date: May 23, 2019Inventors: Allen E Eckhardt, Rijo Pantoja, Sean M Ramirez, Petr Capek, Edwin Li
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Publication number: 20180327832Abstract: An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.Type: ApplicationFiled: May 2, 2018Publication date: November 15, 2018Inventors: Sean M. Ramirez, Brian D. Mather, Edwin Li, Sojeong Moon, Innsu Daniel Kim, Alexandre Richez, Ludovic Vincent, Xavier von Hatten, Hai Quang Tran, Maxwell Zimmerley, Julia Morrison, Gianluca Andrea Artioli, Krystal Sly, Hayden Black, Lewis J. Kraft, Hong Xie, Wei Wei, Ryan Sanford
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Publication number: 20180245142Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: ApplicationFiled: July 21, 2016Publication date: August 30, 2018Inventors: Alex SO, Li LIU, Min-Jui Richard SHEN, Neeraj SALATHIA, Kathryn M. STEPHENS, Anne JAGER, Timothy WILSON, Justin FULLERTON, Sean M. RAMIREZ, Shannon KAPLAN, Rigo PANTOJA, Bala Murali VENKATESAN, Steven MODIANO
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Publication number: 20180195950Abstract: A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.Type: ApplicationFiled: December 20, 2017Publication date: July 12, 2018Inventors: James Tsay, Anmiv Prabhu, David Heiner, Edwin Li, Alexandre Richez, John M. Beierle, Kevan Samiee, Kristina Munoz, Leonid Malevanchik, Ludovic Vincent, Naiqian Zhan, Peyton Shieh, Robert Yang, Samantha Schmitt, Sang Park, Scott Bailey, Sean M. Ramirez, Sunmin Ahn, Valerie Uzzell, Wei Wei, Yuxiang Huang, Tyler Jamison Dill
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Publication number: 20180179575Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.Type: ApplicationFiled: December 20, 2017Publication date: June 28, 2018Inventors: Wayne N. George, Alexandre Richez, M. Shane Bowen, Andrew A. Brown, Dajun M. Yuan, Audrey Rose Zak, Sean M. Ramirez, Raymond Campos
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Patent number: 9394408Abstract: A polymer comprising polymerized units of norbornene fluoroalkyl polyhedral oligomeric silsesquioxane. According to aspects of the present invention, the polymer may be norbornene fluoroalkyl polyhedral oligomeric silsesquioxane. Still other aspects of the present invention may include a polymerized unit of an alkene chain derived from a cyclic alkene.Type: GrantFiled: August 29, 2013Date of Patent: July 19, 2016Assignee: The United States of America as represented by the Secretary of the Air ForceInventors: Sean M. Ramirez, Joseph M. Mabry
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Publication number: 20150239915Abstract: A method of synthesizing peripherally asymmetric aryl polyhedral oligomeric silsesquioxane (ArPOSS) compounds. The method comprises: wherein Ph is phenyl and wherein R is 1-napthyl, 2-naphthyl, 9-anthracenyl, 9-phenanthrenyl, 1-pryeyl, and mixtures thereof.Type: ApplicationFiled: March 19, 2015Publication date: August 27, 2015Applicant: Government of the United States as Represented by the Secretary of the Air ForceInventors: Joseph M. Mabry, Brian M. Moore, Sean M. Ramirez, Gregory R. Yandek