IREF Registrants
| Name | Status | Dept | Interests | Projects | Skills | Poster |
| Andrew, Keith | faculty | physics | Theoretical and mathematical modeling of complex systems. Applications include analytical tools related to the modeling of partial differential equations and nonlinear dynamics and numerical tools related to time and space series data analysis, and applications of quantum mechanics to fundamental processes. | 1. Characterization of phase space trajectories and attractors. 2. Linearization of complex systems and dimensional regularization. 3. Numerical methods for Hurst exponents, power spectra, Lyanpunov exponents, noise and dimension. Application with Atmospheric Radiation Measurement program at Southern Great Plains site, atmospheric column modeling, oscillating Belusov-Zhabotinski type chemical reactions far from equilibrium, soliton and compacton propagation, galactic jets, and cosmological structure formation. |
1. Analytical tools for modeling systems of nonlinear partial differential equations. 2. Numerical tools for extracting nonlinear trends and characterisitcs from time and space series data, Fortran. Maple, Mathematica, C. | no |
| Atici, Ferhan | faculty | math | Recurrence relations (Difference Equations) Modelling with difference equations Theory of Difference Equations Dynamic Equations on Time Scales | Recently, I am working on modelling with dynamic equations. Dynamic equations are unified version of difference and differential equations and others. The domain what we call Time scale is a nonempty closed subset of real numbers. So if we start with any time scale then we are considering R(real numbers), Z (integers), C (cantor set) and many others as examples. | I am also interested in the study of equations and the qualitative behaviors of their solutions. | yes |
| Atici, Mustafa | faculty | cs | Graph Theory nad combinatorial Mathematics. Security-Crypto |
Graph Algorithms
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no | |
| Cook, Kim | other | other | I am a research microbiologist working with the USDA-ARS Animal Waste Management Research Unit. My work focuses on using molecular microbiological methods to obtain data and find solutions for issues related to animal waste and waste storage. | We are using denaturing gradient gel electrophoresis and clonal library sequence analysis to monitor changes/shifts in microbial communities enriched for production of mal-odorous compounds found in animal wastes | Quantitative, real-time PCR Cloning, sequencing | no |
| Davis, Cheryl | faculty | admin | Immunological Aspects of Parasite-Host Relationships. At the present time, our work is primarily focused on the human protozoan parasite, Toxoplasma gondii , using a mouse model system. | Toxoplasmosis, particularly toxoplasmic encephalitis has emerged as a major cause of morbidity and mortality in patients with AIDS. Patients infected with HIV typically experience chronic oxidative stress, and concurrent infection with the intracellular parasite, Toxoplasma gondii, would be expected to further exacerbate this condition. However, previous studies in the laboratory have provided evidence that dietary supplementation with antioxidants is actually harmful during experimental toxoplasmosis in mice, whereas a diet deficient in vitamin E and selenium results in decreased numbers of tissue cysts in the brain and dramatically reduced brain pathology. Spleens obtained from infected mice maintained on the antioxidant diet, show elevated levels of IFN-g, TNF-a_ and IL-10 mRNAs as compared to mice maintained on normal or pro-oxidant diets. IFN-g, levels also are greatly enhanced in splenocyte culture supernatants obtained from infected mice on the antioxidant diet alone, in the absence of infection had no significant effect on the synthesis of cytokine mRNAs. These results demonstrate that diet can have a significant impact on the regulation of potent immuno-regulatory cytokines during T. gondii infection. In collaboration with Dr. Nigel Cooper at the University of Louisville, we have expanded the scope of our study to include microarray analysis. With this analysis, it will be possible to determine the relative abundance of each mRNA expressed in mouse brain tissue, and it will be possible to determine which genes are differentially expressed between T. gondii-infected mice maintained on a diet lacking vitamin E and selenium and those maintained on a diet containing elevated levels of these antioxidants. Although the major focus of our laboratory has been on genes of immunological relevance, with microarray analysis, other genes whose expression is influenced by diet will likely be identified. | no | |
| Doerner, Kinchel | faculty | bio | I am a microbiologist, molecular biologist, biochemist by training and am currently conducting traditioal experiments into the physiology and genetics of odor prodution in bacteria. However I wish to expand into the study of complex microbial populations and microbial ecology. | Microbial ecology is an emerging field that relies heavily on large data sets usually consisting of nucleic acid sequences, use of programs that may be user unfriendly, and use of complex and novel statistical approaches of which I am unfamiliar. I see this group providing a forum to get advise on computing isssues (i.e. task automation, file formating automation), as well as providing assistance in statistical analysis and interpretation.
