Jonathan E. LoTempio

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

This study evaluates the diagnostic yield of long-read genome sequencing in cases where short-read sequencing failed, finding an incremental yield of 4.7% due to LR-GS's ability to detect structural variants and other complex genomic features.

duoNovo identifies de novo variants from parent-proband duos using long-read sequencing, achieving high precision and low error rates in diagnostic evaluations.

Genome sequencing identifies pseudoexons as a common cause of Mendelian disease, with some variants missed by prior exome testing.

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

This study benchmarks long-read genome alignment tools for human genomics, finding that no single tool resolves all structural variants, and recommends using multiple tools for comprehensive analysis.

This paper compares traditional and chatbot-based consent processes for genomics research, finding shorter consent times and positive participant feedback with the chatbot.

The paper identifies a novel SARS-CoV-2 spike variant, S:N679S, in a neonatal patient and finds it present in other samples from the US mid-Atlantic region.