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Research Concentrations

Molecular Biophysics
Ecological and
Evolutionary Modeling
MutS-DNA complex involved in DNA mismatch recognition exhibits allosteric effects that are linked to the initiation of DNA repair. Modeling efforts based on new computational methods that are suitable for such a large system are undertaken in order to gain new insight by complementing experimental data. ( Michael Feig, Biochemistry and Molecular Biology/Chemistry).
A healthy, young, fat, blue, territorial male damselfly guarding his mate from unhealthy, old, lean, green,
Systems Biology
Genomics, Bioinformatics, and Computational Biology
Predicting life processes systems biology: reverse engineering.  (Christina Chan, Chemical and Materials Engineering)
The human apoptosis network adapted from that in the Kegg database.  (Phillip Duxbury, Physics and Astonomy)


Molecular Biophysics

Faculty                           Research Interests

Structural biology
Protein dynamics and reactions in proteins using fast laser spectroscopic methods
Study the relationship between local atomic structure and properties of materials using novel x-ray and neutron scattering techniques
Focus is on understanding the structural and dynamical properties of heterogeneous lipid bilayer structures.
Functional and structural genomics of ribosome assembly
Quantum and classical mechanics methods development for simulation of reaction mechanisms in enzymes

Statistical Mechanics, Disordered Systems, Materials Theory, Computational Physics

Modeling supramolecular assemblies and membrane environments. Protein structure prediction and refinement
Defining functionally important structural features of protein:protein interface between cytochrome c and cytochrome oxidase
Elucidation of structure-function relationships in membrane proteins and molecular complexes using macromolecular crystallography and other biophysical methods
Structure/function studies of enzymes and biological processes involving metal ions
RNA catalysis and RNA-protein interactions; biomolecular NMR and EPR methods and applications
Determining the structures of bacterial transcription factors
Developing computational approaches for protein folding, ligand interactions, and design
Fast protein folding processes studied by optical spectroscopy and ultrarapid mixing; and developing a universal description of the unfolded state of proteins
Development and use of Electron Paramagnetic Resonance (EPR) Spectroscopy for the structural characterization of paramagnetic centers in biologicalsystems
Electronic nanocomponents in Geobacter biofilms
Computational methods (Molecuar Dynamics, Docking) to investigate protein structure function relation-ships in ligand binding and water chain formation for enzyme activity
Developing algorithms for identifying disulfide bonds given mass spectral data
Studying the determinants of protein thermostability using heperthermophilic enzymes as models
Advanced numerical methods for the structure and dynamics of biological macromolecules
NMR and crystallography for structure determination of viral fusion peptides and proteins
Wenkert, David
Collaborations in drug design in the areas of infectious diseases and cancer
Empirical demonstration of the link between protein structure, gene function, and organismal fitness
Protein structure, function and dynamics with applications to protein engineering and structure-based drug design


Ecological and Evolutionary Modeling

Faculty                           Research Interests

Cole, James
The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community
Statistical modeling of growth and shape
Analysis of evolutionary changes in higher primate cytochrome c and cytochrome oxidase
Evolution of signaling, social behavior and life history strategies
The Genetic Algorithms Research and Applications Group (GARAGe) studies and advances evolutionary computation, building on principles abstracted from nature
Host-parasite systems in mathematical ecology: statistical issues in data analysis of microarray experiments; genetic association for complex traits; biological networks
Gene and protein sequence in evolution
Theoretical population, community, ecosystem and evolutionary ecology
Relating structural and conformational changes in proteins to amino acid mutations
Experimental evolution, Escherichia coli and Digital organisms in the Avida system
Experimental evolution with digital organisms; applied evolution for solving computational problems
Molecular phylogenetic analyses
Modeling the developmental regulation and evolution of body and organ size in animals
Comparative and evolutionary genomics, gene family evolution and duplicate gene fate
Evaluating and developing algorithms for phylogeny reconstruction
Changing enzyme substrate and cofactor specificities, changing enzyme stability to temperature and pH
Molecular evolutionary and population genetic simulations with digital organisms


