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BMC Bioinformatics

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https://www.readbyqxmd.com/read/28438115/an-auditory-display-tool-for-dna-sequence-analysis
#1
Mark D Temple
BACKGROUND: DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorithms are logically designed from the simple through to the more complex. Three of these parse individual nucleotides, nucleotide pairs or codons into musical notes to give rise to 4, 16 or 64 notes, respectively. Codons may also be parsed degenerately into 20 notes with respect to the genetic code...
April 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28424069/ankplex-algorithmic-structure-for-refinement-of-near-native-ankyrin-protein-docking
#2
Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee, Chatchai Tayapiwatana
BACKGROUND: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet...
April 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28420344/erratum-to-the-jbei-quantitative-metabolic-modeling-library-jqmm-a-python-library-for-modeling-microbial-metabolism
#3
Garrett W Birkel, Amit Ghosh, Vinay S Kumar, Daniel Weaver, David Ando, Tyler W H Backman, Adam P Arkin, Jay D Keasling, Héctor García Martín
No abstract text is available yet for this article.
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28420343/on-the-association-analysis-of-cnv-data-a-fast-and-robust-family-based-association-method
#4
Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C Elston, Bong-Jo Kim, Sungho Won
BACKGROUND: Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical methods for CNV association analysis can be categorized into two different strategies. First, the copy number is estimated by maximum likelihood and association of the expected copy number with the phenotype is tested. Second, the observed probe intensity measurements can be directly used to detect association of CNV with the phenotypes of interest...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28420341/genetic-sequence-based-prediction-of-long-range-chromatin-interactions-suggests-a-potential-role-of-short-tandem-repeat-sequences-in-genome-organization
#5
Sarvesh Nikumbh, Nico Pfeifer
BACKGROUND: Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions - the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28410574/comparison-of-different-cell-type-correction-methods-for-genome-scale-epigenetics-studies
#6
COMPARATIVE STUDY
Akhilesh Kaushal, Hongmei Zhang, Wilfried J J Karmaus, Meredith Ray, Mylin A Torres, Alicia K Smith, Shu-Li Wang
BACKGROUND: Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular heterogeneity. Algorithms have been developed to measure or adjust for this heterogeneity, and some have been compared in the literature. However, with new methods available, it is unknown whether the findings will be consistent, if not which method(s) perform better. RESULTS: Methods: We compared eight cell-type correction methods including the method in the minfi R package, the method by Houseman et al...
April 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28407731/segmentum-a-tool-for-copy-number-analysis-of-cancer-genomes
#7
Ebrahim Afyounian, Matti Annala, Matti Nykter
BACKGROUND: Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However, due to the limitations of current high throughput sequencing technologies, this task remains challenging. Hence, accurate and reliable detection of such events is crucial for the identification of cancer-related alterations. RESULTS: We introduce a new tool called Segmentum for determining somatic copy numbers using whole genome sequencing from paired tumor/normal samples...
April 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28403836/an-adaptive-threshold-determination-method-of-feature-screening-for-genomic-selection
#8
Guifang Fu, Gang Wang, Xiaotian Dai
BACKGROUND: Although the dimension of the entire genome can be extremely large, only a parsimonious set of influential SNPs are correlated with a particular complex trait and are important to the prediction of the trait. Efficiently and accurately selecting these influential SNPs from millions of candidates is in high demand, but poses challenges. We propose a backward elimination iterative distance correlation (BE-IDC) procedure to select the smallest subset of SNPs that guarantees sufficient prediction accuracy, while also solving the unclear threshold issue for traditional feature screening approaches...
April 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28403823/empirical-bayes-method-for-reducing-false-discovery-rates-of-correlation-matrices-with-block-diagonal-structure
#9
Clare Pacini, James W Ajioka, Gos Micklem
BACKGROUND: Correlation matrices are important in inferring relationships and networks between regulatory or signalling elements in biological systems. With currently available technology sample sizes for experiments are typically small, meaning that these correlations can be difficult to estimate. At a genome-wide scale estimation of correlation matrices can also be computationally demanding. RESULTS: We develop an empirical Bayes approach to improve covariance estimates for gene expression, where we assume the covariance matrix takes a block diagonal form...
