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Recommendations for improving statistical inference in population genomics

PLoS biology, 2022-05, Vol.20 (5), p.e3001669-e3001669

2022

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Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers

PLoS genetics, 2022-02, Vol.18 (2), p.e1010022-e1010022

2022

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Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples

PLoS pathogens, 2023-04, Vol.19 (4), p.e1011265-e1011265

2023

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On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses

PLoS genetics, 2018-12, Vol.14 (12), p.e1007859-e1007859

2018

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Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Science (American Association for the Advancement of Science), 2018-06, Vol.360 (6395), p.1355-1358

2018

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WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Molecular ecology resources, 2015-01, Vol.15 (1), p.87-98

2015

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Interpreting the pervasive observation of U-shaped Site Frequency Spectra

PLoS genetics, 2023-03, Vol.19 (3), p.e1010677-e1010677

2023

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Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection

PLoS genetics, 2013-09, Vol.9 (9), p.e1003735-e1003735

2013

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An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Genetics (Austin), 2016-06, Vol.203 (2), p.831-846

2016

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Experimental illumination of a fitness landscape

Proceedings of the National Academy of Sciences - PNAS, 2011-05, Vol.108 (19), p.7896-7901

2011

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Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Nature biotechnology, 2012-01, Vol.30 (1), p.105-111

2012

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Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions

Genetics (Austin), 2019-03, Vol.211 (3), p.1019-1028

2019

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Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

Science (American Association for the Advancement of Science), 2013-03, Vol.339 (6125), p.1312-1316

2013

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Population genetic inference from genomic sequence variation

Genome research, 2010-03, Vol.20 (3), p.291

2010

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Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants

PLoS pathogens, 2011-05, Vol.7 (5), p.e1001344-e1001344

2011

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Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data

Nature communications, 2024-04, Vol.15 (1), p.3240-3240, Article 3240

2024

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Thinking too positive? Revisiting current methods of population genetic selection inference

Trends in genetics, 2014-12, Vol.30 (12), p.540-546

2014

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The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

Molecular biology and evolution, 2018-04, Vol.35 (4), p.792-806

2018

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On the Origin and Spread of an Adaptive Allele in Deer Mice

Science (American Association for the Advancement of Science), 2009-08, Vol.325 (5944), p.1095-1098

2009

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Limits and patterns of cytomegalovirus genomic diversity in humans

Proceedings of the National Academy of Sciences - PNAS, 2015-07, Vol.112 (30), p.E4120-E4128

2015

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Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

Genetics (Austin), 2020-05, Vol.215 (1), p.173-192

2020

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A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments

Genetics (Austin), 2014-03, Vol.196 (3), p.841-852

2014

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Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Genetics (Austin), 2015-07, Vol.200 (3), p.947-963

2015

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On the unfounded enthusiasm for soft selective sweeps

Nature communications, 2014-10, Vol.5 (1), p.5281-5281, Article 5281

Jensen, Jeffrey D

2014

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Influenza virus drug resistance: a time-sampled population genetics perspective

PLoS genetics, 2014-02, Vol.10 (2), p.e1004185-e1004185

2014

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Recommendations for improving statistical inference in population genomics

Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers

Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples

On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Experimental illumination of a fitness landscape

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

Population genetic inference from genomic sequence variation

Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants

Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data

Thinking too positive? Revisiting current methods of population genetic selection inference

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

On the Origin and Spread of an Adaptive Allele in Deer Mice

Limits and patterns of cytomegalovirus genomic diversity in humans

Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection

A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

On the unfounded enthusiasm for soft selective sweeps

Influenza virus drug resistance: a time-sampled population genetics perspective

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