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» Biology
Develop a high-level understanding in all levels of biological analysis with outstanding research opportunities

» Computer Science, M.S. or Ph.D.
Develop your critical thinking, investigatory and expository skills for a deeper understanding of the limitations and possibilities of using computers to solve problems.

» A - Z Degree Index

Bioinformatics and Computational Biology

M.S. Bioinformatics and Computational Biology, Ph.D. Bioinformatics and Computational Biology

» Bioinformatics & Computational Biology Program » College of College of Graduate Studies

INTRODUCTION
WHAT IT TAKES
WHAT PEOPLE DO
GET INVOLVED
FACULTY

Major technological advancements in molecular and genetic research have resulted in an explosion of new biological information. With a master's or doctorate degree in bioinformatics and computational biology, you will have the specialized expertise and technical skills to decipher this complex data. You may also have opportunities to research and discover new applications that could potentially improve human health and agriculture.

Specialize in one of the following areas:

Biology: Focus on the study and research of biological systems and the understanding of the molecular and genetic data.
Computer Science/Mathematical Sciences: Explore the methods and models used in genetic and molecular biological research and concentrate on skills and techniques to develop and use databases.

Drawing on expertise and resources from nine university departments, this progressive graduate degree merges study and research in biology, mathematics, computer science and statistics. You'll develop the interdisciplinary knowledge and specialized tools to manage, process and analyze complex biological data.

Depending on your area of specialization, you may study and conduct research in:

Molecular biology
Evolution
Statistical genetics
Database management systems
Probability theory
Mathematical methods and models
Biochemistry
Ecology

As a student in the bioinformatics and computational biology program, you will have the opportunity to engage in exciting collaborative research projects through the Institute for Bioinformatics and Evolutionary Studies (IBEST), a group of faculty and students from several disciplines investigating evolutionary phenomena and the bioinformatics tools to explain them.

Prepare for Success

We realize that students will enter our program with multiple backgrounds and perspectives. Our goal is to design a curriculum that builds a strong intellectual foundation in the two focus areas that are integral to Bioinformatics and Computational Biology: Computer Sciences/Mathematical Sciences and Biological Sciences. We encourage undergraduates thinking about graduate school in BCB to plan ahead. Take calculus, statistics, some programing language and biology though genetics and you will be well prepared for our program.

Your First Year

During your first years in the MS and PhD degree programs, you will form an interdisciplinary foundation by completing the following core courses:

Computational Biology: CS 515
Molecular Evolution: Biol 522
Mathematical Genetics: Math 563

Your committee will work with you to build the background in the foundational areas in which you have the least undergraduate training. For example, we have developed a course (Biol 456) which is designed to introduce biologists to the computational tools needed to conduct bioinformatics research. Similarly, we offer courses for mathematician and computer scientists to gain a background in general biology and genetics.

What You Can Do

Depending on your area of specialization, you may become a:

Bioinformatician
Biomedical computer scientist
Geneticist
Computational biologist
Biostatistician
Biomedical chemist
Clinical data manager
Molecular microbiologist
Software/database programmer
Medical writer/technical writer
Research associate and research scientist
Academic professor/researcher

Opportunities

Graduates of the University of Idaho Bioinformatics and Computational Biology Program are at the forefront of a newly emerging science. This ever-evolving field offers many diverse career paths, depending on your specialization and interests.

You'll be in high demand in health care, agriculture, pharmaceutical products, forestry, academia and other industries and governmental agencies that rely on the high-level ability to manage and analyze complex biological information. You could find yourself on the leading edge of human medical discovery, with opportunities to use your expertise to prevent diseases and create new treatments to improve human health.

