Viacheslav Fofanov, Ph.D.I am an Assistant Professor in the Informatics and Computing Program at the Northern Arizona University's College of Engineering, Forestry, and Natural Sciences. My research focuses on applications of High Throughput Sequencing data to pathogen detection in complex clinical and environmental samples. In humans, this includes detection and transmission tracing (person-to-person, surface-to-person, and animal-to-person) of community-acquired Methicillin Resistant Staphylococcus aureus (MRSA) infections, an important cause of soft tissue and skin infections, with significant ethnic health disparities. In animals, this includes development of tools for pathogen surveillance of wildlife reservoirs, including PCR-amplicon and metagenomic sequencing approaches. My particular focus is on bats - an important and ubiquitous animal reservoir of a number of important human-affecting diseases.

Specialties:
  • Bioinformatics, Statistics, and Computer Science
  • Data-structures and algorithm for High Throughput Sequence data analysis
  • Environmental and clinical metagenomics via shotgun sequencing techniques
  • Bacterial and viral quasispecies characterization
  • Pathogen detection
viacheslav.fofanov@nau.edu
Affiliates
Faith M. Walker, Ph.D.I employ a variety of tools in ecology and genetics to understand population biology and natural and evolutionary history of organisms. A uniting theme is how flora and fauna function in natural systems and how population processes are impacted in human-altered ones. My favorite questions have a management component and involve species that are scientifically intractable because they are cryptic, rare, or endangered. I recently incorporated bats into my research because they face many conservation challenges, yet are one of the most difficult mammals to study, being cryptic, nocturnal, and volant, and some cases solitary, non-cave roost-ers. I work with many excellent collaborators and enjoy a global perspective to my research, having spent seven years overseas in various research contexts.Faith.Walker@nau.edu
Carol L. Chambers, Ph.D.I am a Professor of Wildlife Ecology at Northern Arizona University (NAU) with a long-term bat ecology and habitat relationships research program. For almost 20 years, my research has focused on bats, resulting in 15 studies encompassing 22 southwestern bat species, some of which are uncommon and rare species. My work covers a variety of roost types such as snags, caves, and mines, as well as a wide range of methods and techniques including live-trapping mark-recapture, track plates, occupancy modeling, radio telemetry, stable isotopes, and others. Carol.Chambers@nau.edu
Talima Pearson, Ph.D. I am interested in the dispersal of bacterial pathogens over space and time. This entails documenting and tracing mutations that occur over multiple evolutionary time periods. Over long term evolutionary periods, we can trace the spread of disease on a regional or global scale. For some bacterial pathogens, it is possible to track the evolution of an infection within a single host. This may allow us to identify adaptive mutations and the progression of disease. Understanding the evolution and population dynamics at small temporal scales will hopefully help us better understand the more complex dynamics of mutations that accumulate over longer periods of time. Talima.Pearson@nau.edu
Current Students
Isaac Shaffer, PhD StudentI am a graduate student pursuing a PhD in Bioinformatics in the School of Informatics, Computers, and Cyber Systems. I have received a MS in Statistics from Northern Arizona University. My primary areas of research are in the characterization of microbial communities, using of metagenomic sequencing tools, and the simulation of infectious disease dynamics in complex microbial and human communities. I am currently involved with projects that range from the characterization of the behavior of oral plaque to the analysis of composition of intestinal microbial communities. My simulation projects include the estimation of network parameters required to recreate an Susceptible-Infectious-Susceptible (SIS) model of Staphylococcus aureus dynamics that is consistent with observations reported in a selection of published literature. Isaac.Shaffer@nau.edu
Tsosie Schneider PhD StudentTsosie Schneider is graduate student in the SICCS PhD program. He completed his undergraduate degree in Computer Science at NAU in Spring 2016. He claims his doctoral aspirations are merely a means to re-enact the doctor greeting scene from the film "Spies like us". tes87@nau.edu
Daryn Erickson, Senior Undergraduate ResearcherI am a senior at NAU pursuing a B.S. in Microbiology with a Minor in Chemistry. I work closely with Jill Cocking to carry out various wet lab experiments and protocols for Dr. Fofanov. My passion is infectious disease and genetic research which I hope to expand my knowledge on while working in the Fofanov Lab. After I graduate from NAU, I plan to pursue a PhD in Microbiology. My dream is to work for the CDC studying infectious diseases and pathogen genetics. dee35@nau.edu
Ryann Whealy, Senior Undergraduate ResearcherI am a senior at NAU working toward a B.S. in Biomedical Science with minors in Community Health and Psychology. I work on various projects studying the movement, evolution, and prevalence of pathogens under Dr. Fofanov. The projects I have assisted on while working in the Fofanov lab have made me even more excited to pursue a graduate degree in Medical Microbiology after completing my bachelor's at NAU. rnw42@nau.edu
