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dna computing Units Based on Fractional Coding 1

18th international conference on Unconventional Computation and Natural Computation (UCNC)

作者： Salehi, Sayed Ahmad Moore, Peyton Univ Kentucky Lexington KY 40506 USA

ISBN: (数字)9783030193119

ISBN: (纸本)9783030193119;9783030193102

Fractional encoding has been recently proposed as a promising convention to represent information in molecular computing systems. this paper presents new 2-input molecular computing units based on unipolar fractional representation. the units calculate simple computational equations that can be used for the computation of more complex functions. the design of these molecular computing units is inspired by fan-in 2 logic gates in the field of stochastic computing. Each computing unit consists of four chemical reactions with two reactants and one product. We design the dna reactions implementing the chemical reactions of each unit based on the toehold-mediated dna strand-displacement mechanism. Every unit is designed by four input strands and eight fuel gate strands of dna. Since dna molecules related to the input and output of the units have the same form of domain-toehold-domain-toehold, output molecules of each unit can be used as input for other units and this provides the cascading of the units for designing complex circuits. the whole dna pathway for each unit is composed of twenty dna reactions. the simulation results by Visual DSD show that the dna implementations follow the theoretically expected computations of each unit with the maximum of 9.33% error.

关键词： dna computing Fractional coding dna strand-displacement

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

12th International Conference on Practical Applications of C...

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

ISBN: (纸本)9783319987019

the proceedings contain 26 papers. the special focus in this conference is on Practical Applications of Computational Biology and Bioinformatics. the topics include: A bioinformatics protocol for quickly creating large-scale phylogenetic trees;Deep learning analysis of binding behavior of virus displayed peptides to AuNPs;compression of amino acid sequences;NET-ASAR: A tool for dna sequence search based on data compression;Can an integrative SNP approach substitute standard identification in comprehensive case/control analyses?;simple pattern-only heuristics lead to fast subgraph matching strategies on very large networks;in silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum;EvoPPI: A web application to compare protein-protein interactions (PPIs) from different databases and species;a review on metabolomics data analysis for cancer applications;parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search;a framework for the automatic combination and evaluation of gene selection methods;parallel cellular automaton tumor growth model;MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis;metabolite integration pipeline for the improvement of human metabolic models;a genetic programming approach applied to feature selection from medical data;A dna sequence corpus for compression benchmark;17α-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools;in silico modeling and simulation approach for apoptosis caspase pathways;molecular dynamic simulations suggest that P152R mutation within MeCP2 can lead to higher dna binding affinity and loss of selective binding to methylated dna.

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Next-generation HLA typing of 382 international Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th international HLA and Immunogenetics Workshop

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HUMAN IMMUNOLOGY 2019年第7期80卷 449-460页

作者： Creary, Lisa E. Guerra, Sandra G. Chong, Winnie Brown, Colin J. Turner, thomas R. Robinson, James Bultitude, Will P. Mayor, Neema P. Marsh, Steven G. E. Saito, Katsuyuki Lam, Kevin Duke, Jamie L. Mosbruger, Timothy L. Ferriola, Deborah Monos, Dimitrios Willis, Amanda Askar, Medhat Fischer, Gottfried Saw, Chee Loong Ragoussis, Jiannis Petrek, Martin Serra-Pages, Caries Juan, Manel Stavropoulos-Giokas, Catherine Dinou, Amalia Ameen, Reem Al Shemmari, Salem Spierings, Eric Gendzekhadze, Ketevan Morris, Gerald P. Zhang, Qiuheng Kashi, Zahra Hsu, Susan Gangavarapu, Sridevi Mallempati, Kalyan C. Yamamoto, Fumiko Osoegawa, Kazutoyo Vayntrub, Tamara Chang, Chia-Jung Hansen, John A. Fernandez-Vina, Marcelo A. Stanford Univ Sch Med Dept Pathol Palo Alto CA 94304 USA NHS Blood & Transplant Histrocompatibil & Immunogenet Serv Dev Lab London England NHS Blood & Transplant Dept Histocompatibil & Immunogenet London England Royal Free Hosp Anthony Nolan Res Inst London England UCL Canc Inst Royal Free Campus London England Thermo Fisher Sci One Lambda Mol Biol Res Dept Canoga Pk CA USA Childrens Hosp Philadelphia Immunogenet Lab Philadelphia PA 19104 USA Univ Penn Dept Pathol & Lab Med Philadelphia PA USA Baylor Univ Med Ctr Dept Pathol & Lab Med Dallas TX USA Med Univ Vienna Dept Blood Grp Serol & Transfus Med Vienna Austria McGill Univ HLA Lab Div Haematol Hlth Ctr Montreal PQ Canada McGill Univ Dept Human Genet Montreal PQ Canada McGill Univ Montreal PQ Canada Genome Quebec Innovat Ctr Montreal PQ Canada Palacky Univ Fac Med & Dent IMTM Dept Pathol Physiol & Immunogen Olomouc Czech Republic Univ Barcelona IDIBAPS Hosp Clin Barcelona Immunol Dept Barcelona Spain Acad Athens Hellen Cord Blood Bank Biomed Res Fdn Athens Greece Kuwait Univ Hlth Sci Ctr Kuwait Kuwait UMC Utrecht Lab Translat Immunol Utrecht Netherlands City Hope Natl Med Ctr HLA Lab Duarte CA USA Univ Calif San Diego Dept Pathol La Jolla CA 92093 USA UCLA Dept Pathol & Lab Med Immunogenet Ctr Los Angeles CA USA Kashi Clin Labs Inc HLA Dept Portland OR USA Amer Red Cross HLA Lab Philadelphia PA USA Stanford Blood Ctr Histocompatibil Immunogenet & Dis Profiling Lab Palo Alto CA 94025 USA Stanford Genome Technol Ctr Palo Alto CA USA Fred Hutchinson Canc Res Ctr 1124 Columbia St Seattle WA 98104 USA

