IEEE Transactions on NanoBioscience最新文献_第6页

A High-Throughput Microdroplet-Based Single Cell Transfection Method for Gene Knockout Based on the CRISPR/Cas9 System 基于 CRISPR/Cas9 系统的基因敲除高通量微滴单细胞转染方法。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-03-07 DOI: 10.1109/TNB.2024.3373597

Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun

{"title":"A High-Throughput Microdroplet-Based Single Cell Transfection Method for Gene Knockout Based on the CRISPR/Cas9 System","authors":"Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun","doi":"10.1109/TNB.2024.3373597","DOIUrl":"10.1109/TNB.2024.3373597","url":null,"abstract":"The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"378-388"},"PeriodicalIF":3.9,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem 探索 DNA 计算在解决复杂大数据问题方面的潜力：旅行租车问题案例研究》。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-03-06 DOI: 10.1109/TNB.2024.3396142

Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu

{"title":"Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem","authors":"Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu","doi":"10.1109/TNB.2024.3396142","DOIUrl":"10.1109/TNB.2024.3396142","url":null,"abstract":"The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is \u0000<inline-formula> <tex-math>$boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ </tex-math></inline-formula>\u0000 for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"391-402"},"PeriodicalIF":3.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterizations of Centrifugal Electrospun Polyvinyl Alcohol/Sodium Alginate/Tamanu Oil/Silver Nanoparticles Wound Dressing 离心电纺聚乙烯醇/海藻酸钠/柚木油/银纳米粒子伤口敷料的特性。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-03-01 DOI: 10.1109/TNB.2024.3371224

Thi Phuong Anh Tran;Anh Hue Luong;Wei-Chih Lin

{"title":"Characterizations of Centrifugal Electrospun Polyvinyl Alcohol/Sodium Alginate/Tamanu Oil/Silver Nanoparticles Wound Dressing","authors":"Thi Phuong Anh Tran;Anh Hue Luong;Wei-Chih Lin","doi":"10.1109/TNB.2024.3371224","DOIUrl":"10.1109/TNB.2024.3371224","url":null,"abstract":"Known for its water solubility, flexibility, strong adhesion, and eco-friendly nature, polyvinyl alcohol (PVA) is widely used in various industries. In the medical field, it is used for applications such as creating bandages and orthopaedic devices. Incorporating sodium alginate (SA) into PVA membranes enhances their structural integrity, breathability, and permeability, thereby minimising the risk of cellular damage in the wound zone. Moreover, the addition of tamanu oil (C alophyllum inophyllum L.) and silver nanoparticles, both of which are known for their antibacterial properties and benefits in traditional wound healing, further enhances the membranes’ wound-healing effectiveness. Following production, the membranes undergo a series of tests designed to evaluate their physical properties as well as their antioxidant and antibacterial capabilities. Subsequently, in vitro testing is conducted using human skin cells; experiments on Wistar rats are then performed. Numerous experiments have consistently demonstrated that the performance of polyvinyl alcohol/sodium alginate/tamanu oil (PVA/SA/Oil) membrane is superior to that of polyvinyl alcohol/sodium alginate/tamanu oil/silver nanoparticles (PVA/SA/Oil/Ag NP) membrane. Specifically, the polyvinyl alcohol/sodium alginate (PVA/SA) combination exhibits an impressive wound-healing rate of 98.82% after 15 days, with cells maintaining a high viability of 92% in a nourishing environment. Moreover, these membranes exhibit exceptional resistance to the oxidation of free radicals, surpassing the 70% threshold, and they possess antibacterial activity against Staphylococcus aureus subsp. aureus in vitro. Based on the obtained results, the nanofiber membranes composed of polyvinyl alcohol/ alginate/ tamanu oil, with or without silver nanoparticles, have shown potential as wound dressings in the wound care discipline.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"368-377"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10457035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Wireless Body Area Nanonetworks via Vascular Molecular Communication 通过血管分子通信的无线体区纳米网络