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I am familiar with most molecular biology techniques, a little MS Dos experience and a budding linux user. I am willing to learn and co-author papers and grant submissions. | no |
| Ernst, Claus | faculty | math | Knot Theory, Graph Theory, Geometric Algorithms | In the past I have worked together with experimentalists analysing DNA recombination experiments for which the geometry and toplogy of the macromolecules was the key interestto be determined. I am familiar with the current state of research in this particular area. | Mathematica programming. | no |
| Gary, James | faculty | cs | High performance parallel and distributed computing, image processing, computer graphics. | I manage a 24 node beowulf cluster than can be used for research in the college. I am willing to help install or develop software for bioinfomatics research. I'm also willing to consult on new computing equipment for research purposes. I have interest in computer graphics (my knowledge is a bit dated though) and would consider assisting in scientific visualization. | Development of software for parallel and distributed applications. | no |
| Hahn, Lance | faculty | psych | Computational modeling of complex systems with a primary focus on the semantic networks underlying reading processes. Automated model design. Network characteristics and their relationships to function. |
Computational modeling of biological systems. Recently, I have been used a complex system (Petri Nets) to model possible biochemical pathways which mediate the influence of genes on disease states. This Fall, I will use complex systems to model the semantic relationships underlying word recognition. Automated Model design. I have used evolutionary machine learning algorithms (genetic algorithms, grammatical evolution, genetic programming) to design complex systems (Petri Nets, Neural Nets and Cellular Automata) to achieve different goals. Two significant benefits of this approach are a decrease in designer bias and the ability to easily generate models for different datasets. |
Visual Perception. C++ programming. Parallel programming. Machine Learning Algorithm development. Experience with using a large (1000+ CPUs) clusters. Familiar with a range of bioinformatics data: genetic, neuroscience, behavioral. | no |
| Jacobshagen, Sigrid | faculty | bio | I am working on the circadian clock in the model organism Chlamydomonas reinhardtii. | The genome of Chlamydomonas reinhardtii has been sequenced with the third version just recently released. I am interested in the use of simple, basic bioinformatics tools to help me analyze some of the genes with respect to their involvement in the circadian clock in lab bench experiments. I am also interested in modeling gene expression that is regulated by the circadian clock. A third interest is the analysis of circadian rhythms data with respect to period, phase, and amplitude. | Bioinformatics: Limited knowledge of modeling, genome searches and primer designs. Molecular biology/cell physiology: Gene expression, RNA interference, circadian rhythms monitoring |
no |
| Kessler, Bruce | faculty | math | I am a waveleteer by trade, but I am interested in applied harmonic analysis and signal processing in general. | no | ||
| Li, Qi | faculty | cs | It has been known that the development/growing of an embryo can be categorized as different stages, and it is highly desirable for a biologist to have a tool that can automatically classify the stage of an embryo by its image taken in a certain period. Previous work showed that the appearances of an embryo are valuable information for the classification task. Like global appearance based face recognition, a scheme in previous work on embryo stage classification first aligns the global appearance, and then applies projection methods to reduce the dimension of a global appearance. Thus global appearance based embryo stage classification has the same challenge as global appearance based face recognition, such as alignment errors, outlier appearances, etc. It turns out that automatic alignment of embryo images is even harder than automatic face alignment since no consistent salient features have been found in embryo images. I am very interested in the bioinformatics problems mentioned above. I am now collaborating with Professor Jieping Ye who is a member of Evolutionary Functional Genomics Center of the Biodesign Institute at Arizona State University. I am interested in being a member of the BISC at Western Kentukcy University so that | I can contribute my research experience on the bioinformatics to BISC, including the collaboration with other members in writing papers or proposals, and the effort of establishing research connection between the BISC at Western Kentukcy University and external bioinformatics origanization, such as the Genomics Center at Arizona State Univeristy. I believe that I will get valuable suggestions/comments on my research from other members of BISC. | Data mining Machine learning Bioinformatics Appearance based recognition | yes |
| Marcus, Jeffrey | faculty | bio | I am interested in modeling how gene products interact to produce phenotypes. My primary experimental system is butterfly color patterns, and my laboratory has used computational techniques to model how specific gene products interact during development to produce the colors found in the adult butterfly. I am more generally interested in how to employ computational methods to solve problems in genetics, developmental, and evolutionary biology. | I know enough just enough math and computer programming to be dangerous, but not necessarily enough to answer all of the questions I might like to ask. I am hoping through interactions in this center might help me interact with people who have more robust expertise in these fields, but who might not be familiar with the kinds of questions that biologists are trying to address. | Molecular Biology Genetics Pascal Programming (yes, I may be the last person alive who codes in Pascal) | no |
| Niu, Xinnan | staff | bio | 1. Apply data mining techniques to process biological data. 2. Implementing data mining and statistic approaches by efficient algorthmic design with Java, C++, Perl. 3. Implement web-based bioinformatics tools by using Object oriented Perl,Bioperl module, Java, biojava, relational database, biosql-schema/sql, mySql, Appache Server, and Apache Tomcat. 4. Teaching students to learn how to code with Perl and Bioperl to manipulate biological sequence data. 5. Developing web-based tools by which students can easily learn programming techniques and how to use SQL language. 6. Create or implement virus genome databases with associated searching, alignment, clustering, classification, and assocaiton tools. |
