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[ PhD Program: Computational Biology Keyword: ]

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NameEmailPhd ProgramResearch InterestsPublications
Berkowitz, Max email , , , , publications

We use computational techniques (multiscale molecular dynamics computer simulations) to study interactions of proteins and peptides with membranes and to study interactions of shock waves with membranes of neural cells. Specifically, we study the interaction of antimicrobial peptides with bacterial membranes to understand how they destroy such membranes.  In our study of shock wave interacting with brain tissue we investigate the importance of cavitation effect (collapse of bubbles) created by shock waves. Detailed molecular level knowledge of the processes we investigate using computational methodology is very helpful in understanding processes such as TBI (traumatic brain injury).  The computational methodology we use is also playing now an important role in the filed of drug design.  Member of the Molecular & Cellular Biophysics Training Program.

Burch, Christina email , , , , , publications

Experimental Evolution of Viruses.  We use both computational and experimental approaches to understand how viruses adapt to their host environment.  Our research attempts to determine how genome complexity constrains adaptation, and how virus ecology and genetics interact to determine whether a virus will shift to utilizing new host.  In addition, we are trying to develop a framework for predicting which virus genes will contribute to adaptation in particular ecological scenarios such as frequent co-infection of hosts by multiple virus strains.  For more information, and for advice on applying to graduate school at UNC, check out my lab website www.unc.edu/~cburch/lab.

Calabrese, J. Mauro email , , , , , , , , , publications

Our lab is trying to understand the mechanisms by which long noncoding RNAs orchestrate the epigenetic control of gene expression. Relevant examples of this type of gene regulation occur in the case of X-chromosome inactivation and autosomal imprinting. We specialize in genomics, but rely a combination of techniques —  including genetics, proteomics, and molecular, cell and computational biology — to study these processes in both mouse and human stem and somatic cell systems.

Carter, Charles email , , , , , , publications

Molecular evolution and mechanistic enzymology find powerful synergy in our study of aminoacyl-tRNA synthetases, which translate the genetic code. Class I Tryptophanyl-tRNA Synthetase stores free energy as conformational strain imposed by long-range, interactions on the minimal catalytic domain (MCD) when it binds ATP.  We study how this allostery works using X-ray crystallography, bioinformatics, molecular dynamics, enzyme kinetics, and thermodynamics. As coding sequences for class I and II MCDs have significant complementarity, we also pursuing their sense/antisense ancestry.  Member of the Molecular & Cellular Biophysics Training Program.

Chen, Xian email , , , , publications

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.

Crofton, Kevin email , , publications

Our laboratory has research interests that include developmental neurotoxicity, with an emphasis on the use of mode-of-action models to study the impact of endocrine disruptors and the cumulative risk of thyroid disruptors and pesticides.

Dokholyan, Nikolay email , , , , , publications

The mission of my laboratory is to develop and apply integrated computational and experimental strategies to understand, sense, and control misfolded proteins, and uncover the etiologies of human diseases. UNDERSTAND: We are working toward understanding of the protein misfolding diseases, such as Lou Gehrig’s disease and cystic fibrosis.. Other areas of interest include HIV, Graft versus Host disease (fatal autoimmune response to bone marrow transplant), and understanding and developing new drugs for pain. SENSE: We are working toward developing genetically-encoded proteins that bind and report rare/intermediate conformations of target molecules (proteins and RNA). CONTROL: We are working toward developing genetically-encoded proteins that control target proteins with light and/or drugs. We have developed novel approach for drug activation/deactivation of kinases, and light-activatable protein to manipulate protein function with light. We are working toward extending these approaches to other classes of proteins and on multiplexing, whereby we selectively activate/control several distinct cellular pathways via targeting several proteins simultaneously.

Dowen, Jill email , , , , , , publications

My lab studies how genes function within the three-dimensional context of the nucleus to control development and prevent disease. We combine genomic approaches (ChIP-Seq, ChIA-PET) and genome editing tools (CRISPR) to study the epigenetic mechanisms by which transcriptional regulatory elements control gene expression in embryonic stem cells.  Our current research efforts are divided into 3 areas: 1) Mapping the folding pattern of the genome 2) Dynamics of three-dimensional genome organization as cells differentiate and 3) Functional analysis of altered chromosome structure in cancer and other diseases.

Elston, Timothy email , , , , publications

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

Fenton, Suzanne E. email , , , publications

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.

Forest, Greg email , publications

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.

Franco, Hector L. email , , , , , publications

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.

Frohlich, Flavio email , , , , , , publications

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.