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-02-13 DOI: 10.1109/TNB.2024.3365737

Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis

{"title":"Wireless Body Area Nanonetworks via Vascular Molecular Communication","authors":"Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis","doi":"10.1109/TNB.2024.3365737","DOIUrl":"10.1109/TNB.2024.3365737","url":null,"abstract":"Advancements in biotechnology and molecular communication have enabled the utilization of nanomachines in Wireless Body Area Networks (WBAN2) for applications such as drug delivery, cancer detection, and emergency rescue services. To study these networks effectively, it is essential to develop an ideal propagation model that includes the channel response between each pair of in-range nanomachines and accounts for the interference received at each receiver node. In this paper, we employ an advection-diffusion equation to obtain a deterministic channel matrix through a vascular WBAN2. Additionally, the closed forms of inter-symbol interference (ISI) and co-channel interference (CCI) are derived for both full duplex (FDX) and half duplex transmission (HDX) modes. By applying these deterministic formulations, we then present the stochastic equivalents of the ideal channel model and interference to provide an innovative communication model by simultaneously incorporating CCI, ISI, and background noise. Finally, we evaluate the results with numerous experiments and use signal-to-interference-plus-noise ratio (SINR) and capacity as metrics.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"355-367"},"PeriodicalIF":3.9,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimization of Novel 2D Material Based SPR Biosensor Using Machine Learning 利用机器学习优化基于二维材料的新型 SPR 生物传感器。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-25 DOI: 10.1109/TNB.2024.3354810

Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar

{"title":"Optimization of Novel 2D Material Based SPR Biosensor Using Machine Learning","authors":"Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar","doi":"10.1109/TNB.2024.3354810","DOIUrl":"10.1109/TNB.2024.3354810","url":null,"abstract":"Biosensors are needed for today’s health monitoring system for detecting different biomolecules. Graphene is a monolayer material that can be utilized to sense biomolecules and design biosensors. We have proposed a Graphene-Gold-Silver hybrid structure design based on Zinc Oxide which gives sensitive performance to detect hemoglobin biomolecules. The advanced biosensor designed based on this hybrid structure shows the highest sensitivity of 1000 nm/RIU which is far better concerning similar structure previously analyzed. The graphene-gold-silver hybrid structure is presented for its possible reflectance results and electric field results. The E-field results match well with the reflectance results given by the sensitive hybrid structure. The sensing biomolecules are presented above the structure where a combination of graphene-gold-silver hybrid structure improves the sensitivity to a great extent. The optimized parameters are obtained by applying variations in the physical parameters of the design. The machine learning algorithm employed for reflectance prediction shows a high prediction accuracy and can be utilized for simulation resource reduction. The proposed biosensor can be used in real-time hemoglobin monitoring.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"328-335"},"PeriodicalIF":3.9,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139563924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA 用于 DNA 数据存储的与 ASCII 编码相对应的编码表和一种新的纠错方法 HMSA。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-22 DOI: 10.1109/TNB.2024.3356522

