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BMC Bioinformatics

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https://www.readbyqxmd.com/read/27809781/pse-hmm-genome-wide-cnv-detection-from-ngs-data-using-an-hmm-with-position-specific-emission-probabilities
#1
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
BACKGROUND: Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. RESULTS: In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i...
November 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27806697/evaluating-tools-for-transcription-factor-binding-site-prediction
#2
Narayan Jayaram, Daniel Usvyat, Andrew C R Martin
BACKGROUND: Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate prediction of TFBSs for gene annotation and in applications such as evaluating the effects of single nucleotide variations in causing disease. TFBSs are generally recognized by scanning a position weight matrix (PWM) against DNA using one of a number of available computer programs...
November 2, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27806691/indel-marker-detection-by-integration-of-multiple-softwares-using-machine-learning-techniques
#3
Jianqiu Yang, Xinyi Shi, Lun Hu, Daipeng Luo, Jing Peng, Shengwu Xiong, Fanjing Kong, Baohui Liu, Xiaohui Yuan
BACKGROUND: In the biological experiments of soybean species, molecular markers are widely used to verify the soybean genome or construct its genetic map. Among a variety of molecular markers, insertions and deletions (InDels) are preferred with the advantages of wide distribution and high density at the whole-genome level. Hence, the problem of detecting InDels based on next-generation sequencing data is of great importance for the design of InDel markers. To tackle it, this paper integrated machine learning techniques with existing software and developed two algorithms for InDel detection, one is the best F-score method (BF-M) and the other is the Support Vector Machine (SVM) method (SVM-M), which is based on the classical SVM model...
November 2, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27931206/survivalgwas_power-a-user-friendly-tool-for-power-calculations-in-pharmacogenetic-studies-with-time-to-event-outcomes
#4
Hamzah Syed, Andrea L Jorgensen, Andrew P Morris
BACKGROUND: Power calculators are currently available for the design of genetic association studies of binary phenotypes and quantitative traits, but not for "time to event" outcomes, which are of particular relevance in pharmacogenetics. With the rapid emergence of pharmacogenetic association studies of single nucleotide polymorphisms (SNPs), and the complexity of clinical outcomes they consider, there is a need for software to perform power calculations of time to event data over a range of design scenarios and analytical methodologies...
December 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27927171/finding-an-appropriate-equation-to-measure-similarity-between-binary-vectors-case-studies-on-indonesian-and-japanese-herbal-medicines
#5
Sony Hartono Wijaya, Farit Mochamad Afendi, Irmanida Batubara, Latifah K Darusman, Md Altaf-Ul-Amin, Shigehiko Kanaya
BACKGROUND: The binary similarity and dissimilarity measures have critical roles in the processing of data consisting of binary vectors in various fields including bioinformatics and chemometrics. These metrics express the similarity and dissimilarity values between two binary vectors in terms of the positive matches, absence mismatches or negative matches. To our knowledge, there is no published work presenting a systematic way of finding an appropriate equation to measure binary similarity that performs well for certain data type or application...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27927167/development-of-a-group-contribution-method-for-estimating-free-energy-of-peptides-in-a-dodecane-water-system-via-molecular-dynamic-simulations
#6
Camilo Andrés Mora Osorio, Andrés Fernando González Barrios
BACKGROUND: Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27927164/the-role-of-nucleotide-composition-in-premature-termination-codon-recognition
#7
Fouad Zahdeh, Liran Carmel
BACKGROUND: It is not fully understood how a termination codon is recognized as premature (PTC) by the nonsense-mediated decay (NMD) machinery. This is particularly true for transcripts lacking an exon junction complex (EJC) along their 3' untranslated region (3'UTR), and thus degrade through the EJC-independent NMD pathway. RESULTS: Here, we analyzed data of transcript stability change following NMD repression and identified over 200 EJC-independent NMD-targets...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27927161/scifio-an-extensible-framework-to-support-scientific-image-formats
#8
Mark C Hiner, Curtis T Rueden, Kevin W Eliceiri
BACKGROUND: No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27923364/pcan-phenotype-consensus-analysis-to-support-disease-gene-association
#9
Patrice Godard, Matthew Page
BACKGROUND: Bridging genotype and phenotype is a fundamental biomedical challenge that underlies more effective target discovery and patient-tailored therapy. Approaches that can flexibly and intuitively, integrate known gene-phenotype associations in the context of molecular signaling networks are vital to effectively prioritize and biologically interpret genes underlying disease traits of interest. RESULTS: We describe Phenotype Consensus Analysis (PCAN); a method to assess the consensus semantic similarity of phenotypes in a candidate gene's signaling neighborhood...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27923350/coneva-a-toolbox-for-comprehensive-assessment-of-protein-contacts
#10
Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd)...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27923367/integrating-mean-and-variance-heterogeneities-to-identify-differentially-expressed-genes
#11
Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin
BACKGROUND: In functional genomics studies, tests on mean heterogeneity have been widely employed to identify differentially expressed genes with distinct mean expression levels under different experimental conditions. Variance heterogeneity (aka, the difference between condition-specific variances) of gene expression levels is simply neglected or calibrated for as an impediment. The mean heterogeneity in the expression level of a gene reflects one aspect of its distribution alteration; and variance heterogeneity induced by condition change may reflect another aspect...
