Patents by Inventor Ryan T. Koehler
Ryan T. Koehler 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).
-
Publication number: 20230372935Abstract: Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.Type: ApplicationFiled: July 31, 2023Publication date: November 23, 2023Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, Erin R. Chia, Billy W. Colston, Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
-
Publication number: 20220008914Abstract: Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.Type: ApplicationFiled: September 27, 2021Publication date: January 13, 2022Applicant: Bio-Rad Laboratories, Inc.Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, JR., Erin R. Chia, Billy W. Colston, JR., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
-
Publication number: 20200392571Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: June 5, 2020Publication date: December 17, 2020Applicant: APPLIED BIOSYSTEMS, LLCInventors: Ryan T. KOEHLER, Kenneth J. LIVAK, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Dawn MADDEN, Dennis A. GILBERT, Yu N. WANG, Eugene G. SPIER, Xiaoqing YOU, Lily XU, Jeremy HEIL, Emily S. WINN-DEEN, Ivy McMULLEN, Susan EDDINS, Leila G. SMITH
-
Patent number: 10689692Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: GrantFiled: September 6, 2016Date of Patent: June 23, 2020Assignee: APPLIED BIOSYSTEMS, LLCInventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Emily S. Winn-Deen, Ivy McMullen, Susan Eddins, Leila G. Smith
-
Publication number: 20200086312Abstract: Method of detecting a target nucleic acid. In an exemplary method, at least two thermal zones of different temperature may be created using a heating assembly. A first emulsion and a second emulsion may be formed. The first and second emulsions may be thermally cycled by passing them through tubing in a spaced relation to one another, with the tubing being wound around a central axis of the heating assembly and extending through each thermal zone multiple times. Thermally cycling may promote amplification of the target nucleic acid in droplets of each emulsion. Droplets of each emulsion may be passed through a detection channel located downstream of the tubing. Fluorescence may be detected from the droplets being passed through the detection channel.Type: ApplicationFiled: October 29, 2019Publication date: March 19, 2020Applicant: Bio-Rad Laboratories, Inc.Inventors: Amy L. HIDDESSEN, Donald A. MASQUELIER, Kevin D. NESS, Benjamin J. HINDSON, Anthony J. MAKAREWICZ, JR., Erin R. CHIA, Billy W. COLSTON, JR., Serge SAXONOV, Svilen S. TZONEV, Michael Y. LUCERO, Ryan T. KOEHLER
-
Publication number: 20180147573Abstract: Devices and methods for generating droplets. An exemplary device comprises a substantially planar base portion including a bottom surface having a plurality of microfluidic channels formed therein as recessed regions of the bottom surface. The device also comprises a plurality of protrusions projecting from a top surface of the base portion and each formed integrally with the base portion. The device further comprises a sample well, a carrier well, and a droplet well. Each well has an upper portion created by one of the protrusions. A cover layer is attached to the bottom surface of the base portion and seals a bottom side of each microfluidic channel.Type: ApplicationFiled: September 18, 2017Publication date: May 31, 2018Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, Jr., Erin R. Chia, Billy W. Colston, Jr., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
-
Publication number: 20170268051Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: September 6, 2016Publication date: September 21, 2017Inventors: Ryan T. Koehler, Kenneth J. Livak, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Yu N. WANG, Xiaoqing YOU, Michael W. HUNKAPILLER, Janet S. ZIEGLE, Julie WILLIAMS, Dawn MADDEN, Dennis A. GILBERT, Charles R. SCAFE, Hadar I. ISAAC, Eugene G. SPIER, Lily XU, Leila G. SMITH, Jeremy HEIL, Stephen GLANOWSKI, John SCOTT, Emily S. WINN-DEEN, Ivy MCMULLEN, Lini WU, Harold Carey GIRE, Susan EDDINS
-
Publication number: 20170151558Abstract: System, including methods, apparatus, and kits, for forming emulsions. In an exemplary method of generating droplets, a device may be selected that includes a plurality of emulsion-formation units each including a sample well, a continuous-phase well, a droplet well, and a channel network that fluidically interconnects the wells and creates a droplet-generation region. A discrete volume of sample-containing fluid may be placed into the sample well of each emulsion-formation unit, and a discrete volume of continuous-phase fluid into the continuous-phase well of each emulsion-formation unit. Pressure may be applied to the device with a fluidics assembly after the step of placing, such that the plurality of emulsion-formation units generate droplets in parallel with one another. A pressure signal may be detected from the fluidics assembly. Application of the pressure may be stopped when the pressure signal indicates that a sample well is empty.Type: ApplicationFiled: November 14, 2016Publication date: June 1, 2017Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, JR., Erin R. Chia, Billy W. Colston, JR., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
-
Patent number: 9464320Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: GrantFiled: April 27, 2012Date of Patent: October 11, 2016Assignee: Applied Biosystems, LLCInventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Julie Williams, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Stephen Glanowski, Emily S. Winn-Deen, Ivy McMullen, Leila G. Smith
