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@article{kelleher2018efficient,
author = {Kelleher, Jerome AND Thornton, Kevin R. AND Ashander, Jaime AND
Ralph, Peter L.},
journal = {PLoS Computational Biology},
publisher = {Public Library of Science},
title = {Efficient pedigree recording for fast population genetics simulation},
year = {2018},
month = {11},
volume = {14},
pages = {1--21},
number = {11}
}
@article{ralph2020efficiently,
author = {Ralph, Peter and Thornton, Kevin and Kelleher, Jerome},
journal = {Genetics},
title = {Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes},
year = {2020},
volume={215},
number={3},
pages={779--797}
}
@article{wong2024general,
author = {Wong, Yan and Ignatieva, Anastasia and Koskela, Jere and Gorjanc, Gregor and Wohns, Anthony W and Kelleher, Jerome},
title = {A general and efficient representation of ancestral recombination graphs},
journal = {Genetics},
volume = {228},
number = {1},
pages = {iyae100},
year = {2024},
month = {07},
}
@article{brandt2024promise,
author = {Brandt, Débora Y C and Huber, Christian D and Chiang, Charleston W K and Ortega-Del Vecchyo, Diego},
title = {The Promise of Inferring the Past using the {Ancestral Recombination Graph (ARG)}},
journal = {Genome Biology and Evolution},
volume={16},
number={2},
year = {2024},
pages = {evae005},
}
@article{lewanski2024era,
author = {Lewanski, Alexander L. and Grundler, Michael C. and Bradburd, Gideon S.},
title = {The era of the {ARG}: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics},
journal = {PLOS Genetics},
year = {2024},
volume = {20},
number = {1},
pages = {1--24},
}
@article{nielsen2024inference,
title = {Inference and applications of ancestral recombination graphs},
author = {Nielsen, Rasmus and Vaughn, Andrew H. and Deng, Yun},
journal = {Nature Reviews Genetics},
year = {2024},
volume = {26},
pages = {47--58},
}
@article{kelleher2016efficient,
author = {Kelleher, Jerome and Etheridge, Alison M. and McVean, Gilean},
title = {Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes},
journal = {PLOS Computational Biology},
year = {2016},
volume = {12},
number = {5},
pages = {e1004842},
}
@article{andersontrocme2023genes,
author = {Luke Anderson-Trocm{\'e} and Dominic Nelson and Shadi Zabad and Alex Diaz-Papkovich and Ivan Kryukov and Nikolas Baya and Mathilde Touvier and Ben Jeffery and Christian Dina and H{\'e}l{\`e}ne V{\'e}zina and Jerome Kelleher and Simon Gravel},
journal = {Science},
number = {6647},
pages = {849--855},
title = {On the genes, genealogies, and geographies of {Quebec}},
volume = {380},
year = {2023}
}
@article{kelleher2019inferring,
author = {Kelleher, Jerome and Wong, Yan and Wohns, Anthony W. and Fadil, Chaimaa and Albers, Patrick K. and McVean, Gil},
journal = {Nature Genetics},
pages = {1330--1338},
title = {Inferring whole-genome histories in large population datasets},
volume = {51},
year = {2019}
}
@article{wohns2022unified,
author = {Wohns, Anthony Wilder and Wong, Yan and Jeffery, Ben and Akbari, Ali and Mallick, Swapan and Pinhasi, Ron and Patterson, Nick and Reich, David and Kelleher, Jerome and McVean, Gil},
journal = {Science},
pages = {eabi8264},
title = {A unified genealogy of modern and ancient genomes},
volume = {375},
year = {2022}
}
@article{zhan2025pandemic,
author = {Zhan, Shing H. and Wong, Yan and Ignatieva, Anastasia and
Eaton, Katherine and Guthrie, Isobel and Jeffery, Benjamin and
Palmer, Duncan S. and Murall, Carmen Lia and Otto, Sarah P. and
Kelleher, Jerome},
title = {A Pandemic-Scale Ancestral Recombination Graph for {SARS-CoV-2}},
year = {2025},
journal = {bioRxiv}
}
@article{haller2025simHumanity,
author = {Haller, Benjamin C. and Nelson, Chase W. and Rodrigues, Murillo F. and Messer, Philipp W.},
title = {{SimHumanity: Using SLiM} 5.0 to run whole-genome simulations of human evolution},
journal = {Human Population Genetics and Genomics},
year = {2025},
}
@article{pope2026tracing,
author = {Pope, Nathaniel S. and Tallman, Sam and Jeffery, Ben and Robertson, Duncan and Wong, Yan and Karthikeyan, Savita and Ralph, Peter L. and Kelleher, Jerome},
title = {Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs},
journal = {bioRxiv},
year = {2026},
}