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[ PhD Program: Genomics Keyword: ]

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NameEmailPhd ProgramResearch InterestsPublications
Ahmed, Shawn email , , , , , publications

Our research group utilizes the nematode C. elegans to investigate germ cell immortality: mechanisms that allow germ cells remain eternally youthful as they are transmitted from one generation to the next. We also study how telomerase functions at chromosome termini, as well as the consequences of telomere dysfunction.

Amelio, Antonio L. email , , , , , , , publications

Our laboratory is broadly interested in understanding the molecular mechanisms of transcriptional regulation by cell signaling pathways and the role of pathway cross-talk in cancer biology. In particular, the cAMP signaling cascade directs adaptive cellular responses to a variety of stress stimuli via a combination of acute affects arising from GS-protein coupled receptor (GPCR)-mediated activation of PKA and long-term affects resulting from transcriptional reprogramming directed by CREB and the CREB Regulated Transcription Coactivators (CTRCs). We are applying an interdisciplinary approach to study the consequences of aberrant activation of the cAMP/CREB/CRTC signal circuit on these adaptive responses and how cooperative signaling with other pathways promotes oncogenic processes in oral, head, and neck cancers.

Berg, Jonathan email , , , , , publications

My research group is broadly interested in the application of sequencing technologies in medical genetics and genomics, using a combination of wet lab and computational approaches.  As a clinician, I am actively involved in the care of patients with hereditary disorders, and the research questions that my group investigates have direct relevance to patient care.  One project uses genome sequencing in families with likely hereditary cancer susceptibility in order to identify novel genes that may be involved in monogenic forms of cancer predisposition.  Another major avenue of investigation examines the use of genome-scale sequencing in clinical medicine, ranging from diagnostic testing to newborn screening, to screening in healthy adults.

Bultman, Scott email , , , , publications

Our lab is interested in the role of chromatin-modifying factors and epigenetics in mammalian development and disease. We are particularly interested in two major areas both of which make use of mouse models: (1) the role of BRG1 and SWI/SNF nucleosome-remodeling complexes in various aspects of hematopoiesis including regulation of globin gene expression and inflammation; (2) the role of dietary fiber and gut microflora on histone modifications, CpG methylation, and prevention of colorectal cancer.

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.

Coleman, William B. email , , , , , publications

The research in our laboratory involves several major projects related to the molecular pathogenesis of human cancer and investigations related to the biology of liver stem-like progenitor cells, including (i) characterization of human liver tumor suppressor genes, (ii) analysis of genetic determinants of breast cancer, (iii) investigation of mechanisms governing aberrant DNA methylation in breast cancer, (iv) liver progenitor cell responses after toxic liver injury, and (v) transplantation of liver stem-like progenitor cells for correction of genetic liver disease.

Copenhaver, Gregory P. email , , , , , publications

The primary research area my lab is the regulation of meiotic recombination at the genomic level in higher eukaryotes.  Genomic instability and disease states, including cancer, can occur if the cell fails to properly regulate recombination.  We have created novel tools that give our lab an unparalleled ability to find mutants in genes that control recombination. We use a combination of genetics, bioinformatics, computational biology, cell biology and genomics in our investigations.  A second research area in the lab is the role of centromere DNA in chromosome biology.  We welcome undergraduates, graduate students, postdoctoral fellows and visiting scientists to join our team.

Crews, Stephen email , , , , , , publications

Research in the lab is focused on a genetic, cellular, and molecular understanding of Drosophila developmental neuroscience, including the following research areas – (1) Neuronal formation and differentiation, (2) Glial formation, migration, and axon-glial interactions, (3) Synaptic connectivity, and (4) Transcriptional regulation.

Dangl, Jeff email , , , , , , , publications

We use the premier model plant species, Arabidopsis thaliana, and real world plant pathogens like the bacteria Pseudomonas syringae and the oomycete Hyaloperonospora parasitica to understand the molecular nature of the plant immune system, the diversity of pathogen virulence systems, and the evolutionary mechanisms that influence plant-pathogen interactions. All of our study organisms are sequenced, making the tools of genomics accessible.