-
Patent number: 9458511Abstract: System, including methods, apparatus, and compositions, for performing a multiplexed digital assay of at least three targets. In an exemplary method, partitions may be formed each including a portion of a same sample. The sample may include a first target that is a reference sequence, a second target that is a variant sequence from a gene of interest, and a third target that is a normal sequence from the gene of interest. The target may be amplified in the partitions and amplification data may be collected. A level of the second target may be determined. A copy number of the third target may be determined from a level of the first target and a level of the third target.Type: GrantFiled: March 17, 2014Date of Patent: October 4, 2016Assignee: Bio-Rad Laboratories, Inc.Inventors: Ryan T. Koehler, Svilen S. Tzonev
-
Publication number: 20140274799Abstract: System, including methods, apparatus, and compositions, for performing a multiplexed digital assay of at least three targets. In an exemplary method, partitions may be formed each including a portion of a same sample. The sample may include a first target that is a reference sequence, a second target that is a variant sequence from a gene of interest, and a third target that is a normal sequence from the gene of interest. The target may be amplified in the partitions and amplification data may be collected. A level of the second target may be determined. A copy number of the third target may be determined from a level of the first target and a level of the third target.Type: ApplicationFiled: March 17, 2014Publication date: September 18, 2014Inventors: Ryan T. Koehler, Svilen S. Tzonev
-
Publication number: 20140200164Abstract: System, including methods and apparatus, for detection of spaced droplets.Type: ApplicationFiled: January 20, 2014Publication date: July 17, 2014Inventors: Anthony J. Makarewicz, JR., Amy L. Hiddessen, Kevin D. Ness, Donald. A. Masquelier, Billy W. Colston, JR., Benjamin J. Hindson, Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
-
Patent number: 8663920Abstract: Methods of characterizing a nucleic acid library by digital assay.Type: GrantFiled: July 30, 2012Date of Patent: March 4, 2014Assignee: Bio-Rad Laboratories, Inc.Inventors: Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler, Benjamin J. Hindson
-
Publication number: 20130045875Abstract: Methods of characterizing a nucleic acid library by digital assay.Type: ApplicationFiled: July 30, 2012Publication date: February 21, 2013Applicant: BIO-RAD LABORATORIES, INC.Inventors: Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler, Benjamin J. Hindson
-
Publication number: 20120303472Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: April 27, 2012Publication date: November 29, 2012Applicant: APPLIED BIOSYSTEMS, LLCInventors: Ryan T. KOEHLER, Kenneth J. LIVAK, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Janet S. ZIEGLE, Julie WILLIAMS, Dawn MADDEN, Dennis A. GILBERT, Charles R. SCAFE, Hadar I. Isaac, Yu N. WANG, Eugene G. SPIER, Xiaoqing YOU, Lily XU, Jeremy HEIL, Stephen GLANOWSKI, John SCOTT, Emily S. WINN-DEEN, Ivy MCMULLEN, Lini WU, Harold Carey GIRE, Michael W. HUNKAPILLER, Susan EDDINS, Leila G. SMITH
-
Publication number: 20080228589Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: January 16, 2008Publication date: September 18, 2008Applicant: APPLERA CORPORATIONInventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Julie Williams, Dennis A. Gilbert, Charles R. Scafe, Hadar I. Avi-Itzhak, Lily Xu, Susan Eddins, Michael W. Hunkapiller, Leila G. Smith
-
Patent number: 7176002Abstract: The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.Type: GrantFiled: May 16, 2002Date of Patent: February 13, 2007Assignee: Applera CorporationInventors: Kai Qin Lao, Caifu Chen, Ryan T. Koehler, Charles Scafe, Gary Schroth
-
Patent number: 7085652Abstract: Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.Type: GrantFiled: February 14, 2003Date of Patent: August 1, 2006Assignee: Applera CorporationInventors: Charles R. Scaf, Nicolas Peyret, Francisco M. De La Vega, Ryan T. Koehler, Eugene G. Spier
-
Publication number: 20040018506Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: January 2, 2003Publication date: January 29, 2004Inventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Janet S. Ziegle, Julie Williams, Dawn Madden, Dennis A. Gilbert, Charles R. Scafe, Hadar I. Avi-Itzhak, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Stephen Glanowski, John Scott, Emily Winn-Deen, Ivy McMullen, Lini Wu, Harold Carey Gire, Susan Eddins, Michael W. Hunkapiller, Leila G. Smith
-
Publication number: 20030228591Abstract: Methods for determining the binding affinity of a probe to a target or targets in a polynucleotide composite using an automated system. Such methods determine relative binding sites based on thermodynamic principles, using a thermodynamic alphabet and a thermodynamic scoring matrix, with appropriate computer software, such as BLASTP. The invention also provides methods for designing polynucleotide probes to be used in hybridization assays, and minimizing the occurrence of cross-hybridization.Type: ApplicationFiled: February 14, 2003Publication date: December 11, 2003Inventors: Charles R. Scafe, Nicolas Peyret, Francisco M. De La Vega, Ryan T. Koehler, Eugene G. Spier