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John Terbot, Parul Johri, S. Liphardt, Vivak Soni, Susanne P. Pfeifer, Brandon S. Cooper, Jeffrey M. Good, and Jeffrey D. Jensen. 2023. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. (In review)

Parul Johri, Ryan N. Gutenkunst, Kirk E. Lohmueller, Adam Eyre-Walker, Jeffrey D. Jensen. 2022. On the prospect of achieving accurate joint estimation of selective effects together with population history. Genome Biology and Evolution. 14(7): evac088.   PDF

Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, and Jeffrey D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLOS Biology 20(5): e3001669.   PDF     GitHub

Parul Johri, Jean-Francois Gout, Thomas G. Doak, Michael Lynch. 2022. A population-genetic lens into the process of gene duplicate loss after whole-genome duplication. Molecular Biology and Evolution. 39(6): msac118.   PDF    GitHub

Parul Johri, Wolfgang Stephan, Jeffrey D. Jensen. 2022. Soft selective sweeps: addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLOS Genetics 18(2): e1010022.   PDF   GitHub   


Ana Yansi Morales-Arce*, Parul Johri*, Jeffrey D. Jensen. 2022. Inferring the distribution of fitness effects in influenza A virus and human cytomegalovirus. Heredity 128, 79–87.   PDF   GitHub   

Parul Johri*, Brian Charlesworth*, Emma K. Howell, Michael Lynch, & Jeffrey D. Jensen. 2021. Revisiting the notion of deleterious sweeps. Genetics 219(3): iyab094. Highlighted by Genetics    PDF    Github

Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen. 2021. The impact of purifying and background selection on the inference of population history: problems and prospectsMolecular Biology and Evolution. 38(7): 2986-3003.   PDF    GitHub

Parul Johri, Brian Charlesworth, Jeffrey D. Jensen. 2020. Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection. Genetics 215: 173-192.   Highlighted by Genetics    PDF    GitHub

Jean-Francois Gout, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Fréderic Guérin, Sophie Malinsky, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch. 2019. Universal trends of post-duplication evolution revealed by the genomes of 13 Paramecium species sharing an ancestral whole-genome duplication. bioRxiv. doi:

Parul Johri*, Georgi K. Marinov*, Thomas G. Doak, and Michael Lynch. 2019. Population genetics of Paramecium mitochondrial genomes: recombination, mutation spectrum, and efficacy of selection. Genome Biology and Evolution. 11(5): 1398–1416.   PDF    GitHub

Parul Johri, Sascha Krenek, Georgi K. Marinov, Thomas, G. Doak, Thomas U. Berendonk, and Michael Lynch. 2017. Population genomics of Paramecium species. Molecular Biology and Evolution. 34(5): 1194-1216. PDF

Matthew S. Ackerman, Parul Johri, Ken Spitze, Sen Xu, Thomas G. Doak, Kimberly Young, and Michael Lynch. 2017. Estimating seven coefficients of pairwise relatedness using population-genomic data. Genetics. 206:105-118.   PDF   BioRxiv

Casey L. McGrath, Jean-Francois Gout, Parul Johri, Thomas G. Doak, and Michael Lynch. 2014. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research. 24(10): 1665-75.   PDF

*These authors contributed equally.

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