Biomolecular-Semiconductor Information Microsystems
生物分子半导体信息微系统
基本信息
- 批准号:RGPIN-2019-06331
- 负责人:
- 金额:$ 2.04万
- 依托单位:
- 依托单位国家:加拿大
- 项目类别:Discovery Grants Program - Individual
- 财政年份:2021
- 资助国家:加拿大
- 起止时间:2021-01-01 至 2022-12-31
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
I propose the realization of specialized computer chips for biomolecule measurement and analysis, specifically DNA sequencing. Because these chips will be very small and because they will consume very little power, they shall allow DNA measurement machines ("sequencers") to become less costly and small and portable too. In effect, this research will help make DNA sequencing much more accessible and affordable to a broader set of users thus empowering applications such as personalized healthcare, biomolecular environmental sensing, and even next-generation information technologies such as archival data storage using DNA itself. Three chips are proposed, all for a form of sequencing whereby individual DNA molecules slip through a nano-scale aperture (a so-called "nanopore" sensor), an action that generates a minute signature-current of the DNA. An analysis of this current reveals the make-up of the DNA thus achieving sequencing. The first custom chip (analog mixed-signal) is responsible for amplifying and digitizing the extremely weak signature-currents emerging from the DNA-sensing nanopores. The second (digital) custom chip processes these digitized measurement signals to compute the sequence of sub-molecules (the "bases" A, C, G, T) that the measured DNA consists of, a process referred to as "basecalling". The third (digital) semi-custom chip combines the signals from the first and second chip to make even more accurate predictions of the sequence of bases that make up the measured DNA, thus making the results useful for detailed clinical analysis. Each of these three chips aims to significantly advance the state-of-the-art in DNA signal processing. My research into the first chip is focused on extending its speed (so that it can handle more DNA measurements relative to competing approaches) by at least 10X without compromising signal quality. My research also intends to make the first chip programmable and will also enable it to interact with the nanopore sensing apparatus in order to improve the sequencing system's adaptability to manufacturing and experimental variations. My research into the second chip is focused on integrating machine-learning DNA sequence analysis inference algorithms into a sub-0.5 W DNA basecaller. To date, no such integrated basecaller exists for nanopore-based DNA sequencers. My research into the third chip is focused on a field-programmable-gate-array (FPGA) hardware accelerator to work in conjunction with a general-purpose computer to increase the rate at which DNA sequences can be corrected by 100X with a substantial drop in required power consumption. To date, no such hardware-based accelerator for nanopore-based sequencing correction has been reported.
我建议实现专门的计算机芯片,用于生物分子测量和分析,特别是DNA测序。由于这些芯片将非常小,并且因为它们将消耗非常少的功率,它们将允许DNA测量机器(“测序仪”)变得更便宜、更小和更便携。实际上,这项研究将有助于使更广泛的用户更容易获得和负担得起DNA测序,从而为个性化医疗保健,生物分子环境传感,甚至下一代信息技术(如使用DNA本身的档案数据存储)等应用提供支持。提出了三种芯片,都是为了一种测序形式,即单个DNA分子通过纳米尺度的孔径(所谓的“纳米孔”传感器),这一动作产生了DNA的微小签名电流。对该电流的分析揭示了DNA的组成,从而实现测序。第一个定制芯片(模拟混合信号)负责放大和数字化从DNA传感纳米孔中出现的极其微弱的签名电流。第二个(数字)定制芯片处理这些数字化的测量信号,以计算被测DNA组成的亚分子(“碱基”A、C、G、T)的序列,该过程被称为“碱基调用”。第三个(数字)半定制芯片结合了来自第一个和第二个芯片的信号,对构成测量DNA的碱基序列进行更准确的预测,从而使结果可用于详细的临床分析。这三种芯片中的每一种都旨在显着推进DNA信号处理的最新技术。我对第一个芯片的研究重点是在不影响信号质量的情况下,将其速度提高至少10倍(这样它就可以处理相对于竞争方法更多的DNA测量)。我的研究还打算使第一个芯片可编程,并使其能够与纳米孔传感装置相互作用,以提高测序系统对制造和实验变化的适应性。我对第二个芯片的研究重点是将机器学习DNA序列分析推理算法集成到低于0.5 W的DNA碱基识别器中。迄今为止,对于基于纳米孔的DNA测序仪,不存在这样的集成碱基识别器。我对第三种芯片的研究主要集中在现场可编程门阵列(FPGA)硬件加速器上,该硬件加速器与通用计算机一起工作,以将DNA序列的校正率提高100倍,同时大幅降低所需的功耗。迄今为止,还没有报道用于基于纳米孔的测序校正的这种基于硬件的加速器。
项目成果
期刊论文数量(0)
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专利数量(0)
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Magierowski, Sebastian其他文献
Vehicle Routing Problems for Drone Delivery
- DOI:
10.1109/tsmc.2016.2582745 - 发表时间:
2017-01-01 - 期刊:
- 影响因子:8.7
- 作者:
Dorling, Kevin;Heinrichs, Jordan;Magierowski, Sebastian - 通讯作者:
Magierowski, Sebastian
Oral Cells-On-Chip: Design, Modeling and Experimental Results.
