Chong Chu

Accurate detection of mosaic mutations at short tandem repeats from bulk sequencing data

BulkMonSTR detects mosaic STR mutations in bulk sequencing data with improved precision and F1 scores compared to existing methods.

Multi-platform framework for mapping somatic retrotransposition in human tissues

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

LINE-1 ORF1p is a shared and immunogenic antigen in cancer

This study identifies LINE-1 ORF1p as a shared and immunogenic antigen in cancer, showing its expression in tumors, MHC class I presentation, and in vitro immunogenicity.

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.

DeepMosaic: Control-independent mosaic single nucleotide variant detection using deep convolutional neural networks

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder

This study identifies de novo and polymorphic retrotransposon insertions in ASD families, finding increased exonic and intronic insertions in ASD cases compared to controls.

HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data

HiTea uses Hi-C data to detect non-reference transposable element insertions, outperforming whole genome sequencing-based methods in human cell lines.

HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

HiNT detects copy number variations and translocations from Hi-C data with single base-pair resolution, outperforming existing methods on simulated and real data.

CircMarker: A Fast and Accurate Algorithm for Circular RNA Detection

CircMarker detects circular RNA using k-mers instead of read mapping, achieving higher accuracy and efficiency than existing tools.