Hanlee P. Ji

The paper introduces CTLR-Seq, a method to resolve complex genomic regions with high accuracy, and applies it to study CNVs associated with schizophrenia and autism.

The paper combines single cell DNA-Seq and RNA-Seq in gastric cancer to reveal subclonal genomic instability and gene expression patterns, showing evidence of tumor evolution.

This study uses read cloud sequencing to identify mobile elements in Bacteroides caccae that contribute to antibiotic resistance in a patient's microbiome over time.

The paper identifies TP53 genomic deletions as a poor prognosis marker in Stage III colorectal cancer using a new low-coverage whole-genome sequencing protocol.

CRISPRpic provides fast and precise mutation calling by counting exact matches and pattern searches in CRISPR sequencing data.

The paper identifies ATG7 as a genetic risk factor for cholangiocarcinoma through germline mutations and population studies, linking autophagy dysfunction to cancer development.

The paper introduces a targeted sequencing method using linked read sequencing of CRISPR DNA targets to assemble large genomic regions and detect structural variants with high precision.

The paper provides a comprehensive whole-genome analysis of K562, identifying genomic structural features and their impact on functional genomics data.

This paper provides a haplotype-resolved genome analysis of the HepG2 cell line, identifying genomic features and allele-specific regulation to support functional genomics studies.

scPred is a method for predicting cell types from single-cell RNA sequencing data, achieving high accuracy in classifying cell states and subtypes across multiple tissues and disease contexts.

SVEngine simulates genome structural variations with cancer clonal evolution features, producing sequence data with variants and ground truth BED files.

This paper introduces a targeted sequencing method for low-quality DNA that reduces PCR bias and improves variant detection in clinical samples.