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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...
With the significant reduction in the cost of high-throughput sequencing technology, genomic selection technology has been rapidly developed in the field of plant breeding. Although numerous genomic selection ...
In cancer genomic medicine, finding driver mutations involved in cancer development and tumor growth is crucial. Machine-learning methods to predict driver missense mutations have been developed because varian...
An abnormal growth or fatty mass of cells in the brain is called a tumor. They can be either healthy (normal) or become cancerous, depending on the structure of their cells. This can result in increased pressu...
Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to...
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-t...
Autism spectrum disorder(ASD) is a disease associated with the neurodevelopment of the brain. The autism spectrum can be observed in early childhood, where the symptoms of the disease usually appear in childre...
Accurately predicting the binding affinity between proteins and ligands is crucial for drug discovery. Recent advances in graph neural networks (GNNs) have made significant progress in learning representations...
Despite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic du...
Protein methylation, a post-translational modification, is crucial in regulating various cellular functions. Arginine methylation is required to understand crucial biochemical activities and biological functio...
Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are costly and time consuming. Effective computational methods to predict DTIs are...
Drug repurposing is an approach that holds promise for identifying new therapeutic uses for existing drugs. Recently, knowledge graphs have emerged as significant tools for addressing the challenges of drug re...
The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the comp...
The rising risk of diabetes, particularly in emerging countries, highlights the importance of early detection. Manual prediction can be a challenging task, leading to the need for automatic approaches. The maj...
Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases,...
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