lab members indicated
Soni, V., J. Terbot, and J.D. Jensen. 2024. Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Comm 15: 3240. pdf
Terbot, J., B.S. Cooper, J.M. Good, and J.D. Jensen. 2023. A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2. GBE 15: evad204. pdf
Moström, M., S. Yu, D. Tran, F. Saccoccio, C. Versoza, D. Malouli, S. Valencia, M. Gilbert, R. Blair, S. Hansen, P. Barry, K. Fruh, J.D. Jensen, S.P. Pfeifer, T. Kowalik, S. Permar, and A. Kaur. 2023. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. PLOS Pathogens 19: e1011646. pdf
Howell, A.A., J. Terbot, V. Soni, P. Johri, J.D. Jensen(#), and S.P. Pfeifer(#). 2023. Developing an appropriate evolutionary baseline model for the study of human cytomegalovirus. GBE 15: evad059. pdf
Terbot, J., P. Johri, S. Liphardt, V. Soni, S.P. Pfeifer, B.S. Cooper(#), J.M. Good(#), and J.D. Jensen(#). 2023. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLOS Pathogens 19: e1011265. pdf
Sabin, S., A.Y. Morales-Arce, S.P. Pfeifer, and J.D. Jensen. 2022. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis. G3 12: jkac055. pdf
Jiang, L., N. Samant, P. Liu, M. Somasundaran, J.D. Jensen, W. Marasco, C. Schiffer, R.W. Finberg, J.P. Wang, T.F. Kowalik, and D.N. Bolon. 2022. Identification of a permissive secondary mutation that restores the enzymatic activity of oseltamivir resistance mutation H275Y. J Virol 96:e0198221. pdf
Morales-Arce, A.Y.(*), P. Johri(*), and J.D. Jensen. 2022. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity 128: 79-87. pdf
Wang, H.-Y., S.M. Valencia, S.P. Pfeifer, J.D. Jensen, T.F. Kowalik, and S.R. Permar. 2021. Common polymorphisms in the glycoproteins of human cytomegalovirus and associated strain-specific immunity. Viruses 13: 1106. pdf
Jensen, J.D. 2021. Studying population genetic processes in viruses: from drug-resistance evolution to patient infection dynamics. In: Bamford, D.H. and Zuckerman, M. (eds.) Encyclopedia of Virology, 4th edition, vol.5: 227-232. Oxford Academic Press. pdf
Morales-Arce, A.Y., S.J. Sabin, A.C. Stone, and J.D. Jensen. 2021. The population genomics of within-host Mycobacterium tuberculosis. Heredity 126: 1-9. pdf
Jensen, J.D., R.A. Stikeleather, T.F. Kowalik, and M. Lynch. 2020. Imposed mutational meltdown as an antiviral strategy. Evolution 74: 2549-59. pdf
Morales-Arce, A.Y., R.B. Harris, A.C. Stone, and J.D. Jensen. 2020. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 74: 992-1001. pdf
Jensen, J.D., and M. Lynch. 2020. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity 124: 619-20. pdf
Jensen, J.D., and T.F. Kowalik. 2020. A consideration of within-host human cytomegalovirus genetic variation. PNAS 117: 816-7. pdf
Prachanronarong, K., A. Canale, P. Liu, M. Somasundaran, S. Hou, Y.-P. Poh, T. Han, Q. Zhu, N. Renzette, K. Zeldovich, T. Kowalik, N. Kurt-Yilmaz, J.D. Jensen, D. Bolon, W. Marasco, R. Finberg, C. Schiffer, and J.P. Wang. 2019. Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody. J Virol 93(2): e01639. pdf
