Publications

From the Ghedin Lab

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129. Tipton L, Müller CL, Kurtz ZD, Huang L, Kleerup E, Morris A, Bonneau R, Ghedin E. (2018)
Fungi stabilize connectivity in the lung and skin microbial ecosystems.
Microbiome Jan 15;6(1):12. PMC5769346

128. Forst CV, Zhou B, Wang M, Chou TW, Mason G, Song WM, Schadt E, Ghedin E, Zhang B. (2017)
Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections.
NPJ Syst Biol Appl Dec 4;3:35. PMC5712526

127. Grote A, Lustigman S, Ghedin E. (2017)
Lessons from the genomes and transcriptomes of filarial nematodes.
Mol Biochem Parasitol Jul;215:23-29. PMC5474361 [Available on 2018-07-01]

126. Lustigman S, Grote A, Ghedin E. (2017)
The role of ‘omics’ in the quest to eliminate human filariasis.
PLoS Negl Trop Dis. Apr 20;11(4):e0005464. PMC5398502

125. Tipton L, Ghedin E, Morris A. (2017)
The lung mycobiome in the next-generation sequencing era.
Virulence Apr 3;8(3):334-341. PMC5436731

124. Grote A, Voronin D, Ding T, Twaddle A, Unnasch T, Lustigman S, Ghedin E. (2017)
Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq.
PLoS Negl Trop Dis Mar 30;11(3):e0005357. PMC5373514

123.  Bennuru S, Cotton JA, Ribeiro JMC, Grote A, Harsha B, Holroyd N, Mhashilkar A, Molina D, Randall A, Shandling A, Unnasch T, Ghedin E, Berriman M, Lustigman S, Nutman T. (2016)
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont.
MBio Nov 23;7(6). pii: e02028-16. PMC5137501

122. Ray B, Ghedin E, Chunara R. (2016)
Network inference from multimodal data: A review of approaches from infectious disease transmission.
J Biomed Inform Dec;64:44-54. PMID: 27612975

121. 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.
Nature Microbiology Nov 21;2:16216. PMC5310847

120. 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 Jul 8 2016;4(1):38. PMC4939015

119. Voronin, D., Bachu, S., Shlossman, M., Unnasch, T.R., Ghedin, E., Lustigman, S. (2016)
Glucose and glycogen metabolism in Brugia malayi is associated with Wolbachia symbiont fitness.
PLoS One Apr 14;11(4):e0153812. PMC4831766

118. Segal, L.N., Clemente, J.C., Tsay, J.-C. J., Koralov, S.B., Keller, B.C., Wu, B.G., Li, Y., Shen, N., Ghedin, E., Morris, A., Diaz, P., Huang, L., Wikoff, W.R., Ubeda, C., Artacho, A., Rom, W.N., Sterman, S.D., Collman, R.G., Blaser, M.J., Weiden, M.D. (2016)
Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.
Nat Microbiol Apr 4;1:16031. PMC5010013

117. Poon, L.M.L., Song, T., Rosenfeld, R., Lin, X., Rogers, M.B., Halpin, R., Stockwell, T., Wentworth, D.E., Peiris, J.S.M., Cowling, B.J., Ghedin, E. (2016)
Quantifying influenza virus diversity and transmission in humans.
Nature Genetics Jan. 4; 48(2):195-200. PMC4731279

116. Cribbs, S.K., Uppal, K., Li, S., Jones, D.P., Huang, L., Kleerup, E., Tipton, L., Fitch, A., Greenblatt, R., Kingsley, L., Guidot, D.M., Ghedin*, E., Morris*, A. (2016)
Correlation of the Lung Microbiome with Metabolic Profiles in Bronchoalveolar Lavage Fluid in HIV Infection.
Microbiome Jan 20; 4(1):3. PMC4721204 *shared corresponding author

115. Tarabichi, Y., Li, K., Hu, S., Nguyen, C., Wang, X., Elashoff, D., Saira, K., Frank, B., Bihan, M., Ghedin, E., Methé, B.A., Deng. J.C. (2015)
The Administration of Intranasal Live Attenuated Influenza Vaccine Induces Changes in the Nasal Microbiota and Nasal Epithelium Gene Expression Profiles.
Microbiome 3(1):74. PMC4678663

114. Ping, J., Tiago Lopes, T.J.S., Nidom, C.A., Ghedin, E., Macken, C.A., Imai, K., Maher, E.A., Neumann, G., Kawaoka, Y. (2015)
Development of high-yield influenza A virus vaccine viruses.
Nat. Commun 6:8148. PMC4569720

113. Beck, J.M., Schloss, P.D., Venkataraman, A., Twigg III, H., Jablonski, K.A., Bushman, F.D., Campbell, T.B., Charlson, E.S., Collman, R.G., Crothers, K., Curtis, J.L., Drews, K.L., Flores, S.C., Fontenot, A.P., Foulkes, M.A., Frank, I., Ghedin, E., Huang, L., Lynch, S.V., Morris, A., Palmer, B.E., Schmidt, T.M., Sodergren, E., Weinstock, G.M., Young, V.B.; Lung HIV Microbiome Project. (2015)
Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.
Am J Respir Crit Care Med. 2015 Aug 6; 192(11):1335-44. PMC4731698

112. Greenbaum, B.D., Ghedin, E. (2015)
Viral evolution: beyond drift and shift.
Curr Opin Microbiol. 26:109-115. PMID:26189048

111. Sam, I-C., Fang Su, Y.C., Y.F., Chan, Jafar, F.L., Nor’E, S.S., Halpin, R.A., Ghedin, E., Hooi, P.S., Hassan, A., Fourment, M., Hassan, H., AbuBakar, S., Wentworth, D.E., Smith, G.J. (2015)
Evolutionary dynamics of influenza B virus in Kuala Lumpur, Malaysia between 1995 and 2008.
J Virol. 89:9689-9692. PMC4542393

110. Liu, C., Voronin, D., Poole, C.P., Bachu, S., Jin, J. Rogers, M.B., Ghedin, E., Lustigman, S., Unnasch, T.R. (2015)
Functional Analysis of MicroRNA activity in Brugia malayi.
Int J Parasitol. 
45(9-10:579-583. PMC4490087

109. Farooqui, A., Leon, A.J., Huang, L., Wu, S., Cai, Y., Lin, P., Chen, W., Fang, X., Zeng, T., Liu, Y., Zhang, L., Su, T., Chen, W., Ghedin, E., Zhu, H., Guan, Y., Kelvin, D.J. (2015)
Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China.
BMC Infect Dis 15:109. PMC4352237

