Jason G. Underwood

This paper introduces an improved DRS protocol using UltraMarathonRT to generate longer RNA reads and isoform predictions in Oxford Nanopore sequencing.

This paper introduces scrHLA-typing, a method to quantify HLA transcripts in single cells using long-read sequencing, showing its ability to detect allele-specific expression in post-transplant relapse samples.

The paper characterizes the structural variation and diversification of the NPIP gene family in humans using long-read sequencing and identifies evidence of positive selection and novel gene models.

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 uses long-read RNA sequencing to analyze isoform expression in brown bears during active and hibernation seasons, finding differential isoform usage in tissues even when genes are not differentially expressed.

The paper introduces a single-molecule sequencing method to measure nucleosome positions on chromatin fibers and reveals heterogeneous patterns of oligonucleosome occupancy across epigenomic domains.

ORF Capture-Seq enables targeted full-length isoform sequencing by using cloned ORFs as probes, significantly increasing isoform detection compared to unenriched samples.

The paper introduces CAT, a toolkit for simultaneous clade and personal genome annotation, demonstrating its ability to discover novel genes and improve cross-species RNA expression analysis.

This study identifies the causal mechanism of X-linked Dystonia-Parkinsonism (XDP) by integrating genome and transcriptome assembly, revealing a SVA insertion causing intron retention and TAF1 dysfunction.

8-channel GemCode droplet barcoding captures ∼50% of loaded cells for 3′ mRNA counting, profiling 68k peripheral blood mononuclear cells and calling transplant chimerism from transcript variants.