Featured Publications

graphical web showing connections between primates and parasites

Predictions of primate–parasite coextinction

Charlie Nunn worked with Duke professors James Herrera and James Moody to analyze potential effects on parasite existence and biodiversity if primates threatened with extinction go extinct.

Read full text in Phil. Trans. R. Soc.          Read article in Duke Today

Principal components (PCoA) plot based on Bray-Curtis distances showing nasopharyngeal microbiome composition among mothers at delivery (M0) and infants throughout the first year of life

Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy

Matthew Kelly, Sweta Patel, John Rawls and colleagues studied the nasopharyngeal microbiomes of 179 mother-infant dyads in Botswana. They examined changes in microbiome diversity and composition during infancy, evaluated associations  between the nasopharyngeal microbiome and pneumococcal colonization risk, and identified environmental factors that influence nasopharyngeal microbiome composition during infancy. 

Read full text in The ISME Journal

Molecular Mechanism of the Mammalian Circadian Clock. (A) Model for circadian entrainment by light. The “master” clock in the suprachiasmatic nucleus (SCN) in the brain is entrained by neural input from photoreceptors in the retina. The master clock in turn maintains a coherent rhythmicity among clocks in peripheral tissue cells via neural signals and humoral factors. (B) The positive (CLOCK-BMAL1) and negative (CRY-PER-CK1δ) arms of the TTFL are in two separate complexes. Mouse liver nuclei were harvested

Circadian clock, carcinogenesis, chronochemotherapy connections

David Hsu collaborated with UNC Chapel Hill to investigate sites of DNA damage and repair following anti-cancer drug treatments. They mapped these sites genome wide at single nucleotide resolution and as a function of circadian time. This data might help provide valuable information for creating rational chronochemotherapy regimens.

Read full text in the Journal of Biological Chemistry

Circulating long chain acylcarnitines and outcomes in diabetic heart failure

James Bain, Chris Newgard, William Kraus, Robert McGarrah, Svati and team used metabolomic profiling to identify biomarkers that report on exercise capacity, clinical outcomes and differential response to exercise in heart failure patients with and without diabetes mellitus.

Read full text in Cardiovascular Diabetology

Altered skeletal muscle metabolic pathways, age, systemic inflammation, and low cardiorespiratory fitness associate with improvements in disease activity following HIIT in persons with RA

William Kraus, David Bartlett, Kim Huffman and team identified connections between skeletal muscle molecular pathways, rheumatoid arthritis (RA) disease activity, and RA disease activity improvements following high intensity interval training.

Read full text in Arthritis Research & Therapy 

Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity

William Kraus and Svati Shah were part of a large collaboration that sequenced over 640,000 exomes from people in the US, UK and Mexico to estimate associations of rare coding variants with body mass index (BMI). They found that inhibiting GPR75 may be a therapeutic strategy for obesity.

Read full text in Science

Genome-Wide Variants Associated With Longitudinal Survival Outcomes Among Individuals With Coronary Artery Disease

William Kraus, Elizabeth Hauser, Carol Haynes and team used a genome-wide screening approach to identify gene variants associated with all-cause mortality among individuals with clinically phenotyped coronary artery disease.

Read full text in Frontiers in Genetics 

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions

Laura Svetkey, Chris Newgard, William Kraus and Svati Shah worked to identify metabolic biomarkers associated with beneficial metabolic changes to weight loss that identify individuals with obesity who would most benefit from a given type of intervention.

Read full text in Plos One

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility

A team at Duke featuring Ricardo Henao, Micah McClain, Ephraim Tsalik, Geoff Ginsburg, Xiling Shen, Chris Woods, Beth Hauser and Dennis Ko created an interactive web database that helps explore and quickly analyze user-uploaded GWAS summary statistics. The database generated novel hypotheses to explain the pathophysiology of common diseases. 

Read full text in Genome Medicine

Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease

Nenad Bursac, Dwight Koeberl, Priya Kishnani and team developed a 3-D model of infantile-onset Pompe disease that demonstrates the signature pathological features of the disease.

Read the full text in Nature

Mucosal Associated Invariant T Cell Responses Differ by Sex in COVID-1

A collaboration including Ephraim Tsalik, Micah McClain, Chris Woods, Xilng Shen and other Duke faculty carried out sex-balanced sampling of peripheral blood mononuclear cells from confirmed 30 COVID-19 inpatients and outpatients, uninfected close contacts, and healthy controls for 36- 31 color flow cytometry and single cell RNA-sequencing.

Read full text in Med

A Rare Autosomal Dominant Variant in Regulator of Calcineurin Type 1 (RCAN1) Gene Confers Enhanced Calcineurin Activity and May Cause FSGS

Nephrotic syndrome (NS) is a kidney disorder that causes the body to pass too much protein in its urine. Rasheed Gbadegesin and team conducted whole-genome sequencing on 320 individuals of unclear genetic etiology and analyzed data from several patient cohorts to gain insight into the genetic architecture of the condition. 

Read full text in JASN

CHG Bathing Reduces Number of Bloodstream Infections in Adults Undergoing Inpatient Hematopoietic Cell Transplantation

Anthony Sung, Julia Messina, Sin-Ho Jung, Li Ma and team conducted a prospective cohort study with historical controls to assess the impact of chlorhexidine gluconate bathing on the rate of bloodstream infections and gut microbiota composition among adults undergoing inpatient HCT at the Duke University Medical Center. 

Read full text in Transcriptional and Cell Therapy

Clinical implementation of an oncology‐specific family health history risk assessment tool

Ryanne Wu, Geoff Ginsburg, Lori Orlando and colleagues used MeTree, a patient-facing family health history risk assessment platform, in a pilot study to test its impact in an oncology setting.

