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نتیجه جستجو - مقاله رایگان بیوانفورماتیک 2017

تعداد مقالات یافته شده: 90
ردیف عنوان نوع
1 Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches
بهره برداری از پتانسیل محصول طبیعی قارچ با رویکردهای یکپارچه ی omics و زیست شناسی مصنوعی-2017
Fungi are rich, underexploited reservoirs for natural products that may serve as medicines, commodity chemicals, insecticides, pesticides and other valuable chemicals. Moreover, the biochemistry of natural product formation may be repurposed with emerging synthetic biology tools to make valuable non- natural compounds such as biofuels. However, the pathways that lead to these products are poorly understood and frequently inactive under lab conditions making discovery challenging. Recent advances in –omics approaches and synthetic biology tools provide powerful new methods to elucidate and tap this wealth of novel chemistry. In this review, we describe cutting-edge approaches to activate and characterize natural product formation, and discuss the potential of established and emerging fungal systems for natural product discovery
Keywords: fungi | natural products | synthetic biology | integrated omics
مقاله انگلیسی
2 The Reviews and Analysis of the State-of-the-Art Service Workflow Specification Languages
مرور و تحلیل مروری خدمات گردش کار مشخصات زبانها-2017
In the globalized market and business environment, enterprises strive to cope with rapid market changes and competition. To sustain competitiveness, enterprises need to continually adapt their business processes to accommodate changes promptly. This view includes the integration of external services with their internal services for required capabilities to catch new business opportunities. A number of services with similar service functionalities are available, posing a great challenge in composing optimized business processes in a timely manner. This requires effective methodologies and tools in selecting services and composing them as service workflows for specified goals. Service workflow technology facilitates these by providing methodologies to support business process modeling and reengineering to optimize and automate processes according to workflow requirement specifications. This paper provides reviews and analysis of the state-of-the-art service workflow specification languages, including (1) Self-Adaptive Configuration based on HMS (2) BAM, (3) CTR, (4) SOLOIST, and (5) SWSpec. These languages are evaluated against the fundamental principles for general service workflow specification languages.
Keywords: Service | Workflow | Specification Language | Business Processes | Logic | CTL
مقاله انگلیسی
3 An efficient strategy using k-mers to analyse 16S rRNA sequences
یک راهبرد کارآمد با استفاده از k-mer ها برای تحلیل ترتیب های 16S rRNA-2017
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k- mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.http://dx.doi.org/10.1016/j.heliyon.2017.e003702405-8440/ © 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
مقاله انگلیسی
4 Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches
Exploiting the natural product potential of fungi with integrated -omics and synthetic biology approaches-2017
Fungi are rich, underexploited reservoirs for natural products that may serve as medicines, commodity chemicals, insecticides, pesticides and other valuable chemicals. Moreover, the biochemistry of natural product formation may be repurposed with emerging synthetic biology tools to make valuable non natural compounds such as biofuels. However, the pathways that lead to these products are poorly understood and frequently inactive under lab conditions making discovery challenging. Recent advances in –omics approaches and synthetic biology tools provide powerful new methods to elucidate and tap this wealth of novel chemistry. In this review, we describe cutting-edge approaches to activate and characterize natural product formation, and discuss the potential of established and emerging fungal systems for natural product discovery.
keywords: fungi| natural products| synthetic biology| integrated omics 19
مقاله انگلیسی
5 The Reviews and Analysis of the State-of-the-Art Service Workflow Specification Languages
مرور و تحلیل آخرین فناوری ها در زبان های تشخیص گردش کار خدمات-2017
In the globalized market and business environment, enterprises strive to cope with rapid market changes and competition. To sustain competitiveness, enterprises need to continually adapt their business processes to accommodate changes promptly. This view includes the integration of external services with their internal services for required capabilities to catch new business opportunities. A number of services with similar service functionalities are available, posing a great challenge in composing optimized business processes in a timely manner. This requires effective methodologies and tools in selecting services and composing them as service workflows for specified goals. Service workflow technology facilitates these by providing methodologies to support business process modeling and reengineering to optimize and automate processes according to workflow requirement specifications. This paper provides reviews and analysis of the state-of-the-art service workflow specification languages, including (1) Self-Adaptive Configuration based on HMS (2) BAM, (3) CTR, (4) SOLOIST, and (5) SWSpec. These languages are evaluated against the fundamental principles for general service workflow specification languages.
مقاله انگلیسی
6 Parallel gene selection and dynamic ensemble pruning based on Affinity Propagation
انتخاب موازی ژن و هرس دسته جمعی پویا برمبنای تکثیر خویشاوندی-2017
Gene selection and sample classification based on gene expression data are important research areas in bioin formatics. Selecting important genes closely related to classification is a challenging task due to high dimen sionality and small sample size of microarray data. Extended rough set based on neighborhood has been successfully applied to gene selection, as it can select attributes without redundancy and deal with numerical attributes directly. However, the computation of approximations in rough set is extremely time consuming. In this paper, in order to accelerate the process of gene selection, a parallel computation method is proposed to calculate approximations of intersection neighborhood rough set. Furthermore, a novel dynamic ensemble pruning approach based on Affinity Propagation clustering and dynamic pruning framework is proposed to reduce memory usage and computational cost. Experimental results on three Arabidopsis thaliana biotic and abiotic stress response datasets demonstrate that the proposed method can obtain better classification performance than ensemble method with gene pre-selection.
