Chaokun Yan
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View article: Computational models for pan-cancer classification based on multi-omics data
Computational models for pan-cancer classification based on multi-omics data Open
Tumor heterogeneity presents a significant challenge in cancer treatment, limiting the ability of clinicians to achieve accurate early-stage diagnoses and develop customized therapeutic strategies. Early diagnosis is crucial for effective …
View article: KGRDR: a deep learning model based on knowledge graph and graph regularized integration for drug repositioning
KGRDR: a deep learning model based on knowledge graph and graph regularized integration for drug repositioning Open
Computational drug repositioning, serving as an effective alternative to traditional drug discovery plays a key role in optimizing drug development. This approach can accelerate the development of new therapeutic options while reducing cos…
View article: DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering
DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering Open
Gene polymorphism originates from single-nucleotide polymorphisms (SNPs), and the analysis and study of SNPs are of great significance in the field of biogenetics. The haplotype, which consists of the sequence of SNP loci, carries more gen…
View article: GTasm: a genome assembly method using graph transformers and HiFi reads
GTasm: a genome assembly method using graph transformers and HiFi reads Open
Motivation Genome assembly aims to reconstruct the whole chromosome-scale genome sequence. Obtaining accurate and complete chromosome-scale genome sequence serve as an indispensable foundation for downstream genomics analyses. Due to the c…
View article: MSFN: a multi-omics stacked fusion network for breast cancer survival prediction
MSFN: a multi-omics stacked fusion network for breast cancer survival prediction Open
Introduction: Developing effective breast cancer survival prediction models is critical to breast cancer prognosis. With the widespread use of next-generation sequencing technologies, numerous studies have focused on survival prediction. H…
View article: MPASL: multi-perspective learning knowledge graph attention network for synthetic lethality prediction in human cancer
MPASL: multi-perspective learning knowledge graph attention network for synthetic lethality prediction in human cancer Open
Synthetic lethality (SL) is widely used to discover the anti-cancer drug targets. However, the identification of SL interactions through wet experiments is costly and inefficient. Hence, the development of efficient and high-accuracy compu…
View article: Prediction of drug–disease associations based on reinforcement symmetric metric learning and graph convolution network
Prediction of drug–disease associations based on reinforcement symmetric metric learning and graph convolution network Open
Accurately identifying novel indications for drugs is crucial in drug research and discovery. Traditional drug discovery is costly and time-consuming. Computational drug repositioning can provide an effective strategy for discovering poten…
View article: SLHSD: hybrid scaffolding method based on short and long reads
SLHSD: hybrid scaffolding method based on short and long reads Open
In genome assembly, scaffolding can obtain more complete and continuous scaffolds. Current scaffolding methods usually adopt one type of read to construct a scaffold graph and then orient and order contigs. However, scaffolding with the st…
View article: KGANSynergy: knowledge graph attention network for drug synergy prediction
KGANSynergy: knowledge graph attention network for drug synergy prediction Open
Combination therapy is widely used to treat complex diseases, particularly in patients who respond poorly to monotherapy. For example, compared with the use of a single drug, drug combinations can reduce drug resistance and improve the eff…
View article: DACPGTN: Drug ATC Code Prediction Method Based on Graph Transformer Network for Drug Discovery
DACPGTN: Drug ATC Code Prediction Method Based on Graph Transformer Network for Drug Discovery Open
The Anatomical Therapeutic Chemical (ATC) classification system is a drug classification scheme proposed by the World Health Organization, which is widely used for drug screening, repositioning, and similarity research. The ATC system assi…
View article: MultiGATAE: A Novel Cancer Subtype Identification Method Based on Multi-Omics and Attention Mechanism
MultiGATAE: A Novel Cancer Subtype Identification Method Based on Multi-Omics and Attention Mechanism Open
Cancer is one of the leading causes of death worldwide, which brings an urgent need for its effective treatment. However, cancer is highly heterogeneous, meaning that one cancer can be divided into several subtypes with distinct pathogenes…
View article: MI_DenseNetCAM: A Novel Pan-Cancer Classification and Prediction Method Based on Mutual Information and Deep Learning Model
MI_DenseNetCAM: A Novel Pan-Cancer Classification and Prediction Method Based on Mutual Information and Deep Learning Model Open
The Pan-Cancer Atlas consists of original sequencing data from various sources, provides the opportunity to perform systematic studies on the commonalities and differences between diverse cancers. The analysis for the pan-cancer dataset co…
View article: Predicting Drug-Disease Association Based on Ensemble Strategy
Predicting Drug-Disease Association Based on Ensemble Strategy Open
Drug repositioning is used to find new uses for existing drugs, effectively shortening the drug research and development cycle and reducing costs and risks. A new model of drug repositioning based on ensemble learning is proposed. This wor…
View article: SIns: A Novel Insertion Detection Approach Based on Soft-Clipped Reads
SIns: A Novel Insertion Detection Approach Based on Soft-Clipped Reads Open
As a common type of structural variation, an insertion refers to the addition of a DNA sequence into an individual genome and is usually associated with some inherited diseases. In recent years, many methods have been proposed for detectin…
View article: A Novel Biomarker Identification Approach for Gastric Cancer Using Gene Expression and DNA Methylation Dataset
A Novel Biomarker Identification Approach for Gastric Cancer Using Gene Expression and DNA Methylation Dataset Open
As one type of complex disease, gastric cancer has high mortality rate, and there are few effective treatments for patients in advanced stage. With the development of biological technology, a large amount of multiple-omics data of gastric …
View article: LROD: An Overlap Detection Algorithm for Long Reads Based on k-mer Distribution
LROD: An Overlap Detection Algorithm for Long Reads Based on k-mer Distribution Open
Third-generation sequencing technologies can produce large numbers of long reads, which have been widely used in many fields. When using long reads for genome assembly, overlap detection between any pair of long reads is an important step.…
View article: SLR: a scaffolding algorithm based on long reads and contig classification
SLR: a scaffolding algorithm based on long reads and contig classification Open
Background Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the…
View article: A hybrid algorithm based on binary chemical reaction optimization and tabu search for feature selection of high-dimensional biomedical data
A hybrid algorithm based on binary chemical reaction optimization and tabu search for feature selection of high-dimensional biomedical data Open
In recent years, there have been rapid developments in various bioinformatics technologies, which have led to the accumulation of a large amount of biomedical data. The biomedical data can be analyzed to enhance assessment of at-risk patie…