Xuncai Zhang;Fuzhen Zhou

{"title":"An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA","authors":"Xuncai Zhang;Fuzhen Zhou","doi":"10.1109/TNB.2024.3356522","DOIUrl":"10.1109/TNB.2024.3356522","url":null,"abstract":"DNA storage stands out from other storage media due to its high capacity, eco-friendliness, long lifespan, high stability, low energy consumption, and low data maintenance costs. To standardize the DNA encoding system, maintain consistency in character representation and transmission, and link binary, base, and character together, this paper combines the encoding method with ASCII code to construct an ASCII-DNA encoding table. The encoding method can encode not only pure text information but also audio and video information and satisfies the GC content constraint and the homopolymer constraint, with the encoding density reaching 1.4 bits/nt. In particular, when encoding textual information, it directly skips the binary conversion process, which reduces the complexity of encoding, and increasing the encoding density to 1.6 bits/nt. In order to solve the problem of errors in sequences, under the influence of heuristic algorithms, this paper proposes a new error correction method (HMSA) by combining minimum Hamming distance, multiple sequence alignment, and encoding scheme. It can correct not only substitution, insertion, and deletion errors in Reads but also consecutive errors in Reads. It greatly improves the utilization of the Reads and avoids the waste of resources. Simulation results show that the recovery rate of Reads increases with the increasing number of sequencing times. When the number of erroneous bases in a 150nt sequence reaches 5nt, the error correction rate can exceed 96% by sequencing the base sequence only 10 times regardless of whether the errors are consecutive or not. Additionally, the HMSA error correction method is applicable to all coding schemes for lookup code table types.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"344-354"},"PeriodicalIF":3.9,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bimetal Thin Film, Semiconductors, and 2D Nanomaterials in SPR Biosensors: An Approach to Enhanced Urine Glucose Sensing SPR 生物传感器中的双金属薄膜、半导体和二维纳米材料：增强型尿糖传感方法。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-15 DOI: 10.1109/TNB.2024.3354571

Shatrughna Kumar;Archana Yadav;Boris A. Malomed

{"title":"Bimetal Thin Film, Semiconductors, and 2D Nanomaterials in SPR Biosensors: An Approach to Enhanced Urine Glucose Sensing","authors":"Shatrughna Kumar;Archana Yadav;Boris A. Malomed","doi":"10.1109/TNB.2024.3354571","DOIUrl":"10.1109/TNB.2024.3354571","url":null,"abstract":"This work introduces a systematic approach for the development of Kretschmann configuration-based biosensors designed for non-invasive urine glucose detection. The methodology encompasses the utilization of various semiconductors, including Silicon (Si), Germanium (Ge), Gallium Nitride (GaN), Aluminum Nitride (AlN), and Indium Nitride (InN), in combination with a bimetallic layer (comprising Au and Ag films of equal thickness) to enhance the biosensor sensitivity. Additionally, 2D nanomaterials, such as Black Phosphorus and Graphene, are integrated into the semiconductor layers to enhance performance further. These configurations are meticulously optimized through the application of the transfer matrix method (TMM), and the sensing parameters are assessed using the angular modulation method. Among the semiconductors, AlN and GaN exhibit superior results. On these substrates, Graphene and Black phosphorous (BP) layers are applied, resulting in four final structures (thicknesses in nm): BK7/Au(26)/Ag(26)/Si(6)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/AlN(14)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/GaN(12)/BP(0.53)/Biosample, and BK7/Au(26)/Ag(26)/GaN(12)/Graphene(0.34)/Biosample. These biosensors achieve Sensitivity(° /RIU) and Figure of Merit (FoM) (1/RIU) of 380, 360, 440, 400, and 58.5, 90, 90.65, and 82.4, respectively. Subsequently, these high-performing sensors undergo testing with actual urine glucose samples. Among them, two biosensors, BK7/Au(26)/Ag(26)/AlN(14)/BP (0.53)/Biosample and BK7/Au(26)/Ag(26)/GaN(14)/Graphene(0.34)/Biosample, exhibit outstanding performance, with sensitivities (° /RIU) and FoM (1/RIU) of 394.44 & 294.44, and 112.6 & 92.01 respectively. A comparison is also made with relevant previously published work, revealing improved performance in glucose detection.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"336-343"},"PeriodicalIF":3.9,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coordination and Bioorganometallic Chemistry: Exploring the Potential Applications of Metal Coordination and Organometallic Complexes in Medical and Microbiological Advancements. 配位与生物有机金属化学》：探索金属配位和有机金属复合物在医学和微生物学进步中的潜在应用。

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-09 DOI: 10.1109/TNB.2024.3351480

A A Siller-Ceniceros, J C Martinez-Loyola, A Leon-Buitimea, D C Almonte-Flores, M E Sanchez-Castro, J R Morones-Ramirez

