book.bib

@article{Chakravarty2017,
  doi = {10.1200/po.17.00011},
  url = {https://doi.org/10.1200/po.17.00011},
  year = {2017},
  month = nov,
  publisher = {American Society of Clinical Oncology ({ASCO})},
  number = {1},
  pages = {1--16},
  author = {Debyani Chakravarty and Jianjiong Gao and Sarah Phillips and Ritika Kundra and Hongxin Zhang and Jiaojiao Wang and Julia E. Rudolph and Rona Yaeger and Tara Soumerai and Moriah H. Nissan and Matthew T. Chang and Sarat Chandarlapaty and Tiffany A. Traina and Paul K. Paik and Alan L. Ho and Feras M. Hantash and Andrew Grupe and Shrujal S. Baxi and Margaret K. Callahan and Alexandra Snyder and Ping Chi and Daniel C. Danila and Mrinal Gounder and James J. Harding and Matthew D. Hellmann and Gopa Iyer and Yelena Y. Janjigian and Thomas Kaley and Douglas A. Levine and Maeve Lowery and Antonio Omuro and Michael A. Postow and Dana Rathkopf and Alexander N. Shoushtari and Neerav Shukla and Martin H. Voss and Ederlinda Paraiso and Ahmet Zehir and Michael F. Berger and Barry S. Taylor and Leonard B. Saltz and Gregory J. Riely and Marc Ladanyi and David M. Hyman and Jos{\'{e}} Baselga and Paul Sabbatini and David B. Solit and Nikolaus Schultz},
  title = {{OncoKB}: A Precision Oncology Knowledge Base},
  journal = {{JCO} Precision Oncology}
}

@article{Chen2022,
  doi = {10.1101/2022.03.20.485034},
  url = {https://doi.org/10.1101/2022.03.20.485034},
  year = {2022},
  month = mar,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Siwei Chen and Laurent C. Francioli and Julia K. Goodrich and Ryan L. Collins and Masahiro Kanai and Qingbo Wang and Jessica Alf\"{o}ldi and Nicholas A. Watts and Christopher Vittal and Laura D. Gauthier and Timothy Poterba and Michael W. Wilson and Yekaterina Tarasova and William Phu and Mary T. Yohannes and Zan Koenig and Yossi Farjoun and Eric Banks and Stacey Donnelly and Stacey Gabriel and Namrata Gupta and Steven Ferriera and Charlotte Tolonen and Sam Novod and Louis Bergelson and David Roazen and Valentin Ruano-Rubio and Miguel Covarrubias and Christopher Llanwarne and Nikelle Petrillo and Gordon Wade and Thibault Jeandet and Ruchi Munshi and Kathleen Tibbetts and Anne O'Donnell-Luria and Matthew Solomonson and Cotton Seed and Alicia R. Martin and Michael E. Talkowski and Heidi L. Rehm and Mark J. Daly and Grace Tiao and Benjamin M. Neale and Daniel G. MacArthur and Konrad J. Karczewski and},
  title = {A genome-wide mutational constraint map quantified from variation in 76, 156 human genomes}
}

@article{Danos2019,
  doi = {10.1186/s13073-019-0687-x},
  url = {https://doi.org/10.1186/s13073-019-0687-x},
  year = {2019},
  month = nov,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {11},
  number = {1},
  author = {Arpad M. Danos and Kilannin Krysiak and Erica K. Barnell and Adam C. Coffman and Joshua F. McMichael and Susanna Kiwala and Nicholas C. Spies and Lana M. Sheta and Shahil P. Pema and Lynzey Kujan and Kaitlin A. Clark and Amber Z. Wollam and Shruti Rao and Deborah I. Ritter and Dmitriy Sonkin and Gordana Raca and Wan-Hsin Lin and Cameron J. Grisdale and Raymond H. Kim and Alex H. Wagner and Subha Madhavan and Malachi Griffith and Obi L. Griffith},
  title = {Standard operating procedure for curation and clinical interpretation of variants in cancer},
  journal = {Genome Medicine}
}

