Graduate Faculty

The graduate faculty of the BICB graduate program comes from three institutions (University of Minnesota including Hormel Institute; IBM; and Mayo Clinic).

• University of Minnesota Faculty
• Mayo Clinic Faculty
• IBM Faculty

University of Minnesota

Dr. Elizabeth Amin (Assistant Professor, College of Pharmacy)
The Amin laboratory focuses on the design and optimization of metalloprotein-targeted chemical and biological warfare and anticancer therapeutics, incorporating computer-aided drug design, high-throughput screening (HTS), cell-based assays and synthesis. Our primary therapeutic target is the anthrax toxin lethal factor (LF), a Zn metalloprotease that is critical for anthrax pathogenesis.

Dr. Massoud Amin (Professor, Electrical and Computer Engineering)
Dr. Massoud Amin's research focuses on two areas: 1) Global transition dynamics to enhance resilience, security and efficiency of complex dynamic systems. 2) Science and Technology scanning, mapping, assessment and valuation to identify new science and technology-based opportunities that meet the needs and aspirations of today's consumers, companies and the broader society. This thrust builds coherence between short- and longer-term R&D opportunities and their potential impact.

Dr. Ann Bode (Research Associate Professor and Associate Director, Hormel Institute, Cellular and Molecular Biology)
Research focuses on identifying molecular targets of dietary factors applied to signal transduction pathways involved in neoplastic cell transformation and carcinogenesis. A major goal is to elucidate key protein-protein or protein-molecular interactions predicted through computer simulation methods and validated through laboratory bench studies to be used in the development of small molecule inhibitors that specifically target key cancer-related proteins.

Dr. Dan Boley (Professor, Computer Science and Engineering)
Computational methods in linear algebra, scalable data mining algorithms, algebraic models in systems and evolutionary biology, biochemical metabolic networks. Current projects include scalable computation and analysis of elementary pathways through metabolic networks of single-cell organisms, Markov model of evolution of the avian influenza virus, scalable data mining algorithms for corpora of short text fragments.

Dr. John Carlis (Professor, Computer Science and Engineering, Associate DGS)
John Carlis is a professor of Computer Science and Engineering and Associate DGS of the BICB Program. He conducts research in bio-medical databases, focusing on data modeling, and extending DBMS functionality. His current projects include microarray studies of HIV-1 seeking a better understanding of the earliest stages of infection, and proteomic studies of oral cancer via mass spec analysis of saliva seeking biomarkers for early detection.

Dr. Connie White Delaney (Dean and Professor, School of Nursing) RN, FAAN, FACMI
Connie White Delaney is Dean and Professor in the School of Nursing where she also holds an appointment in the School of Medicine, Division of Health Informatics, Department of Laboratory Medicine and Pathology. She has a Professorship at the University of Iceland, Faculty of Medicine and Faculty of Nursing with focused activities in health informatics. Current research focuses on new methods to provide high quality education and research at an affordable cost. This program of research involves computational modeling and simulation.

Dr. Yang Da (Associate Professor, Department of Animal Science)
Dr. Yang Da's current research includes developing quantitative and computational methods for genome-wide association analysis, and QTL and eQTL mapping to detect genes affecting human diseases and animal quantitative traits, and includes finding genes underlying production, reproduction and health phenotypes in the Holstein breed of dairy cattle using genome-wide association and QTL mapping methods.

Dr. Zigang Dong (Hormel Institute, Professor and Executive Director, Hormel Institute, Cellular and Molecular Biology)
The major focus in the Cellular and Molecular Biology section is the molecular mechanisms of cancer development and the actions of chemopreventive agents in cancer prevention. Another main emphasis of our lab is the elucidation of mechanism(s) of the anticancer actions attributed to several chemopreventive compounds. These are compounds considered to have little or no toxicity and are present in commonly consumed foods and beverages.

Dr. Lynda Ellis (Professor, Department of 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, http://umbbd.msi.umn.edu/ and a rule-based Pathway Prediction System, http://umbbd.msi.umn.edu/predict/ to predict biodegradation of compounds not found in the UM-BDD.

