Jonathan Foox

Whole-genome benchmarking reveals context-specific error rates in the Ultima UG100 and Illumina NovaSeqX Platforms.

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

TET2 and TP53 Mutations Cooperatively Modulate the Response to Inflammation to Promote Leukemic Transformation

This study shows that TET2 and TP53 mutations work together to promote leukemic transformation by altering inflammatory responses and chemotherapy tolerance in hematopoietic stem cells.

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection

This study investigates how SARS-CoV-2 infection affects mitochondrial gene expression in different tissues and disease stages, finding targeted inhibition in some organs and upregulation in others.

Betacoronavirus-specific alternate splicing

The paper investigates differential alternative splicing in cells infected by betacoronaviruses and finds characteristic patterns linked to viral load and gene function.

Comparative analysis of single-cell RNA Sequencing Platforms and Methods

The paper compares scRNA-seq platforms and methods using SUM149PT cells treated with TSA, highlighting technical challenges and best practices for low RNA profiling.

Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study

The paper presents whole-genome and whole-exome sequencing datasets from a multi-center, cross-platform study to benchmark NGS technologies and bioinformatics pipelines in cancer genomics.

DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

The paper evaluates DNA methylation calling tools for Oxford Nanopore sequencing using human data and provides an online database for comparing tool performance.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Haplotype Diversity and Sequence Heterogeneity of Human Telomeres

This study uses long-read sequencing to analyze human telomere sequences, revealing sequence heterogeneity and non-canonical motifs.

The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection

The paper identifies miR-2392 as a miRNA involved in SARS-CoV-2 infection, showing its role in inflammation, glycolysis, and hypoxia, and develops a miRNA-based therapeutic targeting it.

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

This study analyzes over 7,000 SARS-CoV-2 datasets to reveal genomic diversity, showing iSNVs and small indels drive variation, and highlights implications for qRT-PCR and transmission tracking.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

The paper evaluates epigenetic methods using reference materials, finding high concordance between assays and differences in performance across platforms.

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

The paper assesses DNA sequencing performance across multiple platforms using human and bacterial reference genomes to evaluate quality and reproducibility.

Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

This study benchmarks eleven metagenomic classifiers using 846 species and evaluates strategies to reduce false positives in taxonomic classification.