Publications
Zhang J, Yao J, Jiang J, Pan Z, Luo M, Xia Y, Fan Q, Ding X, Ruan J, Handel A, Bahl J, Chen W, Zha L, Fu T (2020) "Migration interacts with the local transmission of HIV in developed trade areas: A molecular transmission network analysis in China." Infection, Genetics and Evolution Volume 84, doi: 10.1016/j.meegid.2020.104376
Kwon, J-H, Bahl J, Swayne DE, Lee Y-N, Lee Y-J, Song C-S, Lee D-H (2020) "Domestic ducks play a major role in the maintenance and spread of H5N8 highly pathogenic avian influenza viruses in South Korea. Transboundary and emerging diseases doi: 10.1111/tbed.13406
Hicks JT‡, Lee D-H, Duvuuri‡ VR, Kim Torchetti M, Swayne DE, Bahl J* (2020) "Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak. PLoS Pathog 16(1): e1007857. doi: 10.1371/journal.ppat.1007857
Piedra F-A, Qiu X‡, Teng MN, Avadhanula V, Machado AA, Kim D-K, Hixson J, Bahl J, Piedra PA (2020) "Non-gradient and genotype-dependent patterns of RSV gene expression. PLoS ONE 15(1): e0227558. doi: 10.1371/journal.pone.0227558
Hicks JT‡, Dimitrov KM, Afonso C. Ramey AM, Bahl J* (2019). "Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion. BMC Evol Biol 19, 108 (2019). doi: 10.1186/s12862-019-1431-2
Kwon, J‐H, Bahl, J, Swayne, DE, Lee Y-N, Lee Y-J, Song C-S, Lee D-H (2019). "Domestic ducks play a major role in the maintenance and spread of H5N8 highly pathogenic avian influenza viruses in South Korea." Transbound Emerg Dis. 00: 1– 8. doi: 10.1111/tbed.13406
Dimitrov KM, Abolnik C, Afonso CL, Albina E, Bahl J, Berg M, Briand F-X, Brown IH, Choi K-S, Chvala I, Diel DG, Durr PA, Ferreira HL, Fusaro A, Gil P, Goujgoulova GV, Grund C, Hicks JT‡, Joannis TM, Torchetti MK, Kolosov S, Lambrecht B, Lewis NS, Liu H, Liu H, McCullough S, Miller PJ, Monne I, Muller CP, Munir M, Reischak D, Sabra M, Samal SK, Servan de Almeida R, Shittu I, Snoeck CJ, Suarez DL, Van Borm S, Wang Z, Wong FYK. (2019) "Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus." Infection, Genetics and Evolution, 74. doi: 10.1016/j.meegid.2019.103917
Qiu, X., V. R. Duvvuri and J. Bahl (2019). "Computational Approaches and Challenges to Developing Universal Influenza Vaccines." Vaccines (Basel) 7(2).
Kwon, J. H., J. Bahl, D. E. Swayne, Y. N. Lee, Y. J. Lee, C. S. Song and D. H. Lee (2019). "Domestic ducks play a major role in the maintenance and spread of H5N8 highly pathogenic avian influenza viruses in South Korea."
Kandeil, A., J. T. Hicks and S. G. Young (2019). "Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016-2018." Transbound Emerg Dis 8(1): 1370-1382.
Kandeil, A., M. R. Gomaa, M. M. Shehata, A. N. El Taweel, S. H. Mahmoud, O. Bagato, Y. Moatasim, O. Kutkat, A. S. Kayed, P. Dawson, X. Qiu, J. Bahl, R. J. Webby, W. B. Karesh and G. Kayali (2019). "Isolation and Characterization of a Distinct Influenza A Virus from Egyptian Bats." BMC Evol Biol 93(2).
Hicks, J. T., K. M. Dimitrov, C. L. Afonso, A. M. Ramey and J. Bahl (2019). "Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion." 19(1): 108.
Ali, M. A., K. M. Dimitrov, C. Abolnik, C. L. Afonso, E. Albina, J. Bahl, M. Berg, F. X. Briand, I. H. Brown, K. S. Choi, I. Chvala, D. G. Diel, P. A. Durr, H. L. Ferreira, A. Fusaro, P. Gil, G. V. Goujgoulova, C. Grund, J. T. Hicks, T. M. Joannis, M. K. Torchetti, S. Kolosov, B. Lambrecht, N. S. Lewis, H. Liu, H. Liu, S. McCullough, P. J. Miller, I. Monne, C. P. Muller, M. Munir, D. Reischak, M. Sabra, S. K. Samal, R. Servan de Almeida, I. Shittu, C. J. Snoeck, D. L. Suarez, S. Van Borm, Z. Wang and F. Y. K. Wong (2019). "Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus." Emerg Microbes Infect 74: 103917.