@article{Good2014,
  doi = {10.1186/s13059-014-0438-7},
  url = {https://doi.org/10.1186/s13059-014-0438-7},
  year = {2014},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {15},
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  author = {Benjamin M Good and Benjamin J Ainscough and Josh F McMichael and Andrew I Su and Obi L Griffith},
  title = {Organizing knowledge to enable personalization of medicine in cancer},
  journal = {Genome Biology}
}

@article{Griffith2017,
  doi = {10.1038/ng.3774},
  url = {https://doi.org/10.1038/ng.3774},
  year = {2017},
  month = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {49},
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  author = {Malachi Griffith and Nicholas C Spies and Kilannin Krysiak and Joshua F McMichael and Adam C Coffman and Arpad M Danos and Benjamin J Ainscough and Cody A Ramirez and Damian T Rieke and Lynzey Kujan and Erica K Barnell and Alex H Wagner and Zachary L Skidmore and Amber Wollam and Connor J Liu and Martin R Jones and Rachel L Bilski and Robert Lesurf and Yan-Yang Feng and Nakul M Shah and Melika Bonakdar and Lee Trani and Matthew Matlock and Avinash Ramu and Katie M Campbell and Gregory C Spies and Aaron P Graubert and Karthik Gangavarapu and James M Eldred and David E Larson and Jason R Walker and Benjamin M Good and Chunlei Wu and Andrew I Su and Rodrigo Dienstmann and Adam A Margolin and David Tamborero and Nuria Lopez-Bigas and Steven J M Jones and Ron Bose and David H Spencer and Lukas D Wartman and Richard K Wilson and Elaine R Mardis and Obi L Griffith},
  title = {{CIViC} is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer},
  journal = {Nature Genetics}
}

@article{Hanahan2011,
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}

@article{Horak2022,
  doi = {10.1016/j.gim.2022.01.001},
  url = {https://doi.org/10.1016/j.gim.2022.01.001},
  year = {2022},
  month = may,
  publisher = {Elsevier {BV}},
  volume = {24},
  number = {5},
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  author = {Peter Horak and Malachi Griffith and Arpad M. Danos and Beth A. Pitel and Subha Madhavan and Xuelu Liu and Cynthia Chow and Heather Williams and Leigh Carmody and Lisa Barrow-Laing and Damian Rieke and Simon Kreutzfeldt and Albrecht Stenzinger and David Tamborero and Manuela Benary and Padma Sheila Rajagopal and Cristiane M. Ida and Harry Lesmana and Laveniya Satgunaseelan and Jason D. Merker and Michael Y. Tolstorukov and Paulo Vidal Campregher and Jeremy L. Warner and Shruti Rao and Maya Natesan and Haolin Shen and Jeffrey Venstrom and Somak Roy and Kayoko Tao and Rashmi Kanagal-Shamanna and Xinjie Xu and Deborah I. Ritter and Kym Pagel and Kilannin Krysiak and Adrian Dubuc and Yassmine M. Akkari and Xuan Shirley Li and Jennifer Lee and Ian King and Gordana Raca and Alex H. Wagner and Marylin M. Li and Sharon E. Plon and Shashikant Kulkarni and Obi L. Griffith and Debyani Chakravarty and Dmitriy Sonkin},
  title = {Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource ({ClinGen}),  Cancer Genomics Consortium ({CGC}),  and Variant Interpretation for Cancer Consortium ({VICC})},
  journal = {Genetics in Medicine}
}

@article{HumanGenome2001,
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  title = {Initial sequencing and analysis of the human genome},
  journal = {Nature}
}

@article{Krysiak2022,
  doi = {10.1038/s43018-022-00379-w},
  url = {https://doi.org/10.1038/s43018-022-00379-w},
  year = {2022},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {3},
  number = {5},
  pages = {522--525},
  author = {Kilannin Krysiak and Arpad M. Danos and Susanna Kiwala and Joshua F. McMichael and Adam C. Coffman and Erica K. Barnell and Lana Sheta