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1. 发明申请

US20190147981A1 Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform 审中-公开
公开(公告)号：US20190147981A1
公开(公告)日：2019-05-16
申请号：US16119976
申请日：2018-08-31
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen , Michael Ruehle , Robert McMillen , Mark Hahm
IPC分类号： G16B40/00 , G16B50/00 , G06N3/00 , H03K19/177 , G16B30/00
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. In various instances, each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform one or more steps a variant call operation.

2. 发明授权

US10068183B1 Bioinformatics systems, apparatuses, and methods executed on a quantum processing platform 有权
公开(公告)号：US10068183B1
公开(公告)日：2018-09-04
申请号：US15497149
申请日：2017-04-25
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen
IPC分类号： G06N99/00 , G06F19/18 , G06N7/00 , G06K9/62 , G06F17/30 , G06F19/28 , G06F19/22
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits. The hardwired quantum logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired quantum logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

3. 发明授权

US10068054B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US10068054B2
公开(公告)日：2018-09-04
申请号：US15059221
申请日：2016-03-02
申请人： EDICO GENOME, CORP.
发明人： Pieter Van Rooyen , Michael Ruehle , Robert J. Mcmillen , Mark Hahm
IPC分类号： G06G7/50 , G06F19/24 , G06N3/00 , G06F19/22 , G06F19/28 , H03K19/177
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. In various instances, each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform one or more steps a variant call operation.

4. 发明申请

US20180143914A1 METHOD AND SYSTEM FOR GENOMIC VISUALIZATION 审中-公开
公开(公告)号：US20180143914A1
公开(公告)日：2018-05-24
申请号：US15874851
申请日：2018-01-18
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen , Gavin Stone , Lucian Lancovici
IPC分类号： G06F12/14 , G16H10/60 , G06F19/28 , G06F19/22 , G06F17/30
CPC分类号： G06F12/1408 , G06F16/13 , G06F2212/1052 , G16B30/00 , G16B50/00 , G16H10/60
摘要： A method and system for correlating genome data with EMR/MR data is disclosed herein. The method includes identifying a plurality of sources of genome data. The method also includes generating an index file for each of the plurality of genome files. The method also includes transmitting each index file to a central depository. The method also includes identifying electronic medical record (EMR) and/or personal health record (PHR) data at each source of the plurality of sources of genome data. The method also includes correlating each genome file of the plurality of genome files with a corresponding EMR/MR data.

5. 发明授权

US09953134B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US09953134B2
公开(公告)日：2018-04-24
申请号：US15390303
申请日：2016-12-23
申请人： EDICO GENOME CORP.
发明人： Pieter van Rooyen , Robert J. McMillen , Michael Ruehle
IPC分类号： G06F19/00 , G06F19/28 , G06F19/22
CPC分类号： G06F19/28 , G06F13/16 , G06F13/4068 , G06F13/4265 , G06F19/22 , G06F19/24 , H01L21/768 , H01L21/76886 , H01L23/528 , H01L27/0207 , H01L27/118 , H01L27/11807 , H01L2027/11838 , H01L2027/11883 , H03K19/17736
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

6. 发明申请

US20170255744A1 BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS EXECUTED ON AN INTEGRATED CIRCUIT PROCESSING PLATFORM 有权
公开(公告)号：US20170255744A1
公开(公告)日：2017-09-07
申请号：US15436151
申请日：2017-02-17
申请人： EDICO GENOME, CORP.
发明人： Pieter van Rooyen , Michael Ruehle , Robert J. Mcmillen
IPC分类号： G06F19/22 , H01L27/118 , G06F19/24 , H03K19/177 , H01L23/528 , H01L27/02 , H01L21/768 , G06F19/28
CPC分类号： G06F19/28 , G06F13/16 , G06F13/4068 , G06F13/4265 , G06F19/22 , G06F19/24 , H01L21/768 , H01L21/76886 , H01L23/528 , H01L27/0207 , H01L27/118 , H01L27/11807 , H01L2027/11838 , H01L2027/11883 , H03K19/17736
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

7. 发明授权

US09652588B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
公开(公告)号：US09652588B2
公开(公告)日：2017-05-16
申请号：US15376622
申请日：2016-12-12
申请人： Edico Genome Corp.
发明人： Pieter Van Rooyen , Robert J. Mcmillen , Michael Ruehle
IPC分类号： C40B60/10 , G06F19/22 , H01L21/768 , G06F19/24
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