Dr. Jiali Gao (Professor, Department of Chemistry and Digital Technology Center)
We develop computational methods to study systems of biological or chemical significance. We develop the theory and implement it in a computer program to carry out detailed simulations of the system. In particular, we combine quantum mechanics and molecular mechanics (QM/MM) to model large molecular systems, including proteins and nucleic acids. The focus of our group includes: (1) development of novel combined QM/MM methods to study chemical and biological reactions, (2) an understanding of the origin of enzyme catalysis, and (3) modeling the diffusion and interactions of macromolecular particles in cellular environment.

Dr. Fumi Katagiri (Associate Professor, Plant Biological Sciences)
Our research focuses on inducible defense of plants, particularly pathogen recognition and ensuing signal transduction mechanisms. We take systems biology approaches as well as molecular genetic and biochemical approaches to this biological phenomenon using genomically tractable model plant host and pathogen: Arabidopsis thaliana and Pseudomonas syringae.

Dr. Arkady Khodursky (Associate Professor, Biochemistry, Molecular Biology, and Biophysics)
My laboratory studies transcriptional activity of genomes of model microbes: Escherichia coli, Synechocystis and Saccaromyces cerevisiae. We design, manufacture and use whole genome DNA microarrays to understand relationships between genotypes and phenotypes, structure of the chromosome and its transcriptional activity, as well as between environmental conditions and transcriptional responses.

Dr. Rui Kuang (Assistant Professor, Computer Science and Engineering)
My lab develops machine-learning algorithms to extract and integrate subtle and elusive information hiding in genome-wide large-scale biological data for understanding the association between genomic characteristics and phenotypes. We are particularly interested in designing novel kernel methods and graph-based learning algorithms for a unified analysis of high-throughput data in a data-driven perspective.

Dr. Vipin Kumar (Professor and Head, Computer Science and Engineering)
Motivated by the need to solve important bio-medical problems using computational approaches, Dr. Kumar's group works on several interesting problems using data mining techniques. These include computational approaches for protein function prediction, data mining for connecting disease characteristics with genomic and phenotypic factors, and analyzing information from electronic medical records.

Dr. Mitchell Luskin (Professor, School of Mathematics)
Mitchell Luskin's research expertise is multiscale modeling and computing, numerical analysis, applied mathematics, and differential equations.  He develops theory and algorithms for finite element methods, molecular dynamics, material microstructure, and atomistic-to-continuum coupling methods.

Dr. Mohamed Mokbel (Assistant Professor, Computer Science and Engineering)
Research Areas: Database systems, scalable data management techniques, query processing and optimization, spatial databases, context-aware data management, location-based services, and Geographic Information Systems (GIS)

Dr. Chad Myers (Assistant Professor, Computer Science and Engineering)
Professor Myers's research focuses on machine learning approaches for integrating diverse genomic data to make inferences about gene function and biological networks. He is also interested in experimental and computational characterization of genetic network structure and how it relates to phenotypic properties of biological systems.

Dr. Claudia Neuhauser (Professor and Vice Chancellor for Academic Affairs, UMR, DGS)
Dr. Neuhauser's research focuses on two areas of biology: ecology and genetics. In ecology, she studies the role of space in community dynamics, and in population genetics, how selection affects genealogies. These investigations are theoretical, relying on mathematical models, analytical methods, and partially on computer simulations.

Dr. Hans Othmer (Professor, School of Mathematics)
Pattern formation in development, dynamics of signal transduction and gene control networks, multiscale modeling of chemotaxis

Dr. Wei Pan (Professor, School of Public Health, Division of Biostatistics)
Wei Pan's research interests include statistical and machine learning approaches to analyzing microarray and other high-throughput data, and integrative analysis of genomic and proteomic data.

Dr. Cavan Reilly (Associate Professor, School of Public Health, Division of Biostatistics)
Dr. Reilly received his PhD in Statistics with an emphasis in Bayesian modeling and computation. His current research focuses on finding genes that alter risk for complex diseases and statistical models for microarrays. In addition, he works on problems in image registration with applications to mass spectrometry and liquid chromatography.

