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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,...
Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequenci...
A large number of researchers have devoted to accelerating the speed of genome sequencing and reducing the cost of genome sequencing for decades, and they have made great strides in both areas, making it easie...
Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between heal...
Obtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins...
We consider the problem of finding an accurate representation of neuron shapes, extracting sub-cellular features, and classifying neurons based on neuron shapes. In neuroscience research, the skeleton represen...
Echocardiographic interpretation during the prenatal or postnatal period is important for diagnosing cardiac septal abnormalities. However, manual interpretation can be time consuming and subject to human erro...
In this paper, a fuzzy hierarchical optimization framework is proposed for identifying potential antiviral targets for treating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the hea...
Autism spectrum disorder (ASD) is a serious developmental disorder of the brain. Recently, various deep learning methods based on functional magnetic resonance imaging (fMRI) data have been developed for the c...
The central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation. Understanding gene regulatory relationships is crucial for unravelling t...
Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations betwee...
In cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or place one gene under the control of the promoter of another gene. Thes...
Helicobacter pylori is a prominent causative agent of gastric ulceration, gastric adenocarcinoma and gastric lymphoma and have been categorised as a group 1 carcinogen by WHO. The treatment of H. pylori with prot...
Plant vacuoles are essential organelles in the growth and development of plants, and accurate identification of their proteins is crucial for understanding their biological properties. In this study, we develo...
Tyrosinase is an enzyme involved in melanin production in the skin. Several hyperpigmentation disorders involve the overproduction of melanin and instability of tyrosinase activity resulting in darker, discolo...
Genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with kidney function. By combining these findings with post-GWAS information (e.g., statistical fine-mapping to identi...
Plummeting DNA sequencing cost in recent years has enabled genome sequencing projects to scale up by several orders of magnitude, which is transforming genomics into a highly data-intensive field of research. ...
Breast cancer is a significant health issue for women, and human epidermal growth factor receptor-2 (HER2) plays a crucial role as a vital prognostic and predictive factor. The HER2 status is essential for for...
We published a paper in BMC Bioinformatics comprehensively evaluating the performance of structural variation (SV) calling with long-read SV detection methods based on simulated error-prone long-read data unde...
The original article was published in BMC Bioinformatics 2023 24:350
Cross-linking mass spectrometry (XL-MS) is a powerful technique for detecting protein–protein interactions (PPIs) and modeling protein structures in a high-throughput manner. In XL-MS experiments, proteins are...
A recent paper by Jiang et al. in BMC Bioinformatics presented guidelines on long-read sequencing settings for structural variation (SV) calling, and benchmarked the performance of various SV calling tools, inclu...
The Matters Arising to this article has been published in BMC Bioinformatics 2023 24:352
Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from s...
Plant secondary metabolites are highly valued for their applications in pharmaceuticals, nutrition, flavors, and aesthetics. It is of great importance to elucidate plant secondary metabolic pathways due to the...
The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous comp...
Body composition (BC) is an important factor in determining the risk of type 2-diabetes and cardiovascular disease. Computed tomography (CT) is a useful imaging technique for studying BC, however manual segmen...
Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techn...
Understanding the Mechanism of Action (MoA) of a compound is an often challenging but equally crucial aspect of drug discovery that can help improve both its efficacy and safety. Computational methods to aid M...
Genome-wide association studies (GWASes) aim to identify single nucleotide polymorphisms (SNPs) associated with a given phenotype. A common approach for the analysis of GWAS is single marker analysis (SMA) bas...
Partitioning around medoids (PAM) is one of the most widely used and successful clustering method in many fields. One of its key advantages is that it only requires a distance or a dissimilarity between the i...
Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host cell, the mitochondria contain a sepa...
Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generat...
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