Page 9 of 247
In the field of neuroscience, neural modules and circuits that control biological functions have been found throughout entire neural networks. Correlations in neural activity can be used to identify such neura...
The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as...
This article is part of a Supplement: Volume 23 Supplement 6
Tree-structured neural networks have shown promise in extracting lexical representations of sentence syntactic structures, particularly in the detection of event triggers using recursive neural networks.
Bioinformatics capability to analyze spatio–temporal dynamics of gene expression is essential in understanding animal development. Animal cells are spatially organized as functional tissues where cellular gene...
Hennekam Lymphangiectasia–Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectas...
Metabolomics is a dynamic tool for elucidating biochemical changes in human health and disease. Metabolic profiles provide a close insight into physiological states and are highly volatile to genetic and envir...
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being des...
This article is part of a Supplement: Volume 23 Supplement 11
Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representatio...
Reaction networks are widely used as mechanistic models in systems biology to reveal principles of biological systems. Reactions are governed by kinetic laws that describe reaction rates. Selecting the appropr...
Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used t...
Computational models of cell signaling networks are extremely useful tools for the exploration of underlying system behavior and prediction of response to various perturbations. By representing signaling casca...
GPR151 is a kind of protein belonging to G protein-coupled receptor family that is closely associated with a variety of physiological and pathological processes.The potential use of GPR151 as a therapeutic tar...
High throughput experiments in cancer and other areas of genomic research identify large numbers of sequence variants that need to be evaluated for phenotypic impact. While many tools exist to score the likely...
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecti...
Although the development of sequencing technologies has provided a large number of protein sequences, the analysis of functions that each one plays is still difficult due to the efforts of laboratorial methods...
RNA sequencing (RNA-Seq) is a technique that utilises the capabilities of next-generation sequencing to study a cellular transcriptome i.e., to determine the amount of RNA at a given time for a given biologica...
Protein-DNA binding sites of ChIP-seq experiments are identified where the binding affinity is significant based on a given threshold. The choice of the threshold is a trade-off between conservative region ide...
The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approach...
Lung squamous cell carcinoma (LUSC) is associated with a worse prognosis than other histological subtypes of non-small cell lung cancer. Due to the vital role of CD8+ T cells in anti-tumor immunity, the character...
Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, ...
Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. Th...
Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the...
Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and und...
Three-dimensional structures of protein–ligand complexes provide valuable insights into their interactions and are crucial for molecular biological studies and drug design. However, their high-dimensional and ...
Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories arou...
When it was first introduced in 2000, reverse vaccinology was defined as an in silico approach that begins with the pathogen's genomic sequence. It concludes with a list of potential proteins with a possible, ...
In tissues and organisms, the coordination of neighboring cells is essential to maintain their properties and functions. Therefore, knowing which cells are adjacent is crucial to understand biological processe...
Clinical studies have shown that miRNAs are closely related to human health. The study of potential associations between miRNAs and diseases will contribute to a profound understanding of the mechanism of dise...
Mathematical models of haematopoiesis can provide insights on abnormal cell expansions (clonal dominance), and in turn can guide safety monitoring in gene therapy clinical applications. Clonal tracking is a re...
Entity normalization is an important information extraction task which has recently gained attention, particularly in the clinical/biomedical and life science domains. On several datasets, state-of-the-art met...
This article is part of a Supplement: Volume 23 Supplement 9
The original article was published in BMC Bioinformatics 2023 24:39
Comutation plot is a widely used visualization method to deliver a global view of the mutation landscape of large-scale genomic studies. Current tools for creating comutation plot are either offline packages t...
N6-methyladenosine (m6A) modification is involved in tumorigenesis and progression as well as closely correlated with stem cell differentiation and pluripotency. Moreover, tumor progression includes the acquis...
As a common chronic disease, diabetes is called the “second killer” among modern diseases. Currently, there is no medical cure for diabetes. We can only rely on medication for auxiliary treatment. However, man...
This article is part of a Supplement: Volume 23 Supplement 3
The original article was published in BMC Bioinformatics 2023 24:43
This article is part of a Supplement: Volume 23 Supplement 3
The original article was published in BMC Bioinformatics 2023 24:40
This study aimed to observe the potential impact of known cuproptosis-related genes (CRGs) on triple negative breast cancer (TNBC) development, as well as their associated molecular mechanisms, immune infiltra...
To explore dermatomyositis signature genes as potential biomarkers of hepatocellular carcinoma and their associated molecular regulatory mechanisms.
As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing th...
Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-re...
CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications. Indel analysis has thus become on...
Viral genomics and epidemiology have been increasingly important tools for analysing the spread of key pathogens affecting daily lives of individuals worldwide. With the rapidly expanding scale of pathogen gen...
Single-cell RNA sequencing (scRNA-seq) strives to capture cellular diversity with higher resolution than bulk RNA sequencing. Clustering analysis is critical to transcriptome research as it allows for further ...
Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and pro...
There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these to...
A variety of high-throughput analyses, such as transcriptome, proteome, and metabolome analysis, have been developed, producing unprecedented amounts of omics data. These studies generate large gene lists, of ...
Structural variations (SVs) refer to variations in an organism’s chromosome structure that exceed a length of 50 base pairs. They play a significant role in genetic diseases and evolutionary mechanisms. While ...
Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/l...
This article is part of a Supplement: Volume 24 Supplement 1
Tremendous amounts of omics data accumulated have made it possible to identify cancer driver pathways through computational methods, which is believed to be able to offer critical information in such downstrea...
The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One im...
View featured videos from across the BMC-series journals
2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)
2023 Speed
19 days submission to first editorial decision for all manuscripts (Median)
146 days submission to accept (Median)
2023 Usage
5,987,678 downloads
4,858 Altmetric mentions