Tongwu Zhang

This paper identifies 116 risk loci for melanoma through GWAS, links susceptibility to immunity and Wnt signaling, and develops a PRS improving risk prediction.

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

This study shows that intestinal Bacteroides species degrade tryptophan into indoles, which enhance anti-tumor immunity and limit melanoma growth.

This study identifies ZC3H18 mutations that stabilize endogenous retroviral RNA, linking ERV RNA accumulation to oncogenesis in zebrafish and human cell lines.

The paper identifies non-coding variants in CDKN2B that disrupt CTCF binding, reduce CDKN2A expression, and increase melanoma risk in families.

This study identifies subtype-specific mutational mechanisms and links them to host metabolic factors in endometrial cancer using genomic and transcriptomic data from 440 tumors.

The paper presents an isoform-level lung cell atlas using single-cell long-read RNA-sequencing, revealing genetic effects on isoform regulation that improve cell-type classification and identify novel variants associated with lung cancer risk.

The paper constructs a single-cell eQTL dataset from Asian never-smokers, identifying alveolar cell-specific genes linked to lung cancer susceptibility.

This study identifies RAPGEF1 as a gene modulating melanoma and nevi risk through RAS activation, using fine-mapping, expression data, and functional assays.

This paper develops a deep learning model to predict molecular alterations in never-smoker lung adenocarcinomas from histological images, achieving high accuracy for most features.

The paper identifies rs3769823 as a functional variant near CASP8 influencing its expression in a cell-type specific manner and associated with multiple cancers.

This study identifies three distinct evolutionary trajectories in lung adenocarcinomas using whole-genome sequencing, revealing that some never-smoking tumors follow smoking-like paths driven by KRAS mutations.

GFBioNet identifies genomic factors modulating trait-trait relationships in multi-omics data, revealing host genetics, microbial taxa, and mutations affecting biological networks.

The paper identifies genetic determinants of gene expression noise and links them to complex trait variation using a large-scale human blood cell dataset.

The paper develops and validates multi-ancestry polygenic risk scores for LUAD in East Asian never-smokers, showing improved risk prediction compared to East Asian-only models.

The paper identifies three subtypes of NS-LUAD using RNA-seq data and develops a 60-gene signature that predicts survival across subgroups.

This study identifies a unique mutational signature, SBS87, in testicular germ cell tumors (TGCTs) that resembles thiopurine-induced DNA damage and is associated with tumor latency and telomere elongation.

This study analyzes 1024 lung adenocarcinomas to identify evolutionary patterns and mutational mechanisms, revealing distinct trajectories linked to smoking, ancestry, and retrotransposition.

The paper identifies candidate causal variants and genes at melanoma risk loci using capture-HiC and integrates multi-omics data to prioritize cis-regulatory interactions.

The paper identifies cell-type specific lung cancer susceptibility genes by integrating single-cell multi-omics data with GWAS loci.

The paper identifies two lung cancer subtypes defined by APOBEC mutagenesis levels and shows their association with different genetic mutations, aging, and immune responses.

This paper introduces SATS, a framework for mutational signature analysis in targeted sequencing data, and presents a pan-cancer catalogue of mutational signatures from 111,711 tumors.

The paper identifies TBX3 as a key regulator in pheomelanogenesis and melanoma predisposition through scRNA-seq analysis of RHC mouse models.

This study shows that time to first cigarette strongly influences lung tumor mutational burden, signatures, and survival in smokers.

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

This study identifies genetic loci associated with eye colour in a Canadian European cohort, highlighting the HERC2/OCA2 region and other genes, and explores their molecular mechanisms.

ezQTL provides a web tool for colocalizing GWAS and molecular QTL data to identify causal genes and variants.

This paper identifies rs117132860 as a functional variant at 7p21.1 that regulates AHR expression in response to UVB, contributing to melanoma risk and tanning ability.

The paper identifies cell-type-specific meQTLs in melanocytes and melanomas, enhancing GWAS annotation and revealing regulatory mechanisms involving IRF4.

The paper identifies a novel NRAS variant in a melanoma-prone family and shows it impairs MAPK/AKT signaling while enhancing PI3K signaling.