Using Computational Genomics to Investigate Human Disease

Our Software Our Team

Research

We develop software tools for genomic data analysis using a combination of biological, statistical, and engineering approaches to accurately detect and interpret inherited and somatic genetic variants. We focus on developing easy-to-use, web-based, visually-driven, interactive and real-time software tools for intuitive analysis of genomic data. Our overall goal is to develop and apply software to better the care and outcomes of patients.

Clinical Genomics

We collaborate with medical geneticists and clinicians across a broad spectrum of human diseases, investigating the genetic etiology of these diseases and potential therapeutic opportunities.

Precision Oncology

We build and apply methods and visualizations for comprehensive profiling of tumors and their clonal structure across disease progression and therapeutic interventions to directly impact the patient's care.

Variant Discovery

Building on our lab's previous work, we continue to develop computational algorithms for variant discovery, including the accurate detection of germline de novo and somatic cancer variants.

Visually-driven Genomics

Our software development approach prioritizes intuitive and interactive visual presentations of complex genomic data, making our software broadly accessible, regardless of computational expertise.

Software

iobio

Realtime genomic data visualization and analysis web tools

RUFUS

K-mer based de novo variant calling

  • direct comparison of k-mers in sequencing reads
  • has no reference alignment bias
  • is powered to call all variant types and sizes

freebayes

Bayesian haplotype-based variant calling

superseeker

Computational reconstruction of tumor clones

bayescmg

An applied Bayesian framework for the ACMG/AMP criteria

  • automatically applies ACMG criteria to vcf records
  • calculates a simple pathogencity probability
  • filters and prioritizes variants

ped_draw

Pedigree drawing with ease

  • quick and easy pedigree visualization
  • simple one-liner syntax
  • no dependencies

bamtools

C++ API & command-line toolkit for working with BAM data

Tangram

Fast structural variation detection toolbox

Publications

Some of our recent and featured publications are shown below, but you can find all of our publications on PubMed and Google Scholar

Apply!

We are always looking for talented and motivated people to join our team!

We are currently looking for post-docs with an emphasis in biostatistics and mathematics, as well as graduate students through the Utah Bioscience PhD and MD/PhD programs.

Email us or check our current job postings!

Members

Gabor Marth

Principle Investigator
Professor of Human Genetics

Alistair Ward

Director of Research and Science
CEO, Co-Founder Frameshift Genomics

Xiaomeng Huang

Assoc. Dir. of Research and Science
Precision Oncology

Isabelle Cooperstein

PhD Student
Genotype:Phenotype Correlations

Casey Sederman

MD/PHD Student
ML / Precision Oncology

Stephanie Gardiner

PhD Student
Somatic Mosaicism

Patrick Ozark

MD/PhD Student
ML / Precision Oncology

Taeho Kim

PhD Student
ML / Precision Oncology

Tony DiSera

Senior Software Developer
Clinical Genomics / iobio

Stephanie Georges

Principal Software Engineer
Variant Calling Algorithms / iobio

Anders Pitman

Software and Backend Developer
iobio

Yang Qi

Software Developer
iobio

Emerson Lebleu

Software Developer
iobio

Lab Alumni

Gage Black

Bioinformatics Scientist
Teiko.bio

Yi Qiao

Assistant Professor
U of Utah, Biomedical Informatics

Niki Williams

Sr Manager, Software Test Engineering
bioMérieux

Chase Miller

CTO | Co-Founder
Frameshift Genomics

Matt Velinder

Head of Bioinformatics
Frameshift Genomics

Andrew Farrell

Senior Research Scientist
Oak Ridge National Laboratory

Szabolcs Tarapcsak

Senior Data Scientist
Servier Pharmaceuticals

John Chamberlin

Postdoctoral Researcher
UPF/CRG

Corin Thummel

Business Data Analyst
FLSmidth & Co.

Matthew Bailey

Assistant Professor
Brigham Young University

Preetida Bhetariya

Bioinformatics Analyst / RA
Harvard School of Public Health

Erik Garrison

Postdoctoral Research Fellow
University of California, Santa Cruz

Contact

Our lab is part of the Utah Center for Genetic Discovery (UCGD) and the Department of Human Genetics at the University of Utah

Address

15 N 2030 E, Salt Lake City, UT