Sheng Chih Jin

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis

SnakeAltPromoter provides a reproducible framework for differential alternative promoter analysis using RNA-seq, benchmarked against CAGE data and scalable for large datasets.

Leveraging Human Pangenome for Improved Somatic Variant Detection

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

Mutations in 329 probands with suspected renal electrolyte disorders

The paper identifies genetic mutations in 329 patients with suspected renal electrolyte disorders, finding known/likely disease-causing variants in 295 probands and highlighting non-coding variants and novel mitochondrial mutations.

Heterozygous and Homozygous RFC1 AAGGG Repeat Expansions are Common in Idiopathic Peripheral Neuropathy

The paper identifies RFC1 AAGGG repeat expansions in idiopathic peripheral neuropathy patients using a new computational pipeline and finds both heterozygous and homozygous expansions contribute to the condition.

A novel SMARCC1-mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus

This study identifies SMARCC1 mutations as a cause of congenital hydrocephalus, showing they lead to neural progenitor dysfunction and a new syndrome called SaDDS.

Dual impact of PTEN mutation on CSF dynamics and cortical networks via the dysregulation of neural precursors and their interneuron descendants

This study shows PTEN mutations cause ventriculomegaly and cortical network dysfunction through neural precursor and interneuron dysregulation, with mTORC1 inhibition offering therapeutic potential.

Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations

The paper identifies genetic variants in RASA1 and EPHB4 associated with vein of Galen malformations through exome analysis and single-cell transcriptomics.

Network Assisted Analysis of De Novo Variants Using Protein-Protein Interaction Information Identified 46 Candidate Genes for Congenital Heart Disease

The paper uses a Markov Random Field model with protein-protein interaction data to identify 46 candidate genes for congenital heart disease, including known and highly expressed genes.

Quantifying concordant genetic effects of de novo mutations on multiple disorders

This paper introduces EncoreDNM, a statistical framework to quantify shared genetic effects of de novo mutations between disorders using exome-wide summary data, revealing abundant pairwise enrichment correlations.

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease

This study identifies a haplotype lowering PU.1 expression in myeloid cells that delays Alzheimer’s disease onset by affecting gene expression and function.