important_papers.bib

@article{chalhoub2014early,
  title={Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome},
  author={Chalhoub, Boulos and Denoeud, France and Liu, Shengyi and Parkin, Isobel AP and Tang, Haibao and Wang, Xiyin and Chiquet, Julien and Belcram, Harry and Tong, Chaobo and Samans, Birgit and others},
  journal={Science},
  volume={345},
  number={6199},
  pages={950--953},
  year={2014},
  publisher={American Association for the Advancement of Science}
}

@article{golicz2016pangenome,
  title={The pangenome of an agronomically important crop plant Brassica oleracea},
  author={Golicz, Agnieszka A and Bayer, Philipp E and Barker, Guy C and Edger, Patrick P and Kim, HyeRan and Martinez, Paula A and Chan, Chon Kit Kenneth and Severn-Ellis, Anita and McCombie, W Richard and Parkin, Isobel AP and others},
  journal={Nature Communications},
  volume={7},
  number={1},
  pages={1--8},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{appels2018shifting,
  title={Shifting the limits in wheat research and breeding using a fully annotated reference genome},
  author={Appels, Rudi and Eversole, Kellye and Stein, Nils and Feuillet, Catherine and Keller, Beat and Rogers, Jane and Pozniak, Curtis J and Choulet, Fr{\'e}d{\'e}ric and Distelfeld, Assaf and Poland, Jesse and others},
  journal={Science},
  volume={361},
  number={6403},
  year={2018},
  publisher={American Association for the Advancement of Science}
}


@article{bayer2021sequencing,
  title={Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding},
  author={Bayer, Philipp E and Valliyodan, Babu and Hu, Haifei and Marsh, Jacob I and Yuan, Yuxuan and Vuong, Tri D and Patil, Gunvant and Song, Qijian and Batley, Jacqueline and Varshney, Rajeev K and others},
  journal={The Plant Genome},
  pages={1--12},
  year={2021},
  publisher={Wiley}
}



@article{bayer2021modelling,
  title={Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids},
  author={Bayer, Philipp E and Scheben, Armin and Golicz, Agnieszka A and Yuan, Yuxuan and Faure, Sebastien and Lee, HueyTyng and Chawla, Harmeet Singh and Anderson, Robyn and Bancroft, Ian and Raman, Harsh and others},
  journal={Plant biotechnology journal},
  volume={19},
  number={12},
  pages={2488--2500},
  year={2021}
}

@article{danilevicz2022dnabert,
  title={DNABERT-based explainable lncRNA identification in plant genome assemblies},
  author={Danilevicz, Monica Furaste and Gill, Mitchell and Fernandez, Cassandria G Tay and Petereit, Jakob and Upadhyaya, Shriprabha R and Batley, Jacqueline and Bennamoun, Mohammed and Edwards, David and Bayer, Philipp E},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{gill2022machine,
  title={Machine learning models outperform deep learning models, provide interpretation and facilitate feature selection for soybean trait prediction},
  author={Gill, Mitchell and Anderson, Robyn and Hu, Haifei and Bennamoun, Mohammed and Petereit, Jakob and Valliyodan, Babu and Nguyen, Henry T and Batley, Jacqueline and Bayer, Philipp E and Edwards, David},
  journal={BMC plant biology},
  volume={22},
  number={1},
  pages={1--8},
  year={2022},
  publisher={BioMed Central}
}


@article{bayer2022not,
  title={Not all pathways are the same-unique adaptations to submerged environments emerge from comparative seagrass genomics},
  author={Bayer, Philipp E and Fraser, Matthew W and Martin, Belinda C and Petereit, Jakob and Severn-Ellis, Anita A and Sinclair, Elizabeth A and Batley, Jacqueline and Kendrick, Gary A and Edwards, David},
  journal={bioRxiv},
  pages={2022--11},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{cundy2023seafood,
  title={Seafood label quality and mislabelling rates hamper consumer choices for sustainability in Australia},
  author={Cundy, Megan E and Santana-Garcon, Julia and McLennan, Alexander G and Ayad, Marcelle E and Bayer, Philipp E and Cooper, Madalyn and Corrigan, Shannon and Harrison, Emily and Wilcox, Chris},
  journal={Scientific Reports},
  volume={13},
  number={1},
  pages={10146},
  year={2023},
  publisher={Nature Publishing Group UK London}
}

@article{bayer2024comprehensive,
  title={A comprehensive evaluation of taxonomic classifiers in marine vertebrate eDNA studies},
  author={Bayer, Philipp E and Bennett, Adam and Nester, Georgia and Corrigan, Shannon and Raes, Eric J and McInnes, Allison S and Cooper, Madalyn and Ayad, Marcelle E and McVey, Philip and Kardailsky, Anya and others},
  journal={bioRxiv},
  pages={2024--02},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

@article{khan2024cicer,
  title={Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea},
  author={Khan, Aamir W and Garg, Vanika and Sun, Shuai and Gupta, Saurabh and Dudchenko, Olga and Roorkiwal, Manish and Chitikineni, Annapurna and Bayer, Philipp E and Shi, Chengcheng and Upadhyaya, Hari D and others},
  journal={Nature Genetics},
  pages={1--10},
  year={2024},
  publisher={Nature Publishing Group US New York}
}