引用次数: 0

An AFM-Based Model-Fitting-Free Viscoelasticity Characterization Method for Accurate Grading of Primary Prostate Tumor 基于原子力显微镜的无模型拟合粘弹性表征方法，用于原发性前列腺肿瘤的精确分级

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-09 DOI: 10.1109/TNB.2024.3351768

Na Liu;Tianyuan Zhang;Ziheng Chen;Yue Wang;Tao Yue;Jialin Shi;Gongxin Li;Chen Yang;Haowen Jiang;Yu Sun

{"title":"An AFM-Based Model-Fitting-Free Viscoelasticity Characterization Method for Accurate Grading of Primary Prostate Tumor","authors":"Na Liu;Tianyuan Zhang;Ziheng Chen;Yue Wang;Tao Yue;Jialin Shi;Gongxin Li;Chen Yang;Haowen Jiang;Yu Sun","doi":"10.1109/TNB.2024.3351768","DOIUrl":"10.1109/TNB.2024.3351768","url":null,"abstract":"Viscoelasticity is a crucial property of cells, which plays an important role in label-free cell characterization. This paper reports a model-fitting-free viscoelasticity calculation method, correcting the effects of frequency, surface adhesion and liquid resistance on AFM force-distance (FD) curves. As demonstrated by quantifying the viscosity and elastic modulus of PC-3 cells, this method shows high self-consistency and little dependence on experimental parameters such as loading frequency, and loading mode (Force-volume vs. PeakForce Tapping). The rapid calculating speed of less than 1ms per curve without the need for a model fitting process is another advantage. Furthermore, this method was utilized to characterize the viscoelastic properties of primary clinical prostate cells from 38 patients. The results demonstrate that the reported characterization method a comparable performance with the Gleason Score system in grading prostate cancer cells, This method achieves a high average accuracy of 97.6% in distinguishing low-risk prostate tumors (BPH and GS6) from higher-risk (GS7-GS10) prostate tumors and a high average accuracy of 93.3% in distinguishing BPH from prostate cancer.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"319-327"},"PeriodicalIF":3.9,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139402647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Concatenated Nanopore DNA Codes 并联纳米孔 DNA 代码

IF 3.9 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2024-01-04 DOI: 10.1109/TNB.2024.3350001

Adrian Vidal;V. B. Wijekoon;Emanuele Viterbo

{"title":"Concatenated Nanopore DNA Codes","authors":"Adrian Vidal;V. B. Wijekoon;Emanuele Viterbo","doi":"10.1109/TNB.2024.3350001","DOIUrl":"10.1109/TNB.2024.3350001","url":null,"abstract":"In nanopore sequencers, single-stranded DNA molecules (or k-mers) enter a small opening in a membrane called a nanopore and modulate the ionic current through the pore, producing a channel output in the form of a noisy piecewise constant signal. An important problem in DNA-based data storage is finding a set of k-mers, i.e. a DNA code, that is robust against noisy sample duplication introduced by nanopore sequencers. Good DNA codes should contain as many k-mers as possible that produce distinguishable current signals (squiggles) as measured by the sequencer. The dissimilarity between squiggles can be estimated using a bound on their pairwise error probability, which is used as a metric for code design. Unfortunately, code construction using the union bound is limited to small k’s due to the difficulty of finding maximum cliques in large graphs. In this paper, we construct large codes by concatenating codewords from a base code, thereby packing more information in a single strand while retaining the storage efficiency of the base code. To facilitate decoding, we include a circumfix in the base code to reduce the effect of the nanopore channel memory. We show that the decoding complexity scales as \u0000<inline-formula> <tex-math>$text {O}{(}text {m}^{{2}} text { k}^{{3}}{)}$ </tex-math></inline-formula>\u0000, where m is the number of concatenated k-mers. Simulations show that the base code error rate is stable as m increases.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"310-318"},"PeriodicalIF":3.9,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139953450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0