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 Biosystems Engineering.


Dr. Bonnie Hurwitz

Principal Investigator

Dr. Bonnie Hurwitz is an Assistant Professor of Biosystems Engineering at the University of Arizona and BIO5 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.

Ken Youens-Clark

Sr. Scientific Programmer and Technical Lead

Ken Youens-Clark 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).

Matt Bomhoff

Sr. Software Engineer

Matt Bomhoff is a full-stack developer who works on bioinformatics applications and infrastructure 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 and Planet Microbe projects.

Alise Ponsero

Post-Doctoral Researcher

Alise Ponsero is a postdoctoral fellow from France. She received her PhD in molecular biology and genetics at the University of Paris-Sud in 2016 and a master’s degree in computer science in 2017 at the University of Rennes I. Her scientific interests are de novo comparative metagenomics, machine learning and statistical methods for multi-omics integration.

 

Graduate Students

Kai Blumberg

Kai Blumberg is a PhD student in the University of Arizona Biosystems Engineering department. He is working to create a model cyberinfrastructure system called Planet Microbe to integrate and provide analytical tools to analyze key marine omics and biogeochemical datasets. As a contributor to the Environment Ontology (ENVO), Kai works to create high-quality human and machine-readable meta-data in order to make environmental and genomic data findable, accessible interoperable for the next generation of artificial intelligence systems.

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. He also 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.

Xiang Liu

Xiang Liu’s research aims 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.

 

Previous Lab Staff

Programmers

Name Title Project
Joshua Lynch Sr. Programmer iMicrobe
Vladimir Frolov Web developer VERVE Net
 

Graduate Students

Name Year Department/Focus
Scott Daniel 2014-2018 Microbiology, Gut bacteria dysfunction in TGF-beta deficient colon cancer
James Thornton Jr. 2016-2018 Biosystems Engineering, Human microbiome
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
 

Undergraduate Students

Name Year Project
Andrew Adair 2017 Lab website
Celina Gomez 2015-present VERVE Net
Jeffrey Saccone 2015-2016 VERVE Net
Bill Wilder 2015-2016 Scripting and tool development