Chia‐Lin Wei

IsoRanker uses long-read transcriptomics to prioritize non-coding variants in Mendelian conditions by detecting expression outliers, allelic imbalance, and NMD, leading to the identification of pathogenic variants in one individual.

This study benchmarks nine short-read sequencing chemistries across seven sequencers using donor-specific assemblies to measure sequencing errors against sample-matched references, revealing platform-specific error profiles and highlighting the importance of donor-specific references for unbiased comparison.

The paper introduces a data model and dataset for rare disease research, enabling interoperable multi-omic data integration across clinical sites.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

This study investigates cohesin's role in transcriptional loops and DNA replication using human cells, finding that cohesin loss affects long-range chromatin interactions and up-regulates early initiation zone genes.

The paper maps ecDNA structures in glioblastoma using long-read sequencing and ecLego3, revealing structural variation, evolutionary dynamics, and transcriptional links to tumor adaptation.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

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.

This study shows ecDNA forms nuclear condensates and reorganizes chromatin to enhance oncogenic transcription across cancer types.

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

This study identifies oncogenic-associated 5hmC signatures in cfDNA from cancer patients and validates their consistency with tumor-specific patterns.

The paper uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

This study identifies Fos as a key regulator of neural stem cell self-renewal, showing it rescues proliferation and interacts with Sox2 through a gene regulatory network involving Socs3.

ChIA-PIPE is a fully automated pipeline for analyzing and visualizing ChIA-PET data, including quality assessment and visualization tools.

This study investigates how PML/RARα alters chromatin topology and transcription in APL cells, revealing its role in repressing myeloid differentiation genes.

This study uses nanopore sequencing to identify structural variants in breast cancer with high specificity and sensitivity, revealing repetitive DNA as a major source of variation.

This paper introduces a method to analyze multiplex chromatin interactions with single-molecule precision and shows they contribute to topologically associated domains and gene regulation.