What We Do

Our lab focuses on large-scale –omics datasets, high-throughput computing, and big data analytics. We leverage these technologies to answer questions related to the relationship between microbes, their hosts, and the environment. In particular, we focus on viral-host interactions and co-evolution given environmental factors (i) in aquatic systems and (ii) for phage treatment of diabetic foot ulcers.

Our lab is committed to open science. To this end, we develop bioinformatics tools and support community data resources (via iMicrobe and iVirus). These projects enable large-scale –omics analyses at all levels of computational-ability by using the CyVerse Cyberinfrastructure. To promote community-based learning and protocol sharing in viral ecology we are currently developing VERVENet, a Viral Ecology Research & Virtual Exchange Network in collaboration with protocols.io.

Our lab was established in August, 2014 at the University of Arizona in the Department of Agricultural and Biosystems Engineering.

Who We Are

Bonnie L. Hurwitz, PhD

Principal Investigator

Dr. Bonnie Hurwitz is an Assistant Professor of Biosystems Engineering at the University of Arizona and Bio5 Research Institute Fellow. She has worked as a computational biologist for nearly two decades on interdisciplinary projects in both industry and academia. Her research on the human/earth microbiome incorporates large-scale –omics datasets, high-throughput computing, and big data analytics towards research questions in “One Health”. In particular, Dr. Hurwitz is interested in the relationship between the environment, microbial communities, and their hosts. Dr. Hurwitz is well-cited for her work in computational biology in diverse areas from plant genomics to viral metagenomics with over 1700 citations.

Sr. Scientific Programmer and Technical Lead

Ken Youens-Clark is a Sr. Scientific Programmer who works on computational tools and interfaces for scientists.  Tools are usually implemented via high-performance cluster computers (HPCC) that may include Singularity/Docker/VM development, and interfaces can range from command-line programs (bash, Perl, Python, R) to websites (Perl/Mojolicious, node, Elm).

Ken Youens-Clark

Matt Bomhoff

Sr. Bioinformatics Programmer

Matt Bomhoff develops bioinformatics applications for HPC and the web. His professional interests include genomics, web development, and data visualization. Matt is responsible for software development for the Ocean Cloud Commons project in the Hurwitz Lab. LinkedIn GitHub

Sr. Programmer

Joshua Lynch is a senior bioinformatics programmer. His scientific interests are host-microbiome interaction, machine learning, HPC, software development and testing, and virtualization. In the Hurwitz lab he is building HPC applications for metagenomics research.

Joshua Lynch

Current Lab Staff

Graduate Students

Alise Ponsero
Alise Ponsero is a visiting student in bioinformatics from the Université de Rennes I, France. Her scientific interests are viral-host interactions, metagenomics and machine learning.
Scott Daniel
Scott Daniel, PhD. is a postdoctoral researcher interested in metagenomics, machine learning, and the gut microbiome. He recently completed his Ph.D. at the University of Arizona entitled “Gut bacteria dysfunction in TGF-beta deficient colon cancer”. Before that, Scott worked in IT/IS industry in the San Francisco area and got his Bachelor’s in Psychology from UC Berkeley. When he’s not doing bioinformatics, Scott enjoys oil painting, cycling, and gaming.
James Thornton Jr.
Interests include metagenomics with a focus on the human microbiome and its implication on health and disease. He develops bioinformatics pipelines that can be used to analyze DNA sequence data from clinical samples in order to improve diagnostic procedures. Current research involves computational analysis of blood samples obtained from cancer patients hospitalized with an infection. His goal is to identify possible causative organisms involved with the infection using a streamlined bioinformatics pipeline.
Xiang Lui
My research is to provide a strategy to study diversity, composition, and the longitudinal dynamics of microbial communities from clinical samples using whole genome shotgun sequencing data. This strategy combined k-mers and social network analysis is able to visualize the sample networks and determine the clinical factor driving microbial communities structure.
Illyoung Choi
Illyoung Choi is a Ph.D student in the Computer Science department at the University of Arizona. His research focus is in big data analytics and development of cloud data-storage services. He develops big-data analytic tools to help bio-scientists analyzing large-scale sequence samples. Also, he contributes to development of data-storage platforms such as Syndicate and iRODS.
Chunan Liu
Chunan Liu is a PhD student from Agricultural & Biosystems Engineering (ABE). She received her B.S. degree in Food Science from Sichuan University in 2012, and M.S. degree in Emergency Management and Business Continuity from New Jersey Institute of Technology in 2014. Her current research is Phage Therapy to Diabetic Foot Ulcers (DFU), under the guidance of Dr. Bonnie Hurwitz.

Undergraduate Students

Andrew Adair
Andrew Adair is an undergraduate in the Computer Science department at the University of Arizona. Andrew develops web tools for the Hurwitz Lab. Part of Andrew’s work includes the design of this website.

Previous Lab Staff

Name Title Project
Vladimir Frolov Website Programmer VERVE Net
Co-Advised Graduate Students
Name Year Department Focus
Brian Hallmark 2015-present Statistics Graduate Interdisciplinary Program Comparative Metagenomic Algorithms for Marine Sciences
Chirag Shetty 2014-2015 Management Information Systems iMicrobe
Anu Mary Jacob 2014-2015 Management Information Systems iMicrobe
Name Year Project
Celina Gomez 2015-present VERVE Net
Jeffrey Saccone 2015-2016 VERVE Net
Bill Wilder 2015-2016 Scripting and tool development