Theodore M. Nelson

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

This paper reports the first derivation of elephant induced pluripotent stem cells (emiPSCs) using a modified reprogramming protocol that inhibits TP53 expansion genes.

The paper identifies CSTF2 and CSTF2T as factors that shape the m6A landscape through cleavage-dependent and -independent mechanisms by altering transcript architecture and polyadenylation sites.

The paper investigates how different high-fat diets affect host and microbiome multi-omic states over time and shows that some changes persist even after returning to a control diet.

This study benchmarks two whole-genome sequencing platforms, showing context-specific error rates and highlighting the importance of whole-genome benchmarking for accuracy assessment.

The paper introduces DRAGEN, a scalable mosaic variant caller that detects low VAF variants with high accuracy and efficiency, and presents a benchmark for low-VAF variants.

SAHA creates a multimodal, subcellular-resolution reference atlas of healthy human tissues, revealing spatial organization and disease-associated disruptions across multiple organ systems.

This paper introduces SPLISOSM, a framework for analyzing spatial transcriptomics data to detect isoform-level patterns, identifying spatially variable transcript diversity and regulatory relationships in mouse and human brain tissues.

This paper creates a database of space-flown drugs and identifies spaceflight-related gene targets to advance pharmacogenomics for space missions.

This study fine maps a mouse QTL for lean body mass (Burly1) to a 0.8-Mb region on chromosome 2, showing the B6 allele increases lean body mass without affecting food intake or activity.

The paper fine-maps a QTL for gonadal adipose depot weight in mice using congenic strains, revealing at least four distinct loci within the original QTL region.