Faculty and Resources
The exceptional computer infrastructure at the Minnesota Supercomputing
Institute and the Digital Technology Center, and an outstanding team of
faculty make UMBSI an excellent starting point for students that are
considering careers in bioinformatics.
program faculty
The Program Director PI, Dr. Yiannis Kaznessis
is Assistant Professor in the Department of Chemical Engineering and
Materials Science. He is also a member of the Digital Technology Center
and graduate faculty of the Bioinformatics Program. Dr. Kaznessis is
interested in the development and employment of structural bioinformatics
tools, systems biology models, and statistical mechanics methods. Dr.
Kaznessis is also the Chair of the Executive Committee of UMBSI.
Dr. John Carlis is Associate
Professor in the Department of Computer Science and Engineering and
member of the Bioinformatics Program and the Digital Technology Center.
Dr. Carlis specializes 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.
Dr. John Crow is Director of the
Center for Biomedical Research Informatics at the
University of Minnesota. The group provides computation,
information, and software development resources for UMN biomedical
& biological researchers. We engineer and develop bioinformatics
software systems including databases, online analysis tools, and
workflows.
Dr. Cristian Domnisoru is Associate Professor
in the Graduate Programs in Software Engineering at the University
of St Thomas, in St Paul, MN. Dr. Domnisoru.s research interest is
in the area of signal processing for bioinformatics with specific
applications to DNA base calling. He teaches courses in Bioinformatics
Algorithms, Bioinformatics Data Analysis, and Mathematical Modeling
and Simulation.
Dr. Kevin Dorfman is Assistant Professor in the
Department of Chemical Engineering and Materials Science. Professor
Dorfman is interested in the development of new tools for biology
based on novel physical phenomena at the micro and nanoscale. His
current research is focused on separating long linear DNA and
topoisomers, using a mixture of theory and experiment. Experimental
work takes advantage of the NanoFabrication Center at the University
of Minnesota and single molecule videomicroscopy. Recent theoretical
work has focused on the use of continuous time random walks for modeling
biomolecular separations.
Dr. Lynda Ellis is Professor in Department of
Laboratory Medicine and Pathology. She is also the Director of the
Graduate Program in Bioinformatics. 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 (http://umbbd.ahc.umn.edu/). 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,
is Director of Graduate Studies for the Graduate Program in Bioinformatics,
coordinates the Bioinformatics Journal Club and the Health Informatics
Seminar and teaches courses in Protein Sequence Analysis and Biocatalysis
and Biodegradation.
Dr. Alexander Grosberg is Professor in the
Department of Physics and member of the Bioinformatics Program and
the Digital Technology Center. 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.
Dr. Jeffrey Kahn is Director of the Center for
Bioethics, and Professor in the Department of Medicine at the School
of Medicine, the Division of Health Services Research and Policy at
the School of Public Health, and the Department of Philosophy, at the
University of Minnesota. The Center for Bioethics is one of the leading
research centers for bioethics, with 15 full- and part-time faculty. Its
mission consists of education, research, and service in the area of
bioethics. Dr. Kahn writes and speaks widely on bioethics issues, with
particular focus on ethics and health policy, ethics of research, and
ethics and organ transplantation.
Dr. George Karypis is Associate Professor
in the Department of Computer Science & Engineering and member
of the Bioinformatics Program and the Digital Technology Center. 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.
Dr. Fumiaki Katagiri is Associate Professor in the
Department of Plant Biology. Dr. Katagiri studies inducible defense
mechanisms of plants against pathogen attack using the model plant
Arabidopsis thaliana. One focus is to study pathogen recognition
mechanisms. Plants achieve very broad recognition specificities with only
hundreds of disease resistance genes. A protein-protein interaction
network approach is being applied to elucidate the repertoire of the
recognition and immediate signal transduction mechanisms. Another focus
is to elucidate the entire signaling network that regulates a wide
variety of defense responses following pathogen recognition. A
large-scale reverse genetics approach is combined with mRNA expression
profiling to determine the network topology.
Dr. Arkady Khodursky is Assistant Professor of
Biochemistry, Molecular Biology and Biophysics and a member of the
Bioinformatics Graduate Program. 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. He teaches a course on microbial genomics and
bioinformatics. Dr. Khodursky is a member of the Executive Committee
of UMSBI.
Dr. Eric Klee is Senior Research Fellow at Mayo
Clinic. Dr. Klee is interested in the research areas of
proteomics/genomics/bioinformatics. Specific projects he is involved
in are:
- Developing and improving new
methods for the prediction of secreted proteins in vertebrate organisms.
Identifying and characterizing the vertebrate secretomes.
- Seeking out and identifying new
circulating markers for the diagnosis of prostate cancer. Identifying
prostate specific receptor proteins for diagnostic, prognostic, and
therapeutic targeting. Assembling multi-marker panels for improved
diagnostic and prognostic applications in prostate cancer.
Dr. Ray Kuang is Assistant Professor
in the Department of Computer Science and Engineering.
