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Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ran...
Transcription factors have been studied intensively because they play an important role in gene expression regulation. However, the transcription factors in the CPP family (cystein-rich polycomb-like protein),...
This article is part of a Supplement: Volume 14 Supplement 13
Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional character...
This article is part of a Supplement: Volume 14 Supplement 13
In order to better understand cancer as a complex disease with multiple genetic and epigenetic factors, it is vital to model the fundamental biological relationships among these alterations as well as their re...
This article is part of a Supplement: Volume 14 Supplement 13
With its massive amount of data, gene-expression profiling by RNA-Seq has many advantanges compared with microarray experiments. RNA-Seq analysis, however, is fundamentally different from microarray data analy...
This article is part of a Supplement: Volume 14 Supplement 13
Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides ...
This article is part of a Supplement: Volume 14 Supplement 13
The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. Howeve...
This article is part of a Supplement: Volume 14 Supplement 13
This paper introduces and applies a genome wide predictive study to learn a model that predicts whether a new subject will develop breast cancer or not, based on her SNP profile.
This article is part of a Supplement: Volume 14 Supplement 13
Variant discovery for rare genetic diseases using Illumina genome or exome sequencing involves screening of up to millions of variants to find only the one or few causative variant(s). Sequencing or alignment ...
This article is part of a Supplement: Volume 14 Supplement 13
Ontologies and catalogs of gene functions, such as the Gene Ontology (GO) and MIPS-FUN, assume that functional classes are organized hierarchically, that is, general functions include more specific ones. This ...
The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provid...
Existing tools to model cell growth curves do not offer a flexible integrative approach to manage large datasets and automatically estimate parameters. Due to the increase of experimental time-series from micr...
Identifying genetic variants associated with complex human diseases is a great challenge in genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) arising from genetic background are of...
Concept recognition is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. The development of such solutions is typically performed in an ad-hoc manner o...
Many calssifiers which are constructed with chosen gene markers have been proposed to forecast the prognosis of patients who suffer from breast cancer. However, few of them has been applied in clinical practic...
This article is part of a Supplement: Volume 14 Supplement 12
In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtaine...
This article is part of a Supplement: Volume 14 Supplement 12
Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus,...
This article is part of a Supplement: Volume 14 Supplement 12
Observation of gene expression changes implying gene regulations using a repetitive experiment in time course has become more and more important. However, there is no effective method which can handle such kin...
This article is part of a Supplement: Volume 14 Supplement 12
According to the World Health organization, half the world's population is at risk of contracting malaria. They estimated that in 2010 there were 219 million cases of malaria, resulting in 660,000 deaths and a...
This article is part of a Supplement: Volume 14 Supplement 12
MicroRNAs are a class of short regulatory RNAs that act as post-transcriptional fine-tune regulators of a large host of genes that play key roles in many cellular processes and signaling pathways. A useful ste...
This article is part of a Supplement: Volume 14 Supplement 12
Finding peaks in ChIP-seq is an important process in biological inference. In some cases, such as positioning nucleosomes with specific histone modifications or finding transcription factor binding specificiti...
Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the und...
High-throughput RNA sequencing (RNA-Seq) is a revolutionary technique to study the transcriptome of a cell under various conditions at a systems level. Despite the wide application of RNA-Seq techniques to gen...
Dynamic visualisation interfaces are required to explore the multiple microbial genome data now available, especially those obtained by high-throughput sequencing — a.k.a. “Next-Generation Sequencing” (NGS) — tec...
Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. Identifying the correct orientati...
Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like ...
Many Single Nucleotide Polymorphism (SNP) calling programs have been developed to identify Single Nucleotide Variations (SNVs) in next-generation sequencing (NGS) data. However, low sequencing coverage present...
High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a non-trivial ch...
This article is part of a Supplement: Volume 14 Supplement 11
Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of c...
This article is part of a Supplement: Volume 14 Supplement 11
Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (a...
This article is part of a Supplement: Volume 14 Supplement 11
Gene regulatory network inference remains a challenging problem in systems biology despite the numerous approaches that have been proposed. When substantial knowledge on a gene regulatory network is already av...
High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can ...
Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. The...
DNA pooling constitutes a cost effective alternative in genome wide association studies. In DNA pooling, equimolar amounts of DNA from different individuals are mixed into one sample and the frequency of each ...
Current advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their bio...
Many problems in computational biology require alignment-free sequence comparisons. One of the common tasks involving sequence comparison is sequence clustering. Here we apply methods of alignment-free compari...
Pathway analysis based on Genome-Wide Association Studies (GWAS) data has become popular as a secondary analysis strategy. Although many pathway analysis tools have been developed for case-control studies, the...
The miRNAs, a class of short approximately 22‐nucleotide non‐coding RNAs, often act post‐transcriptionally to inhibit mRNA expression. In effect, they control gene expression by targeting mRNA. They also help ...
Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying seque...
Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is grow...
New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resultin...
RNA-seq, a massive parallel-sequencing-based transcriptome profiling method, provides digital data in the form of aligned sequence read counts. The comparative analyses of the data require appropriate statisti...
The wealth of gene expression values being generated by high throughput microarray technologies leads to complex high dimensional datasets. Moreover, many cohorts have the problem of imbalanced classes where t...
Texture within biological specimens may reveal critical insights, while being very difficult to quantify. This is a particular problem in histological analysis. For example, cross-polar images of picrosirius s...
DNA methylation is an epigenetic event that adds a methyl-group to the 5’ cytosine. This epigenetic modification can significantly affect gene expression in both normal and diseased cells. Hence, it is importa...
Large-scale chromosomal deletions or other non-specific perturbations of the transcriptome can alter the expression of hundreds or thousands of genes, and it is of biological interest to understand which genes...
Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of m...
Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and...
High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to e...
Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and...
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