William J. Rowell

Hunting for microsatellite instability in long-read data with Owl

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns

Whole-genome variant detection in long-read sequencing data from ultra-low input patient samples

This study evaluates ULI-HiFi and dMDA for long-read sequencing of low-input samples, finding ULI-HiFi achieves higher variant detection accuracy and reveals disease-relevant genetic changes in a FAP patient.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

A computational model for quantifying instability of tandem repeats across the genome

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

Identification of de novo variants from parent-proband duos via long-read sequencing

duoNovo identifies de novo variants from parent-proband duos using long-read sequencing, achieving high precision and low error rates in diagnostic evaluations.

Portello: Making global assembly more effective for rare-disease whole genome sequencing

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

Complex structural variant visualization with SVTopo

SVTopo visualizes complex structural variants using high-accuracy long reads, providing clear figures to understand multi-breakpoint events in human genomes.

The Platinum Pedigree: A long-read benchmark for genetic variants

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

Resolving the diagnostic odyssey in inherited retinal dystrophies through long-read genome sequencing

This study uses long-read genome sequencing to diagnose three previously undiagnosed inherited retinal dystrophy cases by identifying structural and deep intronic variants missed by short-read sequencing.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia

This paper uses long-read sequencing to comprehensively identify pathogenic variants in the CYP21A2 locus for Congenital Adrenal Hyperplasia, including phasing and module counts, improving diagnostic accuracy.

Long-Read Sequencing Increases Diagnostic Yield for Pediatric Sensorineural Hearing Loss

This study evaluates the diagnostic yield of long-read sequencing in pediatric sensorineural hearing loss, finding it detects structural variants missed by short-read sequencing.

Small-field visual projection neurons detect translational optic flow and support walking control

The paper identifies a cell type in Drosophila that detects translational optic flow and is essential for forward walking.

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

HiPhase: Jointly phasing small and structural variants from HiFi sequencing

HiPhase jointly phases small and structural variants from HiFi sequencing, achieving improved phase block NG50 and gene phasing rates.

Sentieon DNAscope LongRead - A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads

DNAscope LongRead is a pipeline for germline variant calling from PacBio HiFi reads, achieving high accuracy and efficiency in variant detection.

Benchmarking challenging small variants with linked and long reads

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy

The paper identifies a de novo missense variant in KCNC2 in two affected siblings with autism and epilepsy using long-read sequencing, showing its potential clinical relevance.

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

The paper presents diagnostic analyses of 960 pediatric rare disease families using genomic sequencing and machine learning, finding higher diagnostic rates with long-read sequencing and highlighting challenges in variant interpretation.

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.

A population of descending neurons that regulate the flight motor of Drosophila

The paper identifies a population of descending neurons in Drosophila that regulate wingbeat amplitude through a population code during flight.

DeepConsensus: Gap-Aware Sequence Transformers for Sequence Correction

DeepConsensus improves PacBio HiFi read accuracy and assembly quality using a gap-aware transformer model.

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

The landscape of SNCA transcripts across synucleinopathies: New insights from long reads sequencing analysis

This study uses long-read sequencing to analyze SNCA transcripts in synucleinopathies, revealing new insights into alternative splicing and structural variants.