Kirkpatrick, E., X. Qiu, P. C. Wilson and J. Bahl (2018). "The influenza virus hemagglutinin head evolves faster than the stalk domain." 8(1): 10432.
Jimenez-Bluhm, P., F. Di Pillo, J. Bahl, J. Osorio, S. Schultz-Cherry and C. Hamilton-West (2018). "Circulation of influenza in backyard productive systems in central Chile and evidence of spillover from wild birds." Sci Rep 153: 1-6.
Ali, M. A., D. H. Lee, M. K. Torchetti, J. Hicks, M. L. Killian, J. Bahl, M. Pantin-Jackwood and D. E. Swayne (2018). "Transmission Dynamics of Highly Pathogenic Avian Influenza Virus A(H5Nx) Clade 2.3.4.4, North America, 2014-2015." J Virol 24(10): 1840-1848.
Ramey, A. M., I. V. Goraichuk, J. T. Hicks, K. M. Dimitrov, R. L. Poulson, D. E. Stallknecht, J. Bahl and C. L. Afonso (2017). "Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America." Influenza Other Respir Viruses 14(1): 43.
Qiu, X. and V. R. Duvvuri (2017). "Lineage-specific epitope profiles for HPAI H5 pre-pandemic vaccine selection and evaluation." 11(5): 445-456.
Tan, G. S., P. E. Leon, R. A. Albrecht, I. Margine, A. Hirsh, J. Bahl and F. Krammer (2016). "Broadly-Reactive Neutralizing and Non-neutralizing Antibodies Directed against the H7 Influenza Virus Hemagglutinin Reveal Divergent Mechanisms of Protection." PLoS Pathog 12(4): e1005578.
Shepard, S. S., S. Meno, J. Bahl, M. M. Wilson, J. Barnes and E. Neuhaus (2016). "Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler." BMC Genomics 17: 708.
Shepard, S. S., S. Meno, J. Bahl, M. M. Wilson, J. Barnes and E. Neuhaus (2016). "Erratum to: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler." BMC Genomics 17(1): 801.
Ramey, A. M., A. B. Reeves, J. L. TeSlaa, S. Nashold, T. Donnelly, J. Bahl and J. S. Hall (2016). "Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses." Infect Genet Evol 40: 176-185.
Pham, T. T., S. Meng, Y. Sun, W. Lv and J. Bahl (2016). "Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance." Virus Evol 2(1): vew009.
Lee, D. H., J. Bahl, M. K. Torchetti, M. L. Killian, H. S. Ip, T. J. DeLiberto and D. E. Swayne (2016). "Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014-2015." Emerg Infect Dis 22(7): 1283-1285.
Hussein, I. T. M., E. J. Ma, N. J. Hill, B. W. Meixell, M. Lindberg, R. A. Albrecht, J. Bahl and J. A. Runstadler (2016). "A point mutation in the polymerase protein PB2 allows a reassortant H9N2 influenza isolate of wild-bird origin to replicate in human cells." Infect Genet Evol 41: 279-288.
Dimitrov, K. M., A. M. Ramey, X. Qiu, J. Bahl and C. L. Afonso (2016). "Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus)." Infect Genet Evol 39: 22-34.
Baranovich, T. and J. Bahl (2016). "Influenza A Virus Diversity and Transmission in Exhibition Swine." Nat Commun 213(2): 169-170.
Bahl, J., T. T. Pham, N. J. Hill, I. T. Hussein, E. J. Ma, B. C. Easterday, R. A. Halpin, T. B. Stockwell, D. E. Wentworth, G. Kayali, S. Krauss, S. Schultz-Cherry, R. G. Webster, R. J. Webby, M. D. Swartz, G. J. Smith and J. A. Runstadler (2016). "Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential." PLoS Pathog 12(5): e1005620.
Zaraket, H., T. Baranovich, B. S. Kaplan, R. Carter, M. S. Song, J. C. Paulson, J. E. Rehg and J. Bahl (2015). "Mammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck." 6: 6553.
Su, Y. C. F. and J. Bahl (2015). "Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection." 6: 7952.
Manokaran, G., E. Finol, C. Wang, J. Gunaratne, J. Bahl, E. Z. Ong, H. C. Tan, O. M. Sessions, A. M. Ward, D. J. Gubler, E. Harris, M. A. Garcia-Blanco and E. E. Ooi (2015). "Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness." Science 350(6257): 217-221.
Lewis, N. S., J. H. Verhagen, Z. Javakhishvili, C. A. Russell, P. Lexmond, K. B. Westgeest, T. M. Bestebroer, R. A. Halpin, X. Lin, A. Ransier, N. B. Fedorova, T. B. Stockwell, N. Latorre-Margalef, B. Olsen, G. Smith, J. Bahl, D. E. Wentworth, J. Waldenstrom, R. A. Fouchier and M. de Graaf (2015). "Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data." J Gen Virol 96(8): 2050-2060.
