Duke mentors provide a multidisciplinary mentorship experience for fellows part of the Center for Precision Medicine's Post-doctoral Training Program in Genomic Medicine Research. Supported by NIH, the Center for Precision Medicine administers the two-year training program for M.D.s and Ph.D.s, which is comprised of courses, laboratory rotations and informal learning opportunities individualized to each trainee.

If you are interested in being a mentor, please reach out to Dr. Susanne B. Haga.

“The post-doctoral training program provides access to the best people at Duke doing this kind of work in a mentored environment. I am fortunate to have mentors like Dr. Ann Reed, the Chair of Pediatrics who helped me create a project that directly lets me do research in the patients I care for in the clinic.” - Cory Stingl, MD

Program Directors

Kathleen A. Cooney, MD, MACP, is the George Barth Geller Distinguished Professor of Medicine and Chair of the Department of Medicine, Duke University School of Medicine, in Durham, North Carolina. Dr. Cooney was recruited to Duke University in 2018 to become the tenth chair of the Department of Medicine.  This department is the largest in the School of Medicine and is highly ranked in all missions. New initiatives under Dr. Cooney include completion of strategic planning to guide the research and clinical missions, recruitment of a number of new leaders, and strong commitment to addressing diversity, equity and inclusion. Dr. Cooney is a medical oncologist focused on caring for men with prostate cancer and internationally known for investigations examining the genetic epidemiology of prostate cancer. She discovered a recurrent mutation in the HOXB13 gene that increases the chances of being diagnosed with prostate cancer. Her current research focuses on identifying germline mutations associated with lethal and aggressive prostate cancer as well as prostate cancer in African American men. Dr. Cooney received her MD from the University of Pennsylvania Perelman School of Medicine in Philadelphia and completed her training in Internal Medicine and Hematology/Oncology at the University of Michigan. She previously served as chair of Internal Medicine at the University of Utah; before that, she served for nearly 10 years as the division chief of Hematology/Oncology and deputy director of the Comprehensive Cancer Center at the University of Michigan.

Susanne Haga, PhD, is Co-Director of Educational Programs in the Duke Center for Precision Medicine and as such, currently oversees the undergraduate, graduate and fellow/post doc education initiatives. Her research focuses on exploring barriers and facilitators to the use and integration of genomic applications in a variety of clinical care environments and in diverse populations, using pharmacogenetic testing as an exemplar. She has served as the PI on several NIH funded projects on the delivery models for pharmacogenetics testing, educational interventions related to genetic/genomic applications, and the study of the ethical, legal, and social issues in genetics and genomics, particularly pharmacogenetic testing. She has a diverse background in both science and policy, working on policy issues for several groups including the NIH Office of Science Policy and non-profit sector.

Lori Orlando, MD, MHS, MMCI: (primary mentor) is a Professor of Medicine and Director of the Precision Medicine Program in the Center for Applied Genomics and Precision Medicine at Duke University. She attended Tulane Medical Center for both medical school (1994-1998) and Internal Medicine residency (1998-2000). There she finished AOA and received a number of awards for teaching and clinical care from the medical school and the residency programs, including the Musser-Burch-Puschett award in 2000 for academic excellence. After completing her residency, she served as Chief Medical Resident in Internal Medicine (2001) and then completed a Health Services Research Fellowship at Duke University Medical Center (2002-2004). In 2004 she also received her MHS from the Clinical Research Training Program at Duke University and joined the academic faculty at Duke. In 2005 she received the Milton W. Hamolsky Award for Outstanding Junior Faculty by the Society of General Internal Medicine. Her major research interests are decision making and patient preferences, implementation research, risk stratification for targeting preventive health services, and decision modeling. From 2004-2009 she worked with Dr. David Matchar in the Center for Clinical Heath Policy Research (CCHPR), where she specialized in decision modeling, decision making, and technology assessments. In 2009 she began working with Dr. Geoffrey Ginsburg in what is now the Center for Applied Genomics and Precision Medicine (CAGPM) and in 2014 she became the director of the Center’s Precision Medicine Program. Since joining the CAGPM she has been leading the development and implementation of MeTree, a patient-facing family health history based risk assessment and clinical decision support program designed to facilitate the uptake of risk stratified evidence-based guidelines. MeTree was designed to overcome the major barriers to collecting and using high quality family health histories to guide clinical care and has been shown to be highly effective when integrated into primary care practices. This effort started with the Genomic Medicine Model, a multi-institutional project, whose goal was to implement personalized medicine in primary care practices. The success of that project has led to funding as part of NHGRI’s IGNITE (Implementing Genomics in Clinical Practice) network. She is currently testing methods for integrating patient preferences and decision making processes into clinical decision support recommendations for patients and providers to facilitate management of patients’ risk for chronic disease using mHealth and other behavioral interventions.

Shelby Reed, PhD: (primary mentor) is Professor in the Departments of Population Health Sciences and Medicine at Duke University’s School of Medicine.  She is the director of the Center for Informing Health Decisions and Therapeutic Area leader for Population Health Sciences at the Duke Clinical Research Institute (DCRI).  She also is core faculty at the Duke-Margolis Center for Health Policy. Dr. Reed has over 20 years of experience leading multidisciplinary health outcomes research studies. Dr. Reed has extensive expertise in designing and conducting trial-based and model-based cost-effectiveness analyses of diagnostics, drugs and patient-centered interventions. In 2016, she co-founded the Preference Evaluation Research (PrefER) Group at the DCRI, and she currently serves as its director. She and the group are frequently sought to conduct stated-preference studies to inform regulatory decisions, health policy, care delivery, value assessment and clinical decision making with applied projects spanning a wide range of therapeutic areas. She served as President for ISPOR in 2017-2018, and she currently is Past-Chair of the Society’s Health Science Policy Council.

Thomas Coffman, MD: (primary mentor) My laboratory is interested mechanisms of kidney injury in disease states and the role of the kidney in regulation of blood pressure. Our research addresses issues that are relevant to disorders such as hypertension, diabetic nephropathy, transplant rejection, and autoimmune diseases. We have been particularly interested in two hormone systems that impact these processes: (1) the renin-angiotensin system and (2) lipid mediators derived from cyco-oxygenase metabolism of arachidonic acid. Our studies have taken advantage of available technologies for producing genetic alterations in mice to study the physiology of these systems. As one example, we generated and characterized lines of mice lacking the major physiological receptors for angiotensin II in the mouse. These studies have provided novel information regarding the role of these receptors in blood pressure homeostasis, in promoting kidney injury in disease states, and in the regulation of inflammation. A major objective of our work is to identify new approaches to treatment and disease prevention. To this end, we are using molecular genetic technology to develop and refine mouse models of human diseases such as diabetic nephropathy, kidney transplant rejection, and hypertension.

