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Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Me...
BMC Bioinformatics 2017 18:331
Published on: 10 July 2017
Research Article
Biomarker detection presents itself as a major means of translating biological data into clinical applications. Due to the recent advances in high throughput sequencing technologies, an increased number of met...
BMC Bioinformatics 2017 18:328
Published on: 10 July 2017
Research Article
In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein–small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (M...
BMC Bioinformatics 2017 18:327
Published on: 10 July 2017
Methodology Article
Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that m...
BMC Bioinformatics 2017 18:326
Published on: 6 July 2017
Software
sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA)....
BMC Bioinformatics 2017 18:325
Published on: 4 July 2017
Methodology Article
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This lea...
BMC Bioinformatics 2017 18:324
Published on: 3 July 2017
Software
Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream...
BMC Bioinformatics 2017 18:323
Published on: 30 June 2017
Methodology Article
Current -omics technologies are able to sense the state of a biological sample in a very wide variety of ways. Given the high dimensionality that typically characterises these data, relevant knowledge is often hi...
BMC Bioinformatics 2017 18:322
Published on: 30 June 2017
Software
The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs...
BMC Bioinformatics 2017 18:321
Published on: 28 June 2017
Software
Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been d...
BMC Bioinformatics 2017 18:320
Published on: 28 June 2017
Software
Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study ...
BMC Bioinformatics 2017 18:319
Published on: 28 June 2017
Software
The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose SparkBLAST, a...
BMC Bioinformatics 2017 18:318
Published on: 27 June 2017
Research Article
Personalizing treatment regimes based on gene expression profiles of individual tumors will facilitate management of cancer. Although many methods have been developed to identify pathways perturbed in tumors, ...
BMC Bioinformatics 2017 18:317
Published on: 26 June 2017
Software
Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to re...
BMC Bioinformatics 2017 18:316
Published on: 26 June 2017
Software
Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available...
BMC Bioinformatics 2017 18:314
Published on: 24 June 2017
Software
The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep it...
BMC Bioinformatics 2017 18:315
Published on: 24 June 2017
Methodology Article
Identifying disease correlated features early before large number of molecules are impacted by disease progression with significant abundance change is very advantageous to biologists for developing early dise...
BMC Bioinformatics 2017 18:313
Published on: 23 June 2017
Correspondence
Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science r...
BMC Bioinformatics 2017 18:311
Published on: 21 June 2017
Methodology Article
Transcriptomic approaches (microarray and RNA-seq) have been a tremendous advance for molecular science in all disciplines, but they have made interpretation of hypothesis testing more difficult because of the...
BMC Bioinformatics 2017 18:312
Published on: 21 June 2017
Software
Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multipl...
BMC Bioinformatics 2017 18:310
Published on: 21 June 2017
Methodology Article
Distance based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and relatively high correlation...
BMC Bioinformatics 2017 18:309
Published on: 20 June 2017
Methodology Article
Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, ...
BMC Bioinformatics 2017 18:306
Published on: 19 June 2017
Methodology Article
Recent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyse...
BMC Bioinformatics 2017 18:307
Published on: 19 June 2017
Methodology Article
Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when ...
BMC Bioinformatics 2017 18:308
Published on: 19 June 2017
Research Article
Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interr...
BMC Bioinformatics 2017 18:304
Published on: 17 June 2017
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