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Journal of Integrative Bioinformatics

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https://www.readbyqxmd.com/read/28941356/computational-approaches-to-identify-genetic-interactions-for-cancer-therapeutics
#1
Graeme Benstead-Hume, Sarah K Wooller, Frances M G Pearl
The development of improved cancer therapies is frequently cited as an urgent unmet medical need. Here we describe how genetic interactions are being therapeutically exploited to identify novel targeted treatments for cancer. We discuss the current methodologies that use 'omics data to identify genetic interactions, in particular focusing on synthetic sickness lethality (SSL) and synthetic dosage lethality (SDL). We describe the experimental and computational approaches undertaken both in humans and model organisms to identify these interactions...
September 23, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28941355/a-novel-method-to-detect-bias-in-short-read-ngs-data
#2
Jamie Alnasir, Hugh P Shanahan
Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. We outline a novel method to detect sequence specific bias in short read Next Generation Sequencing data. This is based on determining intra-exon correlations between specific motifs. This requires a mild assumption that short reads sampled from specific regions from the same exon will be correlated with each other. This has been implemented on Apache Spark and used to analyse two D. melanogaster eye-antennal disc data sets generated at the same laboratory...
September 23, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28918420/computer-analysis-of-glioma-transcriptome-profiling-alternative-splicing-events
#3
Vladimir N Babenko, Natalya V Gubanova, Anatoly O Bragin, Irina V Chadaeva, Gennady V Vasiliev, Irina V Medvedeva, Alexey S Gaytan, Alexey L Krivoshapkin, Yuriy L Orlov
Here we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method...
September 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28902625/biological-big-bytes-integrative-analysis-of-large-biological-datasets
#4
EDITORIAL
Ming Chen, Andrew Harrison, Hugh Shanahan, Yuriy Orlov
No abstract text is available yet for this article.
September 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28902624/rna-seq-mou20170024se-brain-regions-expression-data-analysis-focus-on-apoe-functional-network
#5
Vladimir N Babenko, Dmitry A Smagin, Natalia N Kudryavtseva
ApoE expression status was proved to be a highly specific marker of energy metabolism rate in the brain. Along with its neighbor, Translocase of Outer Mitochondrial Membrane 40 kDa (TOMM40) which is involved in mitochondrial metabolism, the corresponding genomic region constitutes the neuroenergetic hotspot. Using RNA-Seq data from a murine model of chronic stress a significant positive expression coordination of seven neighboring genes in ApoE locus in five brain regions was observed. ApoE maintains one of the highest absolute expression values genome-wide, implying that ApoE can be the driver of the neighboring gene expression alteration observed under stressful loads...
September 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28862986/digital-biomass-accumulation-using-high-throughput-plant-phenotype-data-analysis
#6
Md Matiur Rahaman, Md Asif Ahsan, Zeeshan Gillani, Ming Chen
Biomass is an important phenotypic trait in functional ecology and growth analysis. The typical methods for measuring biomass are destructive, and they require numerous individuals to be cultivated for repeated measurements. With the advent of image-based high-throughput plant phenotyping facilities, non-destructive biomass measuring methods have attempted to overcome this problem. Thus, the estimation of plant biomass of individual plants from their digital images is becoming more important. In this paper, we propose an approach to biomass estimation based on image derived phenotypic traits...
September 1, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28796642/mustv2-an-improved-de-novo-detection-program-for-recently-active-miniature-inverted-repeat-transposable-elements-mites
#7
Ruiquan Ge, Guoqin Mai, Ruochi Zhang, Xundong Wu, Qing Wu, Fengfeng Zhou
Background Miniature inverted repeat transposable element (MITE) is a short transposable element, carrying no protein-coding regions. However, its high proliferation rate and sequence-specific insertion preference renders it as a good genetic tool for both natural evolution and experimental insertion mutagenesis. Recently active MITE copies are those with clear signals of Terminal Inverted Repeats (TIRs) and Direct Repeats (DRs), and are recently translocated into their current sites. Their proliferation ability renders them good candidates for the investigation of genomic evolution...
August 10, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28753538/improving-the-quality-of-positive-datasets-for-the-establishment-of-machine-learning-models-for-pre-microrna-detection
#8
Müşerref Duygu Saçar Demirci, Jens Allmer
MicroRNAs (miRNAs) are involved in the post-transcriptional regulation of protein abundance and thus have a great impact on the resulting phenotype. It is, therefore, no wonder that they have been implicated in many diseases ranging from virus infections to cancer. This impact on the phenotype leads to a great interest in establishing the miRNAs of an organism. Experimental methods are complicated which led to the development of computational methods for pre-miRNA detection. Such methods generally employ machine learning to establish models for the discrimination between miRNAs and other sequences...
