# Publications Sort & Filters close ## Filters Publication type expand\_more Book (1) Book Chapter (6) Journal Article (82) Search Within Results Search Within Results search ## 89 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 89 results Download 89 citations download- [BibTeX](/node/1574846/export?format=bibtex) - [EndNote X3 XML](/node/1574846/export?format=endnote8) - [EndNote 7 XML](/node/1574846/export?format=endnote7) - [Endnote tagged](/node/1574846/export?format=tagged) - [Marc](/node/1574846/export?format=marc) - [PubMedId](/node/1574846/export?format=pubmed_id) - [RIS](/node/1574846/export?format=ris) ### 2025 Newman M, Wakeley J, Fan W-T. [Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing](/publication/conditional-gene-genealogies-given-population-pedigree-diploid-moran-model-selfing). *Theoretical Population Biology*. 2025;165:29-44. Newman M, Wakeley J, Fan W-T. [Conditional gene genealogies given the population pedigree for a diploid Moran model with selfing](/publication/conditional-gene-genealogies-given-population-pedigree-diploid-moran-model-selfing). *Theoretical Population Biology*. 2025;165:29-44. - [Publisher's version (with free access though Sept 10, 2025)](https://authors.elsevier.com/c/1lUEB9EXxdegp) - [Publisher's version (with free access though Sept 10, 2025)](https://authors.elsevier.com/c/1lUEB9EXxdegp) ### 2024 Diamantidis D, Fan W-T, Birkner M, Wakeley J. [Bursts of coalescence within population pedigrees whenever big families occur](/publications/bursts-coalescence-within-population-pedigrees-whenever-big-families-occur). *Genetics*. 2024:iyae030. Diamantidis D, Fan W-T, Birkner M, Wakeley J. [Bursts of coalescence within population pedigrees whenever big families occur](/publications/bursts-coalescence-within-population-pedigrees-whenever-big-families-occur). *Genetics*. 2024:iyae030. - [ picture\_as\_pdfAccepted Manuscript](/sites/g/files/omnuum5776/files/wakeleylab/files/iyae030.pdf) - [ picture\_as\_pdfAccepted Manuscript](/sites/g/files/omnuum5776/files/wakeleylab/files/iyae030.pdf) Rivas-González I, Schierup M, Wakeley J, Hobolth A. [TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting](/publications/trails-tree-reconstruction-ancestry-using-incomplete-lineage-sorting). *PLOS Genetics*. 2024;20(2):1-21. Rivas-González I, Schierup M, Wakeley J, Hobolth A. [TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting](/publications/trails-tree-reconstruction-ancestry-using-incomplete-lineage-sorting). *PLOS Genetics*. 2024;20(2):1-21. - [Publisher's version (open access)](https://doi.org/10.1371/journal.pgen.1010836) - [Publisher's version (open access)](https://doi.org/10.1371/journal.pgen.1010836) Fan W-T, Wakeley J. [Latent mutations in the ancestries of alleles under selection](/publication/latent-mutations-ancestries-alleles-under-selection). *Theoretical Population Biology*. 2024;158:20. Fan W-T, Wakeley J. [Latent mutations in the ancestries of alleles under selection](/publication/latent-mutations-ancestries-alleles-under-selection). *Theoretical Population Biology*. 2024;158:20. - [(pdf)](/sites/g/files/omnuum5776/files/2025-08/FanAndWakeley2024.pdf) - [(pdf)](/sites/g/files/omnuum5776/files/2025-08/FanAndWakeley2024.pdf) ### 2023 Wakeley J, Fan W-T, Koch E, Sunyaev S. [Recurrent mutation in the ancestry of a rare variant](/publications/recurrent-mutation-ancestry-rare-variant). *Genetics*. 2023;224:iyad049. Wakeley J, Fan W-T, Koch E, Sunyaev S. [Recurrent mutation in the ancestry of a rare variant](/publications/recurrent-mutation-ancestry-rare-variant). *Genetics*. 2023;224:iyad049. - [Publisher's version (open access)](https://academic.oup.com/genetics/article/224/3/iyad049/7086184) - [Publisher's version (open access)](https://academic.oup.com/genetics/article/224/3/iyad049/7086184) ### 2022 McAvoy A, Wakeley J. [Evaluating the structure-coefficient theorem of evolutionary game theory](/publications/evaluating-structure-coefficient-theorem-evolutionary-game-theory). *Proceedings of the National Academy of Sciences, USA*. 2022;119:e2119656119. McAvoy A, Wakeley J. [Evaluating the structure-coefficient theorem of evolutionary game theory](/publications/evaluating-structure-coefficient-theorem-evolutionary-game-theory). *Proceedings of the National Academy of Sciences, USA*. 