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More and more Cas9 variants with higher specificity are developed to avoid the off-target effect, which brings a significant volume of experimental data. Conventional machine learning performs poorly on these ...
Copy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia. Conse...
The arterial aneurysm refers to localized dilation of blood vessel wall and is common in general population. The majority of aneurysm cases remains asymptomatic until a sudden rupture which is usually fatal an...
Important objectives in cancer research are the prediction of a patient’s risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In ...
The Correction to this article has been published in BMC Bioinformatics 2022 23:32
The original article was published in BMC Bioinformatics 2021 22:387
Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expressio...
The original article was published in BMC Bioinformatics 2021 22:447
Single-cell sequencing technology can address the amount of single-cell library data at the same time and display the heterogeneity of different cells. However, analyzing single-cell data is a computationally ...
Software for nuclear magnetic resonance (NMR) spectrometers offer general functionality of instrument control and data processing; these applications are often developed with non-scripting languages. NMR users...
Autophagy is closely related to the progression of breast cancer. The aim at this study is to establish a prognostic-related model comprised of hub autophagy genes (AGs) to assess patient prognosis. Simultaneo...
The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms a...
Existing computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells,...
Structural variations (SVs) occupy a prominent position in human genetic diversity, and deletions form an important type of SV that has been suggested to be associated with genetic diseases. Although various d...
Single cell profiling has been proven to be a powerful tool in molecular biology to understand the complex behaviours of heterogeneous system. The definition of the properties of single cells is the primary en...
Deep learning is an active bioinformatics artificial intelligence field that is useful in solving many biological problems, including predicting altered epigenetics such as DNA methylation regions. Deep learni...
Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distribution...
With the rapid development of various advanced biotechnologies, researchers in related fields have realized that microRNAs (miRNAs) play critical roles in many serious human diseases. However, experimental ide...
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying...
In-depth analysis of regulation networks of genes aberrantly expressed in cancer is essential for better understanding tumors and identifying key genes that could be therapeutically targeted.
To select the most complete, continuous, and accurate assembly for an organism of interest, comprehensive quality assessment of assemblies is necessary. We present a novel tool, called Evaluation of De Novo As...
Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most euk...
The Correction to this article has been published in BMC Bioinformatics 2021 22:612
Long noncoding RNAs (lncRNAs) have dense linkages with a plethora of important cellular activities. lncRNAs exert functions by linking with corresponding RNA-binding proteins. Since experimental techniques to ...
Experimental verification of a drug discovery process is expensive and time-consuming. Therefore, recently, the demand to more efficiently and effectively identify drug–target interactions (DTIs) has intensified.
BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based o...
Literature-based gene ontology (GO) annotation is a process where expert curators use uniform expressions to describe gene functions reported in research papers, creating computable representations of informat...
For differential abundance analysis, zero-inflated generalized linear models, typically zero-inflated NB models, have been increasingly used to model microbiome and other sequencing count data. A common assump...
Liver cancer (Hepatocellular carcinoma; HCC) prevalence is increasing and with poor clinical outcome expected it means greater understanding of HCC aetiology is urgently required. This study explored a deep le...
The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair.
Ab initio prediction of splice sites is an essential step in eukaryotic genome annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene structures from model organisms. However, ...
Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis.
When analyzing DNA sequence data of an individual, knowing which nucleotide was inherited from each parent can be beneficial when trying to identify certain types of DNA variants. Mendelian inheritance logic c...
The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or ot...
The research landscape of single-cell and single-nuclei RNA-sequencing is evolving rapidly. In particular, the area for the detection of rare cells was highly facilitated by this technology. However, an automa...
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, sc...
Wet-lab experiments for identification of interactions between drugs and target proteins are time-consuming, costly and labor-intensive. The use of computational prediction of drug–target interactions (DTIs), ...
Protein-RNA interactions play key roles in many processes regulating gene expression. To understand the underlying binding preference, ultraviolet cross-linking and immunoprecipitation (CLIP)-based methods hav...
Wearable devices enable monitoring and measurement of physiological parameters over a 24-h period, and some of which exhibit circadian rhythm characteristics. However, the currently available R package cosinor co...
The Correction to this article has been published in BMC Bioinformatics 2022 23:186
With the rapid development of long-read sequencing technologies, it is possible to reveal the full spectrum of genetic structural variation (SV). However, the expensive cost, finite read length and high sequen...
The existing studies show that circRNAs can be used as a biomarker of diseases and play a prominent role in the treatment and diagnosis of diseases. However, the relationships between the vast majority of circ...
The aim of the present paper is to construct an emulator of a complex biological system simulator using a machine learning approach. More specifically, the simulator is a patient-specific model that integrates...
This article is part of a Supplement: Volume 22 Supplement 14
Ancestry estimation of skulls is under a wide range of applications in forensic science, anthropology, and facial reconstruction. This study aims to avoid defects in traditional skull ancestry estimation metho...
Antimicrobial peptides are promising tools to fight against ever-growing antibiotic resistance. However, despite many advantages, their toxicity to mammalian cells is a critical obstacle in clinical applicatio...
Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Sco...
Elementary flux mode (EFM) analysis is a well-established, yet computationally challenging approach to characterize metabolic networks. Standard algorithms require huge amounts of memory and lack scalability w...
Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. ...
Amyloids are insoluble fibrillar aggregates that are highly associated with complex human diseases, such as Alzheimer’s disease, Parkinson’s disease, and type II diabetes. Recently, many studies reported that ...
Dengue epidemics is affected by vector-human interactive dynamics. Infectious disease prevention and control emphasize the timing intervention at the right diffusion phase. In such a way, control measures can ...
This article is part of a Supplement: Volume 22 Supplement 5
Atrial fibrillation is a paroxysmal heart disease without any obvious symptoms for most people during the onset. The electrocardiogram (ECG) at the time other than the onset of this disease is not significantl...
This article is part of a Supplement: Volume 22 Supplement 5
Heart sound measurement is crucial for analyzing and diagnosing patients with heart diseases. This study employed phonocardiogram signals as the input signal for heart disease analysis due to the accessibility...
This article is part of a Supplement: Volume 22 Supplement 5
Doctors can detect symptoms of diabetic retinopathy (DR) early by using retinal ophthalmoscopy, and they can improve diagnostic efficiency with the assistance of deep learning to select treatments and support ...
This article is part of a Supplement: Volume 22 Supplement 5
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