April 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28403817/homology-to-peptide-pattern-for-annotation-of-carbohydrate-active-enzymes-and-prediction-of-function
#10
P K Busk, B Pilgaard, M J Lezyk, A S Meyer, L Lange
BACKGROUND: Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each family makes it a major task to identify new family members and to provide basis for prediction of enzyme function. A fast and reliable method for de novo annotation of genes encoding carbohydrate-active enzymes is to identify conserved peptides in the curated enzyme families followed by matching of the conserved peptides to the sequence of interest as demonstrated for the glycosyl hydrolase and the lytic polysaccharide monooxygenase families...
April 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28399820/multi-scale-structural-community-organisation-of-the-human-genome
#11
Rasha E Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat, Benjamin Audit
BACKGROUND: Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. RESULTS: We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28399797/a-machine-learning-approach-for-viral-genome-classification
#12
Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani, Abdoulaye Baniré Diallo
BACKGROUND: Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28399795/pan-cancer-analysis-of-systematic-batch-effects-on-somatic-sequence-variations
#13
Ji-Hye Choi, Seong-Eui Hong, Hyun Goo Woo
BACKGROUND: The Cancer Genome Atlas (TCGA) is a comprehensive database that includes multi-layered cancer genome profiles. Large-scale collection of data inevitably generates batch effects introduced by differences in processing at various stages from sample collection to data generation. However, batch effects on the sequence variation and its characteristics have not been studied extensively. RESULTS: We systematically evaluated batch effects on somatic sequence variations in pan-cancer TCGA data, revealing 999 somatic variants that were batch-biased with statistical significance (P < 0...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28399794/meta-analysis-approach-as-a-gene-selection-method-in-class-prediction-does-it-improve-model-performance-a-case-study-in-acute-myeloid-leukemia
#14
Putri W Novianti, Victor L Jong, Kit C B Roes, Marinus J C Eijkemans
BACKGROUND: Aggregating gene expression data across experiments via meta-analysis is expected to increase the precision of the effect estimates and to increase the statistical power to detect a certain fold change. This study evaluates the potential benefit of using a meta-analysis approach as a gene selection method prior to predictive modeling in gene expression data. RESULTS: Six raw datasets from different gene expression experiments in acute myeloid leukemia (AML) and 11 different classification methods were used to build classification models to classify samples as either AML or healthy control...
April 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28388874/pgltools-a-genomic-arithmetic-tool-suite-for-manipulation-of-hi-c-peak-and-other-chromatin-interaction-data
#15
William W Greenwald, He Li, Erin N Smith, Paola Benaglio, Naoki Nariai, Kelly A Frazer
BACKGROUND: Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies...
April 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#16
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28381244/disbind-a-database-of-classified-functional-binding-sites-in-disordered-and-structured-regions-of-intrinsically-disordered-proteins
#17
Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
BACKGROUND: Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding regions of human and other genomes, considering that a significant portion of eukaryotic genomes code for intrinsically disordered regions in proteins. RESULTS: DisBind (available at http://biophy.dzu.edu.cn/DisBind ) is a collection of experimentally supported binding sites in intrinsically disordered proteins and proteins with both structured and disordered regions...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28381205/the-jbei-quantitative-metabolic-modeling-library-jqmm-a-python-library-for-modeling-microbial-metabolism
#18
Garrett W Birkel, Amit Ghosh, Vinay S Kumar, Daniel Weaver, David Ando, Tyler W H Backman, Adam P Arkin, Jay D Keasling, Héctor García Martín
BACKGROUND: Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the circumstantial ones, bounding the outcomes of experiments and guiding engineering approaches. Among different modeling schemes, the quantification of intracellular metabolic fluxes (i.e. the rate of each reaction in cellular metabolism) is of particular interest for metabolic engineering because it describes how carbon and energy flow throughout the cell...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28376796/ahcoda-db-a-data-repository-with-web-based-mining-tools-for-the-analysis-of-automated-high-content-mouse-phenomics-data
#19
Bastijn Koopmans, August B Smit, Matthijs Verhage, Maarten Loos
BACKGROUND: Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available for standardized quality control, data analysis and mining at the resolution of individual mice. DESCRIPTION: Here, we present AHCODA-DB, a public data repository with standardized quality control and exclusion criteria aimed to enhance robustness of data, enabled with web-based mining tools for the analysis of individually and group-wise collected mouse phenotypic data...
April 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28376731/ad-libs-inferring-ancestry-across-hybrid-genomes-using-low-coverage-sequence-data
#20
Nathan K Schaefer, Beth Shapiro, Richard E Green
BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA...
April 4, 2017: BMC Bioinformatics
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