108. Taft, A., Ozawa, M., Fitch, A., Depasse, J., Halfmann, P., Hill-Batorski, L., Hatta, M., Friedrich, T., Lopes, T., Maher, E., Ghedin, E., Macken, C., Neumann, G., and Kawaoka, Y. (2015)
Identification of mammalian-adapting mutations in the polymerase complex of an avian H5N1 influenza virus.
Nat. Commun. 6:7491. PMC4557292

107. Rogers, M.B., Song, T., Sebra, R., Greenbaum, B.D., Hamelin, M.-E., Fitch, A., Twaddle, A., Cui, L., Holmes, E.C., Boivin, G., Ghedin, E. (2015)
Intra-host dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment and natural selection.
MBio 6(2). pii: e02464-14. PMC4453542

106. Kerr, P.J., Liu, J., Cattadori, I., Ghedin, E., Read, A.F., Holmes, E.C. (2015)
Myxoma virus and the leporipoxviruses: an evolutionary paradigm.
Viruses. 6;7(3):1020-1061. Review. PMC4379559

105. Cui, L., Lucht, L., Tipton, L., Rogers, M.B., Fitch, A., Kessinger, C., Camp, D., Kingsley, L., Leo, N., Greenblatt, R.M., Fong, S., Stone, S., Dermand, J., Kleerup, E., Huang, L., Morris, A., Ghedin, E. (2015)
Topographical diversity of the respiratory tract mycobiome and alteration in HIV and lung disease.
Am J Resp Crit Care Med. 191:932-942. PMC4435454

104. Bringaud, F., Rogers, M., Ghedin, E. (2015)
Identification and analysis of ingi-related retroposons in the trypanosomatid genomes.
Methods Mol Biol. 2015;1201:109-22. PMID:25388110

103. Allison, A.B., Ballard, J.R., Tesh, R.B., Brown, J.D., Ruder, M.G., Keel, M.K., Munk, B.A., Mickley, R.M., Gibbs, S.E., Travassos da Rosa, A.P., Ellis, J.C., Ip, H.S., Shern-Bochsler, V.I., Rogers, M.B., Ghedin, E., Holmes, E.C., Parrish, C.R., Dwyer, C. (2015)
Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus.
J Virol. 2015 Jan 15;89(2):1389-403. PMC4300652

102. Liu C, Voronin D, Poole CB, Bachu S, Rogers MB, Jin J, Ghedin E, Lustigman S, McReynolds LA, Unnasch TR. (2015)
Functional analysis of microRNA activity in Brugia malayi.
Int J Parasitol. S0020-7519(15)00133-2. PMC4490087

101. Farooqui A, Leon AJ, Huang L, Wu S, Cai Y, Lin P, Chen W, Fang X, Zeng T, Liu Y, Zhang L, Su T, Chen W, Ghedin E, Zhu H, Guan Y, Kelvin DJ. (2015)
Genetic diversity of the 2013-14 human isolates of influenza H7N9 in China.
BMC Infect Dis. 15(1):109. PMC4352237

100. Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin ME, Fitch A, Twaddle A, Cui L, Holmes EC, Boivin G, Ghedin E.
Intrahost dynamics of antiviral resistance in influenza a virus reflect complex patterns of segment linkage, reassortment, and natural selection.
(2015) MBio. 6(2). PMC4453542

99. Kerr PJ, Liu J, Cattadori I, Ghedin E, Read AF, Holmes EC.
Myxoma virus and the Leporipoxviruses: an evolutionary paradigm.
(2015) Viruses. 7(3):1020-61. PMC4379559

98. 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. PMC4435454

97. Lustigman, S., Melnikow, E., Contreras, A., Liu, J., Bell, A., Unnasch, T.R., Rogers, M., 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. PMC4266806

96. Lukens, S., DePasse, J.V., Rosenfeld, R., Ghedin, E., Mochan, E., Brown, S., Grefenstette, J., Burke, D., Swigon, D. Clermont, G. (2014)
A large-scale immuno-epidemiological simulation of influenza A epidemics.
BMC Public Health. 14(1): 1019. PMC4194421

95. Clancy, C.J., Kalil, A.C., Fowler, V.G., Ghedin, E., Kolls, J.K., Nguyen, M.H. (2014)
Emerging and resistant infections.
Ann Am Thorac Soc. Aug;11 Suppl 4:S193-200

94. Cui, L., Morris, A., Huang, L., Beck, J.M., Twigg III, H.L., von Mutius, E., Ghedin, E. (2014)
The microbiome and the lung.
Ann Am Thorac Soc. Aug;11 Suppl 4:S227-32

93. Ghedin, E. (2014).
Panning for molecular gold in whipworm genomes.
Nat. Genet. 46(7):661-663.

92. Vasilakis, N., Guzman, H., Firth, C., Forrester, N.L., Widen, S.G., Wood, T.G., Rossi, S.L., Ghedin, E., Popov, V., Blasdell, K.R., Walker, P.J., Tesh, R.B. (2014).
Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range.
J. Virology 11:97 (May 20). PMC4038087

91. Rogers, M.B., Cui, L., Fitch, A., Vasilakis, N., Tesh, R., Ghedin, E (2014).
Whole genome analysis of Sierra Nevada virus, a novel mononegavirus in the family Nyamiviridae.
American Journal for Tropical medicine and Hygiene 91(1): 159-164. PMC4080556

90. Gardner, C.L., Hritz, J., Sun, C., Song, T.Y., Rogers, M.B., Vanlandingham, D.L., Higgs, S., Ghedin, E., Klimstra, W.B., Ryman, K.D (2014).
Deliberate attenuation of chikungunya virus by adaptation to heparan sulfate-dependent infectivity as a model for rational arbovirus vaccine design PLoS Negl
Trop Dis 8(2):e2719. PMC3930508

89. Vasilakis, N., Castro-Llanos, F., Widen, S.G., Aguilar, P.V., Guzman, H., Guevara, C., Fernandez, R., Auguste, A.J., Wood, T.G., Popov, V., Mundal, K., Ghedin, E., Kochel, T.J., Holmes, E.C., Walker, P.J., Tesh, R.B. (2014)
Arboretum and Puerto Almendras viruses: two novel rhabdoviruses isolated from mosquitoes in Peru.
J. Gen. Virol. 95(4):787-792. PMC3973475