Myles Wolf, MD, M.Med.Sc: (primary mentor) The focus of my research is disordered mineral metabolism across the spectrum of chronic kidney disease, including dialysis, kidney transplantation and earlier stages.

My research has been published in leading general medicine and subspecialty journals, including the New England Journal of Medicine, JAMA, the Journal of Clinical Investigation, Circulation, Cell Metabolism, Journal of the American Society of Nephrology, and Kidney International, among others.

My primary contributions have been in the area of hormonal regulation of phosphate homeostasis. I have helped to characterize the physiological role of fibroblast growth factor 23 in health and in chronic kidney disease, and the impact of elevated fibroblast growth factor 23 levels on adverse clinical outcomes in patients with kidney disease.

William Kraus, MD: (primary mentor) My training, expertise and research interests range from human integrative physiology and genetics to animal exercise models to cell culture models of skeletal muscle adaptation to mechanical stretch. I am trained clinically as an internist and preventive cardiologist, with particular expertise in preventive cardiology and cardiac rehabilitation.  My research training spans molecular biology and cell culture, molecular genetics, and integrative human exercise physiology and metabolism. I practice as a preventive cardiologist with a focus on cardiometabolic risk and exercise physiology for older athletes.  My research space has both a basic wet laboratory component and a human integrative physiology one.

One focus of our work is an integrative physiologic examination of exercise effects in human subjects in clinical studies of exercise training in normal individuals, in individuals at risk of disease (such as pre-diabetes and metabolic syndrome; STRRIDE), and in individuals with disease (such as coronary heart disease, congestive heart failure and cancer).

A second focus of my research group is exploration of genetic determinates of disease risk in human subjects.  We conduct studies of early onset cardiovascular disease (GENECARD; CATHGEN), congestive heart failure (HF-ACTION), peripheral arterial disease (AMNESTI), and metabolic syndrome.  We are exploring analytic models of predicting disease risk using established and innovative statistical methodology.

A third focus of my group’s work is to understand the cellular signaling mechanisms underlying the normal adaptive responses of skeletal muscle to physiologic stimuli, such as occur in exercise conditioning, and to understand the abnormal maladaptive responses that occur in response to pathophysiologic stimuli, such as occur in congestive heart failure, aging and prolonged exposure to microgravity.

Recently we have begun to investigate interactions of genes and lifestyle interventions on cardiometabolic outcomes.  We have experience with clinical lifestyle intervention studies, particularly the contributions of genetic variants to interventions responses.  We call this Lifestyle Medicopharmacogenetics.

Svati Shah, MD: (primary mentor) is Associate Professor of Medicine in the Division of Cardiology, Vice-Chair of Translational Research, and a faculty member in the Duke Molecular Physiology Institute. Her research in genomic medicine focuses on the molecular epidemiology of cardiovascular disease, particularly atherosclerosis, utilizing diverse, integrated genetic and genomic techniques for identification of biomarkers and novel mechanisms. She has substantial experience as a primary and secondary mentor to many postdoctoral fellows, cardiology fellows, graduate students, medical residents and medical students, has served as the Associate Director of the Cardiology Fellowship for ten years, providing research and career mentorship to 40 cardiology fellows enrolled in the program, and has received a mentorship award from the Division of Cardiology at Duke.

Deepak Voora, MD: (co-mentor) is Assistant Professor in the Division of Cardiology. His research in genomic medicine focuses on systems pharmacogenomics of antiplatelet and other drugs that utilizes transcriptomic profiling and metabolomics in drug exposure studies. In order to translate findings from the challenge model to “real world” outcomes in patients with cardiovascular disease, he actively collaborates with investigators at Duke and the Duke Clinical Research Institute, which houses large biorepositories from past studies or from participants in randomized clinical trials, and enables testing of molecular signatures of drug response with outcomes of drug efficacy and toxicity. In addition, he is leading a prospective randomized controlled trial of genotype-guided statin therapy. Dr. Voora is spearheading an effort to create a clinical pharmacogenomics consultation service that should see its first patients in the fall.

Andrew Alspaugh, MD: (co-mentor) The focus of my research is to understand the ways in which microorganisms sense and respond to changes in their environment. As microbial pathogens enter the infected host, dramatic genetic and phenotypic events occur that allow these organisms to survive in this harsh environment. We study the model fungal organism Cryptococcus neoformans to define signal transduction pathways associated with systemic fungal diseases. This pathogenic fungus causes lethal infections of the central nervous system in patients with AIDS and other immunological disorders. In addition to being an important pathogen, C. neoformans displays well-characterized and inducible virulence determinants. It is an outstanding system for dissecting the signaling pathways associated with pathogenicity.

The main techniques used in the lab are those of molecular genetics. We are able to readily mutate C. neoformans genes by homologous recombination. Mutant strains with disruptions in targeted genes are then evaluated in vitro for various phenotypes including altered expression of polysaccharide capsule and melanin. The effects of gene disruption on pathogenicity are also evaluated in animal models of cryptococcal disease. Using these techniques, we have identified a novel G-alpha protein/cAMP-dependent signaling pathway associated with mating and pathogenicity.

This research is complemented by the other investigators in the Duke University Mycology Research Unit. The members of this research community are pursuing studies in fungal pathogenesis, identifying novel antifungal drug targets, and studying the ecology of several medically important fungi.

Vance Fowler. MD: (primary mentor) is Professor of Medicine in the Division of Infectious Disease, and Molecular Genetics and Microbiology. Much of his research on antibiotic resistant bacteria uses genomics-based approaches including GWAS, whole exome sequencing, SNP discovery, and candidate gene discovery with in vivo model systems. In addition, he established the Duke Blood Stream Infection Biorepository, a unique resource of ~2000 prospectively enrolled patients with Gram-Negative Bacterial Blood Stream Infection that includes clinical data, bloodstream isolates, patient DNA, and patient serum for genomic medicine research. Dr. Fowler has extensive experience in mentoring investigators in multidisciplinary research, with 36 research trainees.

