Robert A. Holt

A De Novo Algorithm for Allele Reconstruction from Oxford Nanopore Amplicon Reads, with Application to CYP2D6

This paper introduces a de novo algorithm to reconstruct allele sequences from Oxford Nanopore amplicon reads, demonstrating its application to CYP2D6 and HLA with high accuracy.

Self-multimerization of mRNA LNP-derived antigen improves antibody responses

This study compares multimerization domains in mRNA LNP vaccines, finding that IMX313 enhances antibody responses more than other domains.

Identification of Novel DNA Sequence Motifs that Modulate Transcription in T cells

The paper identifies novel DNA sequence motifs that modulate transcription in T cells using computational and experimental methods.

Comprehensive Functional Self-Antigen Screening to Assess Cross-Reactivity in a Promiscuous Engineered T-cell Receptor

The paper uses Tope-seq to identify cross-reactive epitopes in an engineered T-cell receptor that caused off-target toxicity, highlighting the need for comprehensive screening.

Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device

The paper describes a cost-effective and accurate plasmid sequencing method using the MinION device, achieving 100% accuracy in consensus sequences and detecting small mutations.

Modulation of the host cell transcriptome and epigenome by Fusobacterium nucleatum

This study investigates how three Fusobacterium nucleatum strains modulate host cell transcriptomes and epigenomes through RNA-seq and ChIP-seq, revealing inflammation-related gene upregulation and chromatin remodeling during host cell invasion.

It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)

The paper reports the first draft genome of the North American bullfrog, providing genomic resources for amphibian research and supporting taxonomic classification.

The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

The paper analyzes the interaction between tumor and immune clones in ovarian cancer, finding that immune contexture patterns mirror malignant spread and that foldback inversions correlate with poor outcomes.