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Pleuni Pennings - Publications

Affiliations: 
San Francisco State University, San Francisco, CA, United States 
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20 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Pennings PS, Ogbunugafor CB, Hershberg R. Reversion is most likely under high mutation supply, when compensatory mutations don't fully restore fitness costs. G3 (Bethesda, Md.). PMID 35920784 DOI: 10.1093/g3journal/jkac190  0.48
2022 Tisthammer KH, Solis C, Orcales F, Nzerem M, Winstead R, Dong W, Joy JB, Pennings PS. Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus. Plos Genetics. 18: e1010179. PMID 35500034 DOI: 10.1371/journal.pgen.1010179  0.439
2021 Feder AF, Harper KN, Brumme CJ, Pennings PS. Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity. Elife. 10. PMID 34473060 DOI: 10.7554/eLife.69032  0.333
2021 Tisthammer KH, Dong W, Joy JB, Pennings PS. Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a. Viruses. 13. PMID 33808782 DOI: 10.3390/v13030511  0.371
2021 Feder AF, Pennings PS, Petrov DA. The clarifying role of time series data in the population genetics of HIV. Plos Genetics. 17: e1009050. PMID 33444376 DOI: 10.1371/journal.pgen.1009050  0.405
2020 Gelbart M, Harari S, Ben-Ari Y, Kustin T, Wolf D, Mandelboim M, Mor O, Pennings PS, Stern A. Drivers of within-host genetic diversity in acute infections of viruses. Plos Pathogens. 16: e1009029. PMID 33147296 DOI: 10.1371/journal.ppat.1009029  0.325
2020 Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, ... ... Pennings PS, et al. CpG-creating mutations are costly in many human viruses. Evolutionary Ecology. 34: 339-359. PMID 32508375 DOI: 10.1007/S10682-020-10039-Z  0.591
2020 Williams KA, Pennings P. Drug Resistance Evolution in HIV in the Late 1990s: Hard Sweeps, Soft Sweeps, Clonal Interference and the Accumulation of Drug Resistance Mutations. G3 (Bethesda, Md.). 10: 1213-1223. PMID 32075854 DOI: 10.1534/g3.119.400772  0.4
2020 Melody K, Roy CN, Kline C, Cottrell ML, Evans D, Shutt K, Pennings PS, Keele BF, Bility M, Kashuba ADM, Ambrose Z. Long-acting rilpivirine (RPV LA) pre-exposure prophylaxis does not inhibit vaginal transmission of RPV-resistant HIV-1 nor select for high frequency drug resistance in humanized mice. Journal of Virology. PMID 31969438 DOI: 10.1128/Jvi.01912-19  0.548
2020 Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, ... ... Pennings PS, et al. Correction to: CpG‑creating mutations are costly in many human viruses Evolutionary Ecology. 34: 361-362. DOI: 10.1007/S10682-020-10052-2  0.577
2019 Zinger T, Gelbart M, Miller D, Pennings PS, Stern A. Inferring population genetics parameters of evolving viruses using time-series data. Virus Evolution. 5: vez011. PMID 31191979 DOI: 10.1093/ve/vez011  0.306
2018 Theys K, Feder AF, Gelbart M, Hartl M, Stern A, Pennings PS. Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. Plos Genetics. 14: e1007855. PMID 30532173 DOI: 10.1371/journal.pgen.1007855  0.404
2018 Theys K, Feder AF, Gelbart M, Hartl M, Stern A, Pennings PS. Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. Plos Genetics. 14: e1007420. PMID 29953449 DOI: 10.1371/journal.pgen.1007420  0.578
2017 Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z. A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. Plos Pathogens. 13: e1006358. PMID 28542550 DOI: 10.1371/Journal.Ppat.1006358  0.408
2016 Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS. More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. Elife. 5. PMID 26882502 DOI: 10.7554/eLife.10670  0.481
2014 Pennings PS, Kryazhimskiy S, Wakeley J. Loss and recovery of genetic diversity in adapting populations of HIV. Plos Genetics. 10: e1004000. PMID 24465214 DOI: 10.1371/Journal.Pgen.1004000  0.46
2013 Pennings PS. HIV Drug Resistance: Problems and Perspectives. Infectious Disease Reports. 5: e5. PMID 24470969 DOI: 10.4081/idr.2013.s1.e5  0.333
2012 Pennings PS. Standing genetic variation and the evolution of drug resistance in HIV. Plos Computational Biology. 8: e1002527. PMID 22685388 DOI: 10.1371/journal.pcbi.1002527  0.332
2006 Pennings PS, Hermisson J. Soft sweeps III: the signature of positive selection from recurrent mutation. Plos Genetics. 2: e186. PMID 17173482 DOI: 10.1371/journal.pgen.0020186  0.417
2006 Pennings PS, Hermisson J. Soft sweeps II--molecular population genetics of adaptation from recurrent mutation or migration. Molecular Biology and Evolution. 23: 1076-84. PMID 16520336 DOI: 10.1093/molbev/msj117  0.35
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