Yadong Wang

This study examines energy metabolic changes in aging male bone marrow mesenchymal stem cells and identifies gene expression and metabolic shifts associated with senescence.

The paper constructs a DNA methylation atlas for 106 Chinese individuals using nanopore long-read sequencing, identifying CpG sites and environmental influences on methylation.

The paper investigates the transcriptional effects of rs11607019 on gene expression in 293 cells, finding it upregulates several genes and downregulates APOBEC3G.

The paper introduces cuteSV2, a long-read-based method for accurate structural variant regenotyping, outperforming existing methods in benchmarking.

GFHunter detects gene fusions in long-read cancer transcriptomes with high accuracy, reduced false positives, and improved speed and memory efficiency.

gcSV is a structural variant detection framework that improves accuracy and yield across long, hybrid, and short-read data, identifying over 93,000 novel SVs.

xRead improves scalability and efficiency for constructing read overlapping graphs in long-read sequencing by using a coverage-guided model and heuristic alignment skeleton approach.

SCancerRNA is a database that compiles single-cell expression data and interaction networks of non-coding RNA biomarkers for cancer diagnosis and therapy.

MEAHNE predicts miRNA-disease associations using a heterogeneous network model, achieving high accuracy and verifying predictions against databases.

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

abPOA is a fast partial order alignment library using SIMD acceleration, achieving 15x speed improvement over SPOA with similar accuracy.

cuteSV improves structural variation detection in long-read sequencing by combining signature-based methods with clustering and refinement, achieving better performance on real datasets.

The paper introduces a tool to identify and remove haplotypic duplication in genome assemblies, improving continuity and completeness.

deSALT improves long RNA-seq read alignment by addressing sequencing errors and gene structure complexity through a two-pass graph-based approach.

xQTLImp imputes missing xQTL summary statistics using multivariate Gaussian approximation, rediscovering novel significant eQTL associations in a single-cell dataset.

deSAMBA classifies metagenomics long reads quickly and accurately using a sparse approximate match block-based algorithm, outperforming existing tools.

deGSM constructs large de Bruijn graphs efficiently in limited memory, handling terabase-pair datasets on standard hardware.

rMETL detects mobile element insertions using long read realignment, improving sensitivity and reducing false positives in genomic studies.

This paper introduces FSM, an algorithm for network motif discovery that improves efficiency and shows that large, frequent motifs are better for inferring higher-order biological network structures.

deSPI classifies metagenomic reads using a lightweight de Bruijn graph-based reference index, achieving faster speed and comparable accuracy.