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Faculty

Abdo, Zaid

Zaid Abdo is an Assistant Professor in the Departments of Mathematics and Statistics and in the Bioinformatics and Computational Biology program at the University of Idaho. His research interests combine mathematical modeling and statistical analysis using computationally intensive methods and simulation.

For IBEST/COBRE, Zaid is the project director of COBRE Project 4. His focus in this project is to develop model-based statistical clustering and classification methods. These methods will serve to group microbes within different human organs into different communities and taxa, a step towards a greater understanding of the "human microbiome." Zaid is also involved in COBRE Project 1 as a co-investigator. His focus in this project is to develop mathematical models and statistical methods to identify the parameters of plasmid evolutionary processes.

Brown, Celeste

Celeste Brown is an Associate Research Professor in the Department of Biological Sciences as well as the IBEST Bioinformatics Coordinator at the University of Idaho. Her research follows two avenues: 1) how gene regulation changes in response to selection, and 2) the evolution of disordered proteins. The link between these two disparate areas is that proteins involved in gene regulation are often disordered.

As the Bioinformatics Coordinator, Celeste facilitates the use of the bioinformatics tools, both software and hardware, within the University and across the state of Idaho. As part of the current COBRE grant, Celeste is studying how gene regulation changes in response to selection, and continues her collaboration with Holly Wichman and Gary Daughdrill on the evolution of protein sequences in response to selection.  Celeste has served on the graduate committees for Bioinformatics and Computational Biology (BCB) students in the Departments of Computer Science, Microbiology, Molecular Biology and Biochemistry, Plant, Soils and Entomological Sciences, Mathematics and Biological Sciences.

Forney, Larry

Larry Forney is a Professor in the Department of Biological Sciences at the University of Idaho.  His research program aims to understand the microbial ecology of the human microbiome, the adaptive evolution of prokaryotes in spatially structured environments, and the biogeography of microorganisms on various spatial scales.

Larry is the Director of IBEST, and works to facilitate interdisciplinary collaborations, the mentoring of junior faculty, and the enhancement of research core facilities.  He collaborates with biologists and mathematicians of IBEST on a range of projects including the statistical analysis of microbial community ecology, factors controlling the diversification and maintenance of bacterial populations in biofilms, and analysis of the "virtual genome" of horizontally transferred genes among prokaryotes.

Foster, James

James A. Foster is a Professor in the Department of Biological Sciences, and also an adjunct Professor of Bioinformatics and Computational Biology, Computer Science, and Philosophy. His research currently focuses on the evolutionary constraints on complex dynamic systems ranging from microbial ecologies with Larry Forney to mobile elements in the genome with Holly Wichman to adaptive computing hardware and software.

James co-founded IBEST with Holly.  He has worked with students and faculty in Computer Science, Bioinformatics, Biology, Mathematics, Philosophy, and more.  He has mentored and been mentored by faculty in those departments as well.  Due to his range of interests he has been called, among other things, an autodidactic polymath (see also: "self-taught smartypants").

Harmon, Luke J.

Luke J. Harmon is an Assistant Professor in the Department of Biological Sciences at the University of Idaho. Luke also holds adjunct status in the Department of Statistics. His research group is interested in adaptive radiation. His group conducts field and lab research on a variety of species, including island lizards, stickleback fish, and amphibians.

In collaboration with IBEST and Larry Forney, Luke is investigating the evolution of antibiotic resistance in bacterial biofilms. Biofilms grown in the lab evolve stunning levels of diversity in a short time, including resistance to various types of antibiotics. His lab will use a combination of statistical modeling and laboratory experiments to investigate this process.

Joyce, Paul

Paul Joyce is a Professor of Mathematics, Statistics, Bioinformatics and Computational Biology at the University of Idaho.   His research focuses on developing and rigorously testing methods and predictive models to describe genetic phenomena.  These include models and methods to: predict how viruses adapt; show the effect of antibiotic resistance genes encoded on plasmids; predict ancestral relationships among species; and to understand the ecological structure of bacterial communities in biofilms.

Thanks to the broad scope of his research, Paul has been able to collaborate on a large number of peer reviewed journal articles with IBEST investigators, most of which have involved University of Idaho graduate students.  Paul is a mentor for junior faculty, and since 2003 he has graduated two PhD and two MS students and is currently advising two other PhD students.  He also helped to secure funding for two undergraduate researchers in 2008.

Krone, Steve

Steve Krone is a Professor in the Department of Mathematics at the University of Idaho.  He and his research group use mathematical/computational models to study the ecology and evolution of microbial populations, especially in the presence of spatial structure.

Steve collaborates with Eva Top, Holly Wichman, and Larry Forney from the Department of Biological Sciences in joint theoretical/experimental studies involving bacteria and phage. As part of the current COBRE grant, Steve is also starting his own phage lab to study the effects of spatial structure on the evolution of viral pathogens.