88. Kerr, P.J., Rogers, M., DePasse, J.V., Fitch, A., Cattadori, I., Twaddle, A.C., Hudson, P.J., Tscharke, D.C., Read, A.F., Holmes, E.C., Ghedin, E. (2013) Genome scale evolution of myxoma virus (MYXV) reveals host-pathogen adaptation and rapid geographic spread. J Virol 87(23):12900-15. PMC3838154 [Selected by the editors for inclusion in “Spotlight”, a feature in the Journal that highlights research articles of significant interest]

87. Ghedin, E., Rogers, M.B., Widen, S., Guzman, H., Travassos da Rosa, A.P.A., Wood, T.G., Fitch, A., Popov, V., Holmes, E.C., Walker, P.J., Vasilakis, N., Tesh, R.B. (2013) Kolenté virus, a novel Rhabdovirus species isolated from ticks and bats in the Republic of Guinea. J. Gen. Virol. 94:2609-15. PMC3836499

86. Kerr, P.J., Rogers, M.B., Fitch, A., Depasse, J.V., Cattadori, I.M., Hudson, P.J., Tscharke, D.C., Holmes, E.C., Ghedin, E. (2013) Comparative analysis of the complete genome sequence of the Californian MSW strain of myxoma virus reveals potential host adaptations. J Virol. 87(22): 12080-12089. PMC3807925

85. Cui, L., Morris, A. and Ghedin, E. (2013). Characterizing the Human Mycobiome in Health and Disease. Genome Medicine. Review. Jul 30;5(7):63.

84. Min, J.-Y., Santos, C., Fitch, A., Twaddle, A., Toyoda, Y., DePasse, J.V., Ghedin*, E., Subbarao*, K. (2013) Mammalian adaptation of the PB2 gene of avian H5N1 influenza virus. J Virol. 87(19):10884-10888. PMC3807384 *co-corresponding authors

83. Vasilakis, N., Widen, S., Mayer, S.V., Seymour, R., Wood, T.G., Popov, V., Guzman, H., Travassos da Rosa, A.P., Ghedin, E., Holmes, E.C., Walker, P.J., Tesh, R.B. (2013) Niakha virus: A novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal. Virology, 444(1-2):80-9. PMC3755043

82. Saira, K., Lin, X., DePasse, J.V., Halpin, R., Twaddle, A., Stockwell, T., Angus, B., Cozzi-Lepri, A., Delfino, M., Dugan, V., Dwyer, D.E., Freiberg, M., Horban, A., Losso, M., Lynfield, R., Wentworth, D.N., Holmes, E.C., Davey, R., Wentworth, D., Ghedin, E. (2013) Sequence analysis of in vivo defective-interfering (DI)-like RNA of influenza A H1N1 pandemic virus. J Virol., 87(14):8064-74. PMC3700204

81. Melnikow, E, Xu, S., Liu, J., Bell, A.J., Ghedin, E., Unnasch, T.R., Lustigman, S. (2013) A potential role for the interaction of Wolbachia surface proteins with the Brugia malayi glycolytic enzymes and cytoskeleton in maintenance of endosymbiosis. PLoS Negl Trop Dis, 7(4): e2151 PMC3617236

80. Morris, A., Beck, J.M., Schloss, P.D., Campbell, T.B., Crothers, K., Curtis, J.L., Flores, S.C., Fontenot, A.P., Ghedin, E., Huang, L., Jablonski, K., Kleerup, E., Lynch, S.V., Sodergren, E., Twigg, H., Young, V.B., Bassis, C.M., Venkataraman, A., Schmidt, T.M., Weinstock, G.M. (2013) Comparison of the respiratory microbiome in healthy non-smokers and smokers. Am J Respir Crit Care Med, 187(10):1067-75. PMC3734620

79. Lozupone, C., Cota-Gomez, A., Palmer, B.E., Linderman, D.J., Charlson, E.S., Sodergren, E., Mitreva, M., Abubucker, S., Martin, J., Yao, G., Campbell, T.B., Flores, S.C., Ackerman, G., Stombaugh, J., Ursell, L., Beck, J.M., Curtis, J.L., Young, V.B., Lynch, S.V., Huang, L., Weinstock, G.M., Knox, K.S., Twigg, H., Morris, A., Ghedin, E., Bushman, F.D., Collman, R.G., Knight, R., Fontenot, A.P.; for the Lung HIV Microbiome Project (2013) Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med, 187(10):1110-7. PMC3734615

78. Kerr, P.J., Ghedin, E., DePasse J.V., Fitch, A., Cattadori, I., Hudson, P.J., Tscharke, D.C., Read, A.F., Holmes, E.C. (2012) The evolutionary history and attenuation of myxoma virus on two continents. PLoS Pathogens 8(10):e1002950 PMC3464225

77. Ghedin, E., Holmes, E.C., DePasse, J.V., Pinilla, L.T., Fitch, A., Hamelin, M.-E., Papenburg, J., Boivin, G. (2012) Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. J Infect Dis 206(10):1504-11. PMC3475640

76. Dugan, V., Saira, K., Ghedin, E. (2012) Large-scale sequencing and the natural history of model human RNA viruses. Future Virology 7(6):563-573. Review. PMC3653332

75. Scott, A.L., Ghedin, E., Nutman, T.B., McReynolds, L.A., Poole, C.B., Slatko, B.E., Foster, J.M. (2012) Filarial and Wolbachia Genomics. Parasite Immunol. 34:121-129. PMC3454450

74. Lam, T.T.-Y., Ip, H.S., Ghedin, E., Wentworth, D.E., Halpin, R.A., Stockwell, T.B., Spiro, D.J., Dusek, R.J., Bortner, J.B., Hoskins, J., Bales, B.D., Yparraguirre, D.R., Holmes, E.C. (2012) Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North-American birds. Ecology Letters 15(1):24-33. PMC3228906

73. Ghedin, E., Laplante, J., DePasse, J., Wentworth, D.E., Santos, R.P., Lepow, M.L., Porter, J., Stellrecht, K., Lin, X., Operario, D., Griesemer, S., Fitch, A., Halpin, R.A., Stockwell, T.B., Spiro, D.J., Holmes, E.C., St.George, K. (2011) Deep sequencing reveals mixed infection of pandemic H1N1/2009 viruses and the emergence of oseltamivir resistance. J Infect Dis 203: 168-174. PMC3071067

72. Ping, J., Keleta, L., Forbes, N.E., Dankar, S., Stecho, W., Tyler, S., Zhou, Y., Babiuk, L., Weingartl, H., Halpin, R.A., Boyne, A., Bera, J., Hostetler, J., Fedorova, N.B., Proudfoot, K., Katzel, D.A., Stockwell, T.B., Ghedin, E., Spiro, D.J., Brown, E.G. (2011) Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse. PLoS One 6:e21740. PMC3128085

