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This section incorporates novel results, useful tools, and methods using bioinformatics in new ways, including but not limited to: biological conclusions that are only supported by bioinformatics analyses.
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
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
Research Article
Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their co...
BMC Bioinformatics 2017 18:285
Published on: 30 May 2017
Methodology Article
Random forests are a popular method in many fields since they can be successfully applied to complex data, with a small sample size, complex interactions and correlations, mixed type predictors, etc. Furthermo...
BMC Bioinformatics 2017 18:230
Published on: 2 May 2017
Research Article
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 m...
BMC Bioinformatics 2017 18:217
Published on: 18 April 2017
Research article
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 h...
BMC Bioinformatics 2017 18:216
Published on: 14 April 2017
Research Article
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 pro...
BMC Bioinformatics 2017 18:211
Published on: 11 April 2017
Database
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 ...
BMC Bioinformatics 2017 18:206
Published on: 5 April 2017
Database
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 fo...
BMC Bioinformatics 2017 18:200
Published on: 4 April 2017
Software
Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data...
BMC Bioinformatics 2017 18:192
Published on: 24 March 2017
Methodology article
Finding epistatic interactions in large association studies like genome-wide association studies (GWAS) with the nowadays-available large volume of genomic data is a challenging and largely unsolved issue. Few...
BMC Bioinformatics 2017 18:184
Published on: 21 March 2017
Software
The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers u...
BMC Bioinformatics 2017 18:175
Published on: 17 March 2017
Research article
The random forests algorithm is a type of classifier with prominent universality, a wide application range, and robustness for avoiding overfitting. But there are still some drawbacks to random forests. Theref...
BMC Bioinformatics 2017 18:169
Published on: 14 March 2017
Methodology article
Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested t...
BMC Bioinformatics 2017 18:165
Published on: 11 March 2017
Software
The lipid scrambling activity of protein extracts and purified scramblases is typically measured using a fluorescence-based assay. While the assay has yielded insight into the scramblase activity in crude memb...
BMC Bioinformatics 2017 18:146
Published on: 3 March 2017
Software
The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relate...
BMC Bioinformatics 2017 18:125
Published on: 23 February 2017
Software
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 pro...
BMC Bioinformatics 2017 18:112
Published on: 16 February 2017
Methodology article
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 algorith...
BMC Bioinformatics 2017 18:105
Published on: 13 February 2017
DATABASE
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.
BMC Bioinformatics 2017 18:103
Published on: 11 February 2017
