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BMC Bioinformatics

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https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#1
Diego Pasqualin, Marcos Barbeitos, Fabiano Silva
BACKGROUND: Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes. Common implementations rely on Continuous-time Markov Chain simulations whose parameters are difficult to adjust and subjected to inherent inaccuracy. Thus, researchers must run a large number of simulations in order to obtain adequate estimates...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28228091/exploring-the-transcriptome-of-non-model-oleaginous-microalga-dunaliella-tertiolecta-through-high-throughput-sequencing-and-high-performance-computing
#2
Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee
BACKGROUND: RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microalgal strains with potential as biofuel sources. However, insufficient genomic or transcriptomic information of non-model microalgae has limited the understanding of their regulatory mechanisms and hampered genetic manipulation to enhance biofuel production. As such, an optimal microalgal transcriptomic database construction is a subject of urgent investigation...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28222698/atgc-transcriptomics-a-web-based-application-to-integrate-explore-and-analyze-de-novo-transcriptomic-data
#3
Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego
BACKGROUND: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28222683/manananggal-a-novel-viewer-for-alternative-splicing-events
#4
Matthias Barann, Ralf Zimmer, Fabian Birzele
BACKGROUND: Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is required to select reliable instances of alternative splicing events (ASEs). There are only few tools specifically designed for interactive inspection of ASEs and available visualization approaches can be significantly improved. RESULTS: Here, we present Manananggal, an application specifically designed for the identification of splicing events in next generation sequencing data...
February 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28219348/distribution-based-nearest-neighbor-imputation-for-truncated-high-dimensional-data-with-applications-to-pre-clinical-and-clinical-metabolomics-studies
#5
Jasmit S Shah, Shesh N Rai, Andrew P DeFilippis, Bradford G Hill, Aruni Bhatnagar, Guy N Brock
BACKGROUND: High throughput metabolomics makes it possible to measure the relative abundances of numerous metabolites in biological samples, which is useful to many areas of biomedical research. However, missing values (MVs) in metabolomics datasets are common and can arise due to both technical and biological reasons. Typically, such MVs are substituted by a minimum value, which may lead to different results in downstream analyses. RESULTS: Here we present a modified version of the K-nearest neighbor (KNN) approach which accounts for truncation at the minimum value, i...
February 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28219343/computing-structure-based-lipid-accessibility-of-membrane-proteins-with-mp_lipid_acc-in-rosettamp
#6
Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
BACKGROUND: Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins...
February 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28212605/erratum-to-mirnacle-machine-learning-with-smote-and-random-forest-for-improving-selectivity-in-pre-mirna-ab-initio-prediction
#7
Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro Vasconcelos, Fabio Ribeiro Cerqueira
No abstract text is available yet for this article.
February 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28209135/marv-a-tool-for-genome-wide-multi-phenotype-analysis-of-rare-variants
#8
Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P Morris, Inga Prokopenko
BACKGROUND: Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and recent advances in technology to produce high-dimensional data cost-effectively have led to method development beyond standard common variant analysis, including single-phenotype rare variant and multi-phenotype common variant analysis, with the latter increasing power for locus discovery and providing suggestions of pleiotropic effects...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28209129/orthograph-a-versatile-tool-for-mapping-coding-nucleotide-sequences-to-clusters-of-orthologous-genes
#9
Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis
BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28209127/repo-an-r-package-for-data-centered-management-of-bioinformatic-pipelines
#10
Francesco Napolitano
BACKGROUND: Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and planning effort, which may become impractical in rapidly changing development environments...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28201984/improvement-of-peptide-identification-with-considering-the-abundance-of-mrna-and-peptide
#11
Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu
BACKGROUND: Tandem mass spectrometry (MS/MS) followed by database search is a main approach to identify peptides/proteins in proteomic studies. A lot of effort has been devoted to improve the identification accuracy and sensitivity for peptides/proteins, such as developing advanced algorithms and expanding protein databases. RESULTS: Herein, we described a new strategy for enhancing the sensitivity of protein/peptide identification through combination of mRNA and peptide abundance in Percolator...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28196464/sparse-kernel-canonical-correlation-analysis-for-discovery-of-nonlinear-interactions-in-high-dimensional-data
#12
Kosuke Yoshida, Junichiro Yoshimoto, Kenji Doya
BACKGROUND: Advance in high-throughput technologies in genomics, transcriptomics, and metabolomics has created demand for bioinformatics tools to integrate high-dimensional data from different sources. Canonical correlation analysis (CCA) is a statistical tool for finding linear associations between different types of information. Previous extensions of CCA used to capture nonlinear associations, such as kernel CCA, did not allow feature selection or capturing of multiple canonical components...
February 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28193166/vacsol-a-high-throughput-in-silico-pipeline-to-predict-potential-therapeutic-targets-in-prokaryotic-pathogens-using-subtractive-reverse-vaccinology
#13
Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali
BACKGROUND: With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28193156/ecdomainminer-discovering-hidden-associations-between-enzyme-commission-numbers-and-pfam-domains
#14
Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W Ritchie
BACKGROUND: Many entries in the protein data bank (PDB) are annotated to show their component protein domains according to the Pfam classification, as well as their biological function through the enzyme commission (EC) numbering scheme. However, despite the fact that the biological activity of many proteins often arises from specific domain-domain and domain-ligand interactions, current on-line resources rarely provide a direct mapping from structure to function at the domain level. Since the PDB now contains many tens of thousands of protein chains, and since protein sequence databases can dwarf such numbers by orders of magnitude, there is a pressing need to develop automatic structure-function annotation tools which can operate at the domain level...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28193155/a-comparison-of-reference-based-algorithms-for-correcting-cell-type-heterogeneity-in-epigenome-wide-association-studies
#15
Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck
BACKGROUND: Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorithms have emerged, their potential remains underexplored and a comparative evaluation of these algorithms beyond tissues such as blood is still lacking. RESULTS: Here we present a novel framework for reference-based inference, which leverages cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference DNA methylation database...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187714/tipmt-identification-of-pcr-based-taxon-specific-markers
#16
Gabriela F Rodrigues-Luiz, Mariana S Cardoso, Hugo O Valdivia, Edward V Ayala, Célia M F Gontijo, Thiago de S Rodrigues, Ricardo T Fujiwara, Robson S Lopes, Daniella C Bartholomeu
BACKGROUND: Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187703/ihms-a-database-integrating-human-histone-modification-data-across-developmental-stages-and-tissues
#17
Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou
BACKGROUND: Differences in chromatin states are critical to the multiplicity of cell states. Recently genome-wide histone modification maps of diverse human developmental stages and tissues have been charted. DESCRIPTION: To facilitate the investigation of epigenetic dynamics and regulatory mechanisms in cellular differentiation processes, we developed iHMS, an integrated human histone modification database that incorporates massive histone modification maps spanning different developmental stages, lineages and tissues ( http://www...
February 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187713/novel-methods-to-optimize-gene-and-statistic-test-for-evaluation-an-application-for-escherichia-coli
#18
Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
BACKGROUND: Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187712/vmcmc-a-graphical-and-statistical-analysis-tool-for-markov-chain-monte-carlo-traces
#19
Raja H Ali, Mikael Bark, Jorge Miró, Sayyed A Muhammad, Joel Sjöstrand, Syed M Zubair, Raja M Abbas, Lars Arvestad
BACKGROUND: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187709/the-drosophila-gene-expression-tool-dget-for-expression-analyses
#20
Yanhui Hu, Aram Comjean, Norbert Perrimon, Stephanie E Mohr
BACKGROUND: Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue...
February 10, 2017: BMC Bioinformatics
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