Research Interest: Computational Biology
| Name | PhD Program | Research Interest | Publications |
|---|---|---|
| Wu, Di WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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 PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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 PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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 PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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 PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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. |
| Franco, Hector L. WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
My lab has a long-standing interest in gene regulation, epigenetics, chromatin and RNA biology, especially as it pertains to cancer. We are interested in studying the formation and function of transcriptional enhancers and the non-coding RNAs that are actively produced at enhancers, known as enhancer RNAs, which are involved in modulating several aspects of gene regulation. In addition, we aim to understand how transcriptional enhancers help orchestrate responses to external stimuli found in the tumor microenvironment. We address these research aims by using an interdisciplinary approach that combines molecular and cellular techniques with powerful genomic and computational approaches. |
| Forest, Greg WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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. |
| Fenton, Suzanne E. WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
The Reproductive Endocrinology Group in the National Toxicology Program (NTP) Labs, led by Dr. Fenton, focuses on the role of environmental chemicals in breast developmental timing as it relates to puberty, increased susceptibility to form breast tumors, altered lactational ability, and the effects of chemicals on independent breast cancer risk factors such as obesity, breast density and pubertal timing. The projects within the lab often take a systems biology approach to the problem and instead of delving into exact mechanisms of an insult, which is in line with the missions of the NTP. The group also provides expertise in the use of whole mount mammary gland preparations in evaluating early life development of both male and female rat offspring and lifelong effects in female mice. |
| Elston, Timothy WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
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 |
| Chen, Xian WEBSITE PUBLICATIONS |
PHD PROGRAM RESEARCH INTEREST |
Developing and applying novel mass spectrometry (MS)-based proteomics methodologies for high throughput identification, quantification, and characterization of the pathologically relevant changes in protein expression, post-translational modifications (PTMs), and protein-protein interactions. Focuses in the lab include: 1) technology development for comprehensive and quantitative proteomic analysis, 2) investigation of systems regulation in toll-like receptor-mediated pathogenesis and 3) proteomic-based mechanistic investigation of stress-induced cellular responses/effects in cancer pathogenesis. |