Polygenic adaptation: From sweeps to subtle frequency shifts von Höllinger, Ilse, Pennings, Pleuni S, Hermisson, Joachim

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How the waxing and waning of a mutation determines HIV treatment success von Pennings, Pleuni S

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Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation von Hermisson, Joachim, Pennings, Pleuni S., Kelley, Joanna

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Loss and recovery of genetic diversity in adapting populations of HIV von Pennings, Pleuni S, Kryazhimskiy, Sergey, Wakeley, John

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Soft sweeps III: the signature of positive selection from recurrent mutation von Pennings, Pleuni S, Hermisson, Joachim

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HIV drug resistance: problems and perspectives von Pennings, Pleuni S.

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Standing genetic variation and the evolution of drug resistance in HIV von Pennings, Pleuni Simone

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Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV von Theys, Kristof, Feder, Alison F, Gelbart, Maoz, Hartl, Marion, Stern, Adi, Pennings, Pleuni S

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Drivers of within-host genetic diversity in acute infections of viruses von Gelbart, Maoz, Harari, Sheri, Ben-Ari, Ya'ara, Kustin, Talia, Wolf, Dana, Mandelboim, Michal, Mor, Orna, Pennings, Pleuni S, Stern, Adi

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The clarifying role of time series data in the population genetics of HIV von Feder, Alison F, Pennings, Pleuni S, Petrov, Dmitri A

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Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation von Hermisson, Joachim, Pennings, Pleuni S

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Ten simple rules for designing and running a computing minor for bio/chem students von Reyes, Rochelle-Jan, Hosmane, Nina, Ihorn, Shasta, Johnson, Milo, Kulkarni, Anagha, Nelson, Jennifer, Savvides, Michael, Ta, Duc, Yoon, Ilmi, Pennings, Pleuni S

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Soft sweeps II--molecular population genetics of adaptation from recurrent mutation or migration von Pennings, Pleuni S, Hermisson, Joachim

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Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance von Moreno-Gamez, Stefany, Hill, Alison L., Rosenbloom, Daniel I. S., Petrov, Dmitri A., Nowak, Martin A., Pennings, Pleuni S.

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Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity von Feder, Alison F, Harper, Kristin N, Brumme, Chanson J, Pennings, Pleuni S

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Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV von Theys, Kristof, Feder, Alison F, Gelbart, Maoz, Hartl, Marion, Stern, Adi, Pennings, Pleuni S

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Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper von Orcales, Faye, Moctezuma Tan, Lucy, Johnson-Hagler, Meris, Suntay, John Matthew, Ali, Jameel, Recto, Kristiene, Glenn, Phelan, Pennings, Pleuni

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A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host von Feder, Alison F, Kline, Christopher, Polacino, Patricia, Cottrell, Mackenzie, Kashuba, Angela D M, Keele, Brandon F, Hu, Shiu-Lok, Petrov, Dmitri A, Pennings, Pleuni S, Ambrose, Zandrea

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Evidence for sweep signatures in antibiotic-resistant strains in three species of bacteria von Pradhananga, Anjani, Benitez-Rivera, Lorena, Clark, Candace, Tisthammer, Kaho H, Pennings, Pleuni S

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Soft Selective Sweeps in Evolutionary Rescue von Wilson, Benjamin A, Pennings, Pleuni S, Petrov, Dmitri A

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