Dr. Marc Riedel (Assistant Professor, Electrical and Computer Engineering)
Dr. Riedel's research encompasses topics in nanoscale digital circuits design and in synthetic/computational biology. A broad theme is the application of computational expertise from the former (circuit design) to analysis and design problems in the latter (biology). A specific theme that cuts across both domains is constructing and deconstructing probabilistic behavior.

Dr. William Schuler (Assistant Professor, Computer Science and Engineering)
My research is primarily directed toward the construction of practical real-time spoken language interfaces for machines that mimic the human language understanding process, exploiting natural human psycholinguistic constraints wherever possible.

Dr. Stuart Speedie (Professor, Laboratory Medicine and Pathology, DGS of Health Informatics)
The impact of health information systems and technologies on patient outcomes, provider decision making and health system efficiencies. These technologies include clinical information systems, health information exchange mechanisms, eprescribing, telehealth and home monitoring.

Dr. Ahmed Tewfik (Professor, Electrical and Computer Engineering)
Research interests: search for genomic biomarkers, design of genomic based screening tests, gene expression level analysis, copy number analysis, chemical genetics

Dr. Darrin York (Associate Professor, Chemistry)
The York Group develops and applies computational methods to study the molecular mechanisms of RNA catalysis. Simulations using new multi-scale quantum models provide detailed insight into the origins of catalysis and allosteric control factors that regulate RNA reactivity. Simulation results are used to facilitate design of new biomedical technology.

Dr. Larry Wackett (Professor, Biochemistry, Molecular Biology and Biophysics)
The Wackett laboratory studies biocatalysis, genomics, and web-based computational tools. Microbial enzymes are studied for their feasibility to degrade wastes or manufacture chemicals. Web-based databases have been developed for representing information pertaining to biocatalysis (http://umbbd.msi.umn.edu) or biofuels (http://www.biofuelsdatabase.org). The former contains a tool for predicting metabolic pathways (http://umbbd.msi.umn.edu/predict/).

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Mayo Clinic

Dr. Karla Ballman (Chair of Division of Biostatistics)
Areas of research interest are analytical techniques for high-dimensional data and clinical trial design. Focus areas of high-dimensional data are prediction/classification methods and analysis of copy number variation, gene expression, and next generation (NextGen) sequencing data. A primary interest in clinical trial design is for surgical trials.

Dr. Zeljko Bajzer (Professor, Biochemistry)
My research is devoted to mathematical and computer modeling of biological systems and to methods of data analysis. In particular this includes modeling cancer growth and therapy (i.e. virotherapy), fluorescence data analysis based on multiexponential functions, enzyme kinetics, models of reaction kinetics in environments with macromolecular crowding and T-cell kinetics.

Dr. Christopher Chute (Professor of Medical Informatics, Associate Professor of Epidemiology, Chair of Division of Biomedical Informatics)
Dr. Chute is Professor and Chair of Biomedical Informatics at Mayo Clinic, trained as an internist and epidemiologist. His research focuses upon patient data and clinical knowledge representation, ontologies, information retrieval, and health information standards. He chairs the WHO ICD-11 development work, the US delegation to ISO for Health Informatics, and the NIH BCHI study section.

Dr. Stephen Ekker (Professor, Biochemistry and Molecular Biology, Mayo Clinic Cancer Center)
The Ekker laboratory has pioneered the use of transposons and morpholino antisense oligonucleotides in zebrafish genetics to identify genes with important roles in clinically relevant processes. The Ekker lab has genome-wide efforts that cover processes including angiogenesis, sensory organ and kidney development, and nicotine response and sensitization.

Dr. Jean-Pierre Kocher (Division of Biomedical Informatics)
My research interest is in the domain of life science informatics. More specifically, my research activities focus on the development and application of computational methods to advance the understanding of molecular mechanisms that underlie clinical disorders. These methods span the areas of bioinformatics, computational biology and chemoinformatics.

