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BMC Bioinformatics

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https://www.readbyqxmd.com/read/28931373/improving-contig-binning-of-metagenomic-data-using-formula-see-text-oligonucleotide-frequency-dissimilarity
#1
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
BACKGROUND: Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. RESULTS: According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28931371/vismapper-ultra-fast-exhaustive-cartography-of-viral-insertion-sites-for-gene-therapy
#2
José M Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau, Joaquín Dopazo
BACKGROUND: The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. RESULTS: Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28923005/methods-for-discovering-genomic-loci-exhibiting-complex-patterns-of-differential-methylation
#3
Thomas J Hardcastle
BACKGROUND: Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation 'loci'; contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28923003/cleaning-by-clustering-methodology-for-addressing-data-quality-issues-in-biomedical-metadata
#4
Wei Hu, Amrapali Zaveri, Honglei Qiu, Michel Dumontier
BACKGROUND: The ability to efficiently search and filter datasets depends on access to high quality metadata. While most biomedical repositories require data submitters to provide a minimal set of metadata, some such as the Gene Expression Omnibus (GEO) allows users to specify additional metadata in the form of textual key-value pairs (e.g. sex: female). However, since there is no structured vocabulary to guide the submitter regarding the metadata terms to use, consequently, the 44,000,000+ key-value pairs in GEO suffer from numerous quality issues including redundancy, heterogeneity, inconsistency, and incompleteness...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28923002/deep-learning-methods-for-protein-torsion-angle-prediction
#5
Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng
BACKGROUND: Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins...
September 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28915791/segmentation-and-classification-of-two-channel-c-elegans-nucleus-labeled-fluorescence-images
#6
Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-Mei Li, Meng-Qiu Dong, Heng Mao, Louis Tao
BACKGROUND: Aging is characterized by a gradual breakdown of cellular structures. Nuclear abnormality is a hallmark of progeria in human. Analysis of age-dependent nuclear morphological changes in Caenorhabditis elegans is of great value to aging research, and this calls for an automatic image processing method that is suitable for both normal and abnormal structures. RESULTS: Our image processing method consists of nuclear segmentation, feature extraction and classification...
September 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28915787/mmquant-how-to-count-multi-mapping-reads
#7
Matthias Zytnicki
BACKGROUND: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results. RESULTS: We provide here a tool, called mmquant, for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene...
September 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929974/reconstruction-and-visualization-of-large-scale-volumetric-models-of-neocortical-circuits-for-physically-plausible-in-silico-optical-studies
#8
Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram, Felix Schürmann
BACKGROUND: We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing approaches for creating those models are explained, and then, a multi-stage pipeline is discussed to overcome those limitations. Starting from the neuronal morphologies, we create smooth piecewise watertight polygonal models that can be efficiently utilized to synthesize continuous and plausible volumetric models of the neurons with solid voxelization...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929973/vermont-a-multi-perspective-visual-interactive-platform-for-mutational-analysis
#9
Alexandre V Fassio, Pedro M Martins, Samuel da S Guimarães, Sócrates S A Junior, Vagner S Ribeiro, Raquel C de Melo-Minardi, Sabrina de A Silveira
BACKGROUND: A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929971/medisyn-uncertainty-aware-visualization-of-multiple-biomedical-datasets-to-support-drug-treatment-selection
#10
Chen He, Luana Micallef, Zia-Ur-Rehman Tanoli, Samuel Kaski, Tero Aittokallio, Giulio Jacucci
BACKGROUND: Dispersed biomedical databases limit user exploration to generate structured knowledge. Linked Data unifies data structures and makes the dispersed data easy to search across resources, but it lacks supporting human cognition to achieve insights. In addition, potential errors in the data are difficult to detect in their free formats. Devising a visualization that synthesizes multiple sources in such a way that links between data sources are transparent, and uncertainties, such as data conflicts, are salient is challenging...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929970/bayesian-unidimensional-scaling-for-visualizing-uncertainty-in-high-dimensional-datasets-with-latent-ordering-of-observations
#11
Lan Huong Nguyen, Susan Holmes
BACKGROUND: Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous process, often unknown. Estimating data points' 'natural ordering' and their corresponding uncertainties can help researchers draw insights about the mechanisms involved...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#12
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929968/c-state-an-interactive-web-app-for-simultaneous-multi-gene-visualization-and-comparative-epigenetic-pattern-search
#13
Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K Mishra
BACKGROUND: Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. RESULTS: We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28899361/interactive-visual-exploration-and-refinement-of-cluster-assignments
#14
Michael Kern, Alexander Lex, Nils Gehlenborg, Chris R Johnson
BACKGROUND: With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear...
