Hu Jin

Gene conversion is a key driver of diversity hotspots in M. tuberculosis antigens and virulence-associated loci

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

Correlation-aware discovery of co-occurring mutational signatures in cancer

Cornet improves mutational signature discovery by modeling correlations, identifying new signatures in cancer genomes.

Topographical archetypes of somatic mutagenesis in cancer

The paper introduces MuTopia, a framework that identifies topographic archetypes of mutagenesis in cancer genomes, revealing that mutational processes are constrained by replication timing and chromatin state.

A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection

The paper identifies a sequencing artifact in Illumina NovaSeq 6000 two-color chemistry that causes T>G substitutions, affecting low-VAF somatic variant detection.

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

Systematic artifacts from Illumina two-color chemistry confound variant identification and actionability in clinical panels

This study identifies systematic T>G sequencing artifacts in Illumina two-color chemistry that can create false pathogenic variants and inflate tumor mutational burden in clinical panels.

Timing the onset of homologous recombination deficiency before breast cancer diagnosis

The paper estimates the timing of homologous recombination deficiency (HRD) onset in breast cancers using HRDTimer, finding HRD occurs years before diagnosis in different subtypes.

Tissue specificity and chromosomal alterations shape divergent immune programs in HRD tumors

This study identifies two immune archetypes in HRD tumors—immune-inflamed and immune-evasive—linked to chromosomal instability and lineage, informing biomarker-driven therapies.

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

Contribution of de novo retroelements to birth defects and childhood cancers

The paper identifies de novo retroelements in birth defects and childhood cancers using whole-genome sequencing data and an improved computational tool.

Accurate and sensitive mutational signature analysis with MuSiCal

MuSiCal improves mutational signature analysis by outperforming existing methods in discovery and assignment, revealing new signatures and resolving ambiguities in cancer genomes.

Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures

The paper identifies mutational signatures SBS26 and SBS54 in MMRD tumors that correlate with immune checkpoint blockade response and survival, suggesting their use as prognostic biomarkers.

Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain

The paper compares somatic mutation rates in neurons and oligodendrocytes across aging human brains, finding faster mutation accumulation in oligodendrocytes and distinct genomic distribution patterns.

Chd1 regulates repair of promoter-proximal DNA breaks to sustain hypertranscription in embryonic stem cells

This study identifies Chd1's role in repairing DNA breaks in embryonic stem cells, showing its importance in maintaining hypertranscription during development.

Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members

This study uses yeast to investigate how DNA methylation is regulated by DNMT3 family members and identifies sequence preferences and spatial patterns of methylation.

A unified computational framework for modeling genome-wide nucleosome landscape

This paper develops a computational framework to model genome-wide nucleosome landscape by quantifying sequence features' contributions to occupancy, translational, and rotational positioning in S. cerevisiae.