Davis, Ian email , , , , publications

With a particular interest in pediatric solid tumors, our lab aims to develop a mechanistic understanding of the role of aberrant or dysregulated transcription factors in oncogenesis.

Dittmer, Dirk email , , , , , publications

Our lab tries to understand viral pathogenesis. To do so, we work with two very different viruses – West Nile Virus (WNV) and Kaposi¹s sarcoma-associated herpesvirus (KSHV/HHV-8).

Dohlman, Henrik email , , , , , , publications

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.

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.

Everett, Eric T email , , , , , publications

Our research focuses upon craniofacial and mineralized tissue genetics; gene: environment interactions; mapping of complex traits; normal variation (to the extent that normal variation becomes abnormal); and animal models for oral/dental/craniofacial disorders.

Faber, James E. email , , , , publications

We study mechanisms of formation of the collateral circulation in embryonic and neonatal mice, 2) collateral growth and angiogenesis in models of ischemic disease in adult mice, 3) signaling in collateral endothelial cells, and 4) the genetic and environmental basis for the large variation in collateral vessel formation in the embryo and growth in ischemic disease (see Faber et al Physiol Genom 2007; Circ Res 2008) using genome-wide mapping and expression profiling (QTL, eQTL), consomic and haplotype analyses, plus physiologic, cellular and molecular study of candidate genes. Techniques in addition to those mentioned above include physiologic analysis of mouse models of cerebral, coronary and hindlimb ischemic disease, vascular imaging (angiography, laser Doppler flowmetry, micro-computed tomography), signaling analysis, cell and molecular biology.  We also study adaptive and pathological arterial wall growth and remodeling in the adult. The laboratory collaborates with other groups at UNC and other institutions in the US and elsewhere, providing varied opportunities for professional development.

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.

Grant, Sarah email , , , , , publications

Our research goal is to understand how bacterial pathogens cause disease on their hosts. We are working with a plant pathogen, Pseudomonas syringae which introduces virulence proteins into host cells to suppress immune responses. Our laboratory collaborates with Jeff Dangl’s lab in the UNC Biology Department using genomics approaches to identify P. syringae virulence proteins and to discover how they alter plant cell biology to evade the plant immune system and cause disease.

Hammond, Scott email , , , , , publications

My lab studies a gene silencing phenomenon called RNA interference, or RNAi.  We are interested in the role of RNAi in regulating endogenous genes, particularly those involved in cancer progression pathways.

Han, Zongchao email , , , , publications

My research focus centers on retinal gene/drug therapy using nanotechnologies. My laboratory is interested in developing gene therapies for inherited blinding diseases and eye tumors. We are particularly interested in understanding the gene expression patterns that are regulated by the cis-regulatory elements. We utilize compacted DNA nanoparticles which have the ability to transfer large genetic messages to overcome various technical challenges and to appreciate the translational potential of this technology. This multidimensional technology also facilitated targeted drug delivery. Currently, we are working on the design and development of several specific nano formulations with targeting, bioimaging and controlled release specificities.

Ideraabdullah, Folami Y email , , , , publications

The lab focus is to understand the mechanism of gene-environment interactions by examining the genetic basis of epigenetic response to nutrition and environmental toxicants. The long-term goal is to identify and characterize genetic (naturally occurring and induced) and environmental (toxicant and nutritional) causes of disruption of DNA methylation patterns during development and to determine their role in disease. The primary focus is on DNA methylation patterns during germ cell and early embryonic development during critical windows of epigenetic reprogramming.

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.

Kaufman, David G. email , , , , , publications

Topic 1  We seek genomic targets for carcinogenesis among segments of DNA replicated in early S phase when cells are most susceptible to carcinogens.  We are mapping genomic sites replicated during early S phase, identifying origins of replication activated in this interval, and characterizing temporal sequencing of replication from these origins.  Topic 2  We are reconstructing differentiated and functional human endometrial tissue from epithelial and stromal cells interacting in culture.  We use these co-cultures to study development of endometrial cancer.