Current Research

The Bioinformatics and Computational Biology Program has attracted more than $10 million in grants from a variety of sources for interdisciplinary research. Current faculty research interests include:

Experimental, theoretical, and natural evolution of viruses
Bacteriophage and plasmids
Protein flexibility
Evolution of retrotransposons
Coevolutionary genetics and plant polyploidy
Conservation genetics
Medical ecology
Computational methods for processing biological data
Phylogenetics and systematics
Statistical models for biological processe
Evolved interacting robots and software

Collaborative research projects as part of the Institute for Bioinformatics and Evolutionary Studies (IBEST) include:

Co-Evolutionary Dynamics
Evolution of Ecosystems
Genetics and Molecular Mechanisms of Adaptation
Genome Evolution
Phylogenetics and Speciation
Theory and Evolutionary Algorithms

Hands-On Experience

Collaborate with peers and nationally recognized experts on exciting research in biological, computer and mathematical sciences. Conduct laboratory experiments with one-on-one mentorship from faculty researchers in a variety of disciplines.

Thesis: Both the M.S. and Ph.D. degrees require a thesis. The M.S. degree requires at least nine credits of thesis research and the Ph.D. degree requires at least 30. Each student has a graduate committee of at least four faculty members representing the two BCB disciplines (biology, computer science/mathematical sciences). Past theses titles include:

Function Choice, Resiliency, and Code Growth in Genetic Programming
Using Classic Optimization to Speed up Burn in and Mixing in Markov Chain Monte Carlo Methods for Phylogenetic Inference
Computational Modeling of Cancer Etiology and Progression Using Neural Networks and Genetic Cellular Automata
Bacterial Diversity and Competition from the Population to the Community Level
On the use of Stochastic Population Dynamics Models in Microbial Ecology
Natural Diversity and Experimental Adaptive Evolution of Bacteriophages of the Family Microviridae

Fellowships and Assistantships: You are encouraged to apply for a research assistantship and other funding opportunities for student research. Students who have contacted and identified a specific BCB faculty member who has agreed to direct their research often have accelerated admissions decisions as well as better funding opportunities.

Facilities

IBEST Bioinformatics Core Facility
Bioinformatics Teaching Lab

Eva Top, Ph.D.
Professor
Director of BCB
My research is currently focused on the evolution and ecology of plasmids that transfer to and replicate in a broad range of bacteria. Plasmids are mobile genetic elements found in most bacteria. Because they readily transfer between different types of bacteria under natural conditions, they play an important role in rapid bacterial adaptation to changing environments. A good example is the current epidemic of multiple antibiotic resistance in human pathogens, which is largely due to the spread of multi-drug resistance plasmids. Although plasmid-mediated gene transfer is now recognized as a key mechanism in the alarming rise of antibiotic resistance, little is known about their host range, their ability to invade bacterial populations in the absence of selection, and their genetic diversity. We are addressing these questions using various Proteobacteria and plasmids as model systems.
» View Eva Top's profile

Celeste Brown, Ph.D.
Research Professor
Dr. Celeste Brown has two research areas, how gene regulation changes in response to selection, and the evolution of disordered proteins. The link between these two disparate areas is that often proteins involved in gene regulation are disordered. The gene regulation studies involve laboratory-based research and the disordered protein studies involve bioinformatics approaches.
» View Celeste Brown's profile

Brian Dennis
Professor
Research interests: Statistical Ecology, Biometrics, Mathematical Modeling, Theoretical Ecology, Conservation Biology, Population Dynamics
» View Brian Dennis' profile

Larry J. Forney, Ph.D.
University Distinguished Professor
Director of IBEST
The research done in Dr. Larry Forney’s laboratory centers on the diversity and distribution of prokaryotes. Both field and laboratory studies are done to explore the temporal and spatial patterns of community diversity, as well as factors that influence the dynamics of inter- and intra-species competition. In addition research is done to understand how spatial structure and the resulting environmental gradients influence the tempo and trajectory of adaptive radiations in bacterial species and the maintenance of diversity. Most of these studies are highly interdisciplinary in nature, and done in collaboration with mathematicians, statisticians, computer scientists, geologists, environmental engineers, physicians, and clinical scientists.
» View Larry Forney's profile