Dr. Kuang’s research interests lie
in the development of machine learning techniques for applications in
computational molecular biology. We use support vector machines (SVMs),
structured output learning algorithms, network diffusion algorithms and
various other statistical models such as hidden Markov models to study
biological data.
Dr. Vipin Kumar is Professor of the Department
of Computer Science and Engineering and the Director of the Computer
Science and Engineering Department at the University of Minnesota. Dr.
Kumar is a member of the Executive Committee of UMSBI.
Dr. York Marahrens is an Associate Professor in
the Department of Genetics, Cell Biology, and Development. He studies
the role of epigenetics in human disease. He also studies epigenetic
mechanisms in mice.
Dr. Andrew Odlyzko is Professor in the Department
of Mathematics, and Director of the Digital Technology Center.
He has written over 150 technical papers
in computational complexity, cryptography, number theory, combinatorics,
coding theory, analysis, probability theory, and related fields, and has
three patents. In recent years he has also been working on electronic
publishing, electronic commerce, and economics of data networks. He has
an honorary doctorate from Univ. Marne la Vallee and serves on editorial
boards of over 20 technical journals, as well as on several advisory and
supervisory bodies.
Dr. Hans Othmer is Professor in the Department
of Mathematics, and member of the Digital Technology Center. He is
interested in applied mathematics, mathematical biology, and dynamical
systems, including mathematical models of chemotaxis and individual and
collective cell motion. He teaches numerous courses on mathematical
models of biological complexity.
Dr. Ronald Phillips is Regents Professor in the
Department of Agronomy and Plant Genetics. Dr. Phillips is interested
in plant genetics applied to plant improvement with an attempt to
bridge basic and applied aspects. Dr. Phillips chaired the Interagency
Working Group 5-year plan on the National Plant Genome Program for
Congress, published in January, 1998. Subsequently, his group received
a three-year grant in the program and was recently renewed for four
years at $3.1 million. He has published many papers on cell and tissue
culture, being the first to regenerate corn from cells in culture, as
well as numerous papers on molecular genetics of plants. He teaches a
modern, up-to-date graduate course on cytogenetics. Being a member of
the National Academy of Sciences, Phillips participates in various
advisory capacities to the federal agencies, and served as Chief
Scientist of the U.S. Department of Agriculture in charge of the
National Research Initiative from 1996-98.
Dr. Kevin A Silverstein is Research Associate
in the Department of Plant Biology. Dr. Silverstein focuses on the
development of computational tools for assignment of putative function
to new sequence data.
Dr. Nathan Springer is Assistant Professor
in the Department of Plant Biology. Dr. Springer studies the molecular
basis of epigenetic inheritance in maize using a variety of genetics
and genomics approaches. A suite of ~200 putative chromatin factors
have been identified and are currently being studied as part of the
Plant Chromatin Consortium. Research projects are also underway to
implement oligonucleotide microarrays for mutation detection,
polymorphism validation and genome structure analysis. Genomic
DNA from maize is hybridized to custom-designed microarrays in
order to perform high-throughput mutation detection or to assess
the relative genome content of different varieties of maize. Dr.
Springer teaches a graduate course in cytogenetics.
Dr. Nevin Dale Young is Professor in the
Department of 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.
Dr. Kathryn VandenBosch is Professor and Head
in the Department of Plant Biology. Dr. VandenBosch oversees a
collaborative program on gene expression profiling in a NSF-sponsored
project on Medicago truncatula. This functional genomics project uses
EST analysis and DNA microarrays to study genome function in many
aspects of legume biology. Her particular research focus is the
development of plant/microbe symbioses, with an increasing interest
in comparative and evolutionary approaches. Her experience with these
multi-disciplinary collaborations has emphasized the importance of
engaging young scientists in teamwork approaches.
Dr. George Vasmatzis is a Senior Associate
Consultant in the Experimental Pathology division, in the Department
of Laboratory Medicine and Pathology and a member of the Mayo Clinic
Cancer Center. He was recently appointed as an Assistant Professor in
the Department of Laboratory Medicine at the Mayo Medical School. He
has a Ph.D. in Biomedical Engineering and has acquired experience in
diverse disciplines, including Bioinformatics, Molecular Biology, and
Computational Biology. He has been actively involved with both research
and educational activities at Mayo and is involved in numerous
collaborations with other Mayo Clinic investigators. Dr. Vasmatzis’s
research program consists of bioinformatics specialists, molecular
biologists, epidemiologists, and pathologists. He combines computational
and experimental techniques to facilitate discovery of genes that can be
used as diagnostic and prognostic markers for cancer.
Dr. Darrin York is Associate Professor in Chemistry.
The York Group research involves the development of a broad range of
theoretical methods aimed, ultimately, at providing the computational
biology community with greatly improved tools for the simulation of
biological macromolecules in solution. The main application focus of
our group is on the study of the molecular mechanisms of RNA catalysis
using molecular simulation and combined quantum mechanical.molecular
mechanical methods. This area is immensely important, not only from a
fundamental biological perspective, but also for the design of medical
therapies that target genetic disorders, and new biotechnology such as
allosteric RNA chips.
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