Currently, I am working on developing a database driven website for biotech center. Techniques to build this website: I got trained in Medical Science and worked serveral years as a public health doctor to deal with epidemic and infectious diseases control. I have a M.S. degree in biological science and worked as a molecular biologist at the Medical College of Wisconsin. I worked with adenovirus, adeno-assocated virus, and lentivirus and am familiar with the genome of these viruses and know how to manipulate those viruses with molecualr approaches. I also got trained in computing and obtained another M.S degree from the department of Mathematics, statics, and computer science at Marquette University and Medical College of Wisconsin. There, I used to be a leader in several research projects to study how transpon elements faciliate bacterial genome rearragement, clustering and classification of lung cancer patient's microarray profiling data with statics and machine learning approaches. |
1. Molecualar Biology Wet Bench techniques: such as DNA and RNA manipulation, cloning, sequencing, virus design and construction, cell culture, transfection, transformation, protein extraction and electrophresis, etc. 2. Web and Programming techniques: Familiar with HTML, CSS, Java-Script, CGI-Perl,XML, Apache Server, Unix System, MySql, CVS tool, Java, Perl, C++. 3. Data Mining Techniques: R package, Weka Package, Matlab. |
no |
| Rinehart, Claire | faculty | bio | Bioinformatics. Protein structure and function prediction in proteins with amino acid substitutions. Developing and implementation of bioinformatic tools. | I have a Unix cluster (7 dual processors) that serves over 170 bioinformatics applications through a common web interface. We have local copies of the NCBI genebank database. I could use help on integration of new programs and databases under the web interface. I also have a Mathematica parallel processing package, for this same cluster, which I am using in the development of bioinformatics algorithms. I would like to help and collaborate with others that could use the parallelization of Mathematica processes. I have been working on a method to predict the conservation of protein structure and function upon substitution of one amino acid for another. After a set of trials on 10 different proteins, the method appears to be predictive and I now need help in developing a mathematical/statistical model for the method that will help predict confidence levels. I have applied some of the parsing and pattern matching approaches of wavelets to the identification of related but diverse protein structures. I wish to now extend this into secondary and tertiary structure interactions. I have developed a method to identify potential open reading frames from a codon bias table. This approach optimizes the identification of a single triplet codon that can be used to search a DNA sequence and identify optimal coding frames and sequences.
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I am very familiar with molecular biology, biochemistry, and recombinant DNA techniques. I am becoming increasingly familiar with techniques and programs in bioinformatics. I have programed applications in fortran, basic, pascal, hyperCard, and Mathematica. I have a broad experience base in a number of areas, with little depth in most, and probably, I am well suited to help identify potential collaborations across disciplines. | yes |
| Spraker, John | faculty | math | Recently, my work has been in differential equations and inclusions. | no | ||
| Wu, Di | faculty | math | Bioinformatics and Computational Biology - Bio-system Database - Protein Structure Modeling and Drug Design - System Biology Applied Mathematics - Scientific Computing - Optimization and Linear Programming | Protein structure modeling: Specifically, the knowledge-based method using protein geometric information has been studied, and it involves distance-based protein structure refinement and protein dynamics study. In addition, some mathematical tools regarding protein structure determination have also been investigated. Bio-system database: With the increasing number of DNA sequences or known protein structures, it is important and valuable to investigate the statistical information from them. Geometric information from protein structure database turns out to be very useful in the study of protein structures, and a more detailed study will be conducted. System Biology: Many biological systems, such as gene regulation network and metabolic pathway, could be studied in a system level. However, for the large system, the traditional method might not be very efficient and the interpretation of results might be also very difficult. Here, some developed algorithms and methods will hopefully resolve these problems. | Biology: familiar with basic molecular biology technology and knowledge, such as cloning, PCR, RT-PCR, northern blot, DNA, RNA and protein extraction. Computer Science: familiar with some programming languages, web and database development, such as matlab, fortran, C/C++, perl, MySQL. Mathematics: familiar with numerical (scientific) computing, constrained and unconstrained optimization, combinatorial and linear programming, dynamics simulation involving ODE (or PDE) and finite different methods. Statistics: familiar with fundamental statistical knowledge, knowing a little about SAS, SPSS programming. | yes |
| Wyatt, Robert | faculty | bio | Searchable metadata for learning objects & video. Parsing large data logs for information. | Concatenating and then parsing servers logs for Ip patterns. | Database, web applications, XML, willingness to learn. | no |
| Xia, Zhonghang | faculty | cs | Machine Learning, Data Mining, Combinatorial Optimization | I am designing an intelligent agent framework that classifies Web documents based on structural information for efficient queries, and recommend interesting items to users. The goals are (1) develop an efficient kernel method for representing XML documents as vectorial data for further processing; (2) compare the classification accurate rates by using the kernel method and Landmark Multidimensional Scaling method as data representation; (3) develop a biclustering method for collaborative filtering. | Algorithm designing | no |
| Ziegler, Uta | faculty | cs | Artificial Intelligence, Graph Theory, Algorithms, Computer Networking | AI contains many different methods which can be applied to analyze existing data -- protein sequences, folding patterns, control of gene expressions -- for a variety of purposes: visualization, prediction, detection of abnormalities.
I have experience with neural networks, rule-based expert systems and some reinforcement learning. |
Algorithm development, experience with interdisciplinary work (cognetive science, knot theory), minor in microbiology | no |
