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A variety of high-throughput analyses, such as transcriptome, proteome, and metabolome analysis, have been developed, producing unprecedented amounts of omics data. These studies generate large gene lists, of ...
Structural variations (SVs) refer to variations in an organism’s chromosome structure that exceed a length of 50 base pairs. They play a significant role in genetic diseases and evolutionary mechanisms. While ...
Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/l...
This article is part of a Supplement: Volume 24 Supplement 1
Tremendous amounts of omics data accumulated have made it possible to identify cancer driver pathways through computational methods, which is believed to be able to offer critical information in such downstrea...
The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One im...
Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interacti...
Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of chronic in...
Better understanding the transcriptomic response produced by a compound perturbing its targets can shed light on the underlying biological processes regulated by the compound. However, establishing the relatio...
In the sporadic form of amyotrophic lateral sclerosis (ALS), the pathogenicity of rare variants in the causative genes characterizing the familial form remains largely unknown. To predict the pathogenicity of ...
Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing t...
In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. ...
A major current focus in the analysis of protein–protein interaction (PPI) data is how to identify essential proteins. As massive PPI data are available, this warrants the design of efficient computing methods...
Finding drugs that can interact with a specific target to induce a desired therapeutic outcome is key deliverable in drug discovery for targeted treatment. Therefore, both identifying new drug–target links, as...
Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also...
Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. Whi...
Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superio...
There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transpa...
Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of v...
Atherosclerosis is the common pathological basis for many cardiovascular and cerebrovascular diseases. The purpose of this study is to identify the diagnostic biomarkers related to atherosclerosis through mach...
One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary ef...
Genome-wide association studies (GWAS) seek to identify single nucleotide polymorphisms (SNPs) that cause observed phenotypes. However, with highly correlated SNPs, correlated observations, and the number of S...
All the time, pancreatic cancer is a problem worldwide because of its high degree of malignancy and increased mortality. Neural network model analysis is an efficient and accurate machine learning method that ...
Synaptogyrin-2 (SYNGR2), as a member of synaptogyrin gene family, is overexpressed in several types of cancer. However, the role of SYNGR2 in pan-cancer is largely unexplored.
Gastric cancer is the third leading cause of death from cancer worldwide and has a poor prognosis. Practical risk scores and prognostic models for gastric cancer are lacking. While immunotherapy has succeeded ...
An artificial-intelligence (AI) model for predicting the prognosis or mortality of coronavirus disease 2019 (COVID-19) patients will allow efficient allocation of limited medical resources. We developed an ear...
In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric a...
The limited knowledge of miRNA–lncRNA interactions is considered as an obstruction of revealing the regulatory mechanism. Accumulating evidence on Human diseases indicates that the modulation of gene expression h...
The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF). T...
Genome-wide association studies have systematically identified thousands of single nucleotide polymorphisms (SNPs) associated with complex genetic diseases. However, the majority of those SNPs were found in no...
The original article was published in BMC Bioinformatics 2023 24:74
Alimentary tract malignancies (ATM) caused nearly one-third of all tumor-related death. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in ATM is unknown.
Protein secondary structures that link simple 1D sequences to complex 3D structures can be used as good features for describing the local properties of protein, but also can serve as key features for predictin...
Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the ...
Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) ...
Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamental...
The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailo...
The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, rese...
There is strong evidence to support that mutations and dysregulation of miRNAs are associated with a variety of diseases, including cancer. However, the experimental methods used to identify disease-related mi...
Pyroptosis is closely related to cancer prognosis. In this study, we tried to construct an individualized prognostic risk model for hepatocellular carcinoma (HCC) based on within-sample relative expression ord...
Locomotion behaviors of Caenorhabditis elegans play an important role in drug activity screening, anti-aging research, and toxicological assessment. Previous studies have provided important insights into drug act...
We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely...
The flourishment of machine learning and deep learning methods has boosted the development of cheminformatics, especially regarding the application of drug discovery and new material exploration. Lower time an...
High-dimensional prediction considers data with more variables than samples. Generic research goals are to find the best predictor or to select variables. Results may be improved by exploiting prior informatio...
Complex diseases such as neurodevelopmental disorders (NDDs) exhibit multiple etiologies. The multi-etiological nature of complex-diseases emerges from distinct but functionally similar group of genes. Differe...
Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNAseq data, carry a hig...
Breast cancer is a highly heterogeneous disease that comprises multiple biological components. Owing its diversity, patients have different prognostic outcomes; hence, early diagnosis and accurate subtype pred...
Identification of the cancer subtype plays a crucial role to provide an accurate diagnosis and proper treatment to improve the clinical outcomes of patients. Recent studies have shown that DNA methylation is o...
CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted comp...
Wound healing involves careful coordination among various cell types carrying out unique or even multifaceted functions. The abstraction of this complex dynamic process into four primary wound stages is essent...
Massively parallel sequencing includes many liquid handling steps which introduce the possibility of sample swaps, mixing, and duplication. The unique profile of inherited variants in human genomes allows for ...
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