Carson Holt

Background

About Carson Holt

I am the Director of the Utah Center for Genetic Discovery (UCGD) Core Facility at the University of Utah, and I oversee a team of software developers and research scientists that study human disease through genomic and sequencing based analysis. As core director, I am the architect of the hardware and software based infrastructure supporting hundreds of research and clinical projects at the University of Utah. This includes the management of thousands of terabytes of sequencing datasets from tens of thousands of individuals, and the development of applications for use in the cloud, Linux based systems, and high throughput computer clusters. Significant clinical projects we support include the Utah NeoSeq project which provides rapid genetic diagnosis for critically ill infants at the University of Utah pediatric NICU and the Undiagnosed Disease Network which seeks to solve mysterious clinical conditions using advanced technologies. As a research scientist, I have 15+ years of experience studying topics including genomic variation, evolutionary biology, cancer, and human disease. I have been responsible for developing notable tools such as the genome annotation pipeline MAKER which is used by thousands of genome projects worldwide. I developed the FastQForward sequence analysis pipeline, currently the fastest whole genome sequence analysis pipeline in the world (it can align raw sequencing reads and identify all variation in a whole human genome in just 5 minutes compared to 24 hours or more for comparable software pipelines). I also develop software and methods for managing large datasets including the BGZFast suite of tools which allows researchers to leverage hundreds of CPUs when producing and manipulating compressed datasets compatible with popular sequencing analysis tools like Tabix. As part of my research, I also collaborate on multiple genome mapping projects and provide expertise in genome annotation and downstream comparative genomic and evolutionary analyses. In addition, I am an active participant in the Generic Model Organism Database (GMOD) project, and I have been involved in both software development and educational outreach for GMOD. I am interested in work in human genetics, cancer research, clinical diagnostics, genome annotation, and developing software for biological analysis. Specialties: sequence analysis, genome, annotation, molecular biology, phylogenetics, computer programming (Perl, C, Java, Python, and R), application development, web application development, MPI application development