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Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments an...
For many practical hypothesis testing (H-T) applications, the data are correlated and/or with heterogeneous variance structure. The regression t-test for weighted linear mixed-effects regression (LMER) is a legit...
Neural network based embedding models are receiving significant attention in the field of natural language processing due to their capability to effectively capture semantic information representing words, sen...
Monotonically expressed genes (MEGs) are genes whose expression values increase or decrease monotonically as a disease advances or time proceeds. Non-small cell lung cancer (NSCLC) is a multistage progression ...
Understanding the cellular architecture is a fundamental problem in various biological studies. C. elegans is widely used as a model organism in these studies because of its unique fate determinations. In recent ...
Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It...
Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods f...
Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. ...
Feature selection, as a preprocessing stage, is a challenging problem in various sciences such as biology, engineering, computer science, and other fields. For this purpose, some studies have introduced tools ...
The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cr...
Genome-wide prediction has become the method of choice in animal and plant breeding. Prediction of breeding values and phenotypes are routinely performed using large genomic data sets with number of markers on...
The design of an experiment influences both what a researcher can measure, as well as how much confidence can be placed in the results. As such, it is vitally important that experimental design decisions do no...
Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-paren...
For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential ...
High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolut...
Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells. Analyzing these data, including making comparisons with existing data, remai...
The ab initio approaches to protein structure prediction usually employ the Monte Carlo technique to search the structural conformation that has the lowest energy. However, the widely-used energy functions are us...
This article is part of a Supplement: Volume 20 Supplement 3
In the field of drug repositioning, it is assumed that similar drugs may treat similar diseases, therefore many existing computational methods need to compute the similarities of drugs and diseases. However, t...
This article is part of a Supplement: Volume 20 Supplement 3
The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. The splicing structure of a sequen...
This article is part of a Supplement: Volume 20 Supplement 3
Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal...
This article is part of a Supplement: Volume 20 Supplement 3
Detecting protein complex in protein-protein interaction (PPI) networks plays a significant part in bioinformatics field. It enables us to obtain the better understanding for the structures and characteristics...
This article is part of a Supplement: Volume 20 Supplement 3
Recently, next-generation sequencing techniques have been applied for the detection of RNA secondary structures, which is referred to as high-throughput RNA structural (HTS) analyses, and many different protoc...
This article is part of a Supplement: Volume 20 Supplement 3
Different types of viruses have different envelope proteins, and may have their shared or distinctive host-virus interactions which result in various post-infection effects in humans and animals. These effects...
This article is part of a Supplement: Volume 20 Supplement 3
RNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an ...
This article is part of a Supplement: Volume 20 Supplement 3
Super-enhancers or stretch enhancers are clusters of active enhancers that often coordinate cell-type specific gene regulation during development and differentiation. In addition, the enrichment of disease-ass...
This article is part of a Supplement: Volume 20 Supplement 3
Mapping expression quantitative trait loci (eQTLs) has provided insight into gene regulation. Compared to cis-eQTLs, the regulatory mechanisms of trans-eQTLs are less known. Previous studies suggest that trans...
This article is part of a Supplement: Volume 20 Supplement 3
Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data access...
Fast and accurate automatic segmentation of skeletal muscle cell image is crucial for the diagnosis of muscle related diseases, which extremely reduces the labor-intensive manual annotation. Recently, several ...
Eukaryotic gene regulation is a complex process comprising the dynamic interaction of enhancers and promoters in order to activate gene expression. In recent years, research in regulatory genomics has contribu...
Although there is an enormous number of textual resources in the biomedical domain, currently, manually curated resources cover only a small part of the existing knowledge. The vast majority of these informati...
Biological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional s...
RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such ...
Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well...
Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary ...
Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may r...
Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in ...
Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have be...
Replicability analysis which aims to detect replicated signals attracts more and more attentions in modern scientific applications. For example, in genome-wide association studies (GWAS), it would be of convin...
Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one pla...
Using meta-analysis, high-dimensional transcriptome expression data from public repositories can be merged to make group comparisons that have not been considered in the original studies. Merging of high-dimen...
microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanis...
The segmentation of a 3D image is a task that can hardly be automatized in certain situations, notably when the contrast is low and/or the distance between elements is small. The existing supervised methods re...
Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of...
Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of t...
This article is part of a Supplement: Volume 20 Supplement 2
One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing F...
This article is part of a Supplement: Volume 20 Supplement 2
The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact predictio...
This article is part of a Supplement: Volume 20 Supplement 2
Barrett’s esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor f...
This article is part of a Supplement: Volume 20 Supplement 2
Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP),...
This article is part of a Supplement: Volume 20 Supplement 2
This article is part of a Supplement: Volume 20 Supplement 2
Dermoscopy is one of the common and effective imaging techniques in diagnosis of skin cancer, especially for pigmented lesions. Accurate skin lesion border detection is the key to extract important dermoscopic...
This article is part of a Supplement: Volume 20 Supplement 2
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