71. Choi, Y.-J., Ghedin, E., Berriman, M., McQuillan, J., Holroyd, N., Mayhew, G.F., Christensen, B.M., Michalski, M.L. (2011) A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis. 5(12): e1409 PMC3236722

70. Bahl, J., Nelson, M.I., Chan, K.H., Chen, R., Vijaykrishna, D., Halpin, R., Stockwell, T., Lin, X., Wentworth, D.E., Ghedin, E., Guan, Y., Peiris, J.S.M., Riley, S., Rambaut, A., Holmes, E.C., Smith, G.J.D. (2011) Complex meta-population dynamics and persistence of human influenza A H3N2 virus. Proc Nat Acad Sc U S A 108(48):19359-64 PMC3228450

69. Liu, C., Kelen, P.V., Ghedin, E., Lustigman, S., Unnasch, T.R. (2011) Analysis of transcriptional regulation of tetracycline responsive genes in Brugia malayi. Mol Biochem Parasitol 180:106-111. PMC3205945

68. Dwyer, D.E.; INSIGHT Influenza Study Group (2011) Surveillance of illness associated with pandemic (H1N1) 2009 virus infection among adults using a global clinical site network approach: the INSIGHT FLU 002 and FLU 003 studies. Vaccine Jul 22:29 Suppl 2:B56-62. PMC3703507

67. Melnikow, E., Xu, S., Liu, J., Li, L., Oksov, Y., Ghedin, E., Unnasch, T.R., Lustigman, S. (2011) Interaction of a Wolbachia WSP-like protein with a nuclear-encoded protein of Brugia malayi. International J Parasitol 41:1053-61. PMC3160744

66. Bennuru, S., Meng, Z., Ribeiro, J.M., Semnani, R.T., Ghedin, E., Chan, K., Lucas, D.A., Veenstra, T.D., Nutman, T.B. (2011) Stage-specific proteomic expression patterns of the human filarial parasite Brugia malayi and its endosymbiont Wolbachia. Proc Nat Acad Sci U S A Jun 7;108(23):9649-54. Epub 2011 May 23. PMC3111283

65. Holmes, E.C., Ghedin, E., Halpin, R.A., Stockwell, T.B., Zhang, X.Q., Fleming, R., Davey, R., Benson, C.A., Mehta, S., Taplitz, R., Liu, Y.T., Brouwer, K.C., Wentworth, D.E., Lin, X.; the INSIGHT FLU002 Study Group, Schooley, R.T. (2011) Extensive Geographical Mixing of 2009 Human H1N1 Influenza A Virus in a Single University Community. J Virol Jul;85(14):6923-6929. PMC3126550

64. Vlasova, A.N., Halpin, R., Wang, S., Ghedin, E., Spiro, D.J., Saif, L.J. (2011) Molecular characterization of a new alphacoronavirus species associated with mink epizootic catarrhal gastroenteritis. J Gen Virol Jun;92(Pt 6):1369-79. Epub 2011 Feb 23. PMC3168282

63. Nelson, M.I., Tan, Y., Ghedin, E., Wentworth, D.E., St. George, K., Edelman, L., Beck, E.T., Fan, J., Lam, T.T-Y., Kumar, S., Spiro, D.J., Simonsen, L., Viboud, C., Holmes. E.C., Henrickson, K.J., Musser, J.M. (2011) Phylogeography of the Spring and Fall Waves of the H1N1/09 Pandemic Influenza Virus in the United States. J Virology Jan;85(2):828-834. Epub 2010 Nov 10. PMC3020026

62. Xu, S., Liu, C., Tzertzinis, G., Ghedin, E., Evans, C., Kaplan, R., Unnasch, TR (2010) In vivo transfection of developmentally competent Brugia malayi infective larvae. Int J Parasitol 41:355-362. PMC3046311

61. Ghedin, E., Wentworth, D., Halpin, R.A., Lin, X., Bera, J., DePasse, J., Fitch, A., Griesemer, S., Hine, E., Katzel, D.A., Overton, L., Proudfoot, K., Sitz, J., Szczypinski, B., St. George, K., Spiro, D.J., Holmes, E.C. (2010) Unseasonal Transmission of H3N2 Influenza A Virus during the Swine-Origin H1N1 Pandemic. J Virology Jun;84(11):5715-5718. Epub Mar. 17. PMC2876599

60. Schriml, L.M., Arze, C., Nadendla, S., Ganapathy, A., Felix, V., Mahurkar, A., Phillippy, K., Gussman, A., Angiuoli, S., Ghedin, E., White, O., Hall, N. (2010) GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res. Jan;38(Database issue):D754-64. Epub 2009 Oct 22. PMC2808878

59. Liu, C., Oliveira, A., Chauhan, C., Ghedin, E., Unnasch, T.R. (2010) Functional analysis of putative operons in Brugia malayi. Int J Parasitol Jan;40(1):63-71. Epub 2009 Jul 23. PMC2813416

58. Nelson, M., Spiro, D.J., Wentworth, D., Beck, E., Fan, J., Ghedin, E., Halpin, R., Bera, J., Hine, E., Proudfoot, K., Stockwell, T., Lin, X., Griesemer, S., Kumar, S., Bose, M., Viboud, C., Holmes, E., Henrickson, K. (2009) The early diversification of influenza A/H1N1pdm. PLoS Curr. Nov 3;1:RRN1126. PMC2773564

57. Brindley, P.J., Mitreva, M., Ghedin, E., Lustigman, S. (2009) Helminth genomics: the implications for human health. PLoS Negl Trop Dis. Oct. 26;3(10):e538. Review. PMC2757907

56. Ghedin, E., Hailemariam, T., DePasse, J., Zhang, X., Oksov, Y., Unnasch, T.R., Lustigman, S. (2009) Brugia malayi gene expression in response to the targeting of the Wolbachia endosymbiont by tetracycline treatment. PLoS Negl Trop Dis. Oct.6;3(10):e525. PMC2754610