Dr. Peter Li (Health Sciences Research, Vice Chair of Biomedical Informatics, Mayo Clinic Cancer Center)
My interests range from software architectures to systems bioinformatics. Currently, I am exploring multi-factor interactions in gene expression, genotyping, and individualized clinical states for translational research. In addition, I am interested in domain modeling, large scale databases,
and novel computer architectures to analyze the large amount of biomedical data.

Dr. Armando Manduca (Assistant Professor of Radiology, Associate Professor of Biophysics)
Dr. Manduca's research interests are in image processing, computer-aided diagnosis, and computational intelligence, for projects such as: analysis and inversion of MR elastography data; motion correction in MRI acquisitions; highly undersampled MRI acquisitions; image denoising techniques; analysis of mammograms to predict breast cancer risk; and analyzing aortic pulsatility.

Dr. Yuan-Ping Pang (Professor, Pharmacology)
Explore how particular structures and atomic interactions underlie angiogenesis, apoptosis, metalloenzyme catalysis, and protein folding; develop molecular databases and scalable supercomputer hardware and software to facilitate the integration of biological data in order to understand how biological systems function; and use models of biological systems to develop therapeutics for treating cancers and emerging infectious diseases.

Dr. George Vasmatzis (Assistant Professor, Laboratory Medicine)
Dr. Vasmatzis' research interests are in theoretical and experimental oncology. He applies computational and experimental tools to generate, analyze, and interpret genomics data with the intention to understand disease progression and develop predictive models for cancer prognostics and diagnostics. This is accomplished by setting multidisciplinary clinician/scientist teams that span Bioinformatics, Molecular Biology, clinical oncology, and Anatomic Pathology.

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IBM

Dr. John Eberhard (Software Engineer, Java Data Access)

Drew Flaada (Director Mayo Collaboration, Life Sciences, and BlueGene Software Development)
Drew Flaada is the IBM executive responsible for development of solutions and new technologies in the Health Care and Life Sciences arena, and for the system software for IBM high performance computing platforms including the preeminent Blue Gene and RoadRunner systems. Drew is responsible for founding and managing the multi-year collaborative efforts between IBM and Mayo Clinic which are focused on leveraging information technology in Individualized Medicine and Medical Imaging informatics. Flaada's interests lie in the areas of cross disciplinary collaborations, innovation processes, new technology creation and introduction, business and economic development, business leadership and entrepreneurship. He is a board member for the BioBusiness Alliance of Minnesota, is on the Dean's Advisory Board for the University of Minnesota's Institute of Technology, and is on the UMR BICB program Scientific Advisory Board.

Mike Good (Manager, BlueGene Software Development)
Mike Good is Program Director of High Performance Systems Software and Stream Processing Development at IBM, Rochester, MN. Since joining IBM in 1987, Mike has held numerous technical and management positions.  He has a B.S. degree in Computer Science from the University of Minnesota, Institute of Technology, and a Master of Business Administration from the University of Minnesota, Carlson School of Management.

Paul Mattson (System and Technology Group System Software Portfolio Team)
Paul Mattson is interested in business leadership, business development, new ventures and entrepreneurship especially in the information technology space. He currently works on partnership ideas within IBM's Systems and Technology Group and additionally teaches courses in Augsburg's M.B.A. and M.I.S. programs.

Dr. George Paulik (VLSI Circuit Design Engineer)
My interests are mathematical in nature and I would be more than willing to work with research groups that might benefit from a mathematical/statistical perspective. Most recently, I have been applying statistical techniques to model the yield of arrays (memory structures) in VLSI chips. I also help design VLSI circuits.

Dr. Carlos Sosa (Technical Lead - BlueGene Software Development in Chemistry and Life Sciences)
Sosa’s research interests include the areas of molecular simulations, bioinformatics, and parallel computing. His research in parallel computing focuses on scaling of these applications in these areas to emerging hardware architectures. An important component of his research is the application of these techniques to molecular cellular biology challenges.

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