Xinchang Zheng

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

IsoMatch integrates transcript models across references, showing how reference choice affects estimates of transcript novelty.

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

IsoAtlas provides an interactive database for visualizing and interpreting transcript isoforms using long-read RNA-seq data from humans and mice.

Omni2Tree directly analyzes raw sequencing reads to reconstruct viral phylogenies and identify diversification, outperforming assembly and reference-based methods in low-coverage scenarios.

Isopedia reduces apparent isoform novelty by up to 26-fold in HG002 benchmarks and provides a reference-agnostic framework for population-scale isoform annotation.

TumorLens detects genetic and epigenetic alterations in cancer using long reads, revealing key somatic events and methylation patterns across tumor samples.

The paper introduces DRAGEN, a scalable mosaic variant caller that detects low VAF variants with high accuracy and efficiency, and presents a benchmark for low-VAF variants.

This paper evaluates Illumina Constellation sequencing for rare disease research, showing it can detect structural variants and haplotype phasing with low DNA input and existing infrastructure.

scVar detects low-frequency somatic mutations in single-cell RNA sequencing data and integrates them with transcriptomic profiles to study tumor heterogeneity.

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

STIX annotates structural variants using long-read data, achieving high accuracy and identifying common SVs in population-scale datasets.

The Genome Warehouse (GWH) is a public repository for genome-scale data that provides storage, submission, and visualization tools for genome assemblies across species.

The paper identifies a common postzygotic mutational signature across healthy tissues linked to embryonic hypoxia, observed in both normal and some tumor samples.