Joyce Lee

Optical genome mapping enables accurate repeat expansion testing

This study evaluates optical genome mapping (OGM) for detecting STR repeat expansions and somatic instability, showing high accuracy and efficiency compared to current methods.

Automated assembly of high-quality diploid human reference genomes

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

The paper presents a contiguous de novo genome assembly of sugar beet EL10 using long-read sequencing and scaffolding, showing high congruence with the reference genome and reduced gene copy number variation.

A complete reference genome improves analysis of human genetic variation

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

The paper generates a chromosome-level genome assembly for the functionally extinct northern white rhinoceros and compares it to the southern white rhinoceros.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays

The paper introduces CRISPR-bind, a method using dCas9 to directly label genomic DNA with fluorescent CRISPR-dCas9 complexes for improved mapping and analysis.

Rapid Automated Large Structural Variation Detection in a Diploid Genome by NanoChannel Based Next-Generation Mapping

The paper introduces a method to detect large structural variants in diploid genomes using Bionano Genomics next-generation mapping, achieving high resolution and throughput.

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

This paper presents a de novo mammalian genome assembly for the domestic goat using long-read sequencing, short-read validation, and chromatin interaction mapping, achieving high contiguity and resolving repetitive regions.