Kelada, Samir email , , , , , publications

While both genes and environment are thought to influence human health, most investigations of complex disease only examine one of these risk factors in isolation.  Accounting for both types of risk factors and their complex interactions allows for a more holistic view of complex disease causation.  The Kelada lab is focused on the identification and characterization of these gene-environment interactions in airway diseases, particularly asthma, a disorder of major public health importance.   /  / Additionally, to gain insight into how the airway responds to relevant exposures (e.g., allergens or pathogens), we study gene expression in the lung (particularly airway epithelia). Our goal is identify the genetic determinants of gene expression by measuring gene expression across many individuals (genotypes). / This “systems genetics” approach allows us to identify master regulators of gene expression that may underlie disease susceptibility or represent novel therapeutic targets. /

Knickmeyer Santelli, Rebecca email , , , , publications

Dr. Knickmeyer Santelli’s lab seeks to advance our understanding of neurodevelopmental disorders through the integration of pediatric neuroimaging with genetic, endocrine, and behavioral methodologies. In particular, her research explores the role which common and rare genetic variation plays in explaining individual differences in neurodevelopment during infancy and early childhood and investigates the mechanisms which modulate differential vulnerability to and expression of neurodevelopment disorders in each sex. She is also using MRI to evaluate the effects of prenatal exposure to antidepressants and to understand how microbial colonization of the gut impacts human brain development and anxiety.

Kodavanti, Urmila P email , , , , publications

Our research focuses on understanding mechanisms of cardiovascular and metabolic health effects of inhaled air pollutants. Specific emphasis is given to susceptibility variations due to underlying cardiovascular disease, obesity, and diabetes. The roles of genetic versus physiological factors are examined. We use molecular and high throughput genomics, and proteomics techniques to establish a link with disease phenotype and physiological alterations. State-of-the-art EPA inhalation facilities are used for air pollution exposures in animal models with or without genetic predisposition. The role of environment in disease burden is the focus.

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/

Magnuson, Terry email , , , , , publications

The Magnuson Lab works in three areas – (i) Novel approaches to allelic series of genomic modifications in mammals, (ii)Mammalian polycomb-group complexes and development, (iii) Mammalian Swi/Snf chromatin remodeling complexes

Marchetti, Adrian email , , , , publications

We are a biological oceanography lab that performs inquiry-based science by combining physiological and molecular approaches in laboratory isolates and natural communities to investigate how marine microorganisms are affected by their environment and in turn, influence ocean biogeochemistry and ecosystem dynamics. Particular interests include studying trace metals, such as iron, that are essential for the nutrition of phytoplankton and predicting the effects of future climate changes on phytoplankton distribution and abundance.  We implement the use of environmental genomic approaches (e.g. RNA-seq) to ascertain the ways in which marine microbes have adapted and acclimate to varying environmental conditions.

Markovic-Plese, Silva email , , , , , publications

My long-term goal is to understand and therapeutically target the key mechanisms of disease development in patients with multiple sclerosis (MS).  Our research has been focused on the molecular events involved in the initiation of the autoimmune response in MS, and on the mechanisms of action of immunomodulatory therapies for this disabling disease.  Current projects in the laboratory include transcriptional and proteomic profiling of the peripheral blood cells and cerebrospinal fluid obtained from patients in the early phase of the disease, which lead to the discovery of the high levels of IL-11 in the CSF and its high up-regulation in the blood-derived CD4+ T-cells in patients with clinically isolated syndrome (CIS) suggestive of MS. Our center is uniquely positioned to perform the proposed research, having an access to the clinical samples through the integrated clinical and cellular/molecular biology research.

Marzluff, William email , , , , , , , , , publications

We are interested in the mechanisms by which histone protein synthesis is coupled to DNA replication, both in mammalian cell cycle and during early embryogenesis in Drosophila, Xenopus and sea urchins.

