Elodie Ghedin

Professor of Biology and Global Public Health; Faculty Director of Genomic Sequencing


Areas of Research/Interest

Evolutionary genomics of infectious agents; neglected tropical diseases; microbiome and virus metagenomic studies.


The focus of our laboratory is on defining genomic characteristics of human parasites and other pathogens. Our research is multidisciplinary and draws upon the tools of genomics, molecular virology, and computational biology. Projects include the study of influenza virus evolution and emergence, the analysis of the microbiome and mycobiome (fungal microbiota) associated with the pathogenesis of lung obstruction and emphysema in HIV patients, and the characterization of endosymbiotic interactions between filarial worms and Wolbachia.


To identify the extent of intra- and inter-host microparasite (viruses and bacteria) diversity within the context of transmission and virulence, and parse the relationship between microbial ecology in the respiratory tract and disease progression;

To develop and apply new genomic methods to study microbial pathogens, particularly the associations with their hosts in the context of human disease;

To elucidate the molecular basis behind the adaptation of macroparasites, such as worms, to niches in their human hosts.

Affiliated with other departments or programs

Department of Epidemiology, College of Global Public Health

External Affiliations

Adjunct, Department of Computational & Systems Biology, University of Pittsburgh School of Medicine


Selected Works


Poon LL, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JS, Cowling BJ, Ghedin E. (2016) Quantifying influenza virus diversity and transmission in humans. Nat Genet. 48(2):195-200.

Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin ME, Fitch A, Twaddle A, Cui L, Holmes EC, Boivin G, Ghedin E. (2015) Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection. MBio. 6(2). pii: e02464-14.

Greenbaum BD, Ghedin E. (2015) Viral evolution: beyond drift and shift. Curr Opin Microbiol. 26:109-15.

Kerr PJ, Rogers MB, Fitch A, Depasse JV, Cattadori IM, Twaddle AC, Hudson PJ, Tscharke DC, Read AF, Holmes EC, Ghedin E. (2013) Genome scale evolution of myxoma virus (MYXV) reveals host-pathogen adaptation and rapid geographic spread. J Virol. 87(23):12900-15.


Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol. 2:16216.

Bringaud F, Rogers M, Ghedin E. (2015) Identification and analysis of ingi-related retroposons in the trypanosomatid genomes. Methods Mol Biol. 1201:109-22.

Lustigman S, Melnikow E, Anand SB, Contreras A, Nandi V, Liu J, Bell A, Unnasch TR, Rogers MB, Ghedin E. (2014) Potential involvement of Brugia malayi cysteine proteases in the maintenance of the endosymbiotic relationship with Wolbachia. Int J Parasitol Drugs Drug Resist. 4(3):267-77.

Ghedin E. (2014) Panning for molecular gold in whipworm genomes. Nat Genet. 46(7):661-3.


Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E. (2016) Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome. 4(1):38.

Cribbs SK, Uppal K, Li S, Jones DP, Huang L, Tipton L, Fitch A, Greenblatt RM, Kingsley L, Guidot DM, Ghedin E, Morris A. (2016) Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection. Microbiome. 4:3.

Cui L, Lucht L, Tipton L, Rogers MB, Fitch A, Kessinger C, Camp D, Kingsley L, Leo N, Greenblatt RM, Fong S, Stone S, Dermand JC, Kleerup EC, Huang L, Morris A, Ghedin E. (2015) Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease. Am J Respir Crit Care Med. 191(8):932-42.

Cui L, Morris A and Ghedin E. (2013). Characterizing the Human Mycobiome in Health and Disease. Genome Medicine. Review. 5(7):63.