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Accurate identification of protein complexes in protein-protein interaction (PPI) networks is crucial for understanding the principles of cellular organization. Most computational methods ignore the fact that ...
Identifying splice site regions is an important step in the genomic DNA sequencing pipelines of biomedical and pharmaceutical research. Within this research purview, efficient and accurate splice site detectio...
In the last few years, multi-omics data, that is, datasets containing different types of high-dimensional molecular variables for the same samples, have become increasingly available. To date, several comparis...
Biological age (BA) has been recognized as a more accurate indicator of aging than chronological age (CA). However, the current limitations include: insufficient attention to the incompleteness of medical data...
We used a hybrid machine learning systems (HMLS) strategy that includes the extensive search for the discovery of the most optimal HMLSs, including feature selection algorithms, a feature extraction algorithm,...
Sequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight into genetic determinants of diseases. Protecting the genetic pr...
Artificial intelligence (AI) and machine learning (ML) have resulted in significant enthusiasm for their promise in healthcare. Despite this, prospective randomized controlled trials and successful clinical im...
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...
Oxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover pro...
Identifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein complexes, none of which exceeds 10 in size play an irreplaceable role in life ...
Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did...
Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome sign...
In Alzheimer’s Diseases (AD) research, multimodal imaging analysis can unveil complementary information from multiple imaging modalities and further our understanding of the disease. One application is to disc...
Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variat...
Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate disc...
Twitter is a popular social networking site where short messages or “tweets” of users have been used extensively for research purposes. However, not much research has been done in mining the medical profession...
Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome,...
Brain volume has been widely studied in the neuroimaging field, since it is an important and heritable trait associated with brain development, aging and various neurological and psychiatric disorders. Genome-...
Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to dat...
The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcri...
Making clear what kinds of metabolic pathways a drug compound involves in can help researchers understand how the drug is absorbed, distributed, metabolized, and excreted. The characteristics of a compound suc...
Pathway-based analysis of transcriptomic data has shown greater stability and better performance than traditional gene-based analysis. Until now, some pathway-based deep learning models have been developed for...
Microarrays can perform large scale studies of differential expressed gene (DEGs) and even single nucleotide polymorphisms (SNPs), thereby screening thousands of genes for single experiment simultaneously. How...
Recent research has already shown that circular RNAs (circRNAs) are functional in gene expression regulation and potentially related to diseases. Due to their stability, circRNAs can also be used as biomarkers...
In this paper we introduce a new representation for the multistationarity region of a reaction network, using polynomial superlevel sets. The advantages of using this polynomial superlevel set representation o...
Collagen VI family (COL6A) is a major member of extracellular matrix protein. There is accumulating evidence that COL6A is involved in tumorigenesis and tumor progression. In this study, we performed a systema...
Deep learning’s automatic feature extraction has proven to give superior performance in many sequence classification tasks. However, deep learning models generally require a massive amount of data to train, wh...
In RNA-sequencing studies a large number of hypothesis tests are performed to compare the differential expression of genes between several conditions. Filtering has been proposed to remove candidate genes with...
The recent global focus on big data in medicine has been associated with the rise of artificial intelligence (AI) in diagnosis and decision-making following recent advances in computer technology. Up to now, A...
Public Data Commons (PDC) have been highlighted in the scientific literature for their capacity to collect and harmonize big data. On the other hand, local data commons (LDC), located within an institution or ...
Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge in computational biology. Current...
The placental barrier protects the fetus from exposure to some toxicants and is vital for drug development and risk assessment of environmental chemicals. However, in vivo experiments for assessing the placent...
The technologies advances of single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) allowed to generate thousands of single cells in a relatively easy and economic manner and it i...
Many novel long noncoding RNAs have been discovered in recent years due to advances in high-throughput sequencing experiments. Finding orthologues of these novel lncRNAs might facilitate clarification of their...
DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole gen...
Breast cancer is currently one of the cancers with a higher mortality rate in the world. The biological research on anti-breast cancer drugs focuses on the activity of estrogen receptors alpha (ER
Biclustering algorithm is an effective tool for processing gene expression datasets. There are two kinds of data matrices, binary data and non-binary data, which are processed by biclustering method. A binary ...
Microbial communities are widely studied using high-throughput sequencing techniques, such as 16S rRNA gene sequencing. These techniques have attracted biologists as they offer powerful tools to explore microb...
Metabolomic time course analyses of biofluids are highly relevant for clinical diagnostics. However, many sampling methods suffer from unknown sample sizes, commonly known as size effects. This prevents absolu...
The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative ...
Transcription factors (TFs) play central roles in maintaining “stemness” of embryonic stem (ES) cells and their differentiation into several hundreds of adult cell types. The regulatory competence of TFs is ro...
Long interspersed element 1 (LINE-1 or L1) retrotransposons are mobile elements that constitute 17–20% of the human genome. Strong correlations between abnormal L1 expression and several human diseases have be...
The L1000 technology, a cost-effective high-throughput transcriptomics technology, has been applied to profile a collection of human cell lines for their gene expression response to > 30,000 chemical and genet...
Chimeric antigen receptor T-cell (CAR-T) therapy is a new and efficient cellular immunotherapy. The therapy shows significant efficacy, but also has serious side effects, collectively known as cytokine release...
The main focus of in silico drug repurposing, which is a promising area for using artificial intelligence in drug discovery, is the prediction of drug–disease relationships. Although many computational models ...
Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine Cp...
Development of new methods for analysis of protein–protein interactions (PPIs) at molecular and nanometer scales gives insights into intracellular signaling pathways and will improve understanding of protein f...
Though proposing algorithmic approaches for protein domain decomposition has been of high interest, the inherent ambiguity to the problem makes it still an active area of research. Besides, accurate automated ...
Protein ligand docking is an indispensable tool for computational prediction of protein functions and screening drug candidates. Despite significant progress over the past two decades, it is still a challengin...
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