Experimental & Viral Population Analysis

lab members indicated

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. In press, Cell Reports.

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(2): 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(5): 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 neuraminidaseJ Chem Theory Comput 12: 6098-6108. pdf

Bank, C., N. Renzette, P. Liu, S. MatuszewskiH. ShimM. Foll, D.N. Bolon, 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): 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 resistanceJ Mol Biol 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(1): 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