Wendell D. Jones

This study benchmarks five scCNV inference methods across multiple scRNA-seq platforms and mixed samples, finding variations in performance based on data characteristics and batch effects.

The paper provides comprehensive reference materials with genomic, epigenomic, transcriptomic, scRNA-seq, and proteomic characterizations of two cell lines for benchmarking and validation.

The paper introduces a cloud-based platform called ORCESTRA for reproducible processing and sharing of multimodal biomedical data in a FAIR manner.

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

This study benchmarks seven SARS-CoV-2 whole-genome sequencing protocols using patient samples, finding performance differences based on viral input and sequencing parameters.

This paper develops a targeted NGS method with synthetic internal standards to improve detection of actionable mutations in ctDNA, increasing sensitivity and enabling quality control metrics.