Fragata, I.(*), S. Matuszewski(*), M.A. Schmitz, T. Bataillon, J.D. Jensen, and C. Bank. 2018. The fitness landscape of the codon space across environments. Heredity 121: 422-37. pdf
Canale, A., S. Venev, T. Whitfield, D. Caffrey, W. Marasco, C. Schiffer, T. Kowalik, J.D. Jensen, R.Finberg, K. Zeldovich, J. Wang, and D. Bolon. 2018. Synonymous mutations at the beginning of the influenza A virus hemagglutinin gene impact experimental fitness. JMB 430: 1098-1115. pdf
Sackman, A.M., S.P. Pfeifer, T. F. Kowalik, and J.D. Jensen. 2018. On the demographic and selective forces shaping patterns of human cytomegalovirus variation within hosts. Pathogens 7: 16. pdf
Avnir, Y., K. Prachanronarong, Z. Zhang, S. Hou, E. Peterson, J. Sui, H. Zayed, V. Kurella, A. McGuire, L. Stamatatos, B. Hilbert, M. Bohn, K. Zeldovich, T. Kowalik, J.D. Jensen, D. Bolon, R. Finberg, J. Wang, R. Jefferis, Q. Zhu, N. Yilmaz, C. Shiffer, and W. Marasco. 2017. Structural determination of the broadly reactive anti-IGHV1-69 anti-idiotypic antibody G6 and its idiotope. Cell Reports 21: 3243-55. pdf
Carratala, A., H. Shim, Q. Zhong, V. Bachmann, J.D. Jensen, and T. Kohn. 2017. Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to tolerance to disinfection and mutagenic resistance to ribavirin. Virus Evol 3: 1-11. pdf
Ma, L., J. Boucher, J. Paulsen, S. Matuszewski, J.D. Jensen, C.A. Schiffer, M.R. Green, and D.N. Bolon. 2017. CRISPR-Cas9 mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. PNAS 114: 11751-56. pdf
Zhong, Q., A. Carratala, H. Shim, V. Bachmann, J.D. Jensen, and T. Kohn. 2017. Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness. Environ Sci Technol 51: 10746-55. pdf
Ormond, L., P. Liu, S. Matuszewski, N. Renzette, C. Bank, K. Zeldovich, D. Bolon, T. Kowalik, R. Finberg, J.D. Jensen(#), and J. Wang(#). 2017. The combined effect of oseltamivir and favipiravir on influenza A virus evolution. GBE 9: 1913-24. pdf
Pokalyuk, C., N. Renzette, K.K. Irwin, S.P. Pfeifer, L. Gibson, W.J. Britt, A.Y. Yamamoto, M.M. Mussi-Pinhata, T.F. Kowalik(#), and J.D. Jensen(#). 2017. Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective. Mol Ecol 26: 1980-90. pdf
Renzette, N., S.P. Pfeifer, S. Matuszewski, T.F. Kowalik(#), and J.D. Jensen(#). 2017. On the analysis of intra-host and inter-host viral populations: human cytomegalovirus as a case study of pitfalls and expectations. J Virol 91: e01976-16. pdf
Bank, C.(*), S. Matuszewski(*), R.T. Hietpas, and J.D. Jensen. 2016. On the (un)predictability of a large intragenic fitness landscape. PNAS 113: 14085-90. pdf
Prachanronarong, K., A. Ozen, K. Thayer, L. Yilmaz, K. Zeldovich, D.N. Bolon, T.F. Kowalik, J.D. Jensen, R.W. Finberg, J.P. Wang, N. Kurt-Yilmaz, and C. Schiffer. 2016. Molecular basis for differential patterns of drug resistance in Influenza N1 and N2 neuraminidase. JCTC 12: 6098-6108. pdf
Bank, C., N. Renzette, P. Liu, S. Matuszewski, H. Shim, M. Foll, D.N. Bolon, K.B. Zeldovich, T.F. Kowalik, R.W. Finberg, J.P. Wang(#), and J.D. Jensen(#). 2016. An experimental evaluation of drug induced mutational meltdown as an antiviral treatment strategy. Evolution 70: 2470-84. pdf