Furey, Terry email , , , , , publications

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 1,3-butadiene, a known carcinogen, on chromatin, gene regulation, and gene expression in lung, liver, and kidney tissues of genetically diverse mouse strains. We are also exploring chromatin, transcriptional, and microbial changes in inflammatory bowel diseases to identify biomarkers of disease onset, severity, and progression.

Gomez, Shawn email , , , , publications

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.

Hahn, Klaus email , , , , , , , , , publications

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.

Hayes, David N email , , , publications

Molecular carcinogenesis, research translation, biomarkers, computational toxicology

Hedrick, Tyson email , , publications

Research in my laboratory focuses on how animals produce and control movement, with a particular interest in animal flight.  We use both computational and experimental techniques to examine how organismal components such as the neuromuscular and neurosensory systems interact with the external environment via mechanics and aerodynamics to produce movement that is both accurate and robust.  Keywords: biomechanics, flight, avian, insect, neural control, muscle, locomotion, computational modeling

Ibrahim, Joseph G email , , , publications

My research involves developing statistical methods in computational biology, including  methods Chip-seq data as well as the development of statistical methods for gene expression and sequence data.

Jones, Corbin email , , , , , , publications

The goal of my research is to identify, clone, and characterize the evolution of genes underlying natural adaptations in order to determine the types of genes involved, how many and what types of genetic changes occurred, and the evolutionary history of these changes. Specific areas of research include: 1) Genetic analyses of adaptations and interspecific differences in Drosophila, 2) Molecular evolution and population genetics of new genes and 3) Evolutionary analysis of QTL and genomic data.

Kuhlman, Brian email , , , , publications

We use a combination of experimental and computational methods to redesign protein-protein interactions.  The potential applications for this technology include enhancing protein therapeutic and creating new tools to study signaling pathways.

Lee, Andrew email , , , , publications

We study protein structure and dynamics as they relate to protein function and energetics. We are currently using NMR spectroscopy (e.g. spin relaxation), computation, and a variety of other biophysical techniques to gain a deeper understanding of proteins at atomic level resolution.  Of specific interest is the general phenomenon of long-range communication within protein structures, such as observed in allostery and conformational change.  A. Lee is a member of the Molecular & Cellular Biophysics Training Program.

Li, Yun email , , publications

The Yun Li group develops statistical methods and computational tools for modern genetic, genomic, and epigenomic data. We do both method development and real data applications. The actual projects in the lab vary from year to year because I am motivated by real data problems, and genomics is arguably (few people argue with me though) THE most fascinating field with new types and huge amount of data generated at a pace more than what we can currently deal with. For current projects, please see: http://www.unc.edu/~yunmli/BCBrotationAds/

Liu, Yufeng email , publications

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

Manis, Paul B. email , , , , publications

We are interested in the cellular and network mechanisms of sensory information processing in the central nervous system, with an emphasis on the neural substrates for hearing. We study functional network organization, synaptic function, the roles of ion channels and cellular excitability, and short and long-term synaptic plasticity, in the auditory brainstem and auditory cortex.  Experimentally, we use patch clamp methods in brain slices, optogenetics and laser scanning photostimulation, multiphoton imaging, and computational neuroscience (modeling), in normal and transgenic mouse models. The lab also has collaborative projects related to schizophrenia (prefrontal cortex; Dr. Patricia Maness, UNC) and connectomics (cochlear nucleus and MNTB; Dr. George Spirou, WVU).

Miller, Laura email , , , , , publications

Miller’s research group focuses on topics in integrative biophysics: physics applied to biology at the level of cells to organisms. In particular, the group is interested in the role of fluid forces during locomotion and morphogenesis. One ongoing project is focused on understanding the aerodynamics of flight in the smallest insects. Another current project investigates the role of fluid forces during the development of the embryonic vertebrate heart.

Nylander-French, Leena email , , publications

My research focuses on understanding the relationship between dermal and inhalation exposure and the effect of individual genetic differences on the function of enzymes that detoxify hazardous agents and that affect the development of disease. My research group has pioneered approaches to quantitatively measure skin and inhalation exposures to toxicants; additionally, my group has developed sophisticated exposure modeling tools using mathematical and statistical principles in an effort to standardize and improve exposure and risk assessment.

Pardo-Manuel de Villena, Fernando email , , , , , , publications

Non-Mendelian genetics including, meiotic drive, parent-of-orifin effects and allelic exclusion.

Pielak, Gary J. email , , , , , publications

My graduate students and I use the formalism of equilibrium thermodynamics and the tools of molecular biology and biophysics to understand how nature designs proteins.

Prins, Jan F. email , , , , publications

Our group develops computational methods for the analysis of high throughput sequence data.  Our focus is on transcriptome analysis and its applications.