September 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28882107/statistical-classifiers-for-diagnosing-disease-from-immune-repertoires-a-case-study-using-multiple-sclerosis
#15
Jared Ostmeyer, Scott Christley, William H Rounds, Inimary Toby, Benjamin M Greenberg, Nancy L Monson, Lindsay G Cowell
BACKGROUND: Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated with clinical phenotypes. Indeed, recent studies support the feasibility of this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) and patient outcomes for several diseases...
September 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28877663/high-throughput-pcr-assay-design-for-targeted-resequencing-using-primerxl
#16
Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans, Jo Vandesompele
BACKGROUND: Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only the regions of interest decreases both costs and the complexity of the downstream data-analysis. Various target enrichment strategies are available, but none of them obtain the degree of coverage uniformity, flexibility and specificity of PCR-based enrichment. On the other hand, the biggest limitation of target enrichment by PCR is the need to design large numbers of partially overlapping assays to cover the target...
September 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28874117/bufet-boosting-the-unbiased-mirna-functional-enrichment-analysis-using-bitsets
#17
Konstantinos Zagganas, Thanasis Vergoulis, Maria D Paraskevopoulou, Ioannis S Vlachos, Spiros Skiadopoulos, Theodore Dalamagas
BACKGROUND: A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological processes that may be regulated by a given miRNA group. However, it is computationally intensive and significantly more expensive than its alternatives. RESULTS: We introduce BUFET, a new approach to significantly reduce the time required for the execution of the unbiased miRNA functional enrichment analysis...
September 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28870256/phylo_dcor-distance-correlation-as-a-novel-metric-for-phylogenetic-profiling
#18
Gabriella Sferra, Federica Fratini, Marta Ponzi, Elisabetta Pizzi
BACKGROUND: Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the prediction of protein-protein interactions at a whole genome level in both Prokaryotes and Eukaryotes. For this reason it is considered one of the most promising methods. RESULTS: Here, we propose an improvement of phylogenetic profiling that enables handling of large genomic datasets and infer global protein-protein interactions...
September 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28865443/investigating-microrna-and-transcription-factor-co-regulatory-networks-in-colorectal-cancer
#19
Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang
BACKGROUND: Colorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through targeting critical genes in cellular system. However, it is unclear about which miRNAs play central roles in CRC's pathogenesis and how they interact with transcription factors (TFs) to regulate the cancer-related genes. RESULTS: To address this issue, we systematically explored the major regulation motifs, namely feed-forward loops (FFLs), that consist of miRNAs, TFs and CRC-related genes through the construction of a miRNA-TF regulatory network in CRC...
September 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28865433/rrcrank-a-fusion-method-using-rank-strategy-for-residue-residue-contact-prediction
#20
Xiaoyang Jing, Qiwen Dong, Ruqian Lu
BACKGROUND: In structural biology area, protein residue-residue contacts play a crucial role in protein structure prediction. Some researchers have found that the predicted residue-residue contacts could effectively constrain the conformational search space, which is significant for de novo protein structure prediction. In the last few decades, related researchers have developed various methods to predict residue-residue contacts, especially, significant performance has been achieved by using fusion methods in recent years...
September 2, 2017: BMC Bioinformatics
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