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In the evaluation of Stereo-Electroencephalography (SEEG) signals, the physicist’s workflow involves several operations, including determining the position of individual electrode contacts in terms of both rel...
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 distribut...
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 microal...
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 use...
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 re...
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 prote...
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 (M...
The original article was published in BMC Bioinformatics 2016 17:474
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...
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 ort...
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 rec...
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 s...
In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to ef...
This article is part of a Supplement: Volume 18 Supplement 2
Confocal microscopes deliver detailed three-dimensional data and are instrumental in biological analysis and research. Usually, this three-dimensional data is rendered as a projection onto a two-dimensional di...
This article is part of a Supplement: Volume 18 Supplement 2
Cluster heatmaps are commonly used in biology and related fields to reveal hierarchical clusters in data matrices. This visualization technique has high data density and reveal clusters better than unordered h...
This article is part of a Supplement: Volume 18 Supplement 2
We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology communit...
This article is part of a Supplement: Volume 18 Supplement 2
Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists’ understanding of phenotypic behavior associated with specific genes.
This article is part of a Supplement: Volume 18 Supplement 2
Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the prote...
This article is part of a Supplement: Volume 18 Supplement 2
Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often comp...
This article is part of a Supplement: Volume 18 Supplement 2
Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these d...
This article is part of a Supplement: Volume 18 Supplement 2
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 correlati...
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) n...
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 ...
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...
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 attr...
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.
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 e...
Conventional differential gene expression analysis by methods such as student’s t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them....
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 ...
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 estim...
Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requ...
The Erratum to this article has been published in BMC Bioinformatics 2017 18:194
The identification of immunogenic regions on the surface of antigens, which are able to be recognized by antibodies and to trigger an immune response, is a major challenge for the design of new and effective v...
The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer...
The Erratum to this article has been published in BMC Bioinformatics 2017 18:185
Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL...
The CRISPR–Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR–Cas system consists of a CRISPR array of repeat and spacer units, and a lo...
Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) r...
Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughp...
The original article was published in BMC Bioinformatics 2016 17:497
Tracing stable isotopes, such as 13C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information re...
Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations in the dystrophin gene are responsible for ...
Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the t...
Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes...
Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based o...
ERp is a variable selection and classification method for metabolomics data. ERp uses minimized classification error rates, based on data from a control and experimental group, to test the null hypothesis of n...
Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlat...
The Erratum to this article has been published in BMC Bioinformatics 2017 18:162
The correct protein coding region identification is an important and latent problem in the molecular biology field. This problem becomes a challenge due to the lack of deep knowledge about the biological syste...
Transcription factors are known to play key roles in carcinogenesis and therefore, are gaining popularity as potential therapeutic targets in drug development. A ‘master regulator’ transcription factor often a...
Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can ...
The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proxi...
Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regula...
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