55. Berriman, M., Haas, B.J., LoVerde, P.T., Wilson, R.A., Dillon, G.P., Cerqueira, G.C., Mashiyama, S.T., Al-Lazikani, B., Andrade, L.F., Ashton, P.D., Aslett, M.A., Bartholomeu, D.C., Blandin, G., Caffrey, C.R., Coghlan, A., Coulson, R., Day, T.A., Delcher, A., DeMarco, R., Djikeng, A., Eyre, T., Gamble, J.A., Ghedin, E., Gu, Y., Hertz-Fowler, C., Hirai, H., Hirai, Y., Houston, R., Ivens, A., Johnston, D.A., Lacerda, D., Macedo, C.D., McVeigh, P., Ning, Z., Oliveira, G., Overington, J.P., Parkhill, J., Pertea, M., Pierce, R.J., Protasio, A.V., Quail, M.A., Rajandream, M.-A., Rogers, J., Sajid, M., Salzberg, S.L., Stanke, M., Tivey, A.R., White, O., Williams, D.L., Wortman, J., Wu, W., Zamanian, M., Zerlotini, A., Fraser-Liggett, C.M., Barrell, B.G., El-Sayed, N.M. (2009) The Genome of the blood fluke Schistosoma mansoni. Nature. Jul 16;460(7253):352-358. PMC2756445

54. Ghedin, E., Fitch, A., Boyne, A., Griesemer, S., DePasse, J., Bera, J., Zhang, X., Halpin, R.A., Smit, M., Jennings, L., St George, K., Holmes, E.C., Spiro, D.J. (2009) Mixed infection and the genesis of influenza virus diversity. J Virology Sep;83(17): 8832-8841. PMC2738154

53. Li, B.W., Rush, A.C., Mitreva, M., Yin, Y., Spiro, D., Ghedin, E., Weil, G.J. (2009) Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. BMC Genomics Jun. 15; 10:267. PMC2708187

52. Brower-Sinning, R., Carter, D.M., Crevar, C.J., Ghedin, E., Ross, T.M., Benos, P.V. (2009) The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biology Feb. 12;10(2):R18. PMC2688270

51. Alekseev, K.P., Vlasova, A.N., Jung, K., Hasoksuz, M., Zhang, X., Halpin, R., Wang, S., Ghedin, E., Spiro, D., Saif, L.J. (2008) Bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses based on complete genomic sequences. J Virol. Dec;82(24):12422-12431. PMC2593316

50. Scott, A.L., Ghedin, E. (2009). The genome of Brugia malayi – All worms are not created equal. Parasitol Int. Mar;58(1):6-11. Epub 2008 Sep 24. Review. PMC2668601

49. Ghedin, E., Daehnel. K., Foster, J., Slatko, B. and Lustigman, S. (2008). The symbiotic relationship between filarial parasitic nematodes and their Wolbachia endosymbionts – a resource for a new generation of control measures. Symbiosis. 46: 77-85. Review.

48. Nelson, M.I., Edelman, L., Spiro, D.J., Boyne, A.R., Bera, J., Halpin, R., Ghedin, E., Miller, M.A., Simonsen, L., Viboud, C., Holmes, E.C. (2008) Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States. PLoS Pathog. Aug 22;4(8):e1000133. PMC2495036

47. Dugan, V.G., Chen, R., Spiro, D.J., Sengamalay, N., Zaborsky, J., Ghedin, E., Nolting, J., Swayne, D.E., Runstadler, J.A., Happ, G.M., Senne, D.A., Wang, R., Slemons, R.D., Holmes, E.C., Taubenberger, J.K. (2008) The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathog. May 30;4(5):e1000076. PMC2387073

46. Nelson, M.I., Viboud, C., Simonsen, L., Bennett, R.T., Griesemer, S.B., St. George, K., Taylor, J., Spiro, D.J., Sengamalay, N.A., Ghedin, E., Taubenberger, J.K., Holmes, E.C. (2008) Multiple reassortment events in the evolutionary history of H1N1 influenza A virus since 1918. PLoS Pathog. Feb 29;4(2):e1000012. PMC2262849

45. Bringaud, F., Ghedin, E., El-Sayed, N.M., Papadopoulou B. (2008). Role of transposable elements in trypanosomatids. Microbes Infect. 2008 May;10(6):575-581. Epub 2008 Feb 21. Review.

44. Djikeng, A., Halpin, R.A., Kuzmickas, R., Depasse, J., Feldblyum, J., Sengamalay, N., Afonso, C.L., Zhang, X., Anderson, N.G., Ghedin, E., Spiro, D.J. (2008) Viral genome sequencing by random priming methods. BMC Genomics Jan 7;9:5. PMC2254600

43. Kumar, S., Chaudhary, K., Foster, J.M., Novelli, J., Zhang, Y., Wang, S., Spiro, D.J., Ghedin, E., Carlow, C.K.S. (2007) Mining predicted essential genes of Brugia malayi for nematode drug targets. PLoS One. Nov 14;2(11):e1189. PMC2063515

42. Smith, K.A., Komuniecki, R.W., Ghedin, E., Spiro, D., Gray, J. (2007) Genes encoding putative biogenic amine receptors in the parasitic nematode Brugia malayi. Invert Neurosci. Dec;7(4):227-244. Epub 2007 Nov 20.

41. Ghedin, E., Wang, S., Spiro, D.J., Caler, E., Zhao, Q., Crabtree, J., Allen, J.E., Delcher, A.L., Guiliano, D.B., Miranda-Saavedra, D., Angiuoli, S.V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N.M., Wortman, J.R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S.L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G.J., Carlow, C.K.S., Crawford, M.J., Daub, J., Dimmic, M.W., Estes, C.F., Foster, J.M., Ganatra, M., Gregory, W.F., Johnson, N.M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B.-W., Li, W., Lindblom, T.H., Lustigman, S., Ma, D., Maina, C., Martin, D., McCarter, J.P., McReynolds, L., Mitreva, M., Nutman, T.B., Parkinson, J., Peregrín-Alvarez, J.M., Poole, C., Ren, Q., Saunders, L., Sluder, A.E., Smith, K., Stanke, M., Unnasch, T.R., Ware, J., Wei, A.D., Weil, G., Williams, D.J., Zhang, Y., Williams, S.A., Fraser-Liggett, C., Slatko, B., Blaxter, M.L., Scott, A.L.. (2007) Draft genome sequence of the filarial nematode parasite Brugia malayi. Science Sep 21;317(5845): 1756-1760. PMC2613796
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40. Dunning Hotopp, J.C., Clark, M.E., Oliveira, D.C.S.G. Foster, J.M., Fischer, P., Muñoz Torres, M.C., Giebel, J.D., Wang, S., Ingram, J., Nene, R.H., Shepard, J., Ishmael, N., Kumar, N., Tomkins, J., Richards, S., Spiro, D.J., Ghedin, E., Slatko, B.E., Tettelin, H., Werren, J.H. (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science Sep 21;317(5845): 1753-1756.

