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This study aimed to observe the potential impact of known cuproptosis-related genes (CRGs) on triple negative breast cancer (TNBC) development, as well as their associated molecular mechanisms, immune infiltra...
To explore dermatomyositis signature genes as potential biomarkers of hepatocellular carcinoma and their associated molecular regulatory mechanisms.
As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing th...
Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-re...
CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications. Indel analysis has thus become on...
Viral genomics and epidemiology have been increasingly important tools for analysing the spread of key pathogens affecting daily lives of individuals worldwide. With the rapidly expanding scale of pathogen gen...
Single-cell RNA sequencing (scRNA-seq) strives to capture cellular diversity with higher resolution than bulk RNA sequencing. Clustering analysis is critical to transcriptome research as it allows for further ...
Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and pro...
There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these to...
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...
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...
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...
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2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)
2023 Speed
19 days submission to first editorial decision for all manuscripts (Median)
146 days submission to accept (Median)
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