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NameEmailPhD ProgramResearch InterestPublications
Ward-Caviness, Cavin
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Toxicology

RESEARCH INTEREST
Bioinformatics, Computational Biology, Genomics, Systems Biology, Translational Medicine

We are actively engaged in multiple research arenas centered around understanding the associations between environmental exposures (primarily air pollution) and health outcomes. We use large clinical cohorts and electronic health records to understand associations between air pollution and health outcomes such as cardiovascular disease, metabolic disease, and aging. We use metabolomics and epigenetic data (primarily DNA methylation) to investigate molecular mechanisms, and highlight the integration of ‘omics data in a systems biology framework to better understand dysregulated pathways. Finally, we have projects centered around methods development and causal analyses to improve our understanding of the biology central to environmental health effects.

Liu, Yufeng
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Bioinformatics, Computational Biology

Statistical machine learning and data mining, nonparametric statistics and functional estimation, bioinformatics, design and analysis of experiments

 

Wu, Di
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Bioinformatics, Cancer Biology, Computational Biology, Genomics, Translational Medicine

Our group develops novel statistical bioinformatics tools and applies them in biomedical research to help understanding the precision medicine for cancer (e.g., breast cancer and lung cancer) subtypes, the disease associated integrative pathways across multiple genomic regulatory levels, and the genetics based drug repurposing mechanisms. Our recent focus includes pathway analysis, microbiome data analysis, data integration and electronica medical records (EMR). Our application fields include cancer, stem cell, autoimmune disease and oral biology. In the past, we have developed gene set testing methods with high citations, in the empirical Bayesian framework, to take care of small complex design and genewise correlation structure. These have been widely used in the microarray and RNAseq based gene expression analysis. Contamination detection for data analysis for Target DNA sequencing is work in progress. Recently, we also work on single cell sequencing data for pathway analysis with the local collaborators.

Hahn, Klaus
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Cell Biology & Physiology, Neuroscience, Pharmacology

RESEARCH INTEREST
Biochemistry, Biophysics, Cell Biology, Cell Signaling, Chemical Biology, Computational Biology, Systems Biology

Dynamic control of signaling networks in living cells; Rho family and MAPK networks in motility and network plasticity; new tools to study protein activity in living cells (i.e., biosensors, protein photomanipulation, microscopy). Member of the Molecular & Cellular Biophysics Training Program and the Medicinal Chemistry Program.

Gomez, Shawn
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Bioinformatics, Cancer Biology, Cell Signaling, Computational Biology, Systems Biology

Our primary research is in the area of computational systems biology, with particular interest in the study of biological signaling networks; trying to understand their structure, evolution and dynamics. In collaboration with wet lab experimentalists, we develop and apply computational models, including probabilistic graphical and multivariate methods along with more traditional engineering approaches such as system identification and control theory, to current challenges in molecular biology and medicine. Examples of recent research projects include: prediction of protein interaction networks, multivariate modeling of signal transduction networks, and development of methods for integrating large-scale genomic data sets.

Furey, Terry
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Computational Biology, Genomics, Immunology, Molecular Biology, Systems Biology, Translational Medicine

The Furey Lab is interested in understanding gene regulation processes in specific cell types, especially with respect to complex phenotypes, and the effect of genetic and environmental variation on gene regulation. We have explored these computationally by concentrating on the analysis of genome-wide open chromatin data generated from high-throughput sequencing experiments; and the development of statistical methods and computational tools to investigate underlying genetic and biological mechanisms of complex phenotypes. Our current projects include determining the molecular effects of exposure to ozone on chromatin, gene regulation, and gene expression in alveolar (lung) macrophages of genetically diverse mouse strains. We are also exploring genetics, chromatin, transcriptional, and microbial changes in inflammatory bowel diseases to identify biomarkers of disease onset, severity, and progression.

Frohlich, Flavio
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Cell Biology & Physiology, Neuroscience

RESEARCH INTEREST
Computational Biology, Neurobiology, Physiology, Systems Biology, Translational Medicine

Our goal is to revolutionize the treatment of psychiatric and neurological illness by developing novel brain stimulation paradigms. We identify and target network dynamics of physiological and pathological brain function. We combine computational modeling, optogenetics, in vitro and in vivo electrophysiology in animal models and humans, control engineering, and clinical trials. We strive to make our laboratory a productive, collaborative, and happy workplace.

Forest, Greg
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology

RESEARCH INTEREST
Biomaterials, Computational Biology

Research interests include: transport processes in the lung, flow and structure of nano-materials & macromolecular fluids, weakly compressible transport phenomena, solitons and optical fiber applications, inverse problems for material characterization and modeling of transport in multiphase porous media.

Elston, Timothy
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Bioinformatics & Computational Biology, Pharmacology

RESEARCH INTEREST
Biophysics, Computational Biology, Pharmacology, Systems Biology

The Elston lab is interested in understanding the dynamics of complex biological systems, and developing reliable mathematical models that capture the essential components of these systems. The projects in the lab encompass a wide variety of biological phenomena including signaling through MAPK pathways, noise in gene regulatory networks, airway surface volume regulation, and understanding energy transduction in motor proteins. A major focus of our research is understanding the role of molecular level noise in cellular and molecular processes. We have developed the software tool BioNetS to accurately and efficiently simulate stochastic models of biochemical networks

Dohlman, Henrik
WEBSITE
EMAIL
PUBLICATIONS

PHD PROGRAM
Biochemistry & Biophysics, Bioinformatics & Computational Biology, Pharmacology

RESEARCH INTEREST
Biochemistry, Cell Signaling, Genomics, Pharmacology, Systems Biology

We use an integrated approach (genomics, proteomics, computational biology) to study the molecular mechanisms of hormone and drug desensitization. Our current focus is on RGS proteins (regulators of G protein signaling) and post-translational modifications including ubiquitination and phosphorylation.