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Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic ...
Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically...
With the exponential increase and widespread availability of genomic, transcriptomic, and proteomic data, accessing these ‘-omics’ data is becoming increasingly difficult. The current resources for accessing a...
Somatically acquired structure variations (SVs) and copy number variations (CNVs) can induce genetic changes that are directly related to tumor genesis. Somatic SV/CNV detection using next-generation sequencin...
Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological process...
The Erratum to this article has been published in BMC Bioinformatics 2016 17:39
Several missing value imputation methods for gene expression data have been proposed in the literature. In the past few years, researchers have been putting a great deal of effort into presenting systematic ev...
Gene expression profiling (GEP) via microarray analysis is a widely used tool for assessing risk and other patient diagnostics in clinical settings. However, non-biological factors such as systematic changes i...
Mass spectrometric analysis of microbial metabolism provides a long list of possible compounds. Restricting the identification of the possible compounds to those produced by the specific organism would benefit...
Accurately predicting the binding affinities of large sets of protein-ligand complexes is a key challenge in computational biomolecular science, with applications in drug discovery, chemical biology, and struc...
This article is part of a Supplement: Volume 16 Supplement 4
MicroRNAs (miRNAs) are important key regulators in multiple cellular functions, due to their a crucial role in different physiological processes. MiRNAs are differentially expressed in specific tissues, during...
This article is part of a Supplement: Volume 16 Supplement 4
Beef quality measurement is a complex task with high economic impact. There is high interest in obtaining an automatic quality parameters estimation in live cattle or post mortem. In this paper we set out to o...
This article is part of a Supplement: Volume 16 Supplement 4
Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious exp...
This article is part of a Supplement: Volume 16 Supplement 4
The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number ...
This article is part of a Supplement: Volume 16 Supplement 4
Cellular processes are known to be modular and are realized by groups of proteins implicated in common biological functions. Such groups of proteins are called functional modules, and many community detection met...
This article is part of a Supplement: Volume 16 Supplement 4
Data from biomedical domains often have an inherit hierarchical structure. As this structure is usually implicit, its existence can be overlooked by practitioners interested in constructing and evaluating pred...
This article is part of a Supplement: Volume 16 Supplement 4
The functioning of a protein relies on its location in the cell. Therefore, predicting protein subcellular localization is an important step towards protein function prediction. Recent studies have shown that ...
This article is part of a Supplement: Volume 16 Supplement 4
Allelic specific expression (ASE) increases our understanding of the genetic control of gene expression and its links to phenotypic variation. ASE testing is implemented through binomial or beta-binomial tests...
ChIP-seq has become a routine method for interrogating the genome-wide distribution of various histone modifications. An important experimental goal is to compare the ChIP-seq profiles between an experimental ...
Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunat...
De novo transcriptome assembly of short transcribed fragments (transfrags) produced from sequencing-by-synthesis technologies often results in redundant datasets with differing levels of unassembled, partially a...
Controlled vocabularies such as the Unified Medical Language System (UMLS®) and Medical Subject Headings (MeSH®) are widely used for biomedical natural language processing (NLP) tasks. However, the standard te...
Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which ...
Current biomedical research needs to leverage and exploit the large amount of information reported in scientific publications. Automated text mining approaches, in particular those aimed at finding relationshi...
Few studies have investigated prognostic biomarkers of distant metastases of lung cancer. One of the central difficulties in identifying biomarkers from microarray data is the availability of only a small numb...
The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association ...
The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×1084 po...
Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the pop...
Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library prepa...
Flux balance analysis is traditionally implemented to identify the maximum theoretical flux for some specified reaction and a single distribution of flux values for all the reactions present which achieve this...
Although Linear Discriminant Analysis (LDA) is commonly used for classification, it may not be directly applied in genomics studies due to the large p, small n problem in these studies. Different versions of spar...
Given a set of biallelic molecular markers, such as SNPs, with genotype values on a collection of plant, animal or human samples, the goal of quantitative genetic trait prediction is to predict the quantitativ...
This article is part of a Supplement: Volume 16 Supplement 1
The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in...
Many disease phenotypes are outcomes of the complicated interplay between multiple genes, and multiple phenotypes are affected by a single or multiple genotypes. Therefore, joint analysis of multiple phenotype...
In genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been pro...
Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based...
In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional...
The discovery and mapping of genomic variants is an essential step in most analysis done using sequencing reads. There are a number of mature software packages and associated pipelines that can identify single...
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
This article is part of a Supplement: Volume 16 Supplement 3
In this meeting report, we give an overview of the talks, presentations and posters presented at the third European Symposium of the International Society for Computational Biology (ISCB) Student Council. The ...
This article is part of a Supplement: Volume 16 Supplement 3
Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, id...
Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This resear...
RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been...
DAVID is the most popular tool for interpreting large lists of gene/proteins classically produced in high-throughput experiments. However, the use of DAVID website becomes difficult when analyzing multiple gen...
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