Matera, Greg email , , , , , , , publications

Research in our laboratory is focused on RNA. We aim to understand how ribonucleoprotein particles (snRNPs, mRNPs, etc.) are transcribed, packaged and transported to their final destinations in the cell.  We are also interested in the genetic and epigenetic forces that direct formation of microscopically visible subcellular structures (e.g. nuclear bodies). We use a combination of approaches, including Drosophila genetics, molecular cell biology, biochemistry, digital imaging microscopy and genome-wide analyses. Projects in the lab are focused on two areas:  models of a neurogenetic disease called Spinal Muscular Atrophy (SMA) and the functional analysis of post-translational modifications of chromatin and RNA-binding proteins important in cancer and other diseases.

Miller, C. Ryan email , , , , , , , , , , publications

My laboratory studies diffuse gliomas, devastating primary tumors of the central nervous system for which few effective drugs are currently available.  We utilize genetically engineered mice, cell culture, and human tumor model systems to explore the molecular pathogenesis of gliomas.  We utilize animal model systems to develop drugs and diagnostic markers for their individualized therapy.  Rotating students gain experience with multiple techniques, including cell culture, molecular biology, genomics, genetic lineage tracing, fluorescence microscopy, and digital image analysis.

Mohlke, Karen email , , , , , publications

We identify genetic variants that influence common human traits with complex inheritance patterns, and we examine the molecular and biological mechanisms of the identified variants and the genes they affect. Currently we are investigating susceptibility to type 2 diabetes and obesity, and variation in cholesterol levels, body size, body shape, and metabolic traits. We detect allelic differences in chromatin structure and gene expression and examine gene function in human cell lines and tissues. In addition to examining the primary effects of genes, the lab is exploring the interaction of genes with environmental risk factors in disease pathogenesis. Approaches include genome-wide association studies, molecular biology, cell biology, genetic epidemiology, sequencing, and bioinformatic analysis of genome-wide data sets.

O’Brien, Lori email , , , , publications

Modern technologies from next-gen sequencing to high resolution imaging have advanced our knowledge of kidney development, function, and disease. We are among the pioneers utilizing techniques such as ChIP-seq, RNA-seq, modern genome editing, and imaging to understand how regulatory programs control progenitor populations during kidney development. Our goal is to understand how these programs contribute to progenitor specification and maintenance, and how they are altered during disease and aging. Our ultimate goal is translational applications of our research to develop new therapeutics and regenerative strategies.

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

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

Parker, Joel email , , , publications

Our research is focused in the methodological development and integrated analysis of high throughput genetic and genomic studies. I previously lead the development of algorithms and content resulting in ProsignaTM, the only CE marked and FDA 510(k) cleared breast cancer diagnostic assay for FFPE tissue. We are currently involved in similar diagnostic development in multiple clinical trials where genomics are modeled to predict clinical outcomes in cancer.

 

In a separate role, I currently direct the sequencing, microarray, and other genomics analysis in the Bioinformatics Shared Resource at the Lineberger Comprehensive Cancer Center. The Bioinformatics Shared Resource provides consultation and analytical services primarily for the Cancer Center, but is also involved in collaborations across multiple departments and institutions. This role has brought a number of opportunities for technology development, primarily for sequencing data analysis. Here we are continuously developing algorithms and software to maximize the information content from novel sequencing assays.

Perou, Charles M. email , , , , , , , publications

The focus of my lab is to characterize the biological diversity of human tumors using genomics, genetics, and cell biology, and then to use this information to develop improved treatments that are specific for each tumor subtype and for each patient. A significant contribution of ours towards the goal of personalized medicine has been in the genomic characterization of human breast tumors, which identified the Intrinsic Subtypes of Breast Cancer. We study many human solid tumor disease types using multiple experimental approaches including RNA-sequencing (RNA-seq), DNA exome sequencing, Whole Genome Sequencing, cell/tissue culturing, and Proteomics, with a particular focus on the Basal-like/Triple Negative Breast Cancer subtype. In addition, we are mimicking these human tumor alterations in Genetically Engineered Mouse Models, and using primary tumor Patient-Derived Xenografts, to investigate the efficacy of new drugs and new drug combinations. All of these genomic and genetic studies generate large volumes of data; thus, a significant portion of my lab is devoted to using genomic data and a systems biology approach to create computational predictors of complex cancer phenotypes.