Irwin, K.K., N. Renzette, T.F. Kowalik, and J.D. Jensen. 2016. Antiviral drug resistance as an adaptive process. Virus Evol 2: 1-10. pdf
Jiang, L., P. Liu, C. Bank, N. Renzette, K. Prachanronarong, L. Yilmaz, D.R. Caffrey, K.B. Zeldovich, C.A. Schiffer, T.F. Kowalik, J.D. Jensen, R.W. Finberg, J.P. Wang and D.N. Bolon. 2016. A balance between inhibitor binding and substrate processing confers influenza drug resistance. JMB 428: 538-53. pdf
Alcala, N., J.D. Jensen, A. Telenti, and S. Vuilleumier. 2016. The genomic signature of population reconnection following isolation: from theory to HIV. G3 6: 107-20. pdf
Renzette, N., T.F. Kowalik, and J.D. Jensen, 2016. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus diversity. Mol Ecol 25: 403-13. pdf
Renzette, N., C. Pokalyuk, L. Gibson, M.R. Schleiss, K. Hamprecht, M. Mussi Pinhata, A.Y. Yamamoto, W.J. Britt, J.D. Jensen(#), and T.F. Kowalik(#), 2015. Limits and patterns of cytomegalovirus genomic diversity in humans. PNAS 112: E4120-28. pdf
Zeldovich, K.B., P. Liu, N. Renzette, M. Foll, S.T. Pham, S.V. Venev, D.N. Bolon, E.A. Kurt-Jones, G.R. Gallagher, J.D. Jensen, D.R. Caffrey, C.A. Schiffer, T.F. Kowalik, J.P. Wang, and R.W. Finberg, 2015. Positive selection drives preferred segment combinations during influenza virus reassortment. MBE 32: 1519-32. pdf
Bank, C., R.T. Hietpas, J.D. Jensen, and D.N. Bolon, 2015. A systematic survey of an intragenic epistatic landscape. MBE 32: 229-38. pdf
Renzette, N., L. Gibson J.D. Jensen, and T.F. Kowalik, 2014. Human cytomegalovirus intrahost evolution – a new avenue for understanding and controlling herpesvirus infections. Curr Opin Virol 8C: 109-115. pdf
Bank, C., R.T. Hietpas, A. Wong, D.N.A. Bolon(#), and J.D. Jensen(#), 2014. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genetics 196: 841-52. pdf
Foll, M.(*), Y.-P. Poh(*), N. Renzette, A. Ferrer-Admetlla, H. Shim, A.-S. Malaspinas, G. Ewing, C. Bank, P. Liu, D. Wegmann, D. R. Caffrey, K.B. Zeldovich, D.N.A. Bolon, J. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen, 2014. Influenza virus drug resistance: a time-sampled population genetics perspective. PLOS Genetics 10(2): e1004185. pdf
Renzette, N., D.R. Caffrey, K.B. Zeldovich, P. Liu, G.R. Gallagher, D. Aiello, A.J. Porter, E.A. Kurt-Jones, D.N. Bolon, Y.-P. Poh, J.D. Jensen, C.A. Schiffer, T.F. Kowalik, R.W. Finberg, and J.P. Wang, 2014. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol 88: 272-81. pdf
Hietpas, R.T.(*), C. Bank(*), J.D. Jensen(#), and D.N. Bolon(#), 2013. Shifting fitness landscapes in response to altered environments. Evolution 67: 3512-22. pdf
Renzette, N., L. Gibson, B. Bhattacharjee, D. Fisher, M.R. Schleiss, J.D. Jensen(#), and T.F. Kowalik(#), 2013. Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLOS Genetics 9(9): e1003735. pdf
Renzette, N., B. Bhattarcharjee, J.D. Jensen, L. Gibson, and T.F. Kowalik, 2011. Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. PLOS Pathogens 7(5): e1001344. pdf
Hietpas, R.T., J.D. Jensen, and D.N.A. Bolon, 2011. Experimental illumination of a fitness landscape. PNAS 108: 7896-901. pdf