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Mining DNA Sequences Based on Spatially Coded Technique Using Spatial Light Modulator [article]

Masoome Fazelian, Sajjad AbdollahRamezani, Sima Bahrani, Ata Chizari, Mohammad Vahid Jamali, Pirazh Khorramshahi, Arvin Tashakori, Shadi Shahsavari, Jawad A. Salehi
2016 arXiv   pre-print
By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted  ...  Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species.  ...  coded moiré technique [16] , [17] implemented on spatial light modulators (SLMs) which enables one to investigate useful hiding information in genomes.  ... 
arXiv:1603.08106v1 fatcat:kb4mseauqfflvo3ghqeqr7qeoq

Feature - Circuits and systems for high-throughput biology

C. Nardini, L. Benini, G. De Micheli
2006 IEEE Circuits and Systems Magazine  
We conclude with a perspective on where this field is projected toward the future. Hardware DNA sequencing is the process of finding the exact sequence of bases in a DNA sample.  ...  For example, polymerase chain reaction (PCR) is a well known technique to amplify DNA sub-sequences.  ...  Benini's research interests are in the design of systems for ambient intelligence, from multi-processor systems-on-chip/networks on chip to energy-efficient smart sensors and sensor networks.  ... 
doi:10.1109/mcas.2006.1688198 fatcat:5jn5qh6j4rb7jkbn6e4n5l4h6a

On the Properties of Non-Media Digital Watermarking: A Review of State of the Art Techniques

Arezou Soltani Panah, Ron Van Schyndel, Timos Sellis, Elisa Bertino
2016 IEEE Access  
In this paper, we classify the data in terms of data mining rules on complex types of data such as time-series, symbolic sequences, data streams, and so forth.  ...  INDEX TERMS Digital watermarking, information hiding, data mining, data security, big data.  ...  Based on performed in silico exterminates on Ypt DNA proteins, the presented scheme could embed 16.5 bytes information within the DNA sequence.  ... 
doi:10.1109/access.2016.2570812 fatcat:2xxteahvprepzekaqqbbyey7hi

Mapping Regulatory Determinants in Plants

Mary Galli, Fan Feng, Andrea Gallavotti
2020 Frontiers in Genetics  
Furthermore, relatively little is known about how CREs function to modulate transcription in plants.  ...  We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.  ...  Recently-developed genomics based techniques are paving the way for large-scale mining of putative CREs and begin to outline certain molecular signatures that correlate with gene expression and are conserved  ... 
doi:10.3389/fgene.2020.591194 pmid:33193733 pmcid:PMC7655918 fatcat:fyqms5w3unblthjzlau3jxn73y

Motif Discovery and Data Mining in Bioinformatics

Nooruldeen Qader, Hussein Keitan Al-Khafaji
2014 INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY  
On the other hand, data mining research develops methods for discovering motifs in biosequences. Motif discovery involves benefits and challenges.  ...  We show bridge of the two fields, data mining and Bioinformatics, for successful mining of biological data.  ...  Pattern mining is widely used in the Bioinformatics domain for: BIO SEQUENCESDB The strings of DNA/RNA molecules are called nucleotide sequences, and each element in such a sequence is called a base  ... 
doi:10.24297/ijct.v13i1.2932 fatcat:3h7j7z35t5b3pd3rjekj7r3gla

Integrative approaches for mining transcriptional regulatory programs in Arabidopsis

A. Krishnan, A. Pereira
2008 Briefings in Functional Genomics & Proteomics  
Exciting inroads are being made in mining and interpretation of developmental, physiological and environmental-response 'programs' using sequence and functional information.  ...  The fundamental transcriptional regulatory logic is emerging in Arabidopsis, presently revealed as isolated conditional, spatial or temporal regulatory 'modules'.  ...  Genome-wide high-throughput techniques like DNA sequencing, gene expression, metabolic profiling and large-scale detection of physical interaction have, like in any other organism, revolutionized research  ... 
doi:10.1093/bfgp/eln035 pmid:18632743 fatcat:w4zbyxr2y5hzzl62sr4s2cptoy

Visualization of image data from cells to organisms

Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider (+2 others)
2010 Nature Methods  
First, new imaging techniques allow the generation of massive datasets that cannot be adequately presented on paper nor be browsed and looked at with older software tools.  ...  Second, the availability of high-throughput techniques enables experiments on a large scale, generating large sets of image data, and even though the readout of each single experiment may be easily visualized  ...  Proper downsampling techniques based on Gaussian convolution must be used when changing the scale dimension of the multiresolution data 42 . 34, 52, 53 .  ... 
doi:10.1038/nmeth.1431 pmid:20195255 pmcid:PMC3650473 fatcat:b6nnwhe3t5fjnhxue3ghu4mjoy

Machine Learning Applications for Therapeutic Tasks with Genomics Data [article]

Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow, Greg Gibson, Jimeng Sun
2021 arXiv   pre-print
In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development.  ...  A model predicts missing DNA methylation state based on its neighboring states and DNA sequence (Section 3.1.2). c.  ...  DNA sequences encode these instructions. Like a computer, where we build a program based on 0/1 bit, the basic DNA sequence units are called nucleotides (A, C, G, and T).  ... 
arXiv:2105.01171v1 fatcat:d2nbrjt4tvak7momoxxjlmqk2m

