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The original article was published in BMC Bioinformatics 2022 23:426
Over the last few years, dozens of healthcare surveys have shown a shortage of doctors and an alarming doctor-population ratio. With the motivation of assisting doctors and utilizing their time efficiently, au...
In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The gen...
Autism spectrum disorder (ASD) is the most prevalent disease today. The causes of its infection may be attributed to genetic causes by 80% and environmental causes by 20%. In spite of this, the majority of the...
As a highly aggressive disease, cancer has been becoming the leading death cause around the world. Accurate prediction of the survival expectancy for cancer patients is significant, which can help clinicians m...
Medication recommendation based on electronic medical record (EMR) is a research hot spot in smart healthcare. For developing computational medication recommendation methods based on EMR, an important challeng...
The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.1.617.2 or Omicron variant B.1.1.529). Proportions of these variants circula...
Flux balance analysis (FBA) is an optimization based approach to find the optimal steady state of a metabolic network, commonly of microorganisms such as yeast strains and Escherichia coli. However, the resulting...
Extracting knowledge from heterogeneous data sources is fundamental for the construction of structured biomedical knowledge graphs (BKGs), where entities and relations are represented as nodes and edges in the...
Today’s biomedical imaging technology has been able to present the morphological structure or functional metabolic information of organisms at different scale levels, such as organ, tissue, cell, molecule and ...
As of June 2022, the GISAID database contains more than 11 million SARS-CoV-2 genomes, including several thousand nucleotide sequences for the most common variants such as delta or omicron. These SARS-CoV-2 st...
The human protein atlas (HPA) is an online database containing large sets of protein expression data in normal and cancerous tissues in image form from immunohistochemically (IHC) stained tissue microarrays. I...
Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplic...
The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAS...
Compound–protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many deep learning-based methods have been proposed for predications related ...
During atherosclerosis, the narrowing of the arterial lumen is observed through the accumulation of bio compounds and the formation of plaque within artery walls. A non-linear optical imaging modality (NLOM), ...
Brain tumor segmentation plays a significant role in clinical treatment and surgical planning. Recently, several deep convolutional networks have been proposed for brain tumor segmentation and have achieved im...
This article is part of a Supplement: Volume 22 Supplement 5
Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics ana...
Differential abundance testing is an important aspect of microbiome data analysis, where each taxa is fitted with a statistical test or a regression model. However, many models do not provide a good fit to rea...
With the rapid accumulation of scRNA-seq data, more and more automatic cell type identification methods have been developed, especially those based on deep learning. Although these methods have reached relativ...
Investigating molecular heterogeneity provides insights into tumour origin and metabolomics. The increasing amount of data gathered makes manual analyses infeasible—therefore, automated unsupervised learning a...
Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databas...
Today it is possible to profile the transcriptome of individual cells, and a key step in the analysis of these datasets is unsupervised clustering. For very large datasets, efficient algorithms are required to...
Automatic functional annotation of proteins is an open research problem in bioinformatics. The growing number of protein entries in public databases, for example in UniProtKB, poses challenges in manual functi...
This article is part of a Supplement: Volume 23 Supplement 2
The widespread usage of Cap Analysis of Gene Expression (CAGE) has led to numerous breakthroughs in understanding the transcription mechanisms. Recent evidence in the literature, however, suggests that CAGE su...
This article is part of a Supplement: Volume 23 Supplement 2
Cis-regulatory regions (CRRs) are non-coding regions of the DNA that fine control the spatio-temporal pattern of transcription; they are involved in a wide range of pivotal processes such as the development of...
This article is part of a Supplement: Volume 23 Supplement 2
Rapidly growing genome-wide ChIP-seq data have provided unprecedented opportunities to explore transcription factor (TF) binding under various cellular conditions. Despite the rich resources, development of an...
The central role of proteins in diseases has made them increasingly attractive as therapeutic targets and indicators of cellular processes. Protein microarrays are emerging as an important means of characteris...
The original article was published in BMC Bioinformatics 2022 23:448
Knowing the responses of a patient to drugs is essential to make personalized medicine practical. Since the current clinical drug response experiments are time-consuming and expensive, utilizing human genomic ...
This article is part of a Supplement: Volume 23 Supplement 8
Modern biomedical research is data-driven and relies heavily on the re-use and sharing of data. Biomedical data, however, is subject to strict data protection requirements. Due to the complexity of the data re...
Researchers have tried to identify and count different blood cells in microscopic smear images by using deep learning methods of artificial intelligence to solve the highly time-consuming problem.
This article is part of a Supplement: Volume 22 Supplement 5
Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have bee...
This article is part of a Supplement: Volume 22 Supplement 10
Localization-based super-resolution microscopy resolves macromolecular structures down to a few nanometers by computationally reconstructing fluorescent emitter coordinates from diffraction-limited spots. The ...
Single-cell RNA-sequencing (scRNA-seq) technologies allow for the study of gene expression in individual cells. Often, it is of interest to understand how transcriptional activity is associated with cell-speci...
The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaff...
Preeclampsia (PE) has an increasing incidence worldwide, and there is no gold standard for prediction. Recent progress has shown that abnormal decidualization and impaired vascular remodeling are essential to ...
Drug–drug interactions (DDIs) are preventable causes of medical injuries and often result in doctor and emergency room visits. Previous research demonstrates the effectiveness of using matrix completion approa...
The correct establishment of the barcode classification system for fish can facilitate biotaxonomists to distinguish fish species, and it can help the government to verify the authenticity of the ingredients o...
This article is part of a Supplement: Volume 22 Supplement 10
Accurate estimate of relatedness is important for genetic data analyses, such as heritability estimation and association mapping based on data collected from genome-wide association studies. Inaccurate related...
The roles of antibody and antigen are indispensable in targeted diagnosis, therapy, and biomedical discovery. On top of that, massive numbers of new scientific articles about antibodies and/or antigens are pub...
Glaucoma can cause irreversible blindness to people’s eyesight. Since there are no symptoms in its early stage, it is particularly important to accurately segment the optic disc (OD) and optic cup (OC) from fu...
A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framew...
Protein–protein interactions are widespread in biological systems and play an important role in cell biology. Since traditional laboratory-based methods have some drawbacks, such as time-consuming, money-consu...
Monoclonal antibodies (mAbs) have been used as therapeutic agents, which must overcome many developability issues after the discovery from in vitro display libraries. Especially, polyreactive mAbs can strongly...
Independent Component Analysis (ICA) allows the dissection of omic datasets into modules that help to interpret global molecular signatures. The inherent randomness of this algorithm can be overcome by cluster...
Self-interacting proteins (SIPs), two or more copies of the protein that can interact with each other expressed by one gene, play a central role in the regulation of most living cells and cellular functions. A...
This article is part of a Supplement: Volume 23 Supplement 7
This research aims to increase our knowledge of amyloidoses. These disorders cause incorrect protein folding, affecting protein functionality (on structure). Fibrillar deposits are the basis of some wellknown ...
Drug repositioning is a very important task that provides critical information for exploring the potential efficacy of drugs. Yet developing computational models that can effectively predict drug–disease assoc...
The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is ...
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