Research Concentrations

Molecular Biophysics

Faculty
 
Bagdasarian, M. 

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
 
Blanchard, Gary
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
 
McCracken, John
Development and use of Electron Paramagnetic Resonance (EPR) Spectroscopy for the structural characterization of paramagnetic centers in biologicalsystems
 
Electronic nanocomponents in Geobacter biofilms
 
Seibold, Steve
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
 
Vieille, Claire
Studying the determinants of protein thermostability using heperthermophilic enzymes as models
 
Advanced numerical methods for the structure and dynamics of biological macromolecules
 
Weliky, David
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
 
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
 
Vieille, Claire
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                      
 
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
 
Harrison, Michael
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
 
Vieille, Claire
Comparing flexibility in mesophilic and hyperthermophilic proteins by NMR and molecular dynamics

Genomics, Bioinformatics, and Computational Biology

Faculty
 
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
 
Jiang, Ning
The contribution of transposable elements to genome evolution
 
Knott, Jason
Developmental epigenetics, embryonic development, and embryonic stem (ES) cells; ChIP-chip and RNA
 
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