8. 发明申请

US20170018626A1 GRAPHENE FET DEVICES, SYSTEMS, AND METHODS OF USING THE SAME FOR SEQUENCING NUCLEIC ACIDS 有权
标题翻译：用于测序核酸的石墨FET装置，系统及其使用方法
公开(公告)号：US20170018626A1
公开(公告)日：2017-01-19
申请号：US15182533
申请日：2016-06-14
申请人： EDICO GENOME, CORP.
发明人： Paul Hoffman , Mitchell Lerner , Pieter van Rooyen
IPC分类号： H01L29/66 , H01L27/085 , C12Q1/68 , H01L21/308 , H01L21/3065 , H01L29/45 , H01L29/16 , H01L21/768
CPC分类号： H01L29/66045 , C12Q1/6869 , G01N27/4145 , G01N27/4146 , H01L21/76879 , H01L21/76883 , H01L27/085 , H01L29/1606 , H01L29/45 , H01L29/66409 , H01L29/66969
摘要： Provided herein are devices, systems, and methods of employing the same for the performance of bioinformatics analysis. The apparatuses and methods of the disclosure are directed in part to large scale graphene FET sensors, arrays, and integrated circuits employing the same for analyte measurements. The present GFET sensors, arrays, and integrated circuits may be fabricated using conventional CMOS processing techniques based on improved GFET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense GFET sensor based arrays. Improved fabrication techniques employing graphene as a reaction layer provide for rapid data acquisition from small sensors to large and dense arrays of sensors. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes, including DNA hybridization and/or sequencing reactions. Accordingly, GFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis within a gated reaction chamber of the GFET based sensor.
摘要翻译：本文提供的是使用其进行生物信息学分析的装置，系统和方法。本公开的装置和方法部分地涉及用于分析物测量的大规模石墨烯FET传感器，阵列和采用其的集成电路。目前的GFET传感器，阵列和集成电路可以使用基于改进的GFET像素和阵列设计的传统CMOS处理技术来制造，这增加了测量灵敏度和精度，并且同时促进了显着小的像素尺寸和基于密集的基于GFET传感器的阵列。使用石墨烯作为反应层的改进的制造技术提供从小型传感器到大型和密集传感器阵列的快速数据采集。可以使用这样的阵列来检测各种化学和/或生物过程中各种分析物类型的存在和/或浓度变化，包括DNA杂交和/或测序反应。因此，GFET阵列通过监测基于GFET传感器的门控反应室内与DNA合成相关的氢离子浓度（pH）变化，其他分析物浓度变化和/或与化学过程有关的结合事件，来促进DNA测序技术。

9. 发明授权

US09235680B2 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform 有权
标题翻译：在集成电路处理平台上执行的生物信息学系统，装置和方法
公开(公告)号：US09235680B2
公开(公告)日：2016-01-12
申请号：US14284307
申请日：2014-05-21
申请人： Edico Genome, Corp.
发明人： Pieter Van Rooyen , Robert J. McMillen , Michael Ruehle
IPC分类号： G06F19/22 , H01L21/768 , H01L27/118
CPC分类号： G06F19/28 , G06F13/16 , G06F13/4068 , G06F13/4265 , G06F19/22 , G06F19/24 , H01L21/768 , H01L21/76886 , H01L23/528 , H01L27/0207 , H01L27/118 , H01L27/11807 , H01L2027/11838 , H01L2027/11883 , H03K19/17736
摘要： A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.
摘要翻译：用于在遗传序列数据上执行序列分析管线的系统，方法和装置包括由通过物理电互连互联的一组硬连线数字逻辑电路形成的结构化ASIC。物理电互连之一形成了与电子数据源连接的结构化ASIC的输入，用于接收基因组数据的读取。硬连线数字逻辑电路被布置为一组处理引擎，每个处理引擎由硬连线数字逻辑电路的子集形成，以在序列分析管线中对基因组数据的读取执行一个或多个步骤。硬连线数字逻辑电路的每个子集以有线配置形成，以执行序列分析流水线中的一个或多个步骤。

10. 发明授权

US11049588B2 Bioinformatics systems, apparatuses, and methods for generating a De Brujin graph 有权
公开(公告)号：US11049588B2
公开(公告)日：2021-06-29
申请号：US16120103
申请日：2018-08-31
申请人： Edico Genome, Corp.
发明人： Pieter van Rooyen , Michael Ruehle , Rami Mehio , Gavin Stone , Mark Hahm , Eric Ojard , Amnon Ptashek
IPC分类号： G16B30/00 , G16B20/00 , G16B50/00
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

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