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Journal of Integrative Bioinformatics

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https://www.readbyqxmd.com/read/29236680/uv-vis-and-cielab-based-chemometric-characterization-of-manihot-esculenta-carotenoid-contents
#1
Telma Afonso, Rodolfo Moresco, Virgilio G Uarrota, Bruno Bachiega Navarro, Eduardo da C Nunes, Marcelo Maraschin, Miguel Rocha
Vitamin A deficiency is a prevalent health problem in many areas of the world, where cassava genotypes with high pro-vitamin A content have been identified as a strategy to address this issue. In this study, we found a positive correlation between the color of the root pulp and the total carotenoid contents and, importantly, showed how CIELAB color measurements can be used as a non-destructive and fast technique to quantify the amount of carotenoids in cassava root samples, as opposed to traditional methods...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236679/assessing-public-metabolomics-metadata-towards-improving-quality
#2
João D Ferreira, Bruno Inácio, Reza M Salek, Francisco M Couto
Public resources need to be appropriately annotated with metadata in order to make them discoverable, reproducible and traceable, further enabling them to be interoperable or integrated with other datasets. While data-sharing policies exist to promote the annotation process by data owners, these guidelines are still largely ignored. In this manuscript, we analyse automatic measures of metadata quality, and suggest their application as a mean to encourage data owners to increase the metadata quality of their resources and submissions, thereby contributing to higher quality data, improved data sharing, and the overall accountability of scientific publications...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236678/protein-protein-interaction-article-classification-using-a-convolutional-recurrent-neural-network-with-pre-trained-word-embeddings
#3
Sérgio Matos, Rui Antunes
Curation of protein interactions from scientific articles is an important task, since interaction networks are essential for the understanding of biological processes associated with disease or pharmacological action for example. However, the increase in the number of publications that potentially contain relevant information turns this into a very challenging and expensive task. In this work we used a convolutional recurrent neural network for identifying relevant articles for extracting information regarding protein interactions...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236677/a-chemometrics-approach-for-nuclear-magnetic-resonance-data-to-characterize-the-partial-metabolome-banana-peels-from-southern-brazil
#4
Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
Banana peels are well recognized as a source of important bioactive compounds, such as phenolics, carotenoids, biogenic amines, among others. As such, they have recently started to be used for industrial purposes. However, its composition seems to be strongly affected by biotic or abiotic ecological factors. Thus, this study aimed to investigate banana peels chemical composition, not only to get insights on eventual metabolic changes caused by the seasons, in southern Brazil, but also to identify the most relevant metabolites for these processes...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236676/supervised-learning-and-knowledge-based-approaches-applied-to-biomedical-word-sense-disambiguation
#5
Rui Antunes, Sérgio Matos
Word sense disambiguation (WSD) is an important step in biomedical text mining, which is responsible for assigning an unequivocal concept to an ambiguous term, improving the accuracy of biomedical information extraction systems. In this work we followed supervised and knowledge-based disambiguation approaches, with the best results obtained by supervised means. In the supervised method we used bag-of-words as local features, and word embeddings as global features. In the knowledge-based method we combined word embeddings, concept textual definitions extracted from the UMLS database, and concept association values calculated from the MeSH co-occurrence counts from MEDLINE articles...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236675/selected-extended-papers-of-the-11th-international-conference-on-practical-applications-of-computational-biology-and-bioinformatics-pacbb
#6
EDITORIAL
Florentino Fdez-Riverola, Miguel Rocha
No abstract text is available yet for this article.
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28941356/computational-approaches-to-identify-genetic-interactions-for-cancer-therapeutics
#7
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
#8
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
#9
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
#10
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-mouse-brain-regions-expression-data-analysis-focus-on-apoe-functional-network
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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