Extended molecular characterization of HLA genes in the IHWG reference B-Iymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th international HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic dna samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable;the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. the data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.

关键词： Human leukocyte antigen Next-generation sequencing B-lymphoblastoid cell lines international HLA and Immunogenetics Workshop Multiple-laboratory testing

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Development of Automated Detection and Wireless Reporting for a Handheld Point-of-Care Test

Development of Automated Detection and Wireless Reporting fo...

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international Baltic Electronics conference, BEC

作者： Tamas Pardy Massimo Leonardo Filograno Cindy Baumann Toomas Rang Tallinn University of Technology Tallinn Estonia SelfDiagnostics Deutschland GmbH Leipzig Germany

ISBN: (数字)9781728194448

ISBN: (纸本)9781728194455

Second-generation rapid diagnostic tests, e.g. Lab-on-a-Chip (LoC) molecular diagnostics can help decentralize medical diagnostics for infectious diseases and provide far wider coverage than existing methods. Furthermore, they can provide results far more quickly, enabling early diagnosis and prevention of epidemics. However, to ensure a short turnaround time in testing, a compact, ideally low-cost, automated readout method is required. Preferably, the readout should also have integrated means of communication for automatic report of the results. We demonstrate a readout solution based on an ESP12F microcontroller board to read results from a LoC device demonstrated in our previous works. the readout solution relies on an LED-photodiode setup to read the results of immunochromatographic test strips. We evaluated the device by comparing readouts of positive and negative strips. During the evaluation, the device prototype was run from batteries and transmitted results via Wi-Fi to a PC, where a MATLAB application processed, displayed and saved results.

关键词： Strips Light emitting diodes Matlab Wireless fidelity dna Photodiodes Testing

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A Review of Nanoscale Characterizing Individual dna Behaviors Using Atomic Force Microscopy

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IEEE TRANSACTIONS ON NANOTECHNOLOGY 2018年第5期17卷 920-933页

作者： Li, Mi Dang, Dan Xi, Ning Wang, Yuechao Liu, Lianqing Chinese Acad Sci Shenyang Inst Automat State Key Lab Robot Shenyang 110016 Liaoning Peoples R China Shenyang Pharmaceut Univ Sch Med Devices Shenyang 110016 Liaoning Peoples R China Univ Hong Kong Dept Ind Mfg Syst Engn Hong Kong Hong Kong Peoples R China

Deoxyribonucleic acid (dna), the structural basis of genetics, plays a crucial role in the life of cells. the abnormal behaviors of dna are closely related to the pathological changes of living organisms. the advent of atomic forcemicroscopy (AFM) provides an exciting instrument for biophysically probing the nanoscale dynamic activities of the individual native molecules, considerably complementing the results obtained by traditional biochemical population-averaged measurements. In the past decades, AFM has been widely used in dna studies, significantly providing novel insights into molecular biology. In this paper, the methodologies and progresses of utilizing AFM to characterize the behaviors of individual dna molecules from several facets (including dna topography imaging, dna mechanics measurements, dna origami, and dna nanorobotics) are reviewed, and the future directions are discussed.

关键词： Atomic force microscopy nanoscale dna topography dna mechanics dna origami nanorobotics

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An improved molecular computation model of integer power using self-assembly of dna tiles 20

An improved molecular computation model of integer power usi...

