Donna Marie Muzny

Microbial Dynamics Across Commercial Spaceflights of Varying Duration

This study examines microbiome and immune changes in astronauts after short and long-duration spaceflights, finding stable gut and oral microbiomes but transient skin microbiome shifts and immune activation.

Integrated Clinical-Genomic Reanalysis Identifies Diagnostic Gaps and Candidate Genes in a Pediatric Rare Disease Cohort

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

Cell-type-resolved somatic variant discovery from bulk long-read sequencing

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

Multi-Omics Study of Ancestry in Adults with Intracranial Cancers Glioma (MOSAIC)

This study analyzes a diverse glioma cohort to show ancestry influences on survival, somatic alterations, and mutational processes in diffuse gliomas.

Multi-Omics Characterization of Human Molecular Responses to Spaceflight Across Two Independent Missions

This study analyzes multi-omics data from two spaceflight missions to identify molecular changes in immune, skeletal, and vascular systems, providing insights for mitigating health risks during space travel.

Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq

The paper introduces NanoSeq-MBN, a method improving variant detection in whole-genome sequencing, expanding the GIAB truth set with novel low-frequency variants and enabling somatic variant benchmarking.

Enriching for Answers in Rare Diseases

TBAS enables cost-effective long-read sequencing of rare-disease trios with high variant detection accuracy and a 77% potential solve rate.

Constellation illuminates rare disease genetics

This paper evaluates Illumina Constellation sequencing for rare disease research, showing it can detect structural variants and haplotype phasing with low DNA input and existing infrastructure.

Pre-Sequencing Assessment of RNA-Seq Library Quality Using Real-Time qPCR

This paper introduces a qPCR-based assay to assess rRNA depletion efficiency in RNA-Seq libraries pre-sequencing, showing strong correlation with post-sequencing rRNA rates.

Population-scale Long-read Sequencing in the All of Us Research Program

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

This study analyzes RSV evolutionary dynamics across pre-pandemic, pandemic, and post-pandemic periods in Houston, finding reduced diversity during the pandemic and increased non-synonymous mutations in RSV/B.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region

The paper sequences the rat Y chromosome and reveals a short pseudoautosomal region with high recombination rate and unique evolutionary features.

Population-scale variability at short tandem repeat loci reveals pathogenicity signature

The paper uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

VizCNV: An integrated platform for concurrent phased BAF and CNV analysis with trio genome sequencing data

VizCNV is a tool for analyzing CNVs and phased BAF from trio genome sequencing data, identifying de novo and inherited CNVs in immunodeficiency cases.

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

This paper presents a probe-based capture enrichment method to obtain full-length genomes of RSV and HuNoV from clinical samples, achieving high completeness and improving variant tracking.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

Closing the gap: Solving complex medically relevant genes at scale

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

The impact of the Turkish (TK) population variome on the genomic architecture of rare disease traits

The paper analyzes the Turkish population's variome to understand its impact on rare disease traits, finding that long ROHs and inbreeding contribute to recessive diseases.

Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

Examining intra-host genetic variation of RSV by short read high-throughput sequencing

The paper analyzes intra-host RSV genetic variation using short-read sequencing, finding low variation but differences between genomic and transcriptomic data.

xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments

xAtlas is a scalable variant caller for NGS data that provides faster and accurate SNV and indel detection compared to existing methods.

Genome sequencing in the Parkinson disease clinic

This study performs genome sequencing in Parkinson's disease patients and finds genetic variants in 3.4% for LRRK2 and 10.1% for GBA, with 82% of patients willing to share variants with relatives.

Whole genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

The paper describes the process of obtaining an FDA IDE for returning genomic results via WGS in the All of Us Research Program and presents validation results.

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

The paper presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

Fully resolved assembly of Cryptosporidium parvum

The paper presents a high-quality, complete reference genome for Cryptosporidium parvum using Oxford Nanopore and Illumina reads, enabling comprehensive genomic studies.

Genetic Sex Validation for Sample Tracking in Clinical Testing

The paper validates genetic sex using a 96-SNP PCR panel to track samples in clinical testing and identify inconsistencies.

Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals

This study develops an oligonucleotide capture sequencing method to generate SARS-CoV-2 genomic and transcriptome sequences from clinical samples, revealing differential transcriptional activity and ORF10 expression.