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@article{salehi2025defining,
title={Defining and cataloging variants in pangenome graphs},
author={Salehi Nowbandegani, Pouria and Zhang, Shenghan and Hu, Haoyang and Li, Heng and O’Connor, Luke J},
journal={bioRxiv},
pages={2025--08},
year={2025},
publisher={Cold Spring Harbor Laboratory}
}
@article{milia2025taurine,
title={Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle},
author={Milia, Sotiria and Leonard, Alexander S and Mapel, Xena Marie and Ulloa, Sandra Milena Bernal and Dr{\"o}gem{\"u}ller, Cord and Pausch, Hubert},
journal={Genome Research},
volume={35},
number={4},
pages={1041--1052},
year={2025},
publisher={Cold Spring Harbor Lab}
}
@article{siren2024personalized,
title={Personalized pangenome references},
author={Sir{\'e}n, Jouni and Eskandar, Parsa and Ungaro, Matteo Tommaso and Hickey, Glenn and Eizenga, Jordan M and Novak, Adam M and Chang, Xian and Chang, Pi-Chuan and Kolmogorov, Mikhail and Carroll, Andrew and others},
journal={Nature Methods},
volume={21},
number={11},
pages={2017--2023},
year={2024},
publisher={Nature Publishing Group US New York}
}
@article{chikhi2024logan,
title={Logan: planetary-scale genome assembly surveys life’s diversity},
author={Chikhi, Rayan and Lemane, T{\'e}o and Loll-Krippleber, Rapha{\"e}l and Montoliu-Nerin, Merc{\`e} and Raffestin, Brice and Camargo, Antonio Pedro and Miller, Carson J and Fiamenghi, Mateus Bernabe and Agustinho, Daniel Paiva and Majidian, Sina and others},
journal={bioRxiv},
pages={2024--07},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}
@article{kalbfleisch2024ruminant,
title={The ruminant telomere-to-telomere (rt2t) consortium},
author={Kalbfleisch, Theodore S and McKay, Stephanie D and Murdoch, Brenda M and Adelson, David L and Almansa-Villa, Diego and Becker, Gabrielle and Beckett, Linda M and Ben{\'\i}tez-Galeano, Mar{\'\i}a Jos{\'e} and Biase, Fernando and Casey, Theresa and others},
journal={Nature genetics},
volume={56},
number={8},
pages={1566--1573},
year={2024},
publisher={Nature Publishing Group US New York}
}
@article{guarracino2023recombination,
title={Recombination between heterologous human acrocentric chromosomes},
author={Guarracino, Andrea and Buonaiuto, Silvia and de Lima, Leonardo Gomes and Potapova, Tamara and Rhie, Arang and Koren, Sergey and Rubinstein, Boris and Fischer, Christian and Gerton, Jennifer L and others},
journal={Nature},
volume={617},
number={7960},
pages={335--343},
year={2023},
publisher={Nature Publishing Group UK London}
}
@article{jarvis2022semi,
title={Semi-automated assembly of high-quality diploid human reference genomes},
author={Jarvis, Erich D and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R and Porubsky, David and others},
journal={Nature},
volume={611},
number={7936},
pages={519--531},
year={2022},
publisher={Nature Publishing Group UK London}
}
@article{paten2018superbubbles,
title={Superbubbles, ultrabubbles, and cacti},
author={Paten, Benedict and Eizenga, Jordan M and Rosen, Yohei M and Novak, Adam M and Garrison, Erik and Hickey, Glenn},
journal={Journal of Computational Biology},
volume={25},
number={7},
pages={649--663},
year={2018},
publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA}
}