Christopher Woods, MD, MPH: (primary mentor) is the Executive Director of the Hubert-Yeargan Center for Global Health. He is a professor in the Departments of Medicine and Pathology at Duke University; an adjunct professor in Epidemiology at the University of North Carolina at Chapel Hill School of Public Health; an adjunct professor in the Emerging Infections Program at the Duke-National University of Singapore Graduate Medical School. Clinically, he serves as Chief of Infectious Diseases and clinical microbiology, and hospital epidemiologist for the Durham VA Medical Center. Dr. Woods is board-certified in internal medicine, infectious diseases, and medical microbiology.

Sandeep Dave, MD, MS: (co-mentor) Leukemias and lymphomas are malignancies that arise from immune cells. The majority of these malignancies arise from B cells, a type of immune cell. Leukemias and lymphomas derived from B cells affect over 100,000 Americans every year. The majority of those patients will succumb to their disease. Dr. Dave's research is focused on the application of high-throughput technologies including microarrays and massively parallel sequencing to improve the diagnosis and treatment of leukemias and lymphomas. Active efforts in the laboratory and clinic include:

  1. Integrating genomic technologies with clinical trials to define molecular subgroups of patients who are most likely to respond to therapy.
  2. Exploring the role of microRNA in the differentiation of immune cells and their role in leukemias and lymphomas.
  3. Application of high throughput sequencing to identify means of gene regulation in normal and malignant cells.
  4. Exploiting high throughput genomic and proteomic technologies to develop new prognostic and diagnostic markers in leukemias and lymphomas.

Michael Kelley, MD: (co-mentor) is Professor of Medicine, Duke University Medical Center and National Program Director for Oncology, Department of Veterans Affairs.

1.     A major theme throughout my career has been the biology of and improving outcomes for patients with lung cancer.  Early publications examined the relationship between specific genetic alterations in lung cancer and clinically relevant applications including differential drug sensitivity, differentiation of metastases from second primary cancers, and application of patient-specific mutations as epitopes for immunotherapy.  Correlation of alteration of p16 with drug sensitivity led to identification of a class of CDK4 inhibitor. I served as the primary investigator or co-investigator in all of these studies.  I led a study that demonstrated that tubulin mutations are uncommon in lung cancer and described the artifactual detection of pseudogenes as the origin of a prior report claiming association of tubulin mutation with taxane sensitivity, thus correcting the scientific record. 

2.   A second area of continuing interest in lung cancer is the conduct of therapeutic and prevention clinical trials.  These trials have primarily been translation of hypotheses derived primarily from laboratory-based biological observations including the GRP autocrine growth factor in small cell lung cancer, a phase I study of a pulmonary toxin in non-small cell lung cancer, mutation-specific immunotherapy, and a putative chemopreventive agent for smokers.  More recently, I have been an active member of the Respiratory Committee of CALGB/Alliance including serving as principal investigator on a trial testing the addition of irinotecan to treatment of patients with small cell lung cancer. 

3.  Through my clinical practice, I identified a large family with the May-Hegglin anomaly, an autosomal dominant platelet condition characterized as thrombocytopenia, leukocyte inclusions, and giant platelets.  While the condition had been described in the early 1900s, the genetic basis was unknown.  I conceptualized and led a project to identify the underlying molecular basis of this frequently misdiagnosed disorder through classical genetics.  I then extended that observation to related genetic conditions (now known as MYH9-assocaited disorders) characterized by varying degrees of hematological abnormalities, hearing loss and renal disease.  Analysis of the spectrum of observed mutations and phenotypes resulted in identification of a genotype-phenotype association for the most medically significant aspects of the disorders.  Working with Dan Kiehart’s lab, we described the effect of commonly observed mutations of MYH9 on assembly of non-muscle myosin.  An animal model of the most common MYH9 mutation was created in my lab and demonstrated hematological abnormalities similar to those found in humans. 

4.  I described genetic linkage for a rare familial cancer syndrome characterized by very high penetrance of chordoma.  Subsequent linkage analysis resolved a phenotype mis-assignment and resulted in identification of germline gene duplication of the T-box gene, Brachyury in about half of affected families.  I then confirmed another groups report that a common coding region SNP of the Brachyury gene as well as additional genetic variants are associated with an increased risk for development of chordoma independent of amplification of the Brachyury gen.   To study the biology of chordoma, I established the origin of existing putative chordoma cell lines and working criteria for identification of possible new chordoma cell lines.  Using two confirmed chordoma cell lines, I screened all regulatory-approved drugs for anti-growth activity to determine whether any could be repurposed for clinical use in patients. 

5.  Beginning in 2007, I began to transition my career to a leadership position within the Department of Veterans Affairs as the National Program Director for Oncology.  This led to opportunities to utilize the vast and detailed clinical data sets of nearly 1 million patients with cancer to address questions that have been difficult to study either through randomized trials or in less robust datasets.  The use of surgery to treat early stage non-small cell lung cancer is a standard treatment for which I observed a racial disparity.  The lower rate of use of surgery among African Americans was not explained by association with comorbidity.  In another study, I described the rate of use of adjuvant chemotherapy as having increased temporally after publication of randomized trials showing a modest benefit to its use.  I showed that initially this chemotherapy was primarily carboplatin-based, despite all positive trials having used cisplatin.  Cisplatin use has subsequently increased though there is not a demonstrable improvement is survival associated with its use.  I also showed that survival overall, regardless of use of chemotherapy, has improved suggesting that the application of clinical trial data for adjuvant chemotherapy is improving outcome.  In a related study, I found that elderly patients benefit as much as younger patients from adjuvant chemotherapy.  Patients with stage III non-small cell lung cancer are frequently treated with concurrent chemoradiotherapy, for which there are two commonly used chemotherapy regimens: cisplatin-etoposide and carboplatin-paclitaxel.  I examined the outcome and toxicity of patients treated with these two regimens and found that while there was no significant difference in survival, there was more toxicity associated with cisplatin-etoposide.  This finding may impact one current clinical guideline recommendation that favors cisplatin-etoposide over carboplatin-paclitaxel.  Finally, in stage IV disease, a similar observation was made that cisplatin-based chemotherapy is associated with greater toxicity but not improved survival. 