39. Bringaud, F., Müller, M., Coutinho Cerqueira, G., El-Sayed, N.M.A., Papadopoulou, B., and Ghedin, E. (2007) Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PLoS Pathogens Sep 7;3(9):1291-1307. PMC2323293
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38. Liu, C., de Oliveira, A.; Higazi, T.B., Ghedin, E., DePasse, J., Unnasch, T.R. (2007) Sequences necessary for trans-splicing in transiently transfected Brugia malayi. Molecular and Biochemical Parasitology. Nov;156(1):62-73. Epub 2007 Jul 22. PMC2039923

37. Schriml, L.M., Gussman, A., Phillippy, K., Angiuoli, S., Hari, K., Goates, A., Jain, R., Davidsen, T., Ganapathy, A., Ghedin, E., Salzberg, S., White, O., Hall, N. (2007) Gemina: A Web-Based epidemiology and genomic metadata system designed to identify infectious agents. BioSurveillance 2007: 228-229

36. Salzberg, S.L., Kingsford, C., Cattoli, G., Spiro, D.J., Janies, D.A., Mehrez Aly, M., Brown, I.H., Couacy-Hymann, E., Mario De Mia, G., Dung, D.H., Guercio, A., Joannis, T., Maken. A.S., Padalino, I., Saad, M.G., Savić, V., Sengamalay, N.A., Yingst, S., Zaborsky, J., Zorman-Rojs. O., Ghedin, E., and Capua, I. (2007) Genome analysis links recent European and African H5N1 influenza viruses and shows them to be distinct from earlier outbreak strains. Emerging Infectious Diseases May;13(5):713-718. PMC2432181

35. Zhang, X., Hasoksuz, M., Spiro, D., Halpin, R., Wang, S., Vlasova, A., Janies, D., Jones, L.R., Ghedin, E., Saif, L.J. (2007) Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology. Jun 20;363(1):1-10. Epub 2007 Apr 16.

34. Hasoksuz, M., Alekseev, K., Vlasova, A., Zhang, X., Spiro, D., Halpin, R., Wang, S., Ghedin, E., Saif, L.J. (2007) Biologic, antigenic and full length genomic characterization of a bovine-like coronavirus isolated from a giraffe. J Virol. May; 81(10):4981-4990. Epub 2007 Mar 7.

33. Zhang, X., Hasoksuz, M., Spiro, D., Halpin, R., Wang, S., Stollar, S., Janies, D., Hadya, N., Tang, Y., Ghedin, E., Saif, L. (2007) Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus. Virology. Feb 20;358(2):424-435. PMC1850758

32. Yao, K., Akyani, N., Donati, D., Sengamalay, N., Fotheringham, J., Ghedin, E., Bishop, M., Barrett, J., Kashanchi, F., Jacobson, S. (2006) Detection of HHV-6B in post-mortem central nervous system tissue of a post-bone marrow transplant recipient: a multi-virus array analysis. J Clin Virol. Dec;37 Suppl 1:S57-62.

31. Nelson, M. I., Simonsen, L., Viboud, C., Miller, M.A., Taylor, J., St. George, K., Griesemer, S.B., Ghedin, E., Sengamalay, N.A., Spiro, D.J., Volkov, I., Grenfell, B.T., Lipman, D.J., Taubenberger, J.K., Holmes, E.C. (2006) Stochastic processes are key determinants of short-term evolution in influenza A virus. PLoS Pathog. Dec;2(12):e125

30. Yao, K., Mandel, M., Akyani, N., Maynard, K., Sengamalay, N., Fotheringham, J., Ghedin, E., Kashanchi, F., Jacobson, S. (2006) Differential HHV-6A gene expression in T cells and primary human astrocytes based on multi-virus array analysis. Glia. Jun;53(8):789-798.

29. Bringaud, F., Bartholomeu, D., Blandin, G., Delcher, A., Baltz, T., El-Sayed, N.M.A.and Ghedin, E. (2006). The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site-specificity for insertion. Mol Biol Evol Feb;23(2):411-420. Epub 2005 Nov 2.

28. Bringaud, F., Ghedin, E., Blandin, G., Bartholomeu, D., Levin, M.J., Baltz, T. and El-Sayed, N.M.A. (2006) Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. Mol Biochem Parasitol Feb;145(2):158-170. Epub 2005 Oct 10.

27. Ghedin, E., Sengamalay, N.A., Shumway, M., Zaborsky, J., Feldblyum, T., Subbu, V., Spiro, D.J., Sitz, J., Koo, H., Bolotov, P., Dernovoy, D., Tatusova, T., Bao, Y., St. George, K., Taylor, J., Lipman, D.J., Fraser, C.M., Taubenberger, J.K., Salzberg, S.L. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature Oct 20;437(7062):1162-1166. Epub 2005 Oct 5.

26. Holmes, E.C., Ghedin, E., Miller, N., Taylor, J., Bao, Y., George, K.S., Grenfell, B.T., Salzberg, S.L., Fraser, C.M., Lipman, D.J., Taubenberger, J.K.. (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. Jul 26;3(9):e300. Epub 2005 Jul 26. PMC1180517
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25. Ghedin, E. and Claverie, J.-M. (2005) Mimivirus relatives in the sargasso sea. Virology J Aug 16;2(1):62.

