Kui Wu

Genos-m: a foundation model for human-associated microbial genomes

Genos-m is a foundation model for human-associated microbial genomes that outperforms existing models in gene-fitness prediction and community structure analysis.

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data

The paper develops computational methods combining sequencing and miFISH data to improve accurate inference of clonal copy number evolution in tumors.

Chromatin Accessibility Reveals Potential Prognostic Value of the Peak Set Associated with Smoking History in Patients with Lung Adenocarcinoma

The paper identifies ATAC-seq peaks associated with smoking history in lung adenocarcinoma that correlate with patient survival and are linked to key oncogenic pathways.

Whole genome sequencing of cell-free DNA yields genome-wide read distribution patterns to track tissue of origin in cancer patients

This study uses whole genome sequencing of cell-free DNA to identify tissue-of-origin patterns, achieving high specificity and sensitivity in cancer patients.

Proteogenomics analysis of non-coding region encoded peptides in normal tissues and five cancer types

The paper identifies non-coding region encoded peptides in normal and cancer tissues, showing pseudogene translation and predicting neoantigens for cancer vaccines.

Identification of the associated expression patterns as potential predictive markers for cancer prognosis

The paper identifies gene expression correlation patterns (AEPs) associated with cancer prognosis across 22 cancer types using transcriptomic data from 5,001 patients.

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

The paper develops methods to deconvolve tumor copy number data by integrating bulk and single-cell sequencing data, improving accuracy over bulk data alone.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Intratumor Heterogeneity and Evolution of Colorectal Cancer

This study examines intratumor heterogeneity and evolution patterns in colorectal cancer, finding a Darwinian pattern with differences between right-sided and left-sided tumors.

Molecular subtyping and prognostic assessment based on tumor mutation burden in patients with lung adenocarcinomas

The paper identifies two molecular subtypes of lung adenocarcinomas based on tumor mutation burden and links them to clinical and genomic differences.

Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq

This study uses single-cell RNA-seq to analyze the tumor microenvironment of breast cancer, revealing cell type diversity and immune evasion mechanisms.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.