Yoon-ha Lee

Genomic Annotation Infrastructure (GAIn): Pipelines and Resource Repositories for Annotating Variants, Positions, and Regions

GAIn provides a platform for generating reproducible genomic annotations using declarative pipelines and public repositories of genomic resources.

The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI

The GPF platform manages and analyzes large family genotypic and phenotypic data for autism research, enabling variant analysis and secure data sharing.

Snakeobjects: an object-oriented workflow management system

Snakeobjects extends Snakemake to simplify workflow development, improve readability, and maintain portability and scalability.

De novo indels within introns contribute to ASD incidence

The paper identifies de novo intronic indels in autism target genes from simplex families and finds they contribute to at least 10% of simplex autism.

Indel variant analysis of short-read sequencing data with Scalpel

This paper introduces Scalpel, an open-source tool for accurate indel detection from short-read sequencing data, and demonstrates its application in various analysis modes.

Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly

Scalpel detects de novo and transmitted INDELs in exome data with high specificity and sensitivity, outperforming existing tools in challenging repeat regions and identifying new autism-related genes.