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A large number of long non-coding RNAs (lncRNAs) have been identified over the past decades. Accumulating evidence proves that lncRNAs play key roles in various biological processes. However, the majority of the lncRNAs have not been functionally characterized. The annotation of lncRNA functions has become an area of focus in the fields of biology and bioinformatics. In this paper, we develop a global...
The collaborations of the diseases might be the key to understand the mechanism of the diseases since it is difficult to detect the role of complex genes and micro RNA in diseases. With the rapid development of technology, several metabolites of many kinds of diseases could be obtained by the advanced machines. Some diseases are related to several metabolites, and some metabolites have strong relationship...
Solid state fermentation processes are mediated by the collective metabolism of specialized microbial communities. Monitoring the relative abundance of dominating species is a critical task in quality control, which is traditionally done by wet lab techniques, such as quantitative PCR (qPCR). In this study, we developed a computational method to quantify microbial species in metagenomes based on their...
Effective mining of large amount of DNA and RNA fragments obtained from next generation sequencing technologies, depends on the availability of efficient analytical tools to process them. One of the important aspects of this analysis, dealing with huge number of fragments, is partitioning them based on their level of similarities. In this paper we propose a space transformation based clustering approach...
Genes that share transcription factors are biologically driven to show a more likely measurable correlation in their gene expression. No modern method of visualization displays these intricate co-expression and correlation patterns better than a graph. Structural observations about a co-expression graph can reveal the secrets of the biological system that it models, but experimentally validated co-expression...
Network pharmacology which is based on bioinformatics and system biology knowledge has been employed into the field of Traditional Chinese Medicine (TCM) researches in recent years. In order to summarize current available bioinformatics databases, especially those can be used for TCM formulae study; a systematic search of Chinese literature by May 2017 was conducted. Results showed that research methods...
The rapid increase in available protein structure datasets requires new techniques for fast, yet, effective analysis of protein 3D structures. In this work, we propose a structure-based signature for protein families, suitable for rapid analysis of multidomain domain protein structures. Our method is alignment-free, using protein strings as the basic representation. A key novelty is the two-stage...
Many scientific experiments in Bioinformatics are executed as computational workflows. Frequently, it is necessary to re-run an experiment under the original circumstances in which it was run to recognize and validate it. Data provenance concerns the origin of data. Knowing the data source facilitates the understanding and analysis of the results, by detailing and documenting the history and the paths...
Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. However, it is extremely slow to align a query spectrum against all protein sequences in a large database when the target proteoform that produced the spectrum contains post-translational modifications and/or mutations. As a result, efficient and sensitive protein sequence filtering algorithms are...
The dysregulations of long intergenic non-coding RNAs (lincRNAs) have shown to be linked with a wide variety of human diseases over the past few years. However, there are only a few lincRNA-disease association inference tools available with most of them relying on very specific type of prior knowledge about the lincRNAs and the diseases. They fall short in generalized association predictions when...
An ontology is a framework for describing domain-specific knowledge in a structured format. It is comprised of a set of terms as nodes and a set of relationships between terms as directed edges to form a directed acyclic graph. Gene Ontology (GO) and Human Phenotype Ontology (HPO) are widely referred biological and biomedical ontology databases. They also provide extensive annotations of human genes...
Proteins interact with each other to regulate their functionality and localization. The accumulated protein interaction evidences are represented by protein interaction network using a graph abstraction. Topological properties of protein interaction networks have been explored to characterize proteins and predict undiscovered interactions. Meanwhile, many researchers have tried to explain how protein...
The availability of cost effective and fast genome sequencing techniques has paved the way for a personalized medical practice. The new sequencing technology produces huge datasets with different characteristics and the analysis has evolved from a single program to a workflow of tens of analytical steps, starting from the analysis of raw data until generating clinical reports. The mix between big...
Genetic sequence alignment has always been a computational challenge in bioinformatics. Depending on the problem size, software-based aligners can take multiple CPU-days to process the sequence data, creating a bottleneck point in bioinformatic analysis flow. Reconfigurable accelerator can achieve high performance for such computation by providing massive parallelism, but at the expense of programming...
Development of technologies in bioinformatics resulted into many folds growth of biological data that led to the research for accelerated solutions in various domains of computational bioinformatics. String matching is one of the most widely performed tasks at various stages of computational pipeline and it needs an accelerated and reconfigurable methodology for implementation. In this paper we present...
Article presents method of storing and processing Big Data using object-oriented datatype in commercial relational database server. Methodology was presented based on genomic data. Additionally, some methods of pattern matching implemented in the object were described and commented. Due to set of numerical experiments based on real data the efficiency of the system was testified. Obtain results shows...
Next-generation sequencing (NGS) is becoming feasible for identification or diagnosis of human infectious diseases. In the present study, we aimed to develop a bioinformatic method for dengue virus identification by comparison against different database for variant types of samples and BLASTn and ViPR databases. We collected 12 different types of samples from five dengue-virus-infected patients and...
Big-data bioinformatics workflows are usually complex and data-intensive. They need to analyze large volumes of data using one or more analysis tools either from existing datasets or that from the new intermediate datasets generated during the workflow execution. Traditionally, the workflows are executed by moving the data to analysis tools. With the advent of big-data in bioinformatics workflows,...
In recent years, personal genomic data can be quickly generated in an affordable price. Abundant research results on genetic diseases have also been published in the past two decade. Therefore, it is desired to utilize updated genetic disease research results into personal genomic data analysis and apply them into genomics-based personalized healthcare. However, this is a challenging task for current...
Metabolic pathways provide key information to achieve a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy and other similar areas. The main analysis tool used to study these pathways is based on the idea of pathway comparison, using graph data structures. Graph comparison has been defined as a computationally complex...
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