Keywords: Intersection neighborhood rough set | MapReduce | Affinity Propagation | Dynamic ensemble pruning | Microarray data
مقاله انگلیسی
7 An acceleration of FFT-based algorithms for the match-count problem
شتاب دهی به الگوریتم های مبتنی بر FFT برای مسئله شمارش هماهنگ-2017
The match-count problem on strings is a problem of counting the matches of characters for every possible gap of the starting positions between two strings. This problem for strings of lengths m and n (m ≤ n) over an alphabet of size σ is classically solved in O(σ n logm) time using the algorithm based on the convolution theorem and a fast Fourier transform (FFT). This paper provides a method to reduce the number of computations of the FFT required in the FFT-based algorithm. The algorithm obtained by the proposed method still needs O(σ n logm) time, but the number of required FFT computations is reduced from 3σ to 2σ + 1. This practical improvement of the processing time is also applicable to other algorithms based on the convolution theorem, including algorithms for the weighted version of the match-count problem.
Keywords: Algorithms | Match-count problem | Convolution | FFT | Processing time
مقاله انگلیسی
8 PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization
PGMiner: گردش کار کامل پروتوژنومیک؛ از دستیابی به داده ها تا بصری سازی نتیجه-2017
In parallel with the development of nucleotide sequencing an equally important interest in further describing the sequence in terms of function arose and the latter represents the current bottleneck in the overall research question. Sequencing the transcriptome allows determination of expressed nucleotide sequences and using mass spectrometry allows se quencing on the protein level. Both approaches can only sequence a subset of the exist ing transcripts. Moreover, for example post translational modification events can only be determined on the proteomics level. Therefore, it is essential to combine proteomics and genomics. For that purpose, proteogenomics data analysis pipelines have been described. Here, we describe a novel proteogenomics workflow which encompasses everything from the acquisition of data to result visualization in the Konstanz Information Miner (KNIME), a state of the art workflow management and data analytics platform. We amended KN IME with a number of processes like peptide consensus prediction, peptide mapping, and database equalizing, as well as result visualization. This enabled construction of our new workflow, entitled PGMiner, which not only includes all data analysis steps, but is highly customizable which is rather cumbersome for most existing pipelines. Furthermore, no burdensome installation processes have to be performed making PGMiner the most user friendly tool available.
Keywords: Proteogenomics | Mass spectrometry | Bioinformatics | Workflow management | Computational proteomics
مقاله انگلیسی
9 Modeling regenerative processes with membrane computing
مدلسازی فرآیندهای بازتولیدی با محاسبات غشایی-2017
Understanding the remarkable ability of some organisms to restore their anatomical shape following the amputation of large parts of their bodies is currently a major unsolved ques tion in regenerative biology and biomedicine. Despite rapid advances in the molecular pro cesses required for regeneration, a systems level, algorithmic understanding of this process has remained elusive. For this reason, the field needs new computational paradigms to help model the flow of information during regeneration. Membrane computing is a branch of natural computing that studies the properties and applications of theoretical computing devices known as P systems. These systems are an abstraction of the structure and func tioning of a living cell, as well as its organization in tissues. Here, we propose a model of regenerative processes in planarian worms based on P systems, which recapitulates sev eral aspects of regenerative pattern regulation. Our results demonstrate that it is possible to apply a novel computational framework to help understand pattern regulation in regen erative biology.
Keywords: Planarian | Modeling | Regeneration | P systems | Membrane computing | Bioinformatics
مقاله انگلیسی
10 A shape-independent algorithm for fully-automated gridding of cDNA microarray images
یک الگوریتم مستقل از شکل برای شبکه بندی کاملا" خودکار تصاویر ریز آرایه ای سی دی ان ای-2017
In this paper, a fully-automated microarray gridding algorithm is presented. This algorithm contains the block finding in an image by using variable length Blackman window, image contrast enhancement based on the Otsu thresholding approach, and identification of im age objects including spots and artifacts through the 8-connected labeling method. Fur thermore, a shape-independent algorithm based on the area of pixels in each object is proposed for noise elimination. The final gridding is performed using a new method based on the constructed spot matrix and a refinement procedure is exploited to minimize all probable grid-line errors. The performance of the proposed algorithm is evaluated by five public datasets including the Swiss Institute of Bioinformatics (SIB), Joe DeRisi’s individual tiff files (DeRisi), University of California, San Francisco (UCSF), Gene Expression Omnibus (GEO), and Stanford Microarray Database (SMD). The obtained results reveal that the pro posed algorithm reaches a higher level of accuracy and stability against some restrictions in microarray images such as noise, artifacts, and irregularities regarding the shapes of spots in comparison with other state-of-the-art methods.
Keywords: Microarray | Gridding | Otsu thresholding | De-noising | Image processing
مقاله انگلیسی
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