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20th IEEE international conference on High Performance computing and Communications (HPCC) / 16th IEEE international conference on Smart City (SmartCity) / 4th IEEE international conference on Data Science and Systems (DSS)

作者： Li, Yongnan Peoples Publ Secur Univ China Sch Criminal Invest & Counter Terrorism Beijing 100038 Peoples R China

ISBN: (纸本)9781538666142

this paper proposes how to use self-assembly of dna tiles to calculate integer power over finite field GF(2n) with less assembly processing time. Two key functional components accomplish the computing process. One of them computes modular-multiplication and modularsquare in parallel, and the other one calculates modularsquare and transmits intermediate result. It achieves better performance than previous work for its optimized assembly rules. this tile assembly model requires 5316 types of computation tiles and 12 types of boundary tiles.

关键词： Binary finite field Tile assembly model dna computing Integer power

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Transient Memory in Gene Regulation 17th

Transient Memory in Gene Regulation

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17th international conference on Computational Methods in Systems Biology (CMSB)

作者： Guet, Calin Henzinger, thomas A. Igler, Claudia Petrov, Tatjana Sezgin, Ali Univ Konstanz Dept Comp & Informat Sci Ctr Adv Study Collect Behav D-78464 Constance Germany IST Austria Campus 1 A-34000 Klosterneuburg Austria Aselsan Ankara Turkey

ISBN: (纸本)9783030313043;9783030313036

the expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets. In this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest. the behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the dna, before applying rapid equilibrium assumptions.

关键词： Gene regulation Stochastic modelling Long lived transients dna looping

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dna computing Sequence Design Based on Bacterial Foraging Algorithm 18

DNA Computing Sequence Design Based on Bacterial Foraging Al...

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5th international conference on Bioinformatics Research and Applications (ICBRA)

作者： Ren, Jiankang Yao, Yao Dalian Univ Technol Sch Comp Sci & Technol Dalian Peoples R China

ISBN: (纸本)9781450366113

Since the quantity and quality of dna sequence directly affect the accuracy and efficiency of computation, the design of dna sequence is critical to dna computing. In order to improve the reliability of dna computing, there is a rich literature targeting at making dna sequences specifically hybridize at a lower melting temperature, no non-complementary bases pairs or mismatch hybridization in the reformed double helix. However, most of them are not good enough to control the melting temperature, because dna sequence design problem under the constraints of hamming distance, secondary structure, molecular thermodynamic is known to be NP-hard. For the sake of achieving the lower and similar melting temperature for each dna sequence, we proposed a dna sequence coding method based on Bacterial Foraging Algorithm (BFA). An evaluation criterion is particularly proposed to assess the quality of dna sequence in the optimization process. With BFA, high-quality dna strands are replicated to avoid the participation of inferior strands in the operation. Experiments show our proposed approach significantly outperforms existing methods in terms of continuity and melting temperature.

关键词： dna computing dna sequence design BFA

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Selection of Characteristics and Classification of dna Microarrays Using Bioinspired Algorithms and the Generalized Neuron 17th

Selection of Characteristics and Classification of DNA Micro...

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17th Mexican international conference on Artificial Intelligence (MICAI)

作者： Alejandra Romero-Montiel, Flor Rodriguez-Vazquez, Katya Univ Nacl Autonoma Mexico Inst Invest Matemt Aplicadas & Sistemas IIMAS Mexico City DF Mexico

ISBN: (纸本)9783030044916;9783030044909

dna microarrays are used for the massive quantification of gene expression. this analysis allows to diagnose, identify and classify different diseases. this is a computationally challenging task due to the large number of genes and a relatively small number of samples. Some papers applied the generalized neuron (GN) to solve approximation functions, to calculate density estimates, prediction and classification problems [1,2]. In this work we show how a GN can be used in the task of microarray classification. the proposed methodology is as follows: first reducing the dimensionality of the genes using a genetic algorithm, then the generalized neuron is trained using one bioinspired algorithms: Particle Swarm Optimization, Genetic Algorithm and Differential Evolution. Finally the precision of the methodology it is tested by classifying three databases of dna microarrays: Leukemia benchmarck ALL - AML, Colon Tumor and Prostate cancer.

关键词： Microarrays Genetic algorithms PSO Differential evolution Neural networks Pattern recognition

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dna computing and molecular programming: 21st international conference, dna 21 Boston and Cambridge, MA, USA, August 17-21, 2015 Proceedings 21st

DNA Computing and Molecular Programming: 21st International ...

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21st international conference on dna computing and molecular programming, 2015

作者： Phillips, Andrew Yin, Peng Microsoft Research Cambridge United Kingdom Wyss Institute BostonMA United States

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