July 28, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28753537/comparison-of-different-approaches-for-measuring-tibial-cartilage-thickness
#9
Jennifer Maier, Marianne Black, Serena Bonaretti, Bastian Bier, Bjoern Eskofier, Jang-Hwan Choi, Marc Levenston, Garry Gold, Rebecca Fahrig, Andreas Maier
Osteoarthritis is a degenerative disease affecting bones and cartilage especially in the human knee. In this context, cartilage thickness is an indicator for knee cartilage health. Thickness measurements are performed on medical images acquired in-vivo. Currently, there is no standard method agreed upon that defines a distance measure in articular cartilage. In this work, we present a comparison of different methods commonly used in literature. These methods are based on nearest neighbors, surface normal vectors, local thickness and potential field lines...
July 28, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28731858/a-generalized-approach-for-measuring-relationships-among-genes
#10
Lijun Wang, Md Asif Ahsan, Ming Chen
Several methods for identifying relationships among pairs of genes have been developed. In this article, we present a generalized approach for measuring relationships between any pairs of genes, which is based on statistical prediction. We derive two particular versions of the generalized approach, least squares estimation (LSE) and nearest neighbors prediction (NNP). According to mathematical proof, LSE is equivalent to the methods based on correlation; and NNP is approximate to one popular method called the maximal information coefficient (MIC) according to the performances in simulations and real dataset...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28731857/cytomcs-a-multiple-maximum-common-subgraph-detection-tool-for-cytoscape
#11
Simon J Larsen, Jan Baumbach
Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28688226/towards-multiple-kernel-principal-component-analysis-for-integrative-analysis-of-tumor-samples
#12
Nora K Speicher, Nico Pfeifer
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene expression data). We propose an unsupervised data integration method based on kernel principal component analysis. Principal component analysis is one of the most widely used techniques in data analysis...
July 8, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28686574/prediction-of-primary-tumors-in-cancers-of-unknown-primary
#13
Dan Søndergaard, Svend Nielsen, Christian N S Pedersen, Søren Besenbacher
A cancer of unknown primary (CUP) is a metastatic cancer for which standard diagnostic tests fail to identify the location of the primary tumor. CUPs account for 3-5% of cancer cases. Using molecular data to determine the location of the primary tumor in such cases can help doctors make the right treatment choice and thus improve the clinical outcome. In this paper, we present a new method for predicting the location of the primary tumor using gene expression data: locating cancers of unknown primary (LoCUP)...
July 7, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28682786/application-of-computational-methods-in-planaria-research-a-current-update
#14
Shyamasree Ghosh
Planaria is a member of the Phylum Platyhelminthes including flatworms. Planarians possess the unique ability of regeneration from adult stem cells or neoblasts and finds importance as a model organism for regeneration and developmental studies. Although research is being actively carried out globally through conventional methods to understand the process of regeneration from neoblasts, biology of development, neurobiology and immunology of Planaria, there are many thought provoking questions related to stem cell plasticity, and uniqueness of regenerative potential in Planarians amongst other members of Phylum Platyhelminthes...
July 6, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28678736/lifestyle-specific-islands-lissi-integrated-bioinformatics-platform-for-genomic-island-analysis
#15
Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar de Castro Soares, Sebastian Böcker, Vasco Azevedo, Jan Baumbach
Distinct bacteria are able to cope with highly diverse lifestyles; for instance, they can be free living or host-associated. Thus, these organisms must possess a large and varied genomic arsenal to withstand different environmental conditions. To facilitate the identification of genomic features that might influence bacterial adaptation to a specific niche, we introduce LifeStyle-Specific-Islands (LiSSI). LiSSI combines evolutionary sequence analysis with statistical learning (Random Forest with feature selection, model tuning and robustness analysis)...
July 5, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28675749/randomization-strategies-affect-motif-significance-analysis-in-tf-mirna-gene-regulatory-networks
#16
Sepideh Sadegh, Maryam Nazarieh, Christian Spaniol, Volkhard Helms
Gene-regulatory networks are an abstract way of capturing the regulatory connectivity between transcription factors, microRNAs, and target genes in biological cells. Here, we address the problem of identifying enriched co-regulatory three-node motifs that are found significantly more often in real network than in randomized networks. First, we compare two randomization strategies, that either only conserve the degree distribution of the nodes' in- and out-links, or that also conserve the degree distributions of different regulatory edge types...
July 4, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28672765/discovery-and-annotation-of-plant-endogenous-target-mimicry-sequences-from-public-transcriptome-libraries-a-case-study-of-prunus-persica
#17
Gökhan Karakülah
Novel transcript discovery through RNA sequencing has substantially improved our understanding of the transcriptome dynamics of biological systems. Endogenous target mimicry (eTM) transcripts, a novel class of regulatory molecules, bind to their target microRNAs (miRNAs) by base pairing and block their biological activity. The objective of this study was to provide a computational analysis framework for the prediction of putative eTM sequences in plants, and as an example, to discover previously un-annotated eTMs in Prunus persica (peach) transcriptome...
June 28, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28637931/comparative-miromics-of-salt-tolerant-and-salt-sensitive-rice
#18
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/28609295/clubber-removing-the-bioinformatics-bottleneck-in-big-data-analyses
#19
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
#20
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
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