Read full text in Hereditary Cancer in Clinical Practice

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

Ken Poss and team used a transgenic BioID2 strategy to capture cell-specific proteome changes in cardiomyocytes during heart regeneration in adult zebrafish. 

Read full text in eLife

Benchmarking DNA isolation kits used in analyses of the urinary microbiome

Cindy Amundsen and Nazema Siddiqui collaborated with Oregon Health and Science University and the University of Alabama in Huntsville to compare the performance of several DNA isolation kits used in microbiome studies to see if recovered microbes identified by 16S rRNA sequencing differ based on the DNA isolation protocol.

Read the full text in Scientific Reports

Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression

The Proteomics & Metabolomics Core Facility and Jessica Tennenbaum were part of a large collaboration that used a targeted metabolomics approach utilizing a panel of 180 metabolites to gain insights into mechanisms of action and response to certain SSRIs used to treat major depressive disorder.

Read full text in Translational Psychiatry

The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights

Raphael Valdivia, Lawrence David, Holly Dressman, Christopher Newgard, Svati Shah and John Rawls and team analyzed clinical, metabolomic and microbiome samples from adolescents with obesity as they undergo lifestyle modifications.  

Read full text in Obesity

Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance

Christopher Newgard and Michael Freemark are part of an international team that is comparing metabolic effects of metformin and fermentable fibers in combination with those of metformin or fiber alone in adolescents with obesity. They will also determine if therapeutic responses correlate with compositional and functional features of the gut microbiome.

Read the study protocol in Trials

Mutational processes in cancer preferentially affect binding of particular transcription factors

Raluca Gordan collaborated with Duke-NUS to develop the "Signature-QBiC" model that integrates signature profiles of mutational processes with the QBiC estimates of changes in binding affinity to investigate the effect of mutational signatures on the binding of 582 human transcription factors.

Read full text in PMC

Genome-wide analysis identifies novel susceptibility loci for myocardial infarction

William Kraus and Beth Hauser were part of a large international team that performed GWAS studies for myocardial infarction to see if genetic factors that establish atherosclerosis may be distinct from those that predispose to vulnerable plaques and thrombus formation.

Read full text in European Heart Journal

Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence

Paul Magwene, Joseph Heitman and team describe the genetic architecture of six traits in C. deneoformans and then used GWAS function-valued QTL mapping to identify genetic differences that underlie variation in those six traits. Their work illustrates the complex effects that variants may have with respect to virulence potential.

Read full text in PLOS Genetics

Validation of a host gene expression test for bacterial/viral discrimination in immunocompromised hosts

Several members from the Duke Center for Applied Genomics and Precision Medicine collaborated on a study that evaluated the performance of a host gene expression test to discriminate bacterial, viral, and noninfectious illness in immunocompromised patients. Although test performance was marginally lower than in immunocompetent patients, this approach may provide useful diagnostic information in this high-risk population.

Read full text in Clinical Infectious Diseases

Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction

Avshalom Caspi and Terrie Moffitt were part of a large, international team that used genetic correlation and polygenic score analysis to test if noncognitive skills influence educational and economic attainments and longevity and to investigate traits and behaviors that constitute noncognitive skills. They also conducted hypothesis-free bioinformatic annotation analysis with help from the Genomic Analysis & Bioinformatic core facility to explore the tissues, cell types and brain structures that might distinguish the biology of noncognitive skills from the biology mediating cognitive influences on educational attainment.

Read full text in Nature

Digital Health—The Need to Assess Benefits, Risks, and Value

Geoff Ginsburg, along with Eric Perakslis, published a viewpoint in JAMA about the potential for digital health -- wearable and internal devices, sensors in people, homes, communities and more -- to improve health management. However, the current state of technology development and deployment requires a "buyer beware" cautionary note. Ginsburg was also interviewed by JAMA editor-in-chief Dr. Howard Bauchner.

Read full text in JAMA          Listen to the interview

Air Pollution May Hasten Aging

A collaboration with DMPI, the departments of Biostatistics and Bioinformatics and Psychiatry and Behavorial Sciences, the division of Cardiology, UNC Chapel Hill, Georgia Tech, Durham VA, and EPA found that epigenetic age acceleration may be a biomarker of sensitivity to air pollution, especially traffic-related air pollution in urban cohorts. This research shows a new way to understand sensitivity to air pollution and provides a molecular measure of environmental sensitivity.

Read full text in Aging

Modeling statin myopathy in a human skeletal muscle microphysiological system

Deepak Voora led a collaboration between the Center for Applied Genomics and Precision Medicine and the Department of Biomedical Engineering that developed a "muscle on a chip" platform to study the effects of statin associated musculoskeletal symptoms.

Read full text in Plos One

CRISPR dCas9 used to program pluripotent stem cells into adult neuronal cells

A team of researchers at Duke University led by Dr. Charlie Gersbach has developed a new method to discover gene regulatory networks for programming stem cells to become any cell type. Their work, published today in Cell Reports, demonstrates the potential of the approach in making mature adult neuronal cells, but is broadly applicable.

Read full text on Cell Reports

RT-PCR-based 36-gene signature performance over time

Researchers in the Center for Applied Genomics and Precision Medicine assessed the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before symptoms appear.

Read full text in The Lancet

Novel Murine Models of Cerebral Cavernous Malformations

Doug Marchuk and team developed a genetic mouse model of cerebral cavernous malformations. 

Read full text in Angiogenesis

Identification of Undetected Monogenic Cardiovascular Disorders

A collaboration between DMPI, Division of Cardiology, Center for Applied Genomics and Precision Medicine as well as Regeneron Genetics Center and Vanderbilt Medical Center shows the large burden of undetected monogenetic cardiovascular disorders.

Read full text in the Journal of the American College of Cardiology