Aaron M. Wenger

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

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.

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.

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

The paper develops a novel 6mA-calling pipeline for SMRT sequencing data, improving accuracy and efficiency, and applies it to map nucleosome positioning and transcription factor occupancy at single-molecule resolution.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

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

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

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.

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

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

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

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.

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 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.

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.

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

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.

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

The paper introduces SVCurator, a crowdsourcing app for evaluating structural variants in the human genome, finding high concordance among curators and with existing benchmarks.

AMELIE 2 improves Mendelian disorder diagnosis by matching patient phenotypes and genotypes to primary literature, achieving high accuracy and efficiency.

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

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

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.

The paper presents high-coverage long-read sequencing data from a Han Chinese trio for developing and evaluating long-read bioinformatics methods.

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.

Phrank improves Mendelian disease prioritization by ranking candidate genes or diseases based on phenotype similarity, outperforming existing methods in real patient exome data.

AMELIE automates Mendelian disorder diagnosis by analyzing literature and prioritizing candidate genes, achieving high diagnostic accuracy for singleton patients.

The paper uses long-read whole genome sequencing to identify a pathogenic structural variant in a patient with Carney complex, demonstrating the potential of LRS in diagnosing Mendelian diseases.