24. Berriman, M., Ghedin, E., Hertz-Fowler, C., Blandin, G., Renauld, H., Bartholomeu, D.C., Lennard, N.J., Caler, E., Hamlin, N.E., Haas, B., Böhme, U., Hannick, L., Aslett, M.A., Shallom, J., Marcello, L., Hou, L., Wickstead, B., Alsmark, U.C., Arrowsmith, C., Atkin, R.J., Barron, A.J., Bringaud, F., Brooks, K., Carrington, M., Cherevach, I., Chillingworth, T.J., Churcher, C., Clark, L.N., Corton, C.H., Cronin, A., Davies, R.M., Doggett, J., Djikeng, A., Feldblyum, T., Field, M.C., Fraser, A., Goodhead, I., Hance, Z., Harper, D., Harris, B.R., Hauser, H., Hostetler, J., Ivens, A., Jagels, K., Johnson, D., Johnson, J., Jones, K., Kerhornou, A.X., Koo, H., Larke, N., Landfear, S., Larkin, C., Leech, V., Line, A., Lord, A., Macleod, A., Mooney, P.J., Moule, S., Martin, D.M., Morgan, G.W., Mungall, K., Norbertczak, H., Ormond, D., Pai, G., Peacock, C.S., Peterson, J., Quail, M.A., Rabbinowitsch, E., Rajandream, M.A., Reitter, C., Salzberg, S.L., Sanders, M., Schobel, S., Sharp, S., Simmonds, M., Simpson, A.J., Tallon, L., Turner, C.M., Tait, A., Tivey, A.R., Van Aken, S., Walker, D., Wanless, D., Wang, S., White, B., White, O., Whitehead, S., Woodward, J., Wortman, J., Adams, M.D., Embley, T.M., Gull, K., Ullu, E., Barry, J.D., Fairlamb, A.H., Opperdoes, F., Barrell, B.G., Donelson, J.E., Hall, N., Fraser, C.M., Melville, S.E., El-Sayed, N.M. (2005) The genome sequence of the African trypanosome, Trypanosoma brucei. Science Jul 15;309(5733):416-422.
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23. El-Sayed, N.M.A., Myler, P.J., Bartholomeu, D., Nilsson, D., Aggarwal, G., Tran, A.N., Ghedin, E., Worthey, E.A., Delcher, A.L., Blandin, G., Westenberger, S.J., Caler, E., Cerqueira, G.C., Branche, C., Haas, B., Anupama, A., Arner, E., Aslund, L., Attipoe, P., Bontempi, E., Bringaud, F., Burton, P., Cadag, E., Campbell, D.A., Carrington, M., Crabtree, J., Darban, H., da Silveira, J.F., de Jong, P., Edwards, K., Englund, P.T., Fazelina, G., Feldblyum, T., Ferella, M., Frasch, A.C., Gull, K., Horn, D., Hou, L., Huang, Y., Kindlund, E., Klingbeil, M., Kluge, S., Koo, H., Lacerda, D., Levin, M.J., Lorenzi, H., Louie, T., Machado, C.R., McCulloch, R., McKenna, A., Mizuno, Y., Mottram, J.C., Nelson, S., Ochaya, S., Osoegawa, K., Pai, G., Parsons, M., Pentony, M., Pettersson, U., Pop, M., Ramirez, J.L., Rinta, J., Robertson, L., Salzberg, S.L., Sanchez, D.O., Seyler, A., Sharma, R., Shetty, J., Simpson, A.J., Sisk, E., Tammi, M.T., Tarleton, R., Teixeira, S., Van Aken, S., Vogt, C., Ward, P.N., Wickstead, B., Wortman, J., White, O., Fraser, C.M., Stuart, K.D., Andersson, B. (2005) The genome sequence of Trypanosoma cruzi, etiological agent of Chagas’ disease. Science Jul 15;309(5733):409-415.
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22. El-Sayed, N.M.A., Myler, P.J., Blandin, G., Berriman, M., Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E.A., Hertz-Fowler, C., Ghedin, E., Peacock, C., Haas, B., Angiuoli, S., Anupama, A., Bartholomeu, D., Cadag, E., Carlton, J.M., Creasy, T., Djikeng, A., Hauser, C., Ivens, A.C., Kummerfeld, S., Leal, J., Nilsson, D., Peterson, J., Shallom, J., Silva, J.C., Sundaram, J., Tran, A.-N., Westenberger, S., White, O., Wortman, J., Melville, S.E., Donelson, J.E., Andersson, B., Stuart, K.D., and Hall, N. (2005) Comparative genomics of the trypanosomatids. Science Jul 15;309(5733):404-409.

21. Huete-Perez, J., Flores-Obando, R.E., Ghedin, E., Caffrey, M. (2005) Genomic and Proteomic Approaches for Chagas’ disease: critical analysis of diagnostic methods. Expert Review of Molecular Diagnostics Jul;5(4):521-530. Review.

20. Foster, J, Ganatra, M, Kamal, I, Ware, J, Makarova, K, Ivanova, N, Bhattacharyya, A, Kapatral, V, Kumar, S, Posfai, J, Vincze, T, Ingram, J, Moran, L, Lapidus, A, Omelchenko, M, Kyrpides, N, Ghedin, E., Wang, S, Goltsman, E, Joukov, V, Ostrovskaya, O, Tsukerman, K, Mazur, M, Comb, D, Koonin, E, Slatko, B. (2005) The Wolbachia Genome of Brugia malayi: Endosymbiont evolution within a human pathogenic nematode. PLoS Biol. Mar 29;3(4):e121. Epub 2005 Mar 29.
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19. Ghedin, E. and Fraser, C.M. (2005) A virus with big ambitions. Trends Microbiol. Feb;13(2):56-57. Review.

18. Ghedin, E., Wang, S., Foster, J., Slatko, B. (2004) First sequenced genome of a parasitic nematode. Trends Parasitol. Apr;20(4):151-153.

17. Ghedin, E., Pumfery, A., De La Fuente C., Yao K., Miller, N., Lacoste, V., Quackenbush, J., Jacobson, S., Kashanchi, F. (2004) Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis. Retrovirology May 25;1:10. PMC442135

16. Ghedin, E., Bringaud, F., Peterson, J., Myler, P., Berriman, M., Ivens, A., Andersson, B., Bontempi, E., Eisen, J., Angiuoli, S., Wanless, D., Von Arx, A., Murphy, L., Lennard, N., Salzberg, S., Adams, M., White, O., Hall, N., Stuart, K., Fraser, C.M., El-Sayed, N.M.A. (2004) Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol. Apr:134(2):183-191.

15. Porter-Kelley, J.M., Gerald, N., Engel, J., Ghedin, E., Dwyer, D.M. (2004) LdARF1 in trafficking and structural maintenance of the trans-Golgi cisternal network in the protozoan pathogen Leishmania donovani. Traffic Nov;5(11):868-883.

14. Guiliano, D.B., Hong, X., McKerrow, J.H., Blaxter, M.L., Oksov, Y., Liu, J., Ghedin, E., Lustigman, S. (2004) A gene family of cathepsin L-like proteases of filarial nematodes are associated with larval molting and cuticle and eggshell remodeling. Mol Biochem Parasitol. Aug;136(2):227-242.

13. Bringaud, F., Biteau, N., Zuiderwijk, E., Berriman, M., El-Sayed, N.M., Ghedin, E., Melville, S.E., Hall, N., Baltz, T. (2004) The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. Mol Biol Evol. Mar;21(3):520-528. Epub 2003 Dec 23.