Steven Patierno, PhD: (co-mentor) is Professor of Medicine; Professor of Pharmacology and Cancer Biology; Professor of Community and Family Medicine; and Director of Population Sciences and Health Services at Duke Cancer Institute. Patierno's current translational research interests are focused on the genomics molecular biology of cancer disparities, cancer biology, molecular pharmacology and targeted experimental therapeutics to control prostate, breast and lung tumor aggressiveness. He is an internationally recognized expert in cancer control, cancer causation and molecular carcinogenesis, which includes a broad spectrum of laboratory and population level research.   Patierno is also actively engaged in cancer health disparities and healthcare delivery research focused on patient navigation, survivorship, community-based interventions, mHealth, implementation sciences, cancer care economics, and policy.

Qianben Wang, PhD: (primary mentor) is a Professor of Pathology in the Duke School of Medicine. My laboratory is primarily interested in understanding the epigenetic mechanisms driving progression of hormone-dependent cancers. We focus on studying how transcription factor-centered, multi-layer transcription regulatory networks drive hormone-dependent cancers, which involve transcription factors (e.g. nuclear hormone receptors, FOXA1, and GATA2), transcription coactivators (e.g. Mediator and histone acetyltransferases), and epigenetic regulators (e.g. histone modifications, chromatin looping and nucleosome positioning)

Qingyi Wei, MD, PhD: (primary mentor) Professor in the Department of Medicine, is Associate Director for Cancer Control and Population Sciences, Co-leader of CCPS and Co-leader of Epidemiology and Population Genomics (Focus Area 1). He is a professor of Medicine and an internationally recognized epidemiologist focused on the molecular and genetic epidemiology of head and neck cancers, lung cancer, and melanoma. His research focuses on biomarkers and genetic determinants for the DNA repair deficient phenotype and variations in cell death. He is Editor-in-Chief of the open access journal "Cancer Medicine" and Associate Editor-in-Chief of the International Journal of Molecular Epidemiology and Genetics.

Nelson Chao, MD, PhD: (primary mentor) My research interests are in two broad areas, clinical hematopoietic stem cell and cord blood transplantation and in the laboratory studies related to graft vs. host disease and immune reconstitution. On the clinical side we are currently conducting approximately 50 different clinical protocols ranging from preparatory regimens, supportive care studies and disease specific protocols. Most of these clinical studies are centered around studies of the sources of stem cells and the methods to improve the long term outcome. There are exploratory protocols for novel therapies such as dendritic cell therapy for several malignancies, antiangiogenesis therapy, graft engineering to prevent graft-versus-host disease and antigen specific T cells or non specific NK cells to prevent relapse. Moreover a strong focus of the program is to develop cord-blood transplantation for adult patients with hematologic malignancies. The laboratory studies center on understanding the immunological events that occur with graft-vs-host disease and methods to prevent this disease. The current efforts focus on understanding murine reconstitution following transplantation, use of a peptide polymer to block MHC class II recognition of minor histocompatibility antigens, use of T cell engineering to prevent graft-versus-host disease at the same time preserving a graft-versus-malignancy effect.

Thomas Ortel, MD, PhD: (primary mentor) My research program investigates the molecular mechanisms whereby various congenital and acquired abnormalities result in ‘dysfunctional’ hemostasis (i.e., hemorrhage or thrombosis) to better understand the molecular mechanisms and interactions that are necessary for normal hemostasis. We are particularly interested in the mechanisms whereby antibodies and other inhibitors can interfere with normal hemostatic mechanisms. Several projects extensively overlap and focus on the assembly and function of procoagulant (e.g., factor X-ase and prothrombinase) and anticoagulant (e.g., activated protein C complex) phospholipid membrane-dependent complexes.

We utilize a variety of approaches in these studies. Monoclonal antibodies, single-chain variable domain fragments, polyclonal antibodies prepared from patients with factor VIII inhibitors, and site-specific mutagenesis have all been used to characterize structure-function relationships in coagulation factor VIII. Our laboratory has also extensively characterized anti-factor V antibodies, investigating autoantibodies as well as xenogenic antibodies developing after exposure to topical bovine thrombin preparations which contain trace amounts of contaminating bovine factor V. We have also characterized how antiphospholipid antibodies interfere with the activated protein C complex, a lipid-dependent natural anticoagulant complex that proteolytically inactivates factor Va and factor VIIIa.

Our current studies are focusing on two antibody-mediated thrombotic syndromes, heparin-induced thrombocytopenia and antiphospholipid antibody syndrome. First, we are initiating a large clinical trial investigating the incidence of clinically-significant heparin-induced thrombocytopenia in patients who develop anti-heparin/platelet factor 4 antibodies following cardiac bypass procedures. While these antibodies are commonly seen following cardiac bypass, the true incidence of thromboembolic complications related to these prothrombotic antibodies remains unknown. We are also collaborating with investigators in the Center for Human Genetics on a large, multi-center study exploring the genetics of familial antiphospholipid antibody syndrome. In addition, we have used a genomic strategy to investigate patients with antiphospholipid antibody syndrome and have identified a gene expression profile that appears to be unique to patients with this syndrome in contrast to patients with venous thromboembolism who do not have these autoantibodies.

We also participate in a variety of collaborative research efforts, both with individual investigators as well as participating in multi-center clinical research studies. For example, we are one of seventeen centers participating in the NIH-supported Transfusion Medicine/Hemostasis Network, and we are currently conducting a trial through this network to define the optimal dose of platelets for patients needing platelet transfusions for hypoproliferative thrombocytopenia. We are also part of a multi-center registry of patients with thrombotic thrombocytopenic purpura, and we are one of eight centers in the Hemostasis and Thrombosis Center pilot program sponsored by the Centers for Disease Control and Prevention. Participation in these registries and networks provides us with access to the patient populations that we study in the research laboratory.

Katherine Garman, MD: (co-mentor) My research focuses on injury, repair, and cancer development in the gastrointestinal tract. My laboratory performs translational research with the goal of improving health of the gastrointestinal tract. Our work is based in observations from human clinical research. We use databases of esophageal and colon disease to learn more about clinical risk factors for disease. We also use pathology samples of tumors to study the gastrointestinal tract in different states: healthy, inflamed or damaged, and with cancer.

