Experimental & Pathogen Population Analysis

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. MatuszewskiN. RenzetteC. 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. RenzetteK.K. IrwinS.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 perspectiveMol Ecol 26: 1980-90. pdf

Renzette, N., S.P. PfeiferS. 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 landscapePNAS 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 neuraminidaseJCTC 12: 6098-6108. pdf

Bank, C., N. Renzette, P. Liu, S. MatuszewskiH. ShimM. 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 strategyEvolution 70: 2470-84. pdf

Irwin, K.K.N. Renzette, T.F. Kowalik, and J.D. Jensen. 2016. Antiviral drug resistance as an adaptive processVirus Evol 2: 1-10. pdf

Jiang, L., P. Liu, C. BankN. 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 resistanceJMB 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: 107-20pdf

Renzette, N., T.F. Kowalik, and J.D. Jensen, 2016. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus diversityMol 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 humansPNAS 112: E4120-28. pdf

Zeldovich, K.B., P. Liu, N. RenzetteM. 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 reassortmentMBE 32: 1519-32pdf

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 infectionsCurr Opin Virol 8C: 109-115pdf

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 environmentsGenetics 196: 841-52. pdf

Foll, M.(*)Y.-P. Poh(*)N. RenzetteA. Ferrer-AdmetllaH. Shim, A.-S. Malaspinas, G. EwingC. 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. PohJ.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 vitroJ Virol 88: 272-81pdf

Hietpas, R.T.(*), C. Bank(*)J.D. Jensen(#), and D.N. Bolon(#), 2013. Shifting fitness landscapes in response to altered environmentsEvolution 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