Robison, Barrie D.

Barrie D. Robison is an Assistant Professor in the Department of Biological Sciences at the University of Idaho. His lab is interested in behavioral and physiological genomics using both zebrafish and rainbow trout as model systems. Specific research areas in the lab currently include identification of the genetic basis of adaptation to captivity, the genetic basis of fear-related behaviors, and nutritional genomics in fishes.

In the context of IBEST, Barrie's lab is investigating the potential role of genetic variation in regulating the behavioral response to Selenium supplementation. Barrie also co-advises BCB doctoral student Matt Settles with Terry Soule, and serves on several other graduate committees.

Rosenblum, Erica Bree

Erica Bree Rosenblum is an Assistant Professor in the Department of Biological Sciences at the University of Idaho.  Her research examines the processes that generate and impact biological diversity, with a focus on adaptive evolution across different levels of biological organization, from genes to communities. Her lab is currently combining whole genome assays with ecological field studies to investigate the genetics of the interaction between frog hosts and the deadly chytrid pathogen.

Bree's lab started at UI in the summer of 2008, and her involvement with IBEST will grow over the coming years.  She looks forward to developing new collaborative projects that integrate experimental, functional, and computational approaches to disease research.

Soule, Terence

Terence Soule is an Associate Professor in the Department of Computer Science at the University of Idaho. He also holds adjunct status in the Neuroscience Program. His research group is interested in evolutionary computation - simulated evolution - as both an optimization technique and to further understand natural evolution.

Terry's current research projects include evolving cooperation among computer agents, evolving classifiers to identify disordered regions in proteins, and studying the genetic robustness in evolving populations.

Sullivan, Jack

Jack Sullivan is a Professor in the Department of Biological Sciences at the University of Idaho. His research has three major foci: conservation and ecosystem genetics in Pacific Northwest mesic forests; phylogeny, hybridization, and speciation of chipmunks; and application of decision theory to phylogeny estimation. All three projects involve high performance computing, and the first two involve fieldwork and integration of molecular genetic data with geographic and ecological information.

Jack collaborates with IBEST-coordinated COBRE investigators Paul Joyce and Zaid Abdo on decision theory in phylogenetics. Jack serves as senior faculty mentor to Luke Harmon and Zaid, and has served on the graduate committees of six students associated with IBEST.

Top, Eva M.

Eva M. Top is a Professor in the Department of Biological Sciences at the University of Idaho. Her research is currently focused on the evolution and ecology of broad-host-range (BHR) plasmids. These plasmids play an important role in the rapid adaptation of their bacterial hosts to changing environments. A good example is their ability to rapidly spread resistance to multiple antibiotics among diverse bacteria.

Eva enjoys being involved with IBEST, and views it as a great opportunity to do interdisciplinary research. By collaborating with talented and dedicated researchers outside of her own field, Eva has been able to take her research and findings to new levels of productivity and scope.

Wichman, Holly

Holly Wichman is a Professor in the Department of Biological Sciences at the University of Idaho and is a co-founder of IBEST.  Her research focuses on two distinct areas - mechanisms of adaptive evolution, and genome evolution in mammals, especially the activity and extinction of LINE-1 and retrovirus-like elements.  These elements make up a substantial proportion of our genome and yet remain enigmatic in many respects.

Holly collaborates on many projects with IBEST members.  With Paul Joyce and Steve Krone, she conducts laboratory experiments to provide empirical data to explore basic mechanisms of evolution and test theoretical models.  With Marty Ytreberg and Celeste Brown, she investigates the molecular underpinnings of adaptation.  With Celeste, James Foster, and Luke Harmon she studies genome organization in mammals.  Graduate and undergraduate students, as well as postdoctoral fellows and technicians, contribute to these investigations.  The Wichman lab frequently hosts Math/Stats graduate students doing wet lab rotations for UI's Bioinformatics and Computational Biology program.

 

Williams, Christopher J.

Christopher J. Williams is a Professor in the Department of Statistics at the University of Idaho.  His research involves the development and application of statistical methods in the fields of genetics and natural resources.

For IBEST/COBRE, Chris collaborates Celeste Brown and Larry Forney.  With Celeste, Chris works on the statistical characterization of disordered proteins based on their amino acid sequences.  With Larry, Chris uses statistical methods to address questions in microbial community ecology.

Ytreberg, F. Marty

F. Marty Ytreberg is an Assistant Professor in the Physics Department at the University of Idaho. His research group is interested in applying the principles of computational and theoretical physics to problems in biology, chemistry and physics. Marty has a particular research interest in the molecular mechanisms underlying physical phenomena in biomolecules.

For IBEST/COBRE, Marty is utilizing computational techniques to understand adaptive evolution in bacteriophages. In collaboration with Holly Wichman, Marty's research group is using computer simulations to quantitatively estimate the effect of single amino acid changes on capsid protein interactions and stability.

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