James A. Foster, Ph.D.
Professor
Dr. Foster’s current research is focused on characterizing evolutionarily permissible ecological structures in microbial ecosystems and on developing bioinformatics for very large sequence datasets. He continues to examine simulations of evolutionary processes to design complex artifacts and optimize functions. He works in close collaboration with biologists, statisticians, mathematicians, and computer scientists.
» View James Foster's profile

$Gao$

Frank Gao, Ph.D.
Professor
Research Interests: Interface of Probability Theory, Functional Analysis and Convex Geometry. In particular, small deviations of Gaussian processes; metric entropy of function spaces and operators; and intrinsic volumes of convex bodies.
» View Frank Gao's profile.

Luke J. Harmon, Ph.D.
Associate Professor
Our research investigates ecological and evolutionary aspects of adaptive radiations. Current projects span a wide range of taxa and time scales, including adaptive radiation in E. coli biofilms, evolution of island lizards in the Caribbean and Indian Ocean, and macroevolutionary dynamics of vertebrates. You will find more information about all of these projects on the research and publications pages.
» View Luke Harmon's profile

Robert Heckendorn, Ph.D.
Associate Professor
Robert works with anything that evolves. His research has included bioinformatics work in phylogenetics, new methods of Markov Chain Monte Carlo sampling, and the simulation of the geneics of the onset of breast cancer. He is currently working on evolutionary approaches to agent based simulations of international conflict and the cooperative behavior of swarms of thousands of robots.
» View Robert Heckendorn's profile.

Paul Hohenlohe, Ph.D.
Assistant Professor
Our research focuses on the genomic architecture of evolving populations, developing sophisticated theory and analytical tools to harness the power of modern DNA sequencing technology. We address basic questions of evolutionary biology as well as applications to conservation and cancer biology.
» View Paul Hohenlohe's profile

$Paul Joyce$

Paul Joyce, Ph.D.
Dean of College of Science & Professor
My research focuses on developing and rigorously testing statistical methods and stochastic 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. This broad focus has lead to collaborations with researchers in phylogenetics, population genetics, theoretical ecology, mircobial ecology, experimental evolution, conservation genetics, and the list is growing.
» View Paul Joyce's profile.

Alexander Karasev
Associate Professor

(208) 885-2350 | akarasev@uidaho.edu
» View profile

$Steve Krone$

Steve Krone, Ph.D.
Professor
Research interests: Stochastic Processes and Mathematical Biology; especially interacting particle systems, population genetics and evolutionary biology, coalescent theory, spatial models in (microbial) ecology and epidemiology, combining experimental and theoretical approaches, diffusion processes and differential equations.
» View Steve Krone's profile.

Stephen Sauchi Lee, Ph.D.
Associate Professor
My general research area is Multivariate and Computational Statistics. It includes: Integrating models and methods from statistics, neural networks, machine learning, and data mining communities to discover relationships and recognize patterns in databases; modeling using regression and classification for interpretation and forecasting; extracting information and patterns; and developing computational algorithms to increase efficiency and prediction accuracy.
» View Stephen Sauchi Lee's profile

Mark McGuire, Ph.D.
Department Head/ Professor

(208) 885-7683 | mmcguire@uidaho.edu
» View profile

Gordon Murdoch, Ph.D.
Associate Professor

(208) 885-7370 | gmurdoch@uidaho.edu
» View profile

Scott L. Nuismer, Ph.D.
Professor
My research focuses on the ecology and evolution of species interactions. The overall aim is to better understand how coevolution shapes patterns of biodiversity and the geographic distributions of interacting species. Work in my lab addresses these issues with a combination of mathematical modeling and field studies.
» View Scott Nuismer's profile

Matt Powell, Ph.D.
Associate Professor

(208) 837-9096 | mpowell@uidaho.edu
» View profile

R. Robberecht
Professor
Specialty area of Interest: Physiological plant ecology (Ecophysiology); guided independent learning (use of information technology in science education); scientific visualization and modeling (integration of ecological processes, molecule to globe)
» View R. Robberecht's Site

