Faculty & Staff

Faculty

The following faculty listings give brief descriptions of the wide range of research interests of the Bioinformatics Graduate Faculty. Faculty names link to departmental or divisional home pages, which have more information.

  • Daniel Boley, Ph.D. - Computer Science. Dr. Boley's research includes development of a hierarchical divisive clustering algorithm. Research issues include theoretical foundations of the algorithm, scalability of the methods, extensions to the algorithm capabilities, extensions to applications beyond text document clustering, and validation of algorithm results. The method is being applied to gene expression, toxicology, and medical literature datasets. It will be extended to other paradigms such as hierarchical taxonomies, document rating aids and collaborative filtering. By incorporating it into a Web agent, the method will be made available to a wide audience.

  • Colin Campbell, Ph.D. - Pharmacology. Dr. Campbell works to gain a greater understanding of molecular genetic mechanisms of DNA repair and recombination in mammalian cancer cells. The goal is to identify genes that play important roles in this process, and to determine how their protein products catalyze DNA repair in these cells. The long-term objective of the effort is to identify targets for future therapeutic intervention, in order to increase the effectiveness of cancer treatment. He uses gene transfer and cloning strategies, as well as traditional biochemical approaches to achieve these goals.

  • John Carlis, Ph.D. - Computer Science. Dr. Carlis is a computer scientist specializing in complex, scientific databases. This work includes interdisciplinary teams working to define data models for integrated databases, and retrieval language extensions to support novel queries. Massive databases motivate the creation of new ways to visualize such data.

  • Yang Da, Ph.D. - Animal Science. Dr. Da is interested in quantitative genetics, including statistical analysis for mapping disease genes and quantitative trait loci, statistical procedures to apply genetic markers to animal breeding and genetics, and genetic diversity in animals.

  • Lynda B.M. Ellis, Ph.D. - Laboratory Medicine and Pathology. Dr. Ellis focuses on developing bioinformatics tools that support the work of life science colleagues. With biochemist Larry Wackett, Dr. Ellis has developed an innovative microbial biotechnology database on the World Wide Web: The University of Minnesota Biocatalysis/Biodegradation Database. With developmental cell biologist Stephen Ekker, she develops bioinformatic databases and selects target for Danio rerio (zebrafish) functional genomics. She also studies economic models for the support of the biological database infrastructure.

  • Scott Fahrenkrug, Ph.D. - Animal Science. Dr. Fahrenkrug seeks to understand the cellular and molecular mechanisms underlying the growth and development of tissues important to livestock production. Genomic loci that contribute to production trait variation are identified by linkage and linkage-disequilibrium mapping, as well as comparative embryology and comparative genomics. Candidate genes are assessed in vivo and in vitro using model organisms and cultured cells. He emphasizes the conversion of biological information into tools for the enhancement of animal health and production.

  • Alexander Grosberg, Ph.D. - Physics. Dr. Grosberg's area of research is the statistical mechanics of biopolymers, and the central emphasis in his work is how the physical properties of biological macromolecules depend on their respective primary sequences. In other words, the question is how physical properties of macromolecules are dictated by their biological information. To this end, his group has worked out one of the first computational methods for sequence design of model proteins based on native state energy minimization over the sequences. He is currently writing a book on Disordered Polymers, which includes discussion of these questions.

  • Yiannis Kaznessis, Ph.D. - Chemical Engineering and Materials Science. Dr. Kaznessis is interested in the development and employment of bioinformatics tools and statistical mechanics methods that will enhance our understanding of complex, molecular-level biological events and will confer the ability to design diagnostic and therapeutic solutions. He is particularly interested in the molecular and cellular aspects of protein functionality, protein-protein and protein-membrane interactions. Structural bioinformatics solutions and computer modeling methodologies are developed that tackle the protein sequence-structure-function relationship both from an evolutionary and a biophysical perspective. Such integrated, hierarchical approaches are employed enabling the rational design of novel biomolecular products and the engineering of metabolic pathways.

