Alex R. Hastie

OMKar generates virtual karyotypes from optical genome mapping data to identify constitutional abnormalities with high precision and recall.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

This paper resolves ring chromosomes, Robertsonian translocations, and complex structural variants using long-read sequencing and telomere-to-telomere assembly, revealing breakpoint structures and methylation changes.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

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

This study validates optical genome mapping (OGM) as a high-resolution, cost-effective alternative to traditional prenatal diagnostic methods by demonstrating its ability to detect all classes of structural variants and copy number variations with 100% concordance.

This study compares optical genome mapping (OGM) and chromosomal microarray (CMA) for detecting copy number variants and structural variants, finding high concordance and additional structural insights from OGM.

This study validates optical genome mapping (OGM) as a clinical test for detecting structural variations in hematological malignancies, showing high accuracy and sensitivity compared to standard-of-care methods.

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.

This study validates optical genome mapping (OGM) as a clinical tool for detecting structural variations in hematological neoplasms, showing high sensitivity and specificity compared to standard methods.

This study identifies molecular and functional changes in mouse and human models of 16p11.2 reciprocal genomic disorder, revealing context-specific disruptions in energy metabolism, RNA processing, and neuronal development.

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.

The paper describes an integrated workflow combining optical genome mapping and SNP microarray analysis to improve diagnostic yield in products of conception cases with maternal cell contamination.

This study evaluates the clinical utility of optical genome mapping and a 523-gene NGS panel for comprehensive genomic profiling of myeloid cancers, showing higher sensitivity and resolution compared to standard-of-care methods.

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.

This study uses Optical Replication Mapping to map human DNA replication initiation sites and finds that replication initiation is stochastic and not confined to specific origins.

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.

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

This paper describes a method using optical genome mapping to identify somatic structural variants in solid tumors, showing high reliability and functional relevance.

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.

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.

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.

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

R2OM2 creates fluorescent optical methylation profiles along chromosomal DNA for epigenetic profiling, comparable to WGBS with single-molecule resolution.

This study identifies early-firing human replication origins in HeLa cells using Optical Replication Mapping, revealing that initiation occurs across broad zones rather than confined to efficient origins.

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.

The paper introduces R2OM2, a method combining optical methylation profiling with genome mapping to analyze epigenetic variation in single cells and large structural aberrations.

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