SYNTHETIC DNA AS A SOLUTION TO THE BIG DATA STORAGE PROBLEM

NAJAT RAFALIA MANAR SAIS
2021 Zenodo  
By 2020, the amount of information we want to store it will be around 44 trillion gigabytes. on the one hand the data volumes continue to grow at an even higher speed, However, our traditional databases  ...  DNA molecules as information carriers have many strengths over traditional storage media.  ...  Two years later, a proposal was made in the same way that the coding of amino acid sequences in the DNA Bancroft proposed a method of direct coding of English letters using DNA bases [6] .  ... 
doi:10.5281/zenodo.5353709 fatcat:727mrlcfifaq5fbzdshda27euq

The M2DC Project: Modular Microserver DataCentre

Mariano Cecowski, Giovanni Agosta, Ariel Oleksiak, Michal Kierzynka, Micha vor dem Berge, Wolfgang Christmann, Stefan Krupop, Mario Porrmann, Jens Hagemeyer, Rene Griessl, Meysam Peykanu, Lennart Tigges (+13 others)
2016 2016 Euromicro Conference on Digital System Design (DSD)  
Nevertheless, every application field introduces special requirements to the used computational architecture.  ...  This paper provides an overview of the different topics FPGAs have been used for in the last 15 years of research and why they have been chosen over other processing units like e.g. CPUs.  ...  spatial MIMO channel simulation 2010 [525] Networks Public telephone remote control system 2010 [526] Image processing Message displaying system using scanning technique 2010 [527] Control  ... 
doi:10.1109/dsd.2016.76 dblp:conf/dsd/CecowskiAOKBCKP16 fatcat:bu4nbkqaejebjafrotibui6mkq

Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts

María Parages, José Gutiérrez-Barranquero, F. Reen, Alan Dobson, Fergal O'Gara
2016 Marine Drugs  
A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally  ...  In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and  ...  Metagenomic Sequence-Based Screening The Metagenomic PCR-based approach (also called Metagenomic DNA Sequence-based Screening) is another alternative methodology, primarily based on the analysis of nucleotide  ... 
doi:10.3390/md14030062 pmid:27007381 pmcid:PMC4810074 fatcat:6ejaesu4nfgzjfuqhq53e54dqm

Relationship Identification & Prediction Of Diseases Association Using Micro-RNA Of Genomic Data

G Michael
2019 JOURNAL OF MECHANICS OF CONTINUA AND MATHEMATICAL SCIENCES  
It then detects the edge of the structure after preprocessing it using the SOBEL edge recognition calculation.  ...  In order to handle or to make this system more accurate, we propose this system by using the chromosome structure of the person.  ...  Here we have used modified greedy algorithm to match the same chromosome structure image based on some similarity between two images. G.  ... 
doi:10.26782/jmcms.spl.2019.08.00015 fatcat:3dlnrgt6a5bdpmakxgxua3zpcu

Statistical Analysis of Spatial Expression Pattern for Spatially Resolved Transcriptomic Studies [article]

Shiquan Sun, Jiaqiang Zhu, Xiang Zhou
2019 bioRxiv   pre-print
Recent development of various spatially resolved transcriptomic techniques has enabled gene expression profiling on complex tissues with spatial localization information.  ...  With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on tens of thousands of samples.  ...  Some of these techniques, such as TIVA 4 , LCM 5 , Tomo-Seq 6 and spatial transcriptomics through spatial barcoding 7 , are based on the next generation DNA sequencing.  ... 
doi:10.1101/810903 fatcat:ge4womnbqvculgrop5lw25t5xa

New Dark Matter Detectors using DNA or RNA for Nanometer Tracking [article]

Andrzej Drukier, Katherine Freese, Alejandro Lopez, David Spergel, Charles Cantor, George Church, Takeshi Sano
2015 arXiv   pre-print
Polymerase Chain Reaction (PCR) and ssNA sequencing are used to read-out the detector.  ...  The location of the break can be identified by amplifying and identifying the segments of cut ssNA using techniques well known to biologists.  ...  Cost Estimates using RNA: The detector could be designed using either DNA or RNA.  ... 
arXiv:1206.6809v2 fatcat:jzuyo44ns5gqjbxahbm2ampq5i

Fabrication of three-dimensional proteinaceous micro- and nano-structures by femtosecond laser cross-linking

Daniela Serien, Koji Sugioka
2018 Opto-Electronic Advances  
An overview of previous studies related to fabrication using a variety of proteins and detailed discussions of the associated mechanisms are provided.  ...  Proteins are a class of biomaterials having a vast array of functions, including the catalysis of metabolic reactions, DNA replication, stimuli response and transportation of molecules.  ...  Dynamic mirror device (DMD), spatial light modulator (SLM), or galvano mirrors were used in some of these previous works. galvano scanning or DMD projection techniques, different exposure doses or scanning  ... 
doi:10.29026/oea.2018.180008 fatcat:chmd3zlufzf2zmvmd437wyeoqa
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