678 resources related to DNA Sequencing
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To promote awareness, understanding, advancement and application of ocean engineering and marine technology. This includes all aspects of science, engineering, and technology that address research, development, and operations pertaining to all bodies of water. This includes the creation of new capabilities and technologies from concept design through prototypes, testing, and operational systems to sense, explore, understand, develop, use, and responsibly manage natural resources.
The conference program will consist of plenary lectures, symposia, workshops andinvitedsessions of the latest significant findings and developments in all the major fields ofbiomedical engineering.Submitted papers will be peer reviewed. Accepted high quality paperswill be presented in oral and postersessions, will appear in the Conference Proceedings and willbe indexed in PubMed/MEDLINE & IEEE Xplore
The Annual Meeting is a gathering of experts who work and conduct research in the industrial applications of electrical systems.
2019 IEEE International Symposium on Information Theory (ISIT)
Information theory and coding theory and their applications in communications and storage, data compression, wireless communications and networks, cryptography and security, information theory and statistics, detection and estimation, signal processing, big data analytics, pattern recognition and learning, compressive sensing and sparsity, complexity and computation theory, Shannon theory, quantum information and coding theory, emerging applications of information theory, information theory in biology.
ICASSP is the world’s largest and most comprehensive technical conference focused on signal processing and its applications. The conference will feature world-class presentations by internationally renowned speakers, cutting-edge session topics and provide a fantastic opportunity to network with like-minded professionals from around the world.
The IEEE Transactions on Automation Sciences and Engineering (T-ASE) publishes fundamental papers on Automation, emphasizing scientific results that advance efficiency, quality, productivity, and reliability. T-ASE encourages interdisciplinary approaches from computer science, control systems, electrical engineering, mathematics, mechanical engineering, operations research, and other fields. We welcome results relevant to industries such as agriculture, biotechnology, healthcare, home automation, maintenance, manufacturing, pharmaceuticals, retail, ...
The Transactions on Biomedical Circuits and Systems addresses areas at the crossroads of Circuits and Systems and Life Sciences. The main emphasis is on microelectronic issues in a wide range of applications found in life sciences, physical sciences and engineering. The primary goal of the journal is to bridge the unique scientific and technical activities of the Circuits and Systems ...
Part I will now contain regular papers focusing on all matters related to fundamental theory, applications, analog and digital signal processing. Part II will report on the latest significant results across all of these topic areas.
Specific topics of interest include, but are not limited to, sequence analysis, comparison and alignment methods; motif, gene and signal recognition; molecular evolution; phylogenetics and phylogenomics; determination or prediction of the structure of RNA and Protein in two and three dimensions; DNA twisting and folding; gene expression and gene regulatory networks; deduction of metabolic pathways; micro-array design and analysis; proteomics; ...
Computer, the flagship publication of the IEEE Computer Society, publishes peer-reviewed technical content that covers all aspects of computer science, computer engineering, technology, and applications. Computer is a resource that practitioners, researchers, and managers can rely on to provide timely information about current research developments, trends, best practices, and changes in the profession.
2007 IEEE/ICME International Conference on Complex Medical Engineering, 2007
Today most commercial DNA sequencing systems' signal detection was based on CCD or PMT. The CCD based system needs cooled CCD, whose cost is high and the sensitivity is relatively low. The PMT based system using mechanical scanning to realize multi-channel detection, whose stability is relatively low and the working noise is high. In this paper, a novel multi-channel DNA ...
2017 International Conference on Intelligent Computing, Instrumentation and Control Technologies (ICICICT), 2017
Genetic disorders can be identified and treated in the most suitable manner by knowing the pattern of its bases. DNA sequencing is the process of detection of the order in which these nucleotides are arranged in DNA. To overcome the disadvantages of traditional methods of DNA sequencing CMOS ISFET sensors can be used. Dual mode CMOS ISFET has the provision ...
2016 International Conference on Signal Processing, Communication, Power and Embedded System (SCOPES), 2016
DNA computing is new wave of advancement in the field of cryptography. DNA is an ultra compact information storage medium with high security and theoretically unbreakable algorithm. We present a new technique for securing the image using DNA computing. In practical steganography images can be broken with some assumption on the information theoretic entropy of the plaintext. We discuss a ...
