Ephraim Tsalik, MD, PhD

Associate Professor of Medicine
Associate Professor in the Department of Molecular Genetics and Microbiology
Member of Duke Center for Applied Genomics and Precision Medicine
Campus mail Box 102359 DUMC, Durham, NC 27710
Phone (919) 684-3114
Email address e.t@duke.edu

My research is focused on understanding the dynamic between host and pathogen so as to discover and develop host-response markers that can diagnose and predict health and disease.  This new and evolving approach to diagnosing illness has the potential to significantly impact individual as well as public health considering the rise of antibiotic resistance.

With any potential infectious disease diagnosis, it is difficult, if not impossible, to determine at the time of presentation what the underlying cause of illness is.  For example, acute respiratory illness is among the most frequent reasons for patients to seek care. These symptoms, such as cough, sore throat, and fever may be due to a bacterial infection, viral infection, both, or a non-infectious condition such as asthma or allergies.  Given the difficulties in making the diagnosis, most patients are inappropriately given antibacterials.  However, each of these etiologies (bacteria, virus, or something else entirely) leaves a fingerprint embedded in the host’s response. We are very interested in finding those fingerprints and exploiting them to generate new approaches to understand, diagnose, and manage disease.

These principles also apply to sepsis, defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Just as with acute respiratory illness, it is often difficult to identify whether infection is responsible for a patient’s critical illness.  We have embarked on a number of research programs that aim to better identify sepsis; define sepsis subtypes that can be used to guide future clinical research; and to better predict sepsis outcomes.  These efforts have focused on many systems biology modalities including transcriptomics, miRNA, metabolomics, and proteomics.  Consequently, our Data Science team has utilized these highly complex data to develop new statistical methods, furthering both the clinical and statistical research communities.

Synergy between multi-disciplinary experts is crucial to tackle the threats posed by infectious diseases and the rise in antimicrobial resistance. We have successfully assembled a team of clinical scientists, data scientists, laboratorians, clinical research coordinators, among many others. Potential collaborators are encouraged to contact us.

These examples are just a small sampling of the breadth of research Dr. Tsalik and his colleagues conduct.  Please visit https://precisionmedicine.duke.edu/ for more details.

Education and Training

  • Fellowship in Infectious Diseases, Medicine, Duke University School of Medicine, 2008 - 2011
  • Residency, Medicine, Duke University School of Medicine, 2005 - 2008
  • M.D., Columbia University, College of Physicians and Surgeons, 2005
  • Ph.D., Columbia University, College of Physicians and Surgeons, 2003


Tsalik, Ephraim L., Ricardo Henao, Marshall Nichols, Thomas Burke, Emily R. Ko, Micah T. McClain, Lori L. Hudson, et al. “Host gene expression classifiers diagnose acute respiratory illness etiology.” Sci Transl Med 8, no. 322 (January 20, 2016): 322ra11. https://doi.org/10.1126/scitranslmed.aad6873.

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McClain, Micah T., Bradly P. Nicholson, Lawrence P. Park, Tzu-Yu Liu, Alfred O. Hero, Ephraim L. Tsalik, Aimee K. Zaas, et al. “A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses.” Open Forum Infect Dis 3, no. 1 (January 2016): ofw007. https://doi.org/10.1093/ofid/ofw007.

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Ruopp, Marcus, Karen Chiswell, Joshua T. Thaden, Kunal Merchant, and Ephraim L. Tsalik. “Respiratory Tract Infection Clinical Trials from 2007 to 2012. A Systematic Review of ClinicalTrials.gov.” Ann Am Thorac Soc 12, no. 12 (December 2015): 1852–63. https://doi.org/10.1513/AnnalsATS.201505-291OC.

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Tsalik, Ephraim L., Laurel K. Willig, Brandon J. Rice, Jennifer C. van Velkinburgh, Robert P. Mohney, Jonathan E. McDunn, Darrell L. Dinwiddie, et al. “Renal systems biology of patients with systemic inflammatory response syndrome.” Kidney Int 88, no. 4 (October 2015): 804–14. https://doi.org/10.1038/ki.2015.150.

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Tsalik, Ephraim L., Micah McClain, and Aimee K. Zaas. “Moving toward prime time: host signatures for diagnosis of respiratory infections.” The Journal of Infectious Diseases 212, no. 2 (July 2015): 173–75. https://doi.org/10.1093/infdis/jiv032.

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Yuan, X., R. Henao, E. L. Tsalik, R. J. Langley, and L. Carin. “Non-Gaussian discriminative factor models via the max-margin rank-likelihood.” 32nd International Conference on Machine Learning, Icml 2015 2 (January 1, 2015): 1254–63.