Anna Mae Diehl, MD, PhD: (primary mentor) Our lab has a long standing interest in liver injury and repair. To learn more about the mechanisms that regulate this process, we study cultured cells, animal models of acute and chronic liver damage and samples from patients with various types of liver disease. Our group also conducts clinical trials in patients with chronic liver disease. We are particularly interested in fatty liver diseases, such as alcoholic fatty liver disease and nonalcoholic fatty liver disease (NAFLD).

Research by our group has advanced understanding in two main areas: 1) immune system regulation of liver injury and regeneration and 2)the role of fetal morphogens, such as the hedgehog pathway, in regulating fibrotic responses to liver damage. Our basic research programs have been enjoyed continuous NIH support since 1989. We welcome students, post-doctoral fellows and visiting scientists who have interests in this research area to contact us about training opportunities and potential collaborations.

Since 2001 we have also been an active participant in the NIDDK-funded Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN), a national consortium comprised of 8 university medical centers selected to generate a national registry for patients with NAFLD and to conduct multicenter treatment trials for this disorder. We are actively recruiting patients for this program, as well as a number of other industry-supported NAFLD studies.

Christopher Newgard, PhD: (primary mentor) Over its 16 year history, our laboratory has investigated mechanisms of metabolic regulation and fuel homeostasis in mammalian systems. Major projects include: 1) Mechanisms involved in regulation of insulin secretion from pancreatic islet β-cells by glucose and other metabolic fuels; 2) Development of methods for protection of β-cells against immune-mediated damage; 3) Studies on spatial organization and regulation of systems controlling hepatic glucose balance; 4) Studies on the mechanisms involved in lipid-induced impairment of insulin secretion and action in diabetes.

Scott Palmer, MD, MHS: (primary mentor) Dr. Palmer leads a successful program of clinical, basic and translational research in lung transplantation, idiopathic pulmonary fibrosis (IPF), bronchiolitis obliterans (BO) and other lung diseases. He directs the Medicine Plus Therapeutic Area at the Duke Clinical Research Institute (DCRI) and serves as Vice Chair for Research in the Department of Medicine. He is also the Director of Clinical Research, Duke Transplant Center.

Dr. Palmer has over 250 peer reviewed publications, received numerous awards, including election into the American Society for Clinical Investigation (ASCI) in 2012, chaired many sessions at national and international meetings, serves regularly on NIH study sections, and is on the editorial board of many prominent journals. He is a dedicated mentor to trainees and junior faculty, having personally mentored over 40 pre-and post-doctoral trainees, many of whom are now engaged in their own successful research careers. He is multiple PI on two Duke R38 awards supporting dedicated resident research, and multiple PI for a Duke Pulmonary T32 training program, all reflecting his deep commitment to support and train the next generation of physician investigators. He has received continuous NIH funding since 2002.

His scientific accomplishments include high impact studies that have demonstrated the importance of innate immunity in transplant rejection, a clinical trial that improved cytomegalovirus (CMV) prevention after lung transplantation, and work that identified rare protein coding exome variants that contribute to the development of IPF.  In addition to these studies he has led numerous multicenter studies, registries and clinical trials.  His program of translational research focuses on the use of human tissue and samples in studying pulmonary transplant rejection, and the use of human airway cells epithelial cells in the study of bronchiolitis obliterans including in the transplant and occupational setting. Recent work has employed single cell RNAseq to discover novel cell types and mechanisms involved in lung disease and transplant rejection.

Ashley Chi, MD, PhD: (primary mentor) We are using functional genomic approaches to investigate the nutrient signaling and stress adaptations of cancer cells when exposed to various nutrient deprivations and microenvironmental stress conditions. Recently, we focus on two areas. First, we are elucidating the genetic determinants and disease relevance of ferroptosis, a newly recognized form of cell death. Second, we have identified the mammalian stringent response pathway which is highly similar to bacterial stringent response, but with some very interesting twists and novel mechanisms.

Simon Gregory, PhD: (primary mentor) My research involves elucidating the molecular mechanisms underlying complex neurological diseases, such as multiple sclerosis (MS), autism, Alzheimer's disease (AD), and brain tumors. We use a variety of (epi)genetic, genomic, transcriptomic, and leading edge technologies to identify the underpinnings of disease development and progression. 

With respect to autism, we are investigating the use of oxytocin to improve social reciprocity in children with the disorder and developing (epi)genetic and transcriptomic predictors of plasma levels of oxytocin. We are also unraveling the mechanisms associated with sociability in animal models of autism.

In the fields of AD and brain tumor research, my lab is using or developing leading edge single cell and spatial expression profiling platforms to unravel the molecular mechanisms of pathology or tissue related microenvironmental changes associated with disease development and progression.

My MS laboratory at Duke University is exploring the use of high sensitivity assays to develop a trajectory of disease development in progressive MS; we are exploring the use of endogenous oxysterols to trigger remyelination of white matter injury in MS; and establishing the immune expression and receptor profile in stable or progressive MS patients. I am PI of the MURDOCK-MS collection, a cross sectional MS cohort of ~1000 MS patients that will provide the basis for genetic, genomic and metabolomic biomarker identification of MS disease development and progression. I am Director of the Duke Center for Research in Autoimmunity and MS within the Duke Department of Neurology.

Elizabeth Hauser, PhD: (primary mentor) My research interests are focused on developing and applying statistical methods to search for genes causing common human diseases. Recent work has been in the development of statistical methods for genetic studies and in identifying optimal study designs for genetic studies of complex traits. As application of these methods to specific diseases has progressed it has become apparent that etiologic and genetic heterogeneity is a major stumbling block in the research for genes for common diseases.  I am interested in developing methods to detect and account for genetic heterogeneity as one type of complex genetic model.  I am also interested in the extent to which environmental exposures interact with genetic variants to modify risks of complex diseases.  Both genetic heterogeneity and gene-environment interactions must be taken into account to achieve the goals of personalized medicine.

Collaborative studies under way at Duke University, the Durham VA and elsewhere provide the opportunity to apply new methods to ongoing studies. My main area of application is in identifying genes for cardiovascular conditions using a variety of study designs.  One such study is the GENECARD study to identify genes for early onset coronary artery disease in families. Another study is the AGENDA study based on the CATHGEN cohort of patients from the Duke Cardiac Catheterization Lab. These two studies have been used to successfully identify a number of novel genes for coronary artery disease. I also work on studies of genetic effects in aging, kidney disease and colon cancer.  