2006 International Symposium on Biophotonics, Nanophotonics and Metamaterials, 2006
Capillary electrophoresis - Laser Induced fluorescence (CE - LIF) signals in DNA sequencing analysis are often contaminated by random noise, which has negative influence on the accuracy and detection limit of analysis. Wavelet analysis is a powerful tool for signal denoising comparing with other conventional denoising methods, but it needs more processing time in computer. Especially in some real-time embedded ...
2008 International Conference on Electronic Design, 2008
This paper presents the development of High Speed DNA sequencing accelerator based on Smith-Waterman algorithm using FPGA. The scope of the paper focuses on speed optimization with parallelism. Smith-Waterman algorithm is sensitive algorithm used for procedure of DNA sequence alignments in computational molecular biology. As the number of sequence database increase exponentially, it affects the performance of Smith-Waterman algorithm in ...
Today most commercial DNA sequencing systems' signal detection was based on CCD or PMT. The CCD based system needs cooled CCD, whose cost is high and the sensitivity is relatively low. The PMT based system using mechanical scanning to realize multi-channel detection, whose stability is relatively low and the working noise is high. In this paper, a novel multi-channel DNA sequencing system was presented, which was based on single PMT confocal fluorescence detection and optical scanning adopting an f-theta lens. Capillary electrophoresis experiments were executed in the system for DNA marker pBR322/Hae III. The system's limit of detection was evaluated to be 1.1841times10<sup>-11</sup> mol/L (dsDNA with Thiazole Orange). Its working noise is much lower compared with that based on mechanical scanning one, and the stability and detecting sensitivity is high. The system is expected to be applied to both capillary array and microchip electrophoresis detection based on laser-induced fluorescence.
Genetic disorders can be identified and treated in the most suitable manner by knowing the pattern of its bases. DNA sequencing is the process of detection of the order in which these nucleotides are arranged in DNA. To overcome the disadvantages of traditional methods of DNA sequencing CMOS ISFET sensors can be used. Dual mode CMOS ISFET has the provision for image sensing which makes the DNA sequencing more accurate.
DNA computing is new wave of advancement in the field of cryptography. DNA is an ultra compact information storage medium with high security and theoretically unbreakable algorithm. We present a new technique for securing the image using DNA computing. In practical steganography images can be broken with some assumption on the information theoretic entropy of the plaintext. We discuss a modified DNA sequencing algorithm for encoding image which appear to be more secure. The image is converted to DNA code and divide into fragments. The fragments are sorted and cloned as a bacterial library which acts as cipher. The clones are extracted from the DNA mixture and decrypted using the DNA sequencing technique, Greedy Shortest Common Substring algorithm(GSCS). This algorithm takes the advantage of decreasing the time complexity and increasing the rate of accuracy in the field of image cryptography.
Capillary electrophoresis - Laser Induced fluorescence (CE - LIF) signals in DNA sequencing analysis are often contaminated by random noise, which has negative influence on the accuracy and detection limit of analysis. Wavelet analysis is a powerful tool for signal denoising comparing with other conventional denoising methods, but it needs more processing time in computer. Especially in some real-time embedded analysis system, it may increase hardware investment. Conventional denoising method such as Low-Pass filter, it can realize by cheap hardware, but its denoising quality is not very satisfactory. If we proper combined the low-pass and wavelet denoising method, it will enhance the denoising efficiency and lower the system's cost. In our experiment, a novel method was presented: CE - LIF signals acquired from PMT were preprocessed by Butterworth low-pass filter in hardware circuit and the wavelet denoising was executed in computer. If we properly choose the cut-off frequency and wavelet denoising method, the denoising efficiency was high and the denoising quality was satisfactory. The denoising experiment results indicate that our denoising method can enhance the signal-to-noise ratio (SNR) and meet the requirement of single base pair resolution in DNA sequencing.
