Danny E. Miller

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

Mahi-mahi accurately genotypes repeat expansions from nanopore sequencing data, matching orthogonal methods and identifying pathogenic alleles.

This paper evaluates long-read sequencing with targeted assembly for accurately analyzing the opsin gene cluster, showing high concordance and improved detection of color vision deficiencies and carrier status.

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

The paper identifies a mechanism of gene amplification in yeast involving microhomology-mediated break-induced replication (mmBIR) at telomeres, leading to tandem duplication of chromosomal ends.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The paper recalibrates BAP1 MAVE data for different disease phenotypes to enable accurate variant classification across related disorders.

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

This study evaluates factors affecting haplotype phasing accuracy in long-read sequencing, showing that T2T reference genomes and longer reads improve performance.

The paper develops TRoLR, a pipeline using long-read sequencing to detect and prioritize pathogenic tandem repeat expansions in diverse populations, identifying known and novel expansions with clinical relevance.

This paper introduces an integrated microfluidic workflow for Oxford Nanopore sequencing that reduces hands-on time and sample loss while enabling high-quality library preparation from small sample volumes.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

This study compares long-read sequencing and optical genome mapping in detecting structural variants in Parkinson's disease, finding OGM better detects large variants while ONT provides high-resolution refinement.

This paper presents a SNP-based crossover map for Drosophila mauritiana, showing reduced centromere suppression of crossing over compared to D. melanogaster.

SeqFirst-neo uses a genotype-driven workflow with broad exclusion criteria to increase access to rapid whole genome sequencing in critically ill newborns, significantly improving the rate and equity of precise genetic diagnoses.

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 evaluates whole-genome long-read sequencing for diagnosing Prader-Willi and Angelman syndromes, showing high accuracy in detecting genetic variants and methylation differences.

The paper identifies a common intronic SVA_E insertion in ASPA as the most frequent pathogenic variant in Canavan disease using long-read sequencing.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

This study evaluates genome-wide DNA methylation analysis in genetically unsolved DEEs, identifying 10 causative or candidate genetic causes and refining a CHD2 episignature.

The paper identifies a critical noncoding superenhancer region essential for regulating anterior HOXA genes in craniofacial development, showing its deletion causes severe developmental defects in mice and a human patient.

This study demonstrates rapid whole-genome sequencing and targeted analysis within three hours to assess genetic risk in a newborn, showing they are not affected or a carrier for a specific Mendelian condition.

The paper uses full-length isoform sequencing to identify a splicing defect in MFN2 causing CMT2A in a patient with undiagnosed neuropathy.

The paper presents an improved chromosome-scale genome assembly for the African spiny mouse using long Nanopore reads and validates it with RNA-seq data.

The paper investigates how heterozygous inversion breakpoints suppress meiotic crossovers and shows that noncrossover gene conversions occur at wildtype levels near breakpoints.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

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