Phanstiel, Doug email , , , , publications

It is estimated that less than 2% of the human genome codes for a functional protein.  Scattered throughout the rest of the genome are regulatory regions that can exert control over genes hundreds of thousands of base pairs away through the formation of DNA loops.  These loops regulate virtually all biological functions but play an especially critical role in cellular differentiation and human development. While this phenomenon has been known for thirty years or more, only a handful of such loops have been functionally characterized.  In our lab we use a combination of cutting edge genomics (in situ Hi-C, ATAC-seq, ChIP-seq), proteomics, genome editing (CRISPR/Cas), and bioinformatics to characterize and functionally interrogate dynamic DNA looping during monocyte differentiation.  We study this process both in both healthy cells and in the context of rheumatoid arthritis and our findings have broad implications for both cell biology as well as the diagnosis and treatment of human disease.

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.

Randell, Scott email , , , , , , , publications

Identification of airway epithelial stem cells; innate immunity in the airway; the pathophysiology of post-lung transplant ischemia reperfusion injury and bronchiolitis obliterans syndrome.

Rogers, Steve email , , , , , , publications

The research in our lab is centered on understanding the mechanisms and principles of movement at the cellular level. Cytoskeletal filaments – composed of actin and microtubules – serve as a structural scaffolding that gives cells the ability to divide, crawl, and change their shape.  Our lab uses a combination of cell biological, biochemical, functional genomic, and  high resolution imaging techniques to study cytoskeletal dynamics and how they contribute to cellular motion.

Schisler, Jonathan C. email , , , , publications

The Schisler Lab is geared towards understanding and designing therapies for diseases involving proteinopathies- pathologies stemming from protein misfolding, aggregation, and disruption of protein quality control pathways. We focus on cardiovascular diseases including the now more appreciated overlap with neurological diseases such as CHIPopathy (or SCAR16, discovered here in our lab) and polyQ diseases. We use molecular, cellular, and animal-based models often in combination with clinical datasets to help drive our understanding of disease in translation to new therapies.

Sekelsky, Jeff email , , , , publications

Genome instability is a major cause of cancer. We use the model organism Drosophila melanogaster to study maintenance of genome stability, including DNA double-strand break repair, meiotic and mitotic recombination, and characterization of fragile sites in the genome.  Our primary approaches are genetic (forward and reverse, transmission and molecular), but we are also using biochemistry to study protein complexes of interest, genomics to identify fragile sites and understand the regulation of meiotic recombination, fluorescence and electron microscopy for analysis of mutant phenotypes, and cell culture for experiments using RNA interference.

Shank, Elizabeth email , , , , , , publications

My laboratory studies chemically mediated interactions between microbes, particularly those that lead to alterations in bacterial development. In the natural world, interspecies chemical communication contributes to the stability and function of complex microbial communities. We explore the mechanisms and molecules that microbes use to influence their microbial neighbors both in the laboratory and in natural environments using genetics, microscopy, chemical imaging, and next generation sequencing. Our goal is to gain insights into microbial ecology, identify compounds with novel bioactivities, and obtain chemical tools to manipulate bacterial behavior to our benefit.