This paper presents the development of High Speed DNA sequencing accelerator based on Smith-Waterman algorithm using FPGA. The scope of the paper focuses on speed optimization with parallelism. Smith-Waterman algorithm is sensitive algorithm used for procedure of DNA sequence alignments in computational molecular biology. As the number of sequence database increase exponentially, it affects the performance of Smith-Waterman algorithm in general purpose computer. Therefore, several techniques have been developed in order to speed up the crucial sequence comparison processes. Hence, optimization technique which used parallelism approach has been utilized. Moreover, the technique, which was previously used in cluster computing, has been exploited and implemented on FPGA technology. The potential of FPGA's implementation is vast in term of cost reduction, faster speed and parallelism. The design has been described using Verilog HDL and target to Altera Cyclone II 2C70. In this paper we introduce the new technique of DNA sequencing algorithm with 10 based pair DNA sequences been aligned at single clock cycle. The result of compilation consisting of 821 logic elements with total cell delay 10.472 ns and total interconnect delays 17.592 ns.
New high-throughput sequencing technologies can generate millions of short DNA sequences that need to be mapped to the reference genome accurately. Majority of the mapping algorithms handle variations in the quality of these short sequences by allowing more mismatches and/or gaps in the alignment and focus to improve runtime. In this paper, we investigate ways to classify quality scores of short DNA sequencing reads and integrate them into the mapping process. We specifically studied the quality scores that suggest two alternate bases (the top quality scores for two bases are close to each other at the locus) and use of such bases to improve mapping accuracy. Our method includes generation of alternative sequences when there are alternate-quality bases in a sequence read and mapping of these alternative sequences to the reference genome. In a test using a piece of ChIP-seq data from epigenetic study, we generated and mapped alternatives of 222,755 sequence reads (out of the original 2.5 million reads) that cannot be mapped to the reference genome by the Eland algorithm. With this approach we could be able to map 12.8% of these sequence reads with alternative bases to unique positions in the genome. In this study, we demonstrate that use of alternative bases in mapping algorithms can improve mapping results dramatically.
A 64×64 CMOS ion-image sensor is demonstrated towards accurate high-throughput DNA sequencing. Dual-mode (pH/image) sensing is performed with ion-sensitive field-effect transistor (ISFET) fabricated in standard CMOS image sensor (CIS) process. After addressing physical locations of DNA slices by optical contact imaging, local pH for one DNA slice can be mapped to its physical address with accurate correlation. Moreover, pixel-to-pixel ISFET threshold voltage mismatch is reduced by correlated double sampling (CDS) readout. Measurements show a sensitivity of 103.8mV/pH and fixed-pattern-noise (FPN) reduction from 4% to 0.3% with speed of 1200fps.
A 90×90 fully-electronic biosensor array for charge-based DNA sequence-by- synthesis is implemented in a 0.18μm standard CMOS process. Each 16 μm × 16 μm pixel consists of an integrated charge-sensing electrode connected to an embedded circuitry capable of detecting DNA polymerization and simultaneously measuring the electrode-electrolyte interface capacitance. The detection dynamic range of this sensor is +90dB while consuming 4 mW from a 3.3V supply when operating at 8.1s/frame.
Recent development of next-generation sequencing platforms has dramatically increased the efficiency of obtaining genomic data. Their accuracy, reliability, and achievable read-lengths, however, often lag behind those of the conventional Sanger sequencing method. In this paper, we consider the Illumina sequencing platform and propose a novel DNA base-calling algorithm based on the sequential Monte Carlo method. It is demonstrated on experimental data that the developed algorithm is much faster than the best performing base-calling method currently available, while achieving similar accuracy.
Hidden Markov models (HMM) have largely demonstrated their usefulness in the fields of statistics and pattern recognition, particularly for speech recognition and hand writing recognition. In the field of genetics, the same principles of statistics and probability can be applied. DNA primarily has four bases: adenine, guanine, thymine, and cytosine, which when paired together can form nucleotides. However, the length of a nucleotide chain can be uncertain. The DNA sequence constitutes the heritable genetic information in nuclei that forms the basis for the developmental programs of all living organisms. Determining the DNA sequence is therefore useful in studying fundamental biological processes, as well as in diagnostic or forensic research. In this study, we will utilize hidden Markov models (HMM) to determine DNA sequence likelihoods. A training sequence of nucleotide bases of the first 1000 bases of rice chromosomes will be used, and the transition and emission probabilities would determine a probable DNA sequence of the next 2000 bases. This sequence should be comparable to the actual sequence. However, experimentation did not show this to be the case, despite previous experiments showing otherwise. Only a fourth of a nucleotide sequence was ever classified correctly.
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