Karlsson, E., T. Fabrizio, H. Zhu, Y. Guan, M. Husain, S. Schultz-Cherry, S. Krauss, R. McBride, R. G. Webster, E. A. Govorkova, J. Zhang, C. J. Russell, R. J. Webby, U. Joseph, M. Linster, Y. Suzuki, S. Krauss, R. A. Halpin, D. Vijaykrishna, T. P. Fabrizio, T. M. Bestebroer, S. Maurer-Stroh, R. J. Webby, D. E. Wentworth, R. A. Fouchier, J. Bahl and G. J. Smith (2015). "Correction for Joseph et al., Adaptation of pandemic H2N2 influenza A viruses in humans." Nat Commun 89(8): 4706.
Joseph, U., M. Linster, Y. Suzuki, S. Krauss, R. A. Halpin, D. Vijaykrishna, T. P. Fabrizio, T. M. Bestebroer, S. Maurer-Stroh, R. J. Webby, D. E. Wentworth, R. A. Fouchier and J. Bahl (2015). "Adaptation of pandemic H2N2 influenza A viruses in humans." 89(4): 2442-2447.
Duvvuri, V. R., A. Granados, P. Rosenfeld, J. Bahl, A. Eshaghi and J. B. Gubbay (2015). "Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics." Sci Rep 5: 14268.
Baranovich, T., J. Bahl, B. M. Marathe, M. Culhane, E. Stigger-Rosser, D. Darnell, B. S. Kaplan, J. F. Lowe, R. J. Webby and E. A. Govorkova (2015). "Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes." Antiviral Res 117: 10-19.
Westgeest, K. B., C. A. Russell, X. Lin, M. I. Spronken, T. M. Bestebroer, J. Bahl, R. van Beek, E. Skepner, R. A. Halpin, J. C. de Jong, G. F. Rimmelzwaan, A. D. Osterhaus, D. J. Smith, D. E. Wentworth, R. A. Fouchier and M. de Graaf (2014). "Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011." J Virol 88(5): 2844-2857.
Smith, G. J., S. Duan, E. A. Govorkova, J. Bahl, H. Zaraket, T. Baranovich, P. Seiler, K. Prevost, R. G. Webster and R. J. Webby (2014). "Epistatic interactions between neuraminidase mutations facilitated the emergence of the oseltamivir-resistant H1N1 influenza viruses." J Virol 5: 5029.
Shepard, S. S., C. T. Davis, J. Bahl, P. Rivailler, I. A. York and R. O. Donis (2014). "LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins." Nat Commun 9(1): e86921.
Bahl, J., S. Krauss, D. Kuhnert, M. Fourment, G. Raven, S. P. Pryor, L. J. Niles, A. Danner, D. Walker, I. H. Mendenhall, Y. C. Su, V. G. Dugan, R. A. Halpin, T. B. Stockwell, R. J. Webby, D. E. Wentworth, A. J. Drummond, G. J. Smith and R. G. Webster (2013). "Influenza a virus migration and persistence in North American wild birds." PLoS Pathog 9(8): e1003570.
Smith, G. J., J. Bahl and D. Vijaykrishna (2012). "Genetic analysis." Methods Mol Biol 865: 207-227.
Mendenhall, I. H., J. Bahl, M. J. Blum and D. M. Wesson (2012). "Genetic structure of Culex erraticus populations across the Americas." J Med Entomol 49(3): 522-534.
Vijaykrishna, D., G. J. Smith, O. G. Pybus, H. Zhu, S. Bhatt, L. L. Poon, S. Riley, J. Bahl, S. K. Ma, C. L. Cheung, R. A. Perera, H. Chen, K. F. Shortridge, R. J. Webby, R. G. Webster, Y. Guan and J. S. Peiris (2011). "Long-term evolution and transmission dynamics of swine influenza A virus." Nature 473(7348): 519-522.
Ducatez, M. F., J. Bahl, Y. Griffin, E. Stigger-Rosser, J. Franks, S. Barman, D. Vijaykrishna, A. Webb, Y. Guan, R. G. Webster, G. J. Smith and R. J. Webby (2011). "Feasibility of reconstructed ancestral H5N1 influenza viruses for cross-clade protective vaccine development." Proc Natl Acad Sci U S A 108(1): 349-354.
Bahl, J., M. I. Nelson, K. H. Chan, R. Chen, D. Vijaykrishna, R. A. Halpin, T. B. Stockwell, X. Lin, D. E. Wentworth, E. Ghedin, Y. Guan, J. S. Peiris, S. Riley, A. Rambaut, E. C. Holmes and G. J. Smith (2011). "Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans." Proc Natl Acad Sci U S A 108(48): 19359-19364.