Systems Biology

Center for Systems Biology

Faculty                           Research Interests

Modeling cis-regulatory grammar of Drosophila (with Chichia Chiu, Mathematics)
Bates, Peter
Infinite-dimensional dynamical systems, nonlinear elliptic and parabolic PDE, phase transitions
Gene regulatory network models of vertebrate development
Identifying gene associations in rice to provide a new layer of functional annotation and to formulate new hypotheses on gene and gene networks in this model monocot species

Integrating various levels of information from genetic expression to metabolic data
Structural and functional genomics of disease resistance in chicken.
Statistical (epi)genetics/genomics, longitudinal data analysis
Modelling kinetics and electrostatic interactions of protein assemblies
The plant circadian clock signaling network
Statistical and epidemiological research, including cancer studies, and methodological research in statistical computing and clinical trials
Gardiner, Joseph
Development of models that reflect experience of patients in changing states of health, and methods for analyzing jointly cost & effectiveness measures using multivariate methods from survival analyses

Physics of sensory thresholds in primates: signal-to-noise factors in theoretical neuroscience
Test theories of sound localization and binaural hearing against experiments on human listeners
Determine how fish habitat affects their population dynamics, general ecology of fishes
Host-parasite systems in mathematical ecology: statistical issues in data analysis of microarray experiments; genetic association for complex traits; biological networks
Molecular mechanisms of signaling and gene regulation during bacterial development
Modeling flexibility and folding in proteins by analyzing bond networks
Fractional reproduction-dispersion equations and heavy tailed dispersal kernels. Fractal gene models
Optimal Control Theory and Non-equilibrium Statistical Mechanics of Regulatory Gene Networks
We study metabolic networks in plant systems including developing seeds and mycorrhizas
Evolution of cis-regulatory elements and expression regulatory networks
Signal transduction pathway leading to the activation of the transcriptional factor NF-KappaB
Nanostructures
Comparing flexibility in mesophilic and hyperthermophilic proteins by NMR and molecular dynamics


Genomics, Bioinformatics, and Computational Biology

Faculty                           Research Interests

Identifying design principles of eukaryotic enhancers using embryonic gene expression in Drosophila
Systems biology of probiotic bacteria
Regulatory genomics and data integration pipelines
Sequencing, annotation, and comparative analyses of plant and plant pathogens genomes
Genetic and genomic analysis of biological shape. Including multivariate statistical modeling
Computational and experimental methods for selective control of apoptosis signaling
Protein structure prediction and refinement based on evolutionary information
Statistical genetics, methodology and algorithm; Computational methods for microarray, genotyping, and identification of regulatory motifs
Functional characterization of genes that are predicted to encode Fe(II)/alpha-ketoglutarate -dependent hydroxylases or flavoenzmes
The contribution of transposable elements to genome evolution
Developmental epigenetics, embryonic development, and embryonic stem (ES) cells; ChIP-chip and RNAi
Genome-wide identification of transcription factor binding sites and sigma factor function in bacteria that undergo development
Protein structure and flexibility modeling, and high-throughput structure-based screening for inhibitor discovery
Functional genomics in evolving microbial and digital systems
RNAi & Proteomic Approaches for Quantitative Analysis of Molecular Pathways (kinases & phosphatases)
Bayes and Empirical Bayes methods to analyze microarray data
Genomic plasticity in Ralstonia pickettii and JGI sequencing two isolates
Optimal Control Theory and Non-equilibrium Statistical Mechanics of Regulatory Gene Networks
Search algorithms for Genome Sequence databases and profile Hidden Markov Models
Electronic nanocomponents in Geobacter biofilms
Genome structure underlying ecological strategies of microbes
Bioinformatics and comparative genomics. Gene family and cis-regulatory evolution
Statistical genetics and genomics. Experimental designs and statistical models to uncover the genetics basis of phenotypic and transcriptomic variation in animal species
Similarity search in large-scale database; protein homology classification; ncRNA identification
Proper analysis of efficient microarray experiments based on mixed effects models
Molecular phylogenetics and comparative chloroplast genomics in euglenophytes