Ruibin Xi

SpaCNA improves CNA detection in spatial transcriptomics by integrating spatial and gene expression data, revealing spatially distinct subclones and clone-specific CNAs in cancer.

HiScanner detects high-resolution copy number alterations in single cells, outperforming existing methods and revealing distinct CNA patterns in neurons and oligodendrocytes.

This paper benchmarks algorithms for identifying spatially variable genes in spatial transcriptomics using synthesized and real-world datasets to evaluate their effectiveness and application scenarios.

SpaHDmap improves spatial transcriptomics data resolution by integrating gene expression with histology images, producing interpretable embeddings and detecting refined spatial structures.

This paper introduces Festem, a method that directly selects differentially expressed genes for single-cell clustering, improving cell-type identification and reducing selection bias.

AtaCNV detects high-resolution copy number variations from scATAC-seq data, effectively distinguishing malignant from non-malignant cells and identifying subclones in cancer samples.

This study shows that pre-trained protein language models can predict mutation pathogenicity and patient survival in cancer, outperforming existing methods.

scFusion detects gene fusions in single-cell RNA sequencing data with high sensitivity and low false discovery rate, successfully identifying fusions missed by bulk methods.

CNV-BAC normalizes replication bias in bacterial WGS data to accurately detect copy number variations, outperforming existing methods.

scRMD imputes dropout values in scRNA-seq data using robust matrix decomposition, improving downstream analysis accuracy.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.