Zheng Hu

This study compares the genomic evolution of sporadic and hereditary colorectal precancers using single-crypt whole-genome sequencing, revealing distinct mutation patterns and evolutionary trajectories.

This study shows that many premalignant colorectal polyps contain multiple genetic lineages, indicating polyclonal origins rather than single-cell expansion.

This study uses lineage tracing and single-cell analysis to show tumor plasticity precedes stable immune evasion, with AP-1 regulating EMT stabilization during immunotherapy.

The paper investigates the reliability of mitochondrial DNA variants as lineage markers, finding that most are pre-existing heteroplasmy rather than de novo mutations, and introduces a score to identify reliable markers.

This study develops mathematical models to explore how chemotherapy and immune checkpoint blockade (ICB) combination therapy affects heterogeneous tumors, revealing chemotherapy's role in reducing antigenic heterogeneity and enhancing ICB efficacy through immune recovery.

This study develops a theory to identify Cancer Driving Nucleotides (CDNs) by analyzing mutation recurrence across large cancer datasets, finding that mutations recurring at least three times are likely CDNs.

MitoSort uses mtDNA germline variants to accurately demultiplex pooled single-cell data and detect doublets, outperforming existing methods for scRNA-seq in mtscATAC-seq.

This study identifies Cancer Driving Nucleotides (CDNs) across cancer types and patients, finding that most remain unidentified and highlights the need for larger sample sizes to improve detection.

scPhyloX infers tissue development and tumor evolution dynamics using single-cell phylogenetic trees, revealing novel insights into stem cell overshoot, hematopoietic progenitor clonal expansion, and colorectal tumor subclonal selection.

The paper introduces PhyloVelo, a method that uses monotonically expressed genes to reconstruct cell fate transitions, outperforming existing approaches in embryo development and tumor evolution analysis.

The paper identifies a mitochondrial DNA bottleneck during lymphocyte development, leading to homoplastic mutations despite lower mutational burden.

The study analyzes genetic diversity in multiple hepatocellular carcinomas, finding that low-frequency mutations pre-exist and contribute to drug resistance, presenting challenges and opportunities for cancer therapeutics.