12. Seelamgari, A., Maddukuri, A., Berro, R., de la Fuente, C., Kehn, K., Deng, L., Dadgar, S., Bottazzi, M.E., Ghedin, E., Pumfery, A., and Kashanchi, F. (2004) Role of viral regulatory and accessory proteins in HIV-1 replication. Front Biosci. Sep 1;9:2388-2413. Review.

11. Kehn, K., Berro, R., de la Fuente, C., Strouss, K., Ghedin, E., Dadgar, S., Bottazzi, M.E., Pumfery, A., and Kashanchi, F. (2004) Mechanisms of HTLV-I transformation. Front Biosci. Sep 1;9:2347-2372. Review.

10. El-Sayed, N.M.A., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., Wanless, D., Peterson, J., Hou, L., Taylor, S. Tweedie, A., Biteau, N., Khalak, H.G., Lin, X., Mason, T., Hannick, L., Caler, E., Blandin, G., Bartholomeu, D., Simpson, A.J., Kaul, S., Zhao, H., Pai, G., Van Aken, S., Utterback, T., Haas, B., Koo, H.L., Umayam, L., Suh, B., Gerrard, C., Leech, V., Qi, Q., Schwartz, D., Feldblyum, T., Salzberg, S., Tait, A., Turner, M.R., Ullu, E., White, O., Melville, S., Adams, M.D., Fraser, C.M., Donelson, J.E. (2003). The sequence and analysis of Trypanosoma brucei chromosome II. Nucl Acids Res. Aug 15;31(16):4856-4863. PMC169936
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9. Bringaud, F., Garcia-Perez, J. L., Heras, S. R., Ghedin, E., El-Sayed, N.M., Andersson, B., Baltz, T., & Lopez, M. C. (2002). Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi. Mol Biochem Parasitol. Sep-Oct;124(1-2):73-78.

8. Shakarian, A.M., Joshi, M.B., Ghedin, E., Dwyer, D.M. (2002) Molecular dissection of the functional domains of a unique, tartrate-resistant, surface membrane acid phosphatase in the primitive human pathogen, Leishmania donovani. J Biol Chem. May 17;277(20):17994-18001. Epub 2002 Mar 6.

7. Ghedin, E., Debrabant, A., Engel, J.C., and Dwyer, D.M. (2001) Secretory and endocytic pathways converge in a dynamic endosomal system in a primitive protozoan. Traffic Mar;2(3):175-188.

6. Debrabant, A., Ghedin, E., and Dwyer, D. (2000) Dissection of the functional domains of the Leishmania surface membrane 3’-Nucleotidase/Nuclease, a unique member of the class I nuclease family. J Biol Chem. May 26;275(21):16366-16372.

5. Ghedin, E., Charest, H., Zhang, W.W., Debrabant, A., Dwyer, D., and Matlashewski, G. (1998) Inducible expression of suicide genes in Leishmania donovani amastigotes. J Biol Chem. Sep 4;273(36): 22997-23003. PMC170587

4. Ghedin, E., Charest, H. and Matlashewski, G. (1998) A2rel: a constitutively expressed Leishmania gene linked to an amastigote-stage-specific gene. Mol Biochem Parasitol. May 15;93(1):23-29.

3. Ghedin, E., Zhang, W.W., Charest, H., Sundar, S., Kenney, R.T. and Matlashewski, G. (1997) Antibody response against a Leishmania donovani amastigote-stage-specific protein in patients with visceral leishmaniasis. Clin Diagn Lab Immunol. Sep 4; 4(5):530-535.

2. Zhang, W.W., Charest, H., Ghedin, E. and Matlashewski, G. (1996) Identification and overexpression of the A2 amastigote-specific protein in Leishmania donovani. Mol Biochem Parasitol. Jun;78(1-2):79-90.

1. Ghedin, E., Robidoux, L., Handschumacher, P., Hebrard, G., and Schmit, J.P. (1993) Quality of drinking water sources in two sub-desert sahelian areas in North-Western Senegal. Int J Environ Stud. 44: 113-130.

Comment, Editorial Overview, Letter & Book Chapters

7. Bringaud, F., Rogers, M., Ghedin, E. (2013) Identification and Analysis of Ingi-Related Retroposons in the Trypanosomatid Genomes. Chapter for Parasite Genomics Protocols. C. Peacock, Editor. Methods in Molecular Biology (Springer Science) (in press)

6. Twigg, H.L., Morris, A., Ghedin, E., Curtis, J.L., Huffnagle, G.B., Crothers, K., Campbell, T.B., Flores, S.C., Fontenot, A.P., Beck, J.M., Huang, L., Lynch, S., Knox, K.S., Weinstock, G., on behalf of the Lung HIV Microbiome Project. (2013) Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respir. Med 1: 354-356. Comment

5. Ghedin, E. and Upton, C. (2011) It’s a small world after all – viral genomics and the global dominance of viruses. Current Opinion in Virology 1(4):280-281.

4. Losada, L., Ghedin, E., Morris, A., Chu, H.W., Nierman, W.C. (2011) The Human Lung Microbiome. In: Metagenomics of the Human Body. K.E. Nelson, Editor. Springer

3. Salzberg, S., Ghedin, E., Spiro, D. (2006) Shared data are key to beating threat from flu. Nature. Mar 30;440(7084):605. Letter to the editor

2. Robidoux, L., Ghedin, E., Handschumacher, P., Hébrard, G., Schmit J.P. (1998). Qualité de l’eau de consommation dans les périmètres irrigués de Diomandou et de Nianga : influence de la source d’approvisionnement. In : Hervé Jean-Pierre (ed.), Brengues Jacques (ed.). Aménagements hydro-agricoles et santé (vallée du fleuve Sénégal). Paris : ORSTOM, 1998, p. 87-102. (Colloques et Séminaires). Eau et Santé : Colloque, Dakar (SEN), 1994/11/14-15. ISBN 2-7099-1388-7

1. Robidoux, L., Ghedin, E., Handschumacher, P., Hebrard, G., Schmit, J.P. (1998). La qualite de l’eau de boisson a Richard-Toll: Influence du comportement de l’utilisateur. In: Hervé Jean-Pierre (ed.), Brengues Jacques (ed.). Aménagements hydro-agricoles et santé (vallée du fleuve Sénégal). Paris : ORSTOM, 1998, p. 169-184. (Colloques et Séminaires). Eau et Santé : Colloque, Dakar (SEN), 1994/11/14-15. ISBN 2-7099-1388-72014

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