  • George Karypis, Ph.D. - Computer Science. Dr. Karypis's research interests span the areas of parallel algorithm design, data mining, applications of parallel processing in scientific computing and optimization, sparse matrix computations, parallel preconditioners, and parallel programming languages and libraries. His recent work has been in the areas of serial and parallel graph partitioning algorithms, parallel sparse solvers, data mining, and parallel matrix ordering algorithms. His research has resulted in the development of software libraries for serial and parallel graph partitioning (METIS and ParMETIS), hypergraph partitioning (hMETIS), and for parallel Cholesky factorization (PSPASES). He has coauthored a book entitled "Introduction to Parallel Computing" (Benjamin Cummings/Addison Wesley, 1994).

  • Arkady Khodursky, Ph.D. - Biochemistry, Molecular Biology and Biophysics. Dr. Khodursky's research is focused on using and developing functional genomics tools, such as DNA microarrays, in order to address fundamental questions regarding microbial biology. A characteristic of functional genomics is the parallel analysis of multiple sequences, sometimes representing entire genomes. This massive parallelism provides an enormous opportunity for genetic screening and molecular phenotypic analysis. Interpretation of the resulting highly complex data presents a novel challenge to molecular biologists. In his work on Escherichia coli and Saccaromyces cerevisiae, he generates and uses such whole genome DNA microarrays.

  • Georgiana May, Ph.D. - Ecology, Evolution and Behavior. Dr. May investigates the genetic and molecular basis of plants' evolutionary interactions with other organisms, especially fungi. Projects include the evolutionary interactions between corn and the pathogenic smut fungus, evolution of resistance genes, and the role of genome rearrangement in pathogenesis. Her work encompasses a variety of approaches: field experiments and observations, systematics, genetics, and molecular biology.

  • Claudia Neuhauser, Ph.D. - Ecology, Evolution and Behavior. Dr. Neuhauser is an applied mathematician. Her research interests are in two areas of biology: ecology and genetics. In ecology, she studies the role of space in community dynamics, and in genetics, how selection affects genealogies. These investigations are theoretical, relying on mathematical models, analytical methods, and partially on computer simulations. Most ecological models of communities do not take into account that individuals interact with each other in a spatial environment. She investigates how space affects community dynamics. To interpret population genetic data, genealogical or coalescent methods have proved extremely valuable. This method allows one to estimate population genetic paramenter, such as mutation rate. Her research focuses on how selection shapes the genealogical tree of sampled genes.

  • Hans Othmer, Ph.D. - Mathematics. Dr. Othmer is interested in applied mathematics, mathematical biology, and dynamical systems, including mathematical models of chemotaxis and individual and collective cell motion.

  • Wei Pan, Ph.D. - Biostatistics. Dr. Pan's research interests include the analysis of microarray data. His goal is to develop statistical methods for detecting genes with different expression under two conditions

  • Cavan Reilly, Ph.D. - Biostatistics. Dr. Reilly is interested in applying Bayesian methodology, computation, filtering, and spatial statistics to problems in the natural sciences. As a member of the Great Lakes Center for AIDS Research, he uses statistical genomic methods to understand HIV.

  • Lawrence P. Wackett, Ph.D. - Biochemistry, Molecular Biology and Biophysics. Dr.Wackett studies microbial catabolic enzymology and functional genomics: fundamental biological mechanisms, enzyme evolution and applications for biotechnology. More than ten million organic compounds are known. Most of them do not accumulate in the environment, and this suggests they serve as substrates for one or more microbial enzymes. Microbial enzymes represent the most diverse biocatalytic potential on Earth. Our knowledge of what nature has wrought is increasingly being used for bioremediation to detoxify hazardous waste and biocatalysis to synthesize specialty chemicals. Studies of microbial metabolism are also important in the context of functional genomics. Microbial genome sequencing projects are leading to the accumulation of genes with unknown function. Reverse genomics approaches are being used to discover a broad range of new microbial functions that will be used to identify unknown genes derived from the genome sequencing projects.

  • Nevin Dale Young, Ph.D. - Plant Pathology. Dr. Young focuses on the structural genomics of plants, with special emphasis on disease resistance genes. Through the use of large-insert DNA libraries and high throughput DNA sequencing, his students are physically mapping the genomes of soybean and the model legume species, Medicago truncatula. In the process, they are discovering numerous genomic regions that show similar structure at the level of "microsynteny." Using similar genomic tools, they are isolating complex families of disease resistance genes from soybean and M.truncatula and studying their molecular diversity and evolutionary history.

Staff

  • Doreen Gruebele. Principle Administrative Specialist, ALRT Center