2022;119:e2119656119. - [Publisher's version (open access)](https://www.pnas.org/doi/10.1073/pnas.2119656119) - [Publisher's version (open access)](https://www.pnas.org/doi/10.1073/pnas.2119656119) ### 2021 Salagnac O, Wakeley J. [The consequences of switching strategies in a two-player iterated survival game](/publications/consequences-switching-strategies-two-player-iterated-survival-game). *Journal of Mathematical Biology*. 2021;82:17. Salagnac O, Wakeley J. [The consequences of switching strategies in a two-player iterated survival game](/publications/consequences-switching-strategies-two-player-iterated-survival-game). *Journal of Mathematical Biology*. 2021;82:17. - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/salagnacandwakeley2021.pdf) - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/salagnacandwakeley2021.pdf) Harney É, Patterson N, Reich D, Wakeley J. [Assessing the performance of qpAdm: a statistical tool for studying population admixture](/publications/assessing-performance-qpadm-statistical-tool-studying-population-admixture). *Genetics*. 2021;iyaa045. Harney É, Patterson N, Reich D, Wakeley J. [Assessing the performance of qpAdm: a statistical tool for studying population admixture](/publications/assessing-performance-qpadm-statistical-tool-studying-population-admixture). *Genetics*. 2021;iyaa045. - [ picture\_as\_pdf(article pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/harneyetal2021.pdf) - [ picture\_as\_pdf(supplement pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/harneyetal2021supp.pdf) - [ picture\_as\_pdf(article pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/harneyetal2021.pdf) - [ picture\_as\_pdf(supplement pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/harneyetal2021supp.pdf) Wakeley J. [Coalescent models](/publications/coalescent-models). In: *Human Population Genomics, K. E. Lohmueller, R. Nielsen (eds.)*. Springer Nature Switzerland AG; 2021. Wakeley J. [Coalescent models](/publications/coalescent-models). In: *Human Population Genomics, K. E. Lohmueller, R. Nielsen (eds.)*. Springer Nature Switzerland AG; 2021. - [Publisher's version](https://doi.org/10.1007/978-3-030-61646-5_1) - [Publisher's version](https://doi.org/10.1007/978-3-030-61646-5_1) ### 2020 Wakeley J. [Developments in coalescent theory from single loci to chromosomes](/publications/developments-coalescent-theory-single-loci-chromosomes). *Theoretical Population Biology*. 2020;133:56-64. Wakeley J. [Developments in coalescent theory from single loci to chromosomes](/publications/developments-coalescent-theory-single-loci-chromosomes). *Theoretical Population Biology*. 2020;133:56-64. - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/wakeley2020.pdf) - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/wakeley2020.pdf) ### 2019 Wakeley J, Nowak M. [A two-player iterated survival game](/publications/two-player-iterated-survival-game). *Theoretical Population Biology*. 2019;125:38–55. Wakeley J, Nowak M. [A two-player iterated survival game](/publications/two-player-iterated-survival-game). *Theoretical Population Biology*. 2019;125:38–55. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/wakeleyandnowak2019.pdf) We describe an iterated game between two players, in which the payoff is to survive a number of steps. Expected payoffs are probabilities of survival. A key feature of the game is that individuals have to survive on their own if their partner dies. We... - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/wakeleyandnowak2019.pdf) Palacios JA, Veber A, Cappello L, Wang Z, Wakeley J, Ramachandra S. [Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees](/publications/bayesian-estimation-population-size-changes-sampling-tajima%E2%80%99s-trees). *Genetics*. 2019;213:967-986. Palacios JA, Veber A, Cappello L, Wang Z, Wakeley J, Ramachandra S. [Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees](/publications/bayesian-estimation-population-size-changes-sampling-tajima%E2%80%99s-trees). *Genetics*. 2019;213:967-986. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/palaciosetal2019.pdf) The large state space of gene genealogies is a major hurdle for inference methods based on Kingman’s coalescent. Here, we present a new Bayesian approach for inferring past population sizes, which relies on a lower-resolution coalescent process that we... - [ picture\_as\_pdf(pdf)](/sites/g/files/omnuum5776/files/wakeleylab/files/palaciosetal2019.pdf) - Previous page chevron\_left - [1](?page=0 "Current page") - [2](?page=1 "Go to page 2") - [3](?page=2 "Go to page 3") - [ Last page 8 ](?page=7 "Go to last page") - [ Next page chevron\_right ](?page=1 "Go to next page")