- DOI:
10.3390/bioengineering9050218 - 发表时间:
2022-05-19 - 期刊:
- 影响因子:4.6
- 作者:
Tabrizi, Hamed Osouli;Panahi, Abbas;Forouhi, Saghi;Sadighbayan, Deniz;Soheili, Fatemeh;Khani, Mohammad Reza Haji Hosseini;Magierowski, Sebastian;Ghafar-Zadeh, Ebrahim - 通讯作者:
Ghafar-Zadeh, Ebrahim
A Scalable Discrete-Time Integrated CMOS Readout Array for Nanopore Based DNA Sequencing
- DOI:
10.1109/access.2021.3129171 - 发表时间:
2021-01-01 - 期刊:
- 影响因子:3.9
- 作者:
Dawji, Yunus;Habibi, Mehdi;Magierowski, Sebastian - 通讯作者:
Magierowski, Sebastian
A 4-GHz Active Scatterer in 130-nm CMOS for Phase Sweep Amplify-and-Forward
- DOI:
10.1109/tcsi.2011.2165418 - 发表时间:
2012-03-01 - 期刊:
- 影响因子:5.1
- 作者:
Bousquet, Jean-Francois;Magierowski, Sebastian;Messier, Geoffrey G. - 通讯作者:
Messier, Geoffrey G.
Magierowski, Sebastian的其他文献
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{{ truncateString('Magierowski, Sebastian', 18)}}的其他基金
Biomolecular-Semiconductor Information Microsystems
生物分子半导体信息微系统
- 批准号:
RGPIN-2019-06331 - 财政年份:2022
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Biomolecular-Semiconductor Information Microsystems
生物分子半导体信息微系统
- 批准号:
RGPIN-2019-06331 - 财政年份:2020
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Machine Learning Hardware Exploration via Parametric Analysis Software
通过参数分析软件进行机器学习硬件探索
- 批准号:
538904-2019 - 财政年份:2019
- 资助金额:
$ 2.04万 - 项目类别:
Engage Grants Program
Biomolecular-Semiconductor Information Microsystems
生物分子半导体信息微系统
- 批准号:
RGPIN-2019-06331 - 财政年份:2019
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Nano and Microelectronics for Integrated Sensor Arrays
用于集成传感器阵列的纳米和微电子学
- 批准号:
RGPIN-2014-04710 - 财政年份:2018
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Computational Hardware for Blockchain Network Acceleration
用于区块链网络加速的计算硬件
- 批准号:
515792-2017 - 财政年份:2017
- 资助金额:
$ 2.04万 - 项目类别:
Engage Grants Program
Nano and Microelectronics for Integrated Sensor Arrays
用于集成传感器阵列的纳米和微电子学
- 批准号:
RGPIN-2014-04710 - 财政年份:2017
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Water Contamination Sensor Based on SoC IP for Mobile DNA Sequencing
基于 SoC IP 的水污染传感器,用于移动 DNA 测序
- 批准号:
503163-2016 - 财政年份:2016
- 资助金额:
$ 2.04万 - 项目类别:
Engage Grants Program
Nano and Microelectronics for Integrated Sensor Arrays
用于集成传感器阵列的纳米和微电子学
- 批准号:
RGPIN-2014-04710 - 财政年份:2016
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
Nano and Microelectronics for Integrated Sensor Arrays
用于集成传感器阵列的纳米和微电子学
- 批准号:
RGPIN-2014-04710 - 财政年份:2015
- 资助金额:
$ 2.04万 - 项目类别:
Discovery Grants Program - Individual
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