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Journal of Integrative Bioinformatics

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https://www.readbyqxmd.com/read/28609295/clubber-removing-the-bioinformatics-bottleneck-in-big-data-analyses
#1
Maximilian Miller, Chengsheng Zhu, Yana Bromberg
With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28609294/computational-mirnomics-integrative-approaches
#2
EDITORIAL
Ralf Hofestädt, Falk Schreiber, Björn Sommer, Jens Allmer
No abstract text is available yet for this article.
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28609293/visualization-and-analysis-of-micrornas-within-kegg-pathways-using-vanesa
#3
Hamid Hamzeiy, Rabia Suluyayla, Christoph Brinkrolf, Sebastian Jan Janowski, Ralf Hofestaedt, Jens Allmer
MicroRNAs (miRNAs) are small RNA molecules which are known to take part in post-transcriptional regulation of gene expression. Here, VANESA, an existing platform for reconstructing, visualizing, and analysis of large biological networks, has been further expanded to include all experimentally validated human miRNAs available within miRBase, TarBase and miRTarBase. This is done by integrating a custom hybrid miRNA database to DAWIS-M.D., VANESA's main data source, enabling the visualization and analysis of miRNAs within large biological pathways such as those found within the Kyoto Encyclopedia of Genes and Genomes (KEGG)...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28609292/knowledge-discovery-in-biological-databases-for-revealing-candidate-genes-linked-to-complex-phenotypes
#4
Keywan Hassani-Pak, Christopher Rawlings
Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28600905/omics-data-complementarity-underlines-functional-cross-communication-in-yeast
#5
Noël Malod-Dognin, Nataša Pržulj
Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker's yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein-protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO)...
June 10, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28600904/using-docker-compose-for-the-simple-deployment-of-an-integrated-drug-target-screening-platform
#6
Markus List
Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows...
June 10, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637931/comparative-miromics-of-salt-tolerant-and-salt-sensitive-rice
#7
Kavita Goswami, Anita Tripathi, Neeti Sanan-Mishra
Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage...
June 22, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637930/towards-a-consistent-quantitative-evaluation-of-microrna-evolution
#8
Ali M Yazbeck, Kifah R Tout, Peter F Stadler, Jana Hertel
The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong to more than 1000 families of homologous sequences. Quantitative investigations of miRNA gene evolution requires the construction of data sets that are consistent in their coverage and include those genomes that are of interest in a given study. Given the size and structure of data, this can be achieved only with the help of a fully automatic pipeline that improves the available seed alignments, extends the set of available sequences by homology search, and reliably identifies true positive homology search results...
June 5, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637929/systematic-prediction-of-the-impacts-of-mutations-in-microrna-seed-sequences
#9
Anindya Bhattacharya, Yan Cui
MicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recognition. Mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes. Here we use a knowledge-based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions...
May 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187422/differential-expression-of-hyperhydricity-responsive-peach-mirnas
#10
Ebru Diler, Turgay Unver, Gökhan Karakülah
Hyperhydricity is a syndrome that causes morpho-physiological malformations in tissue culture plantlets. Micro-RNAs (miRNA) are small non-coding RNAs that play important regulatory roles in plant development, stress response, and adaptation to environmental conditions. In this study, differential expression analysis indicated that miRNAs play an underlying role in the responses to the hyperhydricity syndrome in peach Prunus persica (L.) leaves. 24 known and three novel potential miRNAs were characterized in hyperhydric and non-hyperhydric transcriptome libraries...
December 31, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187427/genomic-islands-an-overview-of-current-software-and-future-improvements
#11
Siomar de Castro Soares, Letícia de Castro Oliveira, Arun Kumar Jaiswal, Vasco Azevedo
Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187426/clustering-of-biological-datasets-in-the-era-of-big-data
#12
Richard Röttger
Clustering is a long-standing problem in computer science and is applied in virtually any scientific field for exploring the inherent structure of datasets. In biomedical research, clustering tools have been utilized in manifold areas, among many others in expression analysis, disease subtyping or protein research. A plethora of different approaches have been developed but there is only little guideline what approach is the optimal in what particular situation. Furthermore, a typical cluster analysis is an entire process with several highly interconnected steps; from preprocessing, proximity calculation, the actual clustering to evaluation and optimization...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#13
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187421/mirquant-2-0-an-expanded-tool-for-accurate-annotation-and-quantification-of-micrornas-and-their-isomirs-from-small-rna-sequencing-data
#14
Matthew Kanke, Jeanette Baran-Gale, Jonathan Villanueva, Praveen Sethupathy
Small non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the sequencing data to provide a comprehensive view of the microRNA landscape...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187420/current-progress-of-high-throughput-microrna-differential-expression-analysis-and-random-forest-gene-selection-for-model-and-non-model-systems-an-r-implementation
#15
Jing Zhang, Hanane Hadj-Moussa, Kenneth B Storey
MicroRNAs are short non-coding RNA transcripts that act as master cellular egulators with roles in orchestrating virtually all biological functions. The recent affordability and widespread use of high-throughput microRNA profiling technologies has grown along with the advancement of bioinformatics tools available for analysis of the mounting data flow. While there are many computational resources available for the management of data from genome sequenced animals, researchers are often faced with the challenge of identifying the biological implications of the daunting amount of data generated from these high-throughput technologies...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187419/dynamics-of-mirna-biogenesis-and-nuclear-transport
#16
Aneesh Kotipalli, Ravikumar Gutti, Chanchal K Mitra
MicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS) or transcriptional gene activation (TGA)...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187418/ensemble-clustering-classification-compete-svm-and-one-class-classifiers-applied-on-plant-micrornas-data
#17
Malik Yousef, Waleed Khalifa, Loai AbedAllah
The performance of many learning and data mining algorithms depends critically on suitable metrics to assess efficiency over the input space. Learning a suitable metric from examples may, therefore, be the key to successful application of these algorithms. We have demonstrated that the k-nearest neighbor (kNN) classification can be significantly improved by learning a distance metric from labeled examples. The clustering ensemble is used to define the distance between points in respect to how they co-cluster...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187417/a-machine-learning-approach-for-microrna-precursor-prediction-in-retro-transcribing-virus-genomes
#18
Müserref Duygu Saçar Demirci, Mustafa Toprak, Jens Allmer
Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especially classification. In order to achieve successful classification, many parameters need to be considered such as data quality, choice of classifier settings, and feature selection. For the latter one, we developed a distributed genetic algorithm on HTCondor to perform feature selection...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187414/web-based-hybrid-dimensional-visualization-and-exploration-of-cytological-localization-scenarios
#19
Gökhan Kovanci, Mehmood Ghaffar, Björn Sommer
The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3...
December 21, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187424/feature-fusion-based-svm-classifier-for-protein-subcellular-localization-prediction
#20
Julia Rahman, Md Nazrul Islam Mondal, Md Khaled Ben Islam, Md Al Mehedi Hasan
For the importance of protein subcellular localization in different branches of life science and drug discovery, researchers have focused their attentions on protein subcellular localization prediction. Effective representation of features from protein sequences plays a most vital role in protein subcellular localization prediction specially in case of machine learning techniques. Single feature representation-like pseudo amino acid composition (PseAAC), physiochemical property models (PPM), and amino acid index distribution (AAID) contains insufficient information from protein sequences...
December 18, 2016: Journal of Integrative Bioinformatics
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