Bahl, J., M. C. Lau, G. J. Smith, D. Vijaykrishna, S. C. Cary, D. C. Lacap, C. K. Lee, R. T. Papke, K. A. Warren-Rhodes, F. K. Wong, C. P. McKay and S. B. Pointing (2011). "Ancient origins determine global biogeography of hot and cold desert cyanobacteria." Nat Commun 2: 163.
Schrenzel, M. D., C. L. Witte, J. Bahl, T. A. Tucker, N. Fabian, H. Greger, C. Hollis, G. Hsia, E. Siltamaki and B. A. Rideout (2010). "Genetic characterization and epidemiology of Helicobacters in non-domestic animals." Helicobacter 15(2): 126-142.
Guan, Y., D. Vijaykrishna, J. Bahl, H. Zhu, J. Wang and G. J. Smith (2010). "The emergence of pandemic influenza viruses." Protein Cell 1(1): 9-13.
Smith, G. J., D. Vijaykrishna, T. M. Ellis, K. C. Dyrting, Y. H. Leung, J. Bahl, C. W. Wong, H. Kai, M. K. Chow, L. Duan, A. S. Chan, L. J. Zhang, H. Chen, G. S. Luk, J. S. Peiris and Y. Guan (2009). "Characterization of avian influenza viruses A (H5N1) from wild birds, Hong Kong, 2004-2008." Emerg Infect Dis 15(3): 402-407.
Smith, G. J., D. Vijaykrishna, J. Bahl, S. J. Lycett, M. Worobey, O. G. Pybus, S. K. Ma, C. L. Cheung, J. Raghwani, S. Bhatt, J. S. Peiris, Y. Guan and A. Rambaut (2009). "Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic." Nature 459(7250): 1122-1125.
Smith, G. J., J. Bahl, D. Vijaykrishna, J. Zhang, L. L. Poon, H. Chen, R. G. Webster, J. S. Peiris and Y. Guan (2009). "Dating the emergence of pandemic influenza viruses." Proc Natl Acad Sci U S A 106(28): 11709-11712.
Bahl, J., D. Vijaykrishna, E. C. Holmes, G. J. Smith and Y. Guan (2009). "Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts." Virology 390(2): 289-297.
Wang, J., D. Vijaykrishna, L. Duan, J. Bahl, J. X. Zhang, R. G. Webster, J. S. Peiris, H. Chen, G. J. Smith and Y. Guan (2008). "Identification of the progenitors of Indonesian and Vietnamese avian influenza A (H5N1) viruses from southern China." J Virol 82(7): 3405-3414.
Vijaykrishna, D., J. Bahl, S. Riley, L. Duan, J. X. Zhang, H. Chen, J. S. Peiris, G. J. Smith and Y. Guan (2008). "Evolutionary dynamics and emergence of panzootic H5N1 influenza viruses." PLoS Pathog 4(9): e1000161.
Duan, L., J. Bahl, G. J. Smith, J. Wang, D. Vijaykrishna, L. J. Zhang, J. X. Zhang, K. S. Li, X. H. Fan, C. L. Cheung, K. Huang, L. L. Poon, K. F. Shortridge, R. G. Webster, J. S. Peiris, H. Chen and Y. Guan (2008). "The development and genetic diversity of H5N1 influenza virus in China, 1996-2006." Virology 380(2): 243-254.
Al-Azemi, A., J. Bahl, S. Al-Zenki, Y. Al-Shayji, S. Al-Amad, H. Chen, Y. Guan, J. S. Peiris and G. J. Smith (2008). "Avian influenza A virus (H5N1) outbreaks, Kuwait, 2007." Emerg Infect Dis 14(6): 958-961.
Xu, K. M., G. J. Smith, J. Bahl, L. Duan, H. Tai, D. Vijaykrishna, J. Wang, J. X. Zhang, K. S. Li, X. H. Fan, R. G. Webster, H. Chen, J. S. Peiris and Y. Guan (2007). "The genesis and evolution of H9N2 influenza viruses in poultry from southern China, 2000 to 2005." J Virol 81(19): 10389-10401.
Cheung, C. L., D. Vijaykrishna, G. J. Smith, X. H. Fan, J. X. Zhang, J. Bahl, L. Duan, K. Huang, H. Tai, J. Wang, L. L. Poon, J. S. Peiris, H. Chen and Y. Guan (2007). "Establishment of influenza A virus (H6N1) in minor poultry species in southern China." J Virol 81(19): 10402-10412.
Bahl, J., R. Jeewon and K. D. Hyde (2005). "Phylogeny of Rosellinia capetribulensis sp. nov. and its allies (Xylariaceae)." Mycologia 97(5): 1102-1110.
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