Sheikh, Shehzad Z email , , publications

We seek to understand how information is encoded and dynamically utilized in immune cells from healthy and disease prone intestines (The Inflammatory Bowel Diseases: Crohn’s disease and Ulcerative Colitis). Our lab is multi-disciplinary and combines high-throughput genomics with innate immunity and microbiology. We focus specifically on genes that regulate response to the bacteria that normally reside in our intestines. Many of these genes make products that regulate the immune system in the intestine. These products defend the intestine against the attack of foreign materials; such as bacteria that live in the intestine. We use genome-sequencing technology to precisely identify regions throughout the genome that are potential ‘on’ or ‘off’ switches for these genes. There is a fine balance between the genes that produce inflammatory substances that are necessary to kill bacteria and genes that produce anti-inflammatory substances that are important to prevent damage to the intestine. If this balance between inflammatory and anti-inflammatory substance production in the intestine is disrupted, IBD may result. Our lab focuses on understanding how these important controllers of inflammation are turned on and off in IBD. We also study how inflammatory and anti-inflammatory signals impact disease severity, progression and response to therapy in individuals with IBD. This information has the potential to increase our understanding of causes of IBD (personalized medicine) and to contribute to the development of new treatments.

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.

Sullivan, Patrick email , , , , , publications

I study complex traits using linkage, association, and genetic epidemiological approaches.  Disorders include schizophrenia (etiology and pharmacogenetics), smoking behavior, and chronic fatigue.

Tarantino, Lisa M. email , , , , , , , , publications

The Tarantino lab studies addiction and anxiety-related behaviors in mouse models using forward genetic approaches. We are currently studying a chemically-induced mutation in a splice donor site that results in increased novelty- and cocaine-induced locomotor activity and prolonged stress response. We are using RNA-seq to identify splice variants in the brain that differ between mutant and wildtype animals. We are also using measures of initial sensitivity to cocaine in dozens of inbred mouse strains to understand the genetics, biology and pharmacokinetics of acute cocaine response and how initial sensitivity might be related to addiction. Finally, we have just started a project aimed at studying the effects of perinatal exposure to dietary deficiencies on anxiety, depression and stress behaviors in adult offspring. This study utilizes RNA-seq and a unique breeding design to identify parent of origin effects on behavior and gene expression in response to perinatal diet.

Troester, Melissa email , , , , publications

Dr. Troester’s research focuses on stromal-epithelial interactions, genomics of normal breast tissue, breast cancer microenvironment, and molecular pathology of breast cancer progression. She is a Co-Investigator on the Carolina Breast Cancer Study (CBCS), a resource including breast tumors from thousands of African American women, and she is PI of the Normal Breast Study (NBS), a unique biospecimen resource of normal tissue from women undergoing breast surgery at UNC Hospitals. Dr. Troester has extensive experience in integrating multiple high dimensional data types. She is chair of the Normal Breast Committee for the Cancer Genome Atlas Project where she is leading coordination of histology, copy number, mutation, methylation, mRNA and microRNA expression data. She has more than a decade of experience working with genomic data and molecular biology of breast cancer progression and has published many papers in the area of breast cancer subtypes, breast microenvironment, and stromal-epithelial interactions. She has trained four postdocs, 12 predoctoral students and several undergraduates.

Valdar, William email , , , , publications

We are a quantitative genetics lab interested the relationship between genes and complex disease. Most of our work focuses on developing statistical and computational techniques for the design and analysis of genetic experiments in animal models. This includes, for example: Bayesian hierarchical modeling of gene by drug effects in crosses of inbred mouse strains; statistical methods for identifying quantitative trait loci (QTL) in a variety of experimental mouse populations (including the Collaborative Cross); computational methods for optimal design of studies on parent of origin effects; modeling of diet by gene by parentage interactions that affecting psychiatric disease; detection and estimation of genetic effects on phenotypic variability. For more information, visit the lab website.

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).

Voruganti, Saroja email , , publications

My research interests are focused on understanding the effects of genetic and environmental factors and their interaction on complex human diseases using a combination of statistical, molecular and bioinformatics approaches. My specific interests include understanding the influence of genetic variants on serum uric acid levels (a biomarker for renal-cardiovascular disease), effect of gene by diet interactions on serum uric acid levels and associated renal-cardiovascular disease risk factors and identification of functional variants affecting these disorders that will lead to novel treatment options.