Breezy Brock, Undergraduate ResearcherI am a freshman at NAU pursuing a B.S. in biology with a minor in chemistry. I work at the Fofanov lab as an undergraduate research assistant. After graduating from NAU, I plan to attend a veterinary school where I will specialize in equine medicine. I will also continue my research in infectious diseases through a DVM-PhD combined degree program. My dream is to eventually become an equine surgeon. bnw97@nau.edu
Majesty Greer-Gipson, Undergraduate ResearcherI am currently a junior at Northern Arizona University majoring in Biomedical Science. I work with Ryann and Daryn on various lab experiments and I am currently working on the Office and Cubicle Staphylococcus aureus swabbing project for Dr. Fofanov. Being able to work on these projects has been a great learning experience, because I get hands on time in the research field. I hope to take the knowledge and techniques that I have learned in this lab and be able to apply to my future job. After I graduate with my B.S. I hope to be able to go to medical school to obtain my MD/PhD and become a pediatric oncologist. I want to use the research experience I have gained from working for Dr. Fofanov and hopefully begin my own research on less harmful and more efficient treatments for cancer. mlg472@nau.edu
Samuel Poidmore, Undergraduate ResearcherI am currently a sophomore at NAU pursuing a degree in Biomedical Science with a minor in Chemistry. I am working under Dr. Fofanov to exercise my interests within the field of microbiology. On a typical day I will be assisting Ryann and Daryn performing various wet lab work. My plan is to attend medical school in the fall of 2021 in hopes to fulfill my dream of becoming an orthopedic surgeon. sap369@nau.edu
The Lab
Tara Furstenau, Ph.D.Dr. Furstenau (Ph.D. Molecular and Cellular Biology, Arizona State University) is interested in the development and application of computational and statistical methods to analyze genomic sequence data. She is currently involved with several projects in the Fofanov lab, including the development of a PCR amplicon-based pathogen detection panel as well as the construction of a bioinformatic pipeline which uses metagenomic sequence data to provide species level classification of organisms within complex samples. Her previous work involved developing simulations and statistical methods for analyzing spatial population genetic data.
[Website](http://tfursten.github.io)
[CV](http://tfursten.github.io/assets/TaraFurstenauCV.pdf)
[Twitter: @TaraFurstenau](https://twitter.com/tara_furstenau)
[Github](https://github.com/tfursten)
[Bitbucket](https://bitbucket.org/TaraFurstenau/)
tara.furstenau@nau.edu
Jill Cocking, Research Specialist, SeniorI grew up here in Flagstaff and have a BS in microbiology along with a Masters in biology from NAU. I have worked in a variety of fields including cancer research, forensics, and toxicology. I am excited to be working with the School of Informatics, Computing and Cyber Systems and I hope I can make a contribution to all the exciting work on human pathogens and their genetics happening in the department. Jill.Cocking@nau.edu
Former Students
Michael Deberg Undergraduate StudentI am currently pursuing a Bachelor's in Computer Science here at NAU and I've always been interested in biology, working for Dr. Fofanov has provided me the opportunity to combine these two interests. In my time here I have had the opportunity to work on smaller pipelines to calculate genome coverage and test primer sets as well as work on several iterations of a much more in depth pipeline which has taught me quite a lot. Being new to bioinformatics the various projects Dr. Fofanov has taken on and enlisted my assistance with have provided a plethora of learning opportunities. mike.deberg@gmail.com
Christopher Philabaum Undergraduate StudentI am a senior undergraduate student pursuing a Bachelor's of Science in Computer Science degree at NAU. Currently, I'm researching under Dr. Fofanov to better understand how to properly research. I hope to continue on to graduate school to pursue research in the many interesting fields under Computer Science! Some topics that interest me is theoretical computer science (such as computational complexity theory), combinatorics, artificial intelligence, and quantum computing. cp723@nau.edu
Nicole Pagel Masters StudentNicole is a Masters student in Computer Science at NAU and received her undergraduate degree in Economics and Finance from the University of Arizona. She is working in the Fofanov Lab as the Data Science/Informatics research assistant for the team and assists on a variety of projects involving data analysis and developing models in metagenomics and bioinformatics. Her interests include data analytics, large scale data modeling and machine learning. nsp5@nau.edu
Ryan Lancione, Undergraduate ResearcherI am a senior in Microbiology and undergraduate researcher for the Fovanov lab here at NAU. I help out with variety of projects including studying the prevalence of Strep mutans, sobrinus, and Staph aureus in caries patients across Northern Arizona, and the development of effective bioinformatic tools for analysis of Baccilus anthracis. Working on these projects is an amazing learning experience and allows me to explore my interests in microbial ecology, genetics, and bioinformatics under other extremely talented and motivated people. rl579@nau.edu