In turn these Collaborative studies continue to raise methodological research questions such as the effect of model misspecification on the results of linkage studies, the interpretation of confirmation studies to replicate linkage results, and the utility of a method for including additional phenotypic information when assessing linkage results.

Tim Reddy, PhD: (co-mentor) is an Assistant Professor in the Duke Duke Center for Genomic and Computational Biology and the Department of Biostatistics & Bioinformatics, and holds a secondary appointment in the Department of Molecular Genetics and Microbiology. He completed his doctoral work in Bioinformatics at Boston University in 2007, followed by a postdoctoral fellowship at the HudsonAlpha Institute for Biotechnology.

Dr. Reddy has long been interested in understanding the regulatory code that determines which genes are used, and which are not. His research has spanned the gamut from computational biology on yeast gene regulation, to developing and applying high-throughput sequencing based techniques to study the regulation of human genes. His current research is on understanding how changes in gene regulation contribute to human traits and increase or decrease risk for common human diseases including diabetes. His research relies on close connections between experimental and computational studies, with a particular focus on the use of high-throughput methodologies to develop a “big-picture” understanding of biological processes.

Greg Crawford, PhD: (co-mentor) My research involves identifying gene regulatory elements across the genome to help us understand how chromatin structure dictates cell function and fate. For the last 30 years, mapping chromatin accessible sites has been the gold standard method to identify the location of active regulatory elements, including promoters, enhancers, silencers, and locus control regions. I have developed technologies that can identify most DNase I hypersensitive sites from potentially any cell type from any species with a sequenced genome. We are combining this data with other wet-lab and computational data types to better understand how these regulatory regions control global gene expression in a set of diverse tissues (normal and diseased) representative of the human body.

Rasheed Gbadegesin, MD: (co-mentor) is Professor of Pediatrics and Nephrology. The overarching objective of his research program is to understand the genetic basis, pathogenesis, and determinants of variable therapy response in nephrotic syndrome (NS) especially the FSGS variant. He is currently PI on multiple NIH/NIDDK sponsored studies that focus on the molecular pathogenesis of kidney diseases including nephrotic syndrome. In collaboration with colleagues around the World, his team has established a biorepository of rigorously characterized phenotype and biosamples from over 700 children with nephrotic syndrome. He has mentored over ten trainees ranging from high school students to post-doctoral fellows and junior faculty members and he was a recipient of the Doris Duke Charitable Foundation Clinical Research Mentorship award.

Matthew Kelly, MD: (primary mentor) My research is broadly focused on elucidating the complex interactions that exist between the host microbiome and exogenous pathogens that cause infections in children. We have several ongoing projects evaluating: 1) the impact of the upper respiratory microbiome on the risk of colonization and invasion by bacterial respiratory pathogens among infants in Botswana; 2) associations between the gut microbiome of pediatric stem cell transplant recipients and the risk of infections (bloodstream infection, C. difficile infection) and graft-versus-host disease; and 3) the role of the gut and respiratory microbiomes in mediating COVID-19 infection susceptibility and disease severity in children. Ultimately, I aim to develop strategies that use targeted modification of the microbiome for the prevention of infections in children.

Mohamad Mikati, MD: (co-mentor) is the Wilburt C. Davison Professor of Pediatrics, Professor of Neurobiology, and Chief of the Division of Pediatric Neurology. Dr. Mikati’s clinical research has centered on characterization and therapy of pediatric epilepsy and neurology syndromes, describing several new pediatric neurological entities with two carrying his name (POSSUM syndromes # 3708 and 4468), developing novel therapeutic strategies for epilepsy and related disorders particularly Alternating Hemiplegia of Childhood, and applying cutting edge genetic and Magnetic Resonance Imaging techniques to drug resistant pediatric epilepsy.  In the laboratory he has elucidated mechanisms of seizure related neuronal injury, particularly those related to the ceramide pathway, and demonstrated neuroprotective effects of several agents including erythropoietin. Most recently he has concentrated his laboratory research on the pathophysiology of ATP1A3 dysfunction in the brain as model for epilepsy and of Alternating Hemiplegia of Childhood. He has more than 290 peer reviewed publications, 400 abstracts 41 chapters one book and two booklets. He also has more than 10,497 citations in the literature with an h-index of 58 and an i-10index of 190. Dr. Mikati has written chapters on epilepsy and related disorders in the major textbooks of Pediatrics and Pediatric Neurology including Swaiman’s Pediatric Neurology and Nelson’s Pediatrics. Before joining Duke in 2008 he had completed his M.D. and Pediatric training at the American University of Beirut, his Neurology at the Massachusetts General Hospital, his Neurophysiology at Boston Children’s Hospital and had been on the Faculty at Harvard as Director of Research in the Epilepsy Program at Boston Children’s Hospital and then as Professor and Chairman, Department of Pediatrics, Founder and Director of the Adult and Pediatric Epilepsy Program at the American University of Beirut. Dr. Mikati has had several international leadership roles including being President of the Union of the Middle Eastern and Mediterranean Pediatric Societies, on the Standing Committee of the International Pediatric Association (IPA), Chair of the Strategic Advisory Group on Early Childhood Development of the IPA, Officer of the International Child Neurology Association, Consultant to UNICEF, WHO, and the American Board of Pediatrics. He was selected to organize and chair the American Epilepsy Society's Merritt-Putnam Symposium and was one of only two Pediatric Neurologists, initially chosen worldwide, on the WHO advisory committee for the International Classification of Disease. He has received several national and international honors including, among others, Merritt Putnam American Epilepsy Society Fellowship Award, Harvard Community Health Plan Peer recognition Award, Debs Research Award, Hamdan Award for contributions to Medicine, Hans Zellweger Award for contributions to Pediatric Neurology, Patient Choice Award and the Michael Frank Award for research and lifetime contributions to the field of Pediatric Neurology.

