Chengpeng Bi

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Expanded map of genomic imprinting reveals insight into human disease

The paper expands the human genomic imprinting map using long-read sequencing and GWAS integration, revealing new disease-associated loci and maternal/paternal imprinting patterns.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.