Yilei Fu

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

IsoMatch integrates transcript models across references, showing how reference choice affects estimates of transcript novelty.

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

TumorLens detects genetic and epigenetic alterations in cancer using long reads, revealing key somatic events and methylation patterns across tumor samples.

TBAS enables cost-effective long-read sequencing of rare-disease trios with high variant detection accuracy and a 77% potential solve rate.

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

Olivar automates variant-aware primer design for tiled amplicon sequencing of pathogens, improving mapping rates and coverage compared to existing methods.

MethPhaser improves haplotype phasing by using methylation signals from Oxford Nanopore data, increasing phase length N50 by 3-fold with minimal error increase.

Vulcan improves long-read mapping and structural variant calling by using dual-mode alignment, enhancing accuracy for Oxford Nanopore Technology reads.

deGSM constructs large de Bruijn graphs efficiently in limited memory, handling terabase-pair datasets on standard hardware.