Barrie Robison, Ph.D.
Associate Professor
My general research interests lie at the interface between genomics, evolutionary biology, and fisheries biology. Specific areas of research emphasis in my lab include the genetic architecture of complex traits, the evolution of locally adaptive phenotypes, and genomic analysis of behavioral variation in fish. I employ two study systems to investigate these issues, the rainbow trout and the zebrafish.
» View Barrie Robison's profile

Terry Soule, Ph.D.
Professor
Research Areas: Evolutionary computation, biological modeling
» View Terry Soule's profile

Deborah Stenkamp, Ph.D.
Professor
Stenkamp’s research interests center on the examination of cellular and molecular mechanisms of vertebrate retinal development and regeneration, with a specific focus on photoreceptor differentiation, using zebrafish as the primary experimental model.
» View Deborah Stenkamp's profile

John "Jack" M. Sullivan, Ph.D.
Professor
Our understanding of the processes of nucleotide substitution (DNA sequence evolution) has been expanding greatly over the last 10 years. Furthermore, it has become apparent that ignoring such processes as heterogeneity of base composition, substitution pattern, and rate variation among nucleotide sites can compromise attempts to estimate phylogeny from DNA sequence data. Therefore, model-based analyses of DNA sequence data have become increasingly wide spread because such approaches afford the investigator the opportunity to account for such processes explicitly.
» View Jack Sullivan's profile

David C. Tank
Assistant Professor & Director, Stillinger Herbarium
I am a plant systematist and am broadly interested in the investigation of the patterns and processes that shape plant biodiversity. In general, my research is focused on the use of molecular methods to reconstruct phylogenetic relationships in plants and the application of phylogenetic methods to understand plant evolution. The evolutionary causes and consequences of processes such as hybridization, polyploidy, pollination biology, biogeography, rapid diversification, and niche evolution can only be understood in light of a robust phylogenetic hypothesis, and these hypotheses are a necessary component of modern taxonomic treatments and classification systems. Research in my lab is directed at multiple levels of plant phylogeny and current projects range from comparative phylogeography of the Pacific Northwest inland rainforest communities, to the study of species boundaries and diversification among very closely related species, to patterns of diversification among some of the major lineages comprising the plant tree of life.
» View David Tank's faculty profile

Lisette Waits
Professor; Affiliate faculty member CATIE Costa Rica
Research interests: Conservation Genetics, Landscape Genetics, Molecular Ecology, Molecular Systematics
» View Lisette Waits' profile

Holly A. Wichman, Ph.D.
University Distinguished Professor
The Wichman Lab studies viruses and their subcellular relatives, transposable elements. These two lines of research are united by a molecular approach and a strong evolutionary context. L1 elements have been active in mammals for over 150 million years and make up about 20% of the genome. Most of the copies in the genome are ancient molecular fossils, so it is a challenge to sift through all of the old copies to find those that have been recently active.
» View Holly Wichman's profile

Michelle Wiest, Ph.D.
Assistant Professor
Michelle’s research interests lie in epidemiological and biostatistical methods. Her work includes developing multivariate diagnostic and prognostic tools for evaluation of metabolic status, study design for nutrition interventions, and evaluation of risk factors for mining injuries. She plays a large role in supporting research across UI as a statistical consultant and in training master’s level statistics students in consulting.
» View Michelle Wiest's profile

Christopher Williams, Ph.D.
Department Chair and Professor
Affiliate Professor of Bioinformatics and Computational Biology
My research interests are on problems in statistical genetics, biostatistics, and statistical methods applied to issues in natural resources. One of the topics that I work on is the analysis of human twin data. Another area of interest is the estimation of disease prevalence from various types of data, such as in groups of fish that are collected and have their tissue pooled to test for disease status.
» View Chris Williams' profile

F. Marty Ytreberg, Ph.D.
Associate Professor
Developing computational methods for proteins and using these approaches to understand the underlying biophysical mechanisms that define protein structure, function and evolution.
» View Marty Ytreberg's profile