Publications

Lab members indicated

Jacob I Marsh, Sachin Kaushik, and Parul Johri. 2025. Effects of rescaling forward-in-time population genetic simulations. doi: https://doi.org/10.1101/2025.04.24.650500. bioRxiv Github (submitted)

Parul Johri and Brian Charlesworth. 2025. A gene-based model of fitness and its implications for genetic variation: Genetic and inbreeding loads. doi: https://doi.org/10.1101/2025.02.19.639162. BioRxiv GitHub (submitted)

Parul Johri and Brian Charlesworth. 2024. A gene-based model of fitness and its implications for genetic variation: linkage disequilibrium. doi: https://doi.org/10.1101/2024.09.12.612686. BioRxiv GitHub (submitted)

Sachin Kaushik*, Kavita Jain*, and Parul Johri. 2024. Genetic diversity during selective sweeps in non-recombining populations. doi: https://doi.org/10.1101/2024.09.12.612756. BioRxiv Github (submitted)

2024

Austin T. Daigle and Parul Johri. Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species. Evolution. (in press) BioRxiv GitHub

Jacob I. Marsh and Parul Johri. 2024. Biases in ARG-based inference of historical population size in populations experiencing selection. Molecular Biology and Evolution 41(7):msae118. Link BioRxiv GitHub

2023

Vivak Soni, Parul Johri, and Jeffrey D. Jensen. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. 2023. Evolution qpad120. (Editor's Choice at Evolution) BioRxiv

Hongan Long, Parul Johri, Jean-Francois Gout, Jiahao Ni, Yue Hao, Timothy Licknack, Yaohai Wang, Jiao Pan, Berenice Jiménez-Marín, and Michael Lynch. 2023. Paramecium Genetics, Genomics, and Evolution. Annual Review of Genetics 57:391-410.

Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Fréderic Guérin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, and Michael Lynch. 2023. Dynamics of gene loss following ancient whole-genome duplication in the cryptic Paramecium complex. Molecular Biology and Evolution 40(5): msad107.

Parul Johri, Susanne P. Pfeifer, and Jeffrey D. Jensen. 2023. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. Molecular Biology and Evolution 40(5): msad100. BioRxiv GitH ub

Abigail A. Howell, John Terbot, Vivak Soni, Parul Johri, Jeffrey D. Jensen, and Susanne P. Pfeifer. 2023. Developing an appropriate evolutionary baseline model for the study of human cytomegalovirus. Genome Biology and Evolution 15(4): evad059. Link

John Terbot, Parul Johri, Schuyler 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. PLOS Pathogens 19(4): e1011265. PDF

2022

Parul Johri, Ryan N. Gutenkunst, Kirk E. Lohmueller, Adam Eyre-Walker, and 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, and 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, and 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*, and Jeffrey D. Jensen. 2022. Inferring the distribution of fitness effects in influenza A virus and human cytomegalovirus. Heredity 128, 79–87. PDF GitHub

2021

Parul Johri*, Brian Charlesworth*, Emma K. Howell, Michael Lynch, and 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, and Jeffrey D. Jensen. 2021. The impact of purifying and background selection on the inference of population history: problems and prospects. Molecular Biology and Evolution 38(7): 2986-3003. PDF GitHub

2020

Parul Johri, Brian Charlesworth, and 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

Before 2019

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.