Purvis, Jeremy email , , , , , publications

We study the behavior of individual cells with a specific focus on “irreversible” cell fate decisions such as apoptosis, senescence, and differentiation. Why do genetically identical cells choose different fates? How much are these decisions controlled by the cell itself and how much is influenced by its environment? We address these questions using a variety of experimental and computational approaches including time-lapse microscopy, single-molecule imaging, computational modeling, and machine learning. Our ultimate goal is to not only understand how cells make decisions under physiological conditions—but to discover how to manipulate these decisions to treat disease.

Sethupathy, Praveen email , , , , , publications

The overall goal of my research program is to define the role of non-coding RNAs in gene regulatory networks that contribute to the molecular pathology of complex diseases, with a primary focus on diabetes and related metabolic disorders.  Specifically, my lab investigates: (1) the contribution of small RNA networks to gene expression dynamics; (2) small RNA mediated regulation of metabolic pathways; (3) non-coding RNAs as both biomarkers of physiologic status and therapeutic targets; (4) regulatory variants within the microRNA (miRNA) regulome that predispose to disease; and (5) novel forms of intercellular communication via regulated transfer of small RNAs.

Snoeyink, Jack email , publications

My primary research area is computational geometry, in which one studies the design and analysis of algorithms for geometric computation. Computational geometry finds application in problems from solid modeling, CAD/CAM, computer graphics, molecular biology, data structuring, and robotics, as well as problems from discrete geometry and topology.  Most of my work involves identifying, representing, and exploiting geometric and topological information that permit efficient computation.  My current focus is on applications of computational geometry in Molecular Biology and Geographic Information Systems (GIS). Examples of the former include docking and folding problems, and scoring protein structures using Delaunay tetrahedralization.

Stein, Jason email , , , , , publications

We are a lab exploring how variations in the genome change the structure and development of the brain, and in doing so, create risk for neuropsychiatric illness. We study genetic effects on multiple aspects of the human brain, from macroscale phenotypes like gross human brain structure measured with MRI to molecular phenotypes like gene expression and chromatin accessibility measured with genome-sequencing technologies. We also use neural progenitor cells as a modifiable and high fidelity model system to understand how disease-associated variants affect brain development.

Tropsha, Alexander email , , , , , , , publications

The major area of our research is Biomolecular Informatics, which implies understanding relationships between molecular structures (organic or macromolecular) and their properties (activity or function). We are interested in building validated and predictive quantitative models that relate molecular structure and its biological function using statistical and machine learning approaches. We exploit these models to make verifiable predictions about putative function of untested molecules.

Vision, Todd email , , , , , , publications

Our lab uses computational and molecular tools to study the evolution of genome organization, primarily in the flowering plants. Areas of
investigation include the origin and consequences of differences in gene order within populations and between species, the evolutionary and functional diversification of gene families (phytome.org), and the application of genomics to evolutionary model organisms (mimulusevolution.org).  We also are involved in a number of cyberinfrastructure initiatives through the National Evolutionary Synthesis Center (nescent.org), including work on digital scientific libraries (datadryad.org), open bioinformatic software development (e.g. gmod.org) and the application of semantic web technologies to biological data integration (phenoscape.org).

Weeks, Kevin email , , , , , , publications

The Weeks group invents novel chemical microscopes for understanding the structure and function of RNA and then applies these technologies to leading, and previously intractable, problems in biology. Most projects in the laboratory span fundamental chemistry or technology development and ultimately lead to practical applications in virology (especially HIV), next-generation structure analysis, drug design, and understanding RNA structure in living cells.  Collectively, this work has led to extensive recognition of graduate student colleagues in the laboratory.

Wright, Fred email , publications

Statistical genetics, bioinformatics, likelihood- based inference

Wu, Di email , , , , publications

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.

Zhang, Qi email , , , , publications

Our laboratory is focusing on developing and applying solution-state NMR methods, together with computational and biochemical approaches, to understand the molecular basis of nucleic acid functions that range from enzymatic catalysis to gene regulation. In particular, we aim to visualize, with atomic resolution, the entire dynamic processes of ribozyme catalysis, riboswitch-based gene regulation, and co-transciptional folding of mRNA. The principles deduced from these studies will provide atomic basis for rational manipulation of RNA catalysis and folding, and for de novo design of small molecules that target specific RNA signals. Research program in the laboratory provides diverse training opportunities in areas of spectroscopy, biophysics, structural biology, computational modeling, and biochemistry.

Zou, Fei email , , publications

My research has been concentrated on the areas of statistical genetics and genomics to investigate the role of genetic variations on complex quantitative traits and diseases. I work primarily in the development, as well as the examination of statistical properties, of theoretical methodologies appropriate for the interpretation of genetic data.