Page 7 of 249
Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estima...
Deep generative models naturally become nonlinear dimension reduction tools to visualize large-scale datasets such as single-cell RNA sequencing datasets for revealing latent grouping patterns or identifying o...
Liquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature...
Antibody-mediated immune responses play a crucial role in the immune defense of human body. The evolution of bioengineering has led the progress of antibody-derived drugs, showing promising efficacy in cancer ...
As an irreversible post-translational modification, protein carbonylation is closely related to many diseases and aging. Protein carbonylation prediction for related patients is significant, which can help cli...
Diabetes is a metabolic disorder usually caused by insufficient secretion of insulin from the pancreas or insensitivity of cells to insulin, resulting in long-term elevated blood sugar levels in patients. Pati...
Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments....
Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by ...
Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical As...
Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resour...
The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics o...
Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial ...
In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a ...
Complex biological systems are described as a multitude of cell–cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand–receptor (L–R) gene co-expression but the analy...
The performance of machine learning classification methods relies heavily on the choice of features. In many domains, feature generation can be labor-intensive and require domain knowledge, and feature selecti...
The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentrat...
Categorizing cells into distinct types can shed light on biological tissue functions and interactions, and uncover specific mechanisms under pathological conditions. Since gene expression throughout a populati...
Network graphs allow modelling the real world objects in terms of interactions. In a multilayer network, the interactions are distributed over layers (i.e., intralayer and interlayer edges). Network alignment ...
Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack ...
Enhancers play a crucial role in gene regulation, and some active enhancers produce noncoding RNAs known as enhancer RNAs (eRNAs) bi-directionally. The most commonly used method for detecting eRNAs is CAGE-seq...
During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipit...
The PubMed archive contains more than 34 million articles; consequently, it is becoming increasingly difficult for a biomedical researcher to keep up-to-date with different knowledge domains. Computationally e...
Identifying variants associated with complex traits is a challenging task in genetic association studies due to linkage disequilibrium (LD) between genetic variants and population stratification, unrelated to ...
LncRNA–protein interactions are ubiquitous in organisms and play a crucial role in a variety of biological processes and complex diseases. Many computational methods have been reported for lncRNA–protein inter...
A Raman spectroscopy method can quickly and accurately measure the concentration of ofloxacin in solution. This method has the advantages of accuracy and rapidity over traditional detection methods. However, t...
Gene-wise differential expression is usually the first major step in the statistical analysis of high-throughput data obtained from techniques such as microarrays or RNA-sequencing. The analysis at gene level ...
Dimension reduction, especially feature selection, is an important step in improving classification performance for high-dimensional data. Particularly in cancer research, when reducing the number of features,...
The commercial adoption of BCI technologies for both clinical and non-clinical applications is drawing scientists to the creation of wearable devices for daily living. Emotions are essential to human existence...
Extracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of canc...
Chromatographic peakpicking continues to represent a significant bottleneck in automated LC–MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require research...
Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, needing to have t...
High-throughput experiments provide deep insight into the molecular biology of different species, but more tools need to be developed to handle this type of data. At the transcriptomics level, quantitative Pol...
Recent advancements in computing power and state-of-the-art algorithms have helped in more accessible and accurate diagnosis of numerous diseases. In addition, the development of de novo areas in imaging scien...
Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, ...
We consider two key problems in genomics involving multiple traits: multi-trait genome wide association studies (GWAS), where the goal is to detect genetic variants associated with the traits; and multi-trait ...
In this paper, we are interested in interactions between a high-dimensional -omics dataset and clinical covariates. The goal is to evaluate the relationship between a phenotype of interest and a high-dimension...
N6, 2'-O-dimethyladenosine (m6Am) is an abundant RNA methylation modification on vertebrate mRNAs and is present in the transcription initiation region of mRNAs. It has recently been experimentally shown to be as...
Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. For a given sequence, we usually use smaller subsequences (anchors) to find possible candi...
Transcription factors (TF) play a crucial role in the regulation of gene transcription; alterations of their activity and binding to DNA areas are strongly involved in cancer and other disease onset and develo...
The original article was published in BMC Bioinformatics 2023 24:318
An important problem in toxicology in the context of gene expression data is the simultaneous inference of a large number of concentration–response relationships. The quality of the inference substantially dep...
Feature selection is important in high dimensional data analysis. The wrapper approach is one of the ways to perform feature selection, but it is computationally intensive as it builds and evaluates models of ...
The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obta...
This Supplement issue, presents five research articles which are distributed, mainly due to the subject they address, from the 8th International Work-Conference on Bioinformatics and Biomedical Engineering (IW...
This article is part of a Supplement: Volume 24 Supplement 2
Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experienc...
Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational too...
Image segmentation pipelines are commonly used in microscopy to identify cellular compartments like nucleus and cytoplasm, but there are few standards for comparing segmentation accuracy across pipelines. The ...
Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential to...
Melanoma is one of the deadliest tumors in the world. Early detection is critical for first-line therapy in this tumor pathology and it remains challenging due to the need for histological analysis to ensure c...
Spatial genetic variation is shaped in part by an organism’s dispersal ability. We present a deep learning tool, disperseNN2, for estimating the mean per-generation dispersal distance from georeferenced polymorph...
View featured videos from across the BMC-series journals
Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
Speed 2023
Submission to first editorial decision (median days): 12
Submission to acceptance (median days): 146
Usage 2023
Downloads: 5,987,678
Altmetric mentions: 4,858