December 6, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27923348/comparison-of-different-statistical-approaches-for-urinary-peptide-biomarker-detection-in-the-context-of-coronary-artery-disease
#12
Eleanor Stanley, Eleni Ioanna Delatola, Esther Nkuipou-Kenfack, William Spooner, Walter Kolch, Joost P Schanstra, Harald Mischak, Thomas Koeck
BACKGROUND: When combined with a clinical outcome variable, the size, complexity and nature of mass-spectrometry proteomics data impose great statistical challenges in the discovery of potential disease-associated biomarkers. The purpose of this study was thus to evaluate the effectiveness of different statistical methods applied for urinary proteomic biomarker discovery and different methods of classifier modelling in respect of the diagnosis of coronary artery disease in 197 study subjects and the prognostication of acute coronary syndromes in 368 study subjects...
December 6, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27919220/deepqa-improving-the-estimation-of-single-protein-model-quality-with-deep-belief-networks
#13
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. RESULTS: We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27919219/ston-exploring-biological-pathways-using-the-sbgn-standard-and-graph-databases
#14
Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray
BACKGROUND: When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks. RESULTS: We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27912731/predicting-the-recurrence-of-noncoding-regulatory-mutations-in-cancer
#15
Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi
BACKGROUND: One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncoding mutations owing to a limited amount of whole-genome sequenced samples. Hence, it is required to develop a method to predict potentially recurrent mutations. RESULTS: In this work, we developed a random forest classifier that predicts regulatory mutations that may recur based on the features of the mutations repeatedly appearing in a given cohort...
December 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27905885/mefit-merging-and-filtering-tool-for-illumina-paired-end-reads-for-16s-rrna-amplicon-sequencing
#16
Hardik I Parikh, Vishal N Koparde, Steven P Bradley, Gregory A Buck, Nihar U Sheth
BACKGROUND: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27905880/the-lair-a-resource-for-exploratory-analysis-of-published-rna-seq-data
#17
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data in the Sequence Read Archive, that together have allowed us to build an easily extendable resource for analysis of data underlying published papers. Our system makes the exploration of data easily accessible and usable without technical expertise...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27887574/fluxfix-automatic-isotopologue-normalization-for-metabolic-tracer-analysis
#18
Sophie Trefely, Peter Ashwell, Nathaniel W Snyder
BACKGROUND: Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [(13)C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27887571/lbsizecleav-improved-support-vector-machine-svm-based-prediction-of-dicer-cleavage-sites-using-loop-bulge-length
#19
Yu Bao, Morihiro Hayashida, Tatsuya Akutsu
BACKGROUND: Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites...
November 25, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27887570/metamis-a-metagenomic-microbial-interaction-simulator-based-on-microbial-community-profiles
#20
Grace Tzun-Wen Shaw, Yueh-Yang Pao, Daryi Wang
BACKGROUND: The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data. RESULTS: In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles...
November 25, 2016: BMC Bioinformatics
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