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Journal of Integrative Bioinformatics

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https://www.readbyqxmd.com/read/28187422/differential-expression-of-hyperhydricity-responsive-peach-mirnas
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28187413/dato-an-atlas-of-biological-databases-and-tools
#12
Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187412/omics-fusion-a-platform-for-integrative-analysis-of-omics-data
#13
Benedikt G Brink, Annica Seidel, Nils Kleinbölting, Tim W Nattkemper, Stefan P Albaum
We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/.
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187411/new-insights-into-genotype-phenotype-correlation-in-individuals-with-different-level-of-general-non-specific-reactivity-of-an-organism
#14
Alexander Mulik, Valery Novochadov, Alexander Bondarev, Sofya Lipnitskaya, Irina Ulesikova, Yulia Shatyr
The objective of the study was to investigate the genetic basis of general non-specific reactivity of an organism. Systematic search in PubMedCentral, PDB, KEGG and SNP databases identified a set of genes and their polymorphisms that can determine pain sensitivity and therefore the level of general non-specific reactivity of the human organism. Six SNPs were selected for genotyping kit design; 230 healthy volunteers were enrolled in the study. It was revealed that very high pain threshold was associated with allele A in rs1851048 and allele C in rs6777055...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187410/jllumina-a-comprehensive-java-based-api-for-statistical-illumina-infinium-humanmethylation450-and-methylationepic-data-processing
#15
Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, Richard Röttger
Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187409/pgminer-reloaded-fully-automated-proteogenomic-annotation-tool-linking-genomes-to-proteomes
#16
Canan Has, Sergey A Lashin, Alexey V Kochetov, Jens Allmer
Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187408/analysis-of-differential-gene-expression-by-rna-seq-data-in-brain-areas-of-laboratory-animals
#17
Vladimir N Babenko, Anatoly O Bragin, Anastasia M Spitsina, Irina V Chadaeva, Elvira R Galieva, Galina V Orlova, Irina V Medvedeva, Yuriy L Orlov
Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions – friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187407/synthetic-biology-open-language-sbol-version-2-1-0
#18
Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John Gennari, Chris Myers, Herbert Sauro, Anil Wipat
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187406/sbml-level-3-package-groups-version-1-release-1
#19
Michael Hucka, Lucian P Smith
Biological models often contain components that have relationships with each other, or that modelers want to treat as belonging to groups with common characteristics or shared metadata. The SBML Level 3 Version 1 Core specification does not provide an explicit mechanism for expressing such relationships, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Groups package for SBML Level 3 adds the necessary features to SBML to allow grouping of model components to be expressed...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187405/specifications-of-standards-in-systems-and-synthetic-biology-status-and-developments-in-2016
#20
Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Walthemath
Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.
December 18, 2016: Journal of Integrative Bioinformatics
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