RESEARCH

Our research focus areas include Genomic Medicine and Genome Biology

Genomic Medicine

Genetics of inherited disease

Genetics of Inherited Disease

We analyze genome sequences to determine the genetic cause of a broad range of inherited disorders, including heart and lung disease, familial cancers, inflammatory and immune conditions, metabolic disease, and neurological conditions.

We participate in large-scale genome sequencing projects including the Utah Genome Project, the Pediatric Cardiac Genomics Consortium, the Simon’s Foundation Autism Research Initiativeand the Sudden Cardiac Death in the Young Consortium. We also partner with life sciences and technology companies to develop novel software tools, diagnostics, and precision therapies based on our research.

Browse our inherited disease publications here.

Cancer Genomics

Smart Cancer Genomics Technologies

Cancer is notoriously difficult to eradicate because tumors vary in their genetic makeup and in their susceptibility to cancer treatments. Furthermore, tumors adapt over time, allowing them to escape chemotherapies, metastasize, and ultimately end the patient’s life.

We have developed computational methods to track genetic changes in metastatic breast cancer tumors over the course of disease and treatment. Our goal is to help determine which genetic signatures predict aggressive growth or metastasis, which tumors respond to different treatments, and which changes signal emerging drug resistance. By following the evolutionary trajectories of individual tumors, we hope to develop precise and dynamic treatment regimens that will reduce unnecessary treatments and prevent disease relapse.

Browse our cancer genomics publications here.

Infectious disease and micro biome

Infectious Disease and Metagenomics

Microorganisms inhabiting the human body outnumber human cells ten to one and are critical for our health and survival.  Infectious disease is a global health problem, killing nearly 5 million children worldwide each year.  Yet only a fraction of the microbes that promote human health or cause disease can be identified using traditional techniques. 

In collaboration with ARUP Laboratories and IDbyDNA, Inc., we have developed Taxonomer, an ultrafast metagenomics tool that identifies all organisms present in a sample by rapidly analyzing the DNA and RNA sequences present.  Taxonomer can identify microbes from many sample types, including body fluid, soil, food, and water.  Taxonomer is already being deployed in University of Utah emergency room to diagnose respiratory infections, and for research analyses for children with Acute Respiratory Distress.  Unlike other command-line metagenomics tools, Taxonomer is available over the web via iobio, and displays results in real time, using elegant graphics and interactive displays.  

Browse our metagenomics publications here.
Learn more and try Taxonomer here

Data visualization

Data Visualization

Computational genomics technologies have exploded in recent years, but most tools still require a bioinformatician and significant computational horsepower to use.  We aim to change that with iobio, a web-based genomics tool suite that puts the power of a supercomputer into the hands of ordinary users. 

The iobio platform allows researchers, clinicians, and data analysts to drive powerful genomic analyses themselves, using only a laptop computer.  iobio analyzes genomic sequences in real time and generates interactive, visual, and intuitive displays.  To date, four genomics applications have been deployed within iobio, including the metagenomics app Taxonomer, a variant prioritization app called gene.iobio, and two data quality inspection apps vcf.iobio and bam.iobio.  

Browse our data visualization publications here.
Learn more and try iobio here.

Understanding Genomes

Genetic variation

Genome Structure and Variation

Despite decades of effort, the genetic basis of most human diseases is poorly understood. Less than 5% of the heritability of most diseases can be explained by known genetic variation.

We develop tools and methods to discover, catalogue, and characterize genomic variation, including single nucleotide polymorphisms and structural rearrangements such as deletions, duplications, copy number variation, insertions, inversions and translocations. We also study the role of genomic variation in human health and disease.  

Browse our genomic structure and variation publications here.

Loblolly pine

Genome Annotation

Accurate genome annotations form the basis for all future genetic and molecular biology research.  The sequence of the first human genome took a decade and billions of dollars to assemble.  Today, an individual lab can use our MAKER tool to assemble and annotate a new genome in a matter of hours, and the software is free for academic use.  

MAKER and MAKER-P (optimized for plant genomes) have become the gold standard software for annotation of novel genomes, with hundreds of licenses issued worldwide.  The tools have been used to annotate the genomes of the loblolly pine, the king cobra, the long-living sacred lotus, the spotted gar, the Burmese python, the desert woodrat, and dozens of others, nucleating entirely new research programs in the process.

Browse our genome annotation publications here.

 

Genome evolution - gibbon

Evolution of Genomes and Populations

Every genome is a treasure trove of information about the genetic and selective forces that drive molecular evolution and variation across and within species.

Our comparative genomics tools are used to identify molecular mechanisms of gene regulation and protein function, reveal ancient host-microbe conflicts, derive insights into global migration and population stratification, understand how mobile elements and viral infections generate genomic variation, and identify molecular changes underlying evolutionary transitions.

Browse our evolutionary genomics publications here.

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BIG DATA IN PERSPECTIVE

Because every living organism has a genome, computational genomics can inform all areas of biology and health.

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