Wang, Greg Gang email , , , , , publications

With an emphasis on chromatin biology and cancer epigenetics, our group focuses on mechanistic understandings of how chemical modifications of chromatin define distinct patterns of human genome, control gene expression, and regulate cell proliferation versus differentiation during development, and how their deregulations lead to oncogenesis. Multiple on-going projects employ modern biological technologies to: 1) biochemically isolate and characterize novel factors that bind to histone methylation on chromatin, 2) examine the role of epigenetic factors (chromatin-modifying enzymes and chromatin-associated factors) during development and tumorigenesis using mouse knockout models, 3) analyze epigenomic and transcriptome alternation in cancer versus normal cells utilizing next-generation sequencing technologies, 4) identify novel oncogenic or tumor suppressor genes associated with leukemia and lymphoma using shRNA library-based screening. We are also working together with UNC Center of Drug Discovery to develop small-molecule inhibitors for chromatin-associated factors as novel targeted cancer therapies.

Wilhelmsen, Kirk email , , , , publications

The Wilhelmsen lab is engaged in the genetic mapping of susceptibility loci for complex neurological diseases and has been developing large-scale automated gene mapping technologies to facilitate these mapping efforts. They have invested heavily in automation that enables high-throughput genotyping and data processing. As data accumulates, this will enable parametric and nonparametric linkage analysis of large numbers of traits at regular intervals for the entire genome. The Wilhelmsen lab is applying these techniques to two projects: (1) the genetics of alcoholism and (2) positional cloning of the gene responsible for a family of disorders called frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17).

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.

Yeh, Jen Jen email , , , , publications

We are a translational research lab. The overall goal of our research is to find therapeutic targets and biomarkers for patients with pancreatic and colorectal cancer and to translate this to the clinic. In order to accomplish this, we analyze patient tumors using microarray analysis, identify and validate targets using forward and reverse genetic approaches in both cell lines and mouse models. At the same time, we evaluate novel therapeutics for promising targets in mouse models in order to better predict clinical response in humans. We also collaborate with the DeSimone and Huang labs to apply nanotechnology to drug delivery and therapeutics. Keywords: genomics, biomarkers, translational research, microarray, signaling, pancreatic cancer, colon cancer, mouse models, GEMM, drug discovery, nanoparticles.

Zhang, Qing email , , , , , publications

The oxygen-sensing pathway contributes largely to the development of tumors. One of the central players in this pathway is prolyl hydroxylase (EglN1, 2 and 3). Our lab currently studies hypoxia signaling, prolyl hydroxylase and cancer, specifically breast and renal cell carcinoma. One project focuses on using proteomic and genomic approaches to screen for novel prolyl hydroxylase substrates that play important roles in cancer. The other project involves integrating CHIP-seq strategy with gene expression profiling in order to identify EglN2 prolyl hydroxylase and hypoxia inducible factor (HIF) targets in the malignant diseases. The ultimate goal is to understand mechanistically how oxygen-sensing pathways contribute to cancer progression, which will facilitate our design of efficient treatment strategies to specifically target cancer.

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.

Zylka, Mark J. email , , , , , , , publications

Our research is focused on two general areas:  1. Autism and 2. Pain.  Our autism research is focused on topoisomerases and other transcriptional regulators that were recently linked to autism.  We use genome-wide approaches to better understand how these transcriptional regulators affect gene expression in developing and adult neurons (such as RNA-seq, ChIP-seq, Crispr/Cas9 for knocking out genes).  We also assess how synaptic function is affected, using calcium imaging and electrophysiology.   In addition, we are performing a large RNA-seq screen to identify chemicals and drugs that increase risk for autism.   /  / Our pain research is focused on lipid kinases that regulate pain signaling and sensitization.  This includes work with cultured dorsal root ganglia (DRG) neurons, molecular biology and behavioral models of chronic pain.  We also are working on drug discovery projects, with an eye towards developing new therapeutics for chronic pain.