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Rapid development of nucleic acid diagnostics
 Proc. IEEE
, 2002
"... There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for viruses and bacteria. This paper presents a computerassisted process that begins with nucleic acid sequence information and produces highly speci ..."
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Cited by 15 (7 self)
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There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for viruses and bacteria. This paper presents a computerassisted process that begins with nucleic acid sequence information and produces highly specific pathogen signatures. When combined with instrumentation using the polymerase chain reaction, the resulting diagnostics are both specific and sensitive. The computational and engineering aspects of converting raw sequence data into pathogenspecific and instrumentready assays are presented. Examples and data are presented for specific pathogens, including footandmouth disease virus and the human immunodeficiency virus. Keywords—Deoxyribonucleic acid (DNA), diagnostics, genomics, nucleic acid, ribonucleic acid (RNA), suffix tree. I.
A DNA sequence design for molecular computation of HPP with output visualization based on RealTime PCR
 IEEE Congress on Evolutionary Compution, Sept. 2528, IEEE Xplore, Singapore
, 2007
"... computing. Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a new readout method tailored specifically to HPP in DNA computing using real ..."
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Cited by 1 (1 self)
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computing. Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a new readout method tailored specifically to HPP in DNA computing using realtime PCR for output visualization. Six nodes HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully.
Application of LengthBased DNA Computing for Complex Scheduling Problem
"... Abstract. This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator traveled paths are represented by DNA sequence of spe ..."
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Abstract. This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator traveled paths are represented by DNA sequence of specific length that represent the elevator’s traveling time in a proportional way based on certain initial conditions such as elevator’s present and destination floors, and hall calls for an elevator from a floor. Parallel overlap assembly method is employed for initial pool generation for a more efficient generation of all possible elevator traveled paths. The initial pool generation solution is then subjected to polymerase chain reaction and gel electrophoresis to extract the required optimal path. Experimental result obtained shows that DNA computing approach can be wellsuited for solving such realworld application in the near future. 1
EXPERIMENTAL IMPLEMENTATION OF DIRECT PROPORTIONAL LENGTHBASED DNA COMPUTING FOR ELEVATOR SCHEDULING PROBLEM
"... Abstract: Previously, ideas and implementation methods for solving elevator scheduling problem using DNA computing method had been proposed. In this paper, results of biochemical experiments that have been carried out to realize the computing approach are presented. Every possible elevators travel p ..."
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Abstract: Previously, ideas and implementation methods for solving elevator scheduling problem using DNA computing method had been proposed. In this paper, results of biochemical experiments that have been carried out to realize the computing approach are presented. Every possible elevators travel path combinations are encoded by DNA sequences of length directly proportional to the elevator’s traveling time based on certain initial conditions such as elevators present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for an efficient initial pool generation of all possible travel path combinations and polymerase chain reaction for sequence amplification. Finally, gel electrophoresis is performed to separate the DNA sequence according to its length, and the shortest DNA sequence representing the elevator’s optimal path can thus be visualized from the gel electrophoresis image. The experimental result shows that the DNA computing approach can be wellsuited for solving such realworld problem of this type of nature.
A Design and Implementation Method for Elevator Scheduling Problem Using DNA Computing Approach
"... We present a design and implementation method to solve an elevator scheduling problem using DNA computing in this research. DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial condition ..."
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We present a design and implementation method to solve an elevator scheduling problem using DNA computing in this research. DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial conditions such as present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for initial pool generation and polymerase chain reaction for amplification. Gel electrophoresis is then performed to separate the sequences according to its length and its image is captured to visualize the optimal path. Experimental result obtained verifies that this approach can be wellsuited to solve such realworld problem of this nature. Key words: Elevator scheduling problem, DNA computing, gel electrophoresis, optimal path.
DNA Computing for . . .
, 2003
"... Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, ..."
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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry,
ConcentrationControlled LengthBased DNA Computing for Weighted Graph Problems with Novel Readout Approach using RealTime PCR
, 2006
"... To my family who loves me, especially to my wife who is always with me and my parents for the education they gave throughout their supports and understandings. ii Acknowledgement First of all, thanks to Allah SWT for giving me the strength and the priceless chances in completing this research, withi ..."
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To my family who loves me, especially to my wife who is always with me and my parents for the education they gave throughout their supports and understandings. ii Acknowledgement First of all, thanks to Allah SWT for giving me the strength and the priceless chances in completing this research, within three years of study. Secondly, I wish to express my sincere thanks to my supervisors, Professor Osamu Ono and cosupervisor, Professor Marzuki Khalid for their guidance, financial support, and encouragement during this PhD research. I greatly appreciate their care and dedication in constructively criticizing my work, including my thesis. I have truly enjoyed working with them. And also, I would like to thank Professor Honda and Professor Miki from Meiji University for reviewing thoroughly this dissertation. I am also particularly thankful to John Anthony Rose from Tokyo University for his permission to use part of his contents of presentation as references and guidance during the writing of this thesis. Special thanks go to Prof Masami Hagiya of Tokyo University, for his discussions and explanations on a lot of aspects of DNA computing, while I was in Singapore, for delivering a tutorial on the introduction of DNA computing, in IEEE CISRAM 2005 conference, together with him.
Application of LengthBased DNA Computing for an Elevator Scheduling Problem Application of LengthBased DNA Computing for an Elevator Scheduling Problem
"... This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator travel paths are represented by DNA sequences of specific lengt ..."
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This paper discussed the implementation ideas and experimental procedures to solve an engineering related combinatorial problem using DNA computing approach. An elevator scheduling problem is chosen as a benchmark where all the elevator travel paths are represented by DNA sequences of specific lengths that represent the elevators traveling time in a proportional way based on certain initial conditions such as elevator’s present and destination floors, and hall calls for an elevator from a floor. Parallel overlap assembly method is employed for initial pool generation for a more efficient generation of all possible elevator travel paths. The initial pool generation solution is then subjected to polymerase chain reaction and gel electrophoresis to extract the required optimal path. Experimental result obtained shows that DNA computing approach can be wellsuited for solving such realworld application in the near future.
Design and Implementation Method for a Scheduling Problem Using DNA Computing Approach
"... Abstract — A design and implementation method to solve a scheduling problem using DNA computing approach is presented. Here, an elevator scheduling problem is chosen as the input problem where DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all ..."
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Abstract — A design and implementation method to solve a scheduling problem using DNA computing approach is presented. Here, an elevator scheduling problem is chosen as the input problem where DNA sequences of length directly proportional to the elevator’s traveling time are encoded to represent all possible travel path combinations based on certain initial conditions such as present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for initial pool generation and polymerase chain reaction for amplification. Gel electrophoresis is then performed to separate the sequences according to its length and its image is captured to visualize the optimal path. Experimental result obtained verifies that this approach can be wellsuited to solve such realworld problem of this nature. T I.