Ann Reed, MD, PhD: (primary mentor) I have spent my career caring for children with autoimmune disorders and immune dysfunction. I have focused my work caring for children with juvenile dermatomyositis and auto inflammatory disorders.  I have overseen a research program for 24 years studying the  genetics and cause of human autoimmune disease, focused on dermatomyositis in children and adults. The long-term goal of my research team is to develop new biomarkers of diseases to identify those predisposed to develop disease, as well as monitor disease activity and response to treatment. My team makes extensive use of genomics, gene expression, protein expression and immunohistochemical techniques to study the inflammatory and non-inflammatory aspects of dermatomyositis diseases. Other autoimmune disease processes, including systemic lupus and vasculitis, have been focused on as well.

Charlie Gersbach, PhD: (co-mentor) is The Rooney Family Associate Professor, Department of Biomedical Engineering and Co-Director of the Center for Biomolecular and Tissue Engineering. Dr. Gersbach’s laboratory is focused on engineering new methods for directing cell behavior to regenerate diseased or damaged tissues and treat genetic diseases. Our work capitalizes on the products of the Genomic Revolution and modern advances in the fields of genetic reprogramming, gene delivery, protein engineering, stem cell transplantation, and synthetic biology to create innovative biologic approaches to improving human health. These studies also facilitate a better understanding of complex processes including organogenesis, cell lineage determination, and gene regulation that will ultimately lead to improved design of drugs and biotherapeutics. Our efforts are catalyzed by interdisciplinary collaborations with investigators in engineering and medicine at Duke and other institutions.

Tuan Vo-Dinh, PhD: (primary mentor) Dr. Vo-Dinh’s research activities and interests involve biophotonics, nanophotonics, plasmonics, laser-excited luminescence spectroscopy, room temperature phosphorimetry, synchronous luminescence spectroscopy, and surface-enhanced Raman spectroscopy for multi-modality bioimaging, and theranostics (diagnostics and therapy) of diseases such as cancer and infectious diseases.

We have pioneered the development of a new generation of gene biosensing probes using surface-enhanced Raman scattering (SERS) detection with “Molecular Sentinels” and Plasmonic Coupling Interference (PCI) molecular probes for multiplex and label-free detection of nucleic acid biomarkers (DNA, mRNA, microRNA) in early detection of a wide variety of diseases.

In genomic and precision medicine, nucleic acid-based molecular diagnosis is of paramount importance with many advantages such as high specificity, high sensitivity, serotyping capability, and mutation detection. Using SERS-based plasmonic nanobiosensors and nanochips, we are developing novel nucleic acid detection methods that can be integrated into lab-on-a-chip systems for point-of-care diagnosis  (e.g., breast, GI cancer) and global health applications (e.g., detection of malaria and dengue).

In bioimaging, we are developing a novel multifunctional gold nanostar (GNS) probe for use in multi-modality bioimaging in pre-operative scans with PET, MRI and CT, intraoperative margin delineation with optical imaging, SERS and two-photon luminescence (TPL). The GNS can be used also for cancer treatment with plasmonics enhanced photothermal therapy (PTT), thus providing an excellent platform for seamless diagnostics and therapy (i.e., theranostics). Preclinical studies have shown its great potential for cancer diagnostics and therapeutics for future clinical translation.

For fundamental studies, various nanobiosensors are being developed for monitoring intracellular parameters (e.g., pH) and biomolecular processes (e.g., apoptosis, caspases), opening the possibility for fundamental molecular biological research as well as biomedical applications (e.g., drug discovery) at the single cell level in a systems biology approach. For point of care diagnostics, nanoprobes and nanochips with highly multiplex SERS detection and imaging use artificial intelligence and machine learning for data analysis.

Our research activities in immunotherapy involve unique plasmonics-active gold “nanostars.” These star-shaped nanobodies made of gold work like “lightning rods,” concentrating the electromagnetic energy at their tips and allowing them to capture photon energy more efficiently when irradiated by laser light. Teaming with medical collaborators, we have developed a novel cancer treatment modality, called synergistic immuno photothermal nanotherapy (SYMPHONY), which combines immune-checkpoint inhibition and gold nanostar–mediated photothermal immunotherapy that can unleash the immunotherapeutic efficacy of checkpoint inhibitors. This combination treatment can eradicate the primary tumors as well as distant “untreated” tumors, and induce immunologic memory like a “anti-cancer vaccine” effect in murine model.

Greg Wray, PhD: (primary mentor) I study the evolution of genes and genomes with the broad aim of understanding the origins of biological diversity. My approach focuses on changes in the expression of genes using both empirical and computational approaches and spans scales of biological organization from single nucleotides through gene networks to entire genomes. At the finer end of this spectrum of scale, I am focusing on understanding the functional consequences and fitness components of specific genetic variants within regulatory sequences of several genes associated with ecologically relevant traits. At the other end of the scale, I am developing molecular and analytical methods to detect changes in gene function throughout entire genomes, including statistical frameworks for detecting natural selection on regulatory elements and empirical approaches to identify functional variation in transcriptional regulation. At intermediate scales, I am investigating functional variation within a dense gene network in the context of wild populations and natural perturbations. My research leverages the advantages of several different model systems, but primarily focuses on sea urchins and primates (including humans)

David Dunson, PhD: (primary mentor) My research focuses on developing new tools for probabilistic learning from complex data - methods development is directly motivated by challenging applications in ecology/biodiversity, neuroscience, environmental health, criminal justice/fairness, and more.  We seek to develop new modeling frameworks, algorithms and corresponding code that can be used routinely by scientists and decision makers.  We are also interested in new inference framework and in studying theoretical properties of methods we develop.  

Some highlight application areas: 
(1) Modeling of biological communities and biodiversity - we are considering global data on fungi, insects, birds and animals including DNA sequences, images, audio, etc.  Data contain large numbers of species unknown to science and we would like to learn about these new species, community network structure, and the impact of environmental change and climate.

(2) Brain connectomics - based on high resolution imaging data of the human brain, we are seeking to developing new statistical and machine learning models for relating brain networks to human traits and diseases.

(3) Environmental health & mixtures - we are building tools for relating chemical and other exposures (air pollution etc) to human health outcomes, accounting for spatial dependence in both exposures and disease.  This includes an emphasis on infectious disease modeling, such as COVID-19.

Some statistical areas that play a prominent role in our methods development include models for low-dimensional structure in data (latent factors, clustering, geometric and manifold learning), flexible/nonparametric models (neural networks, Gaussian/spatial processes, other stochastic processes), Bayesian inference frameworks, efficient sampling and analytic approximation algorithms, and models for "object data" (trees, networks, images, spatial processes, etc).

Sayan Mukherjee, PhD: (primary mentor) is Associate Professor in the Departments of Statistical Science, Computer Science, and Mathematics. His research focuses on genetics and molecular applications of computational biology and statistical modeling. He is particularly interested in tumor progression and has published work in this field. In addition, he is very interested in both simple analyses regarding addition of stroma information data in more accurate prediction of outcomes. He has mentored or is currently mentoring several pre- and post-doctoral trainees.

Ricardo Henao, PhD: (co-mentor) is an assistant professor in Biostatistics and Bioinformatics and Electrical and Computer Engineering at Duke University. A quantitative scientist whose research focuses on the development of novel statistical methods and machine learning algorithms primarily based on probabilistic modeling, his expertise spans several fields, including applied statistics, signal processing, pattern recognition, and machine learning. His methods research targets hierarchical or multilayer probabilistic models to describe complex data for the purposes of hypothesis generation and improved predictive modeling. Most of his applied work is dedicated to the analysis of biological data such as gene expression, proteomics, medical imaging, clinical narrative, and electronic health records. His recent work has been focused on the development of sophisticated machine learning models, including deep learning approaches, for the analysis and interpretation of clinical and biological data with applications to predictive modeling for diverse clinical outcomes.

Michael Pencina, PhD: (primary mentor)

As Vice Dean for Data Science, Dr. Pencina is responsible for developing and implementing quantitative science strategies as they pertain to the education and training, and laboratory, clinical science, and data science missions of the School of Medicine. Dr. Pencina is a Professor of Biostatistics and Bioinformatics at Duke University and Director of Duke AI Health. Previously, he served as Director of Biostatistics at the Duke Clinical Research Institute.

Dr. Pencina is an internationally recognized authority in risk prediction model development and evaluation. Expert panels and guideline groups frequently recommend methods proposed in his research and have adopted them as the most promising new statistical tools in assessing and quantifying model performance.

Dr. Pencina is actively involved in the design, conduct and analysis of clinical studies with particular focus on novel and efficient designs and applications of machine learning for medical decision support. He interacts regularly with investigators from academic and industry institutions as well as the Food and Drug Administration. 

Thomson Reuters/Clarivate Analytics recognized Dr. Pencina as a Highly Cited Researcher in two fields, social sciences and clinical medicine, for the years 2014 – 2020. He is co-author of more than 370 manuscripts published in peer-reviewed journals and has been cited over 90,000 times in professional publications. He serves as Deputy Editor for Statistics at JAMA-Cardiology and Associate Editor for Statistics in Medicine.

In 2003, Dr. Pencina received his PhD in Mathematics and Statistics from Boston University. He holds master’s degrees from the University of Warsaw in actuarial mathematics and business culture. He joined the Duke University faculty in 2013. Dr. Pencina served as an Associate Professor in the Department of Biostatistics at Boston University and the Framingham Heart Study and as Director of Statistical Consulting at the Harvard Clinical Research Institute.

strategies as they pertain to the education and training, and laboratory, clinical science, and data science missions of the School of Medicine. Dr. Pencina is a Professor of Biostatistics and Bioinformatics at Duke University and Director of Duke AI Health. Previously, he served as Director of Biostatistics at the Duke Clinical Research Institute.

Dr. Pencina is an internationally recognized authority in risk prediction model development and evaluation. Expert panels and guideline groups frequently recommend methods proposed in his research and have adopted them as the most promising new statistical tools in assessing and quantifying model performance.

Dr. Pencina is actively involved in the design, conduct and analysis of clinical studies with particular focus on novel and efficient designs and applications of machine learning for medical decision support. He interacts regularly with investigators from academic and industry institutions as well as the Food and Drug Administration.

Thomson Reuters/Clarivate Analytics recognized Dr. Pencina as a Highly Cited Researcher in two fields, social sciences and clinical medicine, for the years 2014 – 2020. He is co-author of more than 370 manuscripts published in peer-reviewed journals and has been cited over 83,000 times in professional publications. He serves as Deputy Editor for Statistics at JAMA-Cardiology and Associate Editor for Statistics in Medicine.

In 2003, Dr. Pencina received his PhD in Mathematics and Statistics from Boston University. He holds master’s degrees from the University of Warsaw in actuarial mathematics and business culture. He joined the Duke University faculty in 2013. Dr. Pencina served as an Associate Professor in the Department of Biostatistics at Boston University and the Framingham Heart Study and as Director of Statistical Consulting at the Harvard Clinical Research Institute

Katherine Heller, PhD: (co-mentor) is an Assistant Professor at Duke University, in the Department of Statistical Science and at the Center for Cognitive Neuroscience. Prior to joining Duke she was an National Science Foundation Postdoctoral Fellow, in the Computational Cognitive Science group at MIT, and an EPSRC Postdoctoral Fellow at the University of Cambridge. Her Ph.D. is from the Gatsby Unit, where her advisor was Zoubin Ghahramani. Her research interests lie in the fields of machine learning and Bayesian statistics. Specifically, she develops new methods and models to discover latent structure in data, including cluster structure, using Bayesian nonparametrics, hierarchical Bayes, techniques for Bayesian model comparison, and other Bayesian statistical methods.

Erich Huang, MD, PhD: (co-mentor) Dr. Huang’s research interests span applied machine learning, research provenance and data infrastructure. Projects include building data provenance tools funded by the NIH’s Big Data to Knowledge program, regulatory science funded by the Burroughs Wellcome Foundation. Applied machine learning applications include “Deep Care Management” a highly interdisciplinary project with Duke Connected Care, Duke’s Accountable Care Organization, that integrates claims and EHR data for predicting unplanned admissions and risk stratifying patients for case management; CALYPSO, a collaboration with the Department of Surgery for utilizing machine learning to predict surgical complications. My team is also building the data platform for the Department of Surgery's "1000 Patients Project" an intensive biospecimen and biomarker study based around patients undergoing the controlled injury of surgery.

As Director of Duke Forge, Dr. Huang is working to build a data science culture and infrastructure across Duke University that focuses on actionable health data science. The Forge emphasizes scientific rigor, awareness that technology does not supersede clinicians’ responsibilities and human relationship with their patients, and the role of data science in society.