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Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma and accounts for cancer-related deaths. Survival rates are very low when the tumor is discovered in the late-stage. Th...
During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research field. While numerous existing methods focus on the in...
Inferring diseases related to the patient’s electronic medical records (EMRs) is of great significance for assisting doctor diagnosis. Several recent prediction methods have shown that deep learning-based meth...
Circular RNA (circRNA) has been extensively identified in cells and tissues, and plays crucial roles in human diseases and biological processes. circRNA could act as dynamic scaffolding molecules that modulate...
Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all ...
Quantitative phase imaging (QPI) is an established tool for the marker-free classification and quantitative characterization of biological samples. For spherical objects, such as cells in suspension, microgel ...
Advances in DNA sequencing have offered researchers an unprecedented opportunity to better study the variety of species living in and on the human body. However, the analysis of microbiome data is complicated ...
Currently the combination of molecular tools, imaging techniques and analysis software offer the possibility of studying gene activity through the use of fluorescent reporters and infer its distribution within...
The latest works on CRISPR genome editing tools mainly employs deep learning techniques. However, deep learning models lack explainability and they are harder to reproduce. We were motivated to build an accura...
Genome-wide ligation-based assays such as Hi-C provide us with an unprecedented opportunity to investigate the spatial organization of the genome. Results of a typical Hi-C experiment are often summarized in a...
The use of RNA-sequencing (RNA-seq) in molecular biology research and clinical settings has increased significantly over the past decade. Despite its widespread adoption, there is a lack of simple and interact...
The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly incre...
Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among t...
Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th...
The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a m...
Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell o...
Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription ...
Semantic resources such as knowledge bases contains high-quality-structured knowledge and therefore require significant effort from domain experts. Using the resources to reinforce the information retrieval fr...
Apoptosis, also called programmed cell death, refers to the spontaneous and orderly death of cells controlled by genes in order to maintain a stable internal environment. Identifying the subcellular location o...
GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used t...
Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary str...
Visualization of multiple sequence alignments often includes colored symbols, usually characters encoding amino acids, according to some (physical) properties, such as hydrophobicity or charge. Typically, colo...
Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification,...
Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite...
With the explosion in the number of methods designed to analyze bulk and single-cell RNA-seq data, there is a growing need for approaches that assess and compare these methods. The usual technique is to compar...
Power analysis becomes an inevitable step in experimental design of current biomedical research. Complex designs allowing diverse correlation structures are commonly used in RNA-Seq experiments. However, the f...
Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not be...
Compared to the many uses of DNA-level testing in clinical oncology, development of RNA-based diagnostics has been more limited. An exception to this trend is the growing use of mRNA-based methods in early-sta...
The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purp...
Finding combinations of homotypic or heterotypic genomic sites obeying a specific grammar in DNA sequences is a frequent task in bioinformatics. A typical case corresponds to the identification of cis-regulato...
The necessity to analyze medium-throughput data in epidemiological studies with small sample size, particularly when studying biomedical data may hinder the use of classical statistical methods. Support vector...
The Correction to this article has been published in BMC Bioinformatics 2020 21:371
Single cell RNA sequencing (scRNAseq) has provided invaluable insights into cellular heterogeneity and functional states in health and disease. During the analysis of scRNAseq data, annotating the biological i...
Most organisms cannot be cultivated, as they live in unique ecological conditions that cannot be mimicked in the lab. Understanding the functionality of those organisms’ genes and their interactions by perform...
In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we pres...
Cardiotoxicity, characterized by severe cardiac dysfunction, is a major problem in patients treated with different classes of anticancer drugs. Development of predictable human-based models and assays for drug...
Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. Howe...
Microorganisms are important occupants of many different environments. Identifying the composition of microbes and estimating their abundance promote understanding of interactions of microbes in environmental ...
With the rapid development of single-cell genomics, technologies for parallel sequencing of the transcriptome and genome in each single cell is being explored in several labs and is becoming available. This br...
Even though R is one of the most commonly used statistical computing environments, it lacks a graphical user interface (GUI) that appeals to students, researchers, lecturers, and practitioners in medicine and ...
In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determin...
Recently, DNA methylation has drawn great attention due to its strong correlation with abnormal gene activities and informative representation of the cancer status. As a number of studies focus on DNA methylat...
In recent years, increasing evidences have indicated that long non-coding RNAs (lncRNAs) are deeply involved in a wide range of human biological pathways. The mutations and disorders of lncRNAs are closely ass...
Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution....
Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of di...
In the current supplement, we are proud to present seventeen relevant contributions from the 6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2018), which was held during ...
This article is part of a Supplement: Volume 21 Supplement 7
Cervical cancer is the fourth most common tumor in women worldwide, mostly resulting from high-risk human papillomavirus (HR-HPV) with persistent infection.
This article is part of a Supplement: Volume 21 Supplement 7
As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-di...
Genome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells,...
Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior ge...
In the last decade, a large number of common variants underlying complex diseases have been identified through genome-wide association studies (GWASs). Summary data of the GWASs are freely and publicly availab...
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