Hugh E. Olsen

The paper introduces methods for haplotype-resolved de novo assembly using Shasta and GFAse, showing improved assembly quality with newer Oxford Nanopore reads.

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 introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

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 introduces NRCeq, a method to identify capped full-length SARS-CoV-2 transcripts, revealing new insights into sgRNA structure and expression.

The paper identifies high-confidence full-length human RNA isoform scaffolds using nanopore sequencing by improving 5' cap detection and 3' polyadenylation site identification.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper surveys rare epigenetic variation in 23,116 human genomes, identifies disease-relevant epivariations, and discovers novel CGG expansions linked to folate-sensitive fragile sites.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.

The paper uses nanopore sequencing to assemble and characterize the centromeric region of a human Y chromosome, overcoming challenges posed by repetitive DNA.

The paper assembles a complex C. elegans genome using MinION long-read sequencing and identifies genomic rearrangements not detectable with Illumina data.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.

The paper uses long-read RNAseq to identify and quantify complex isoforms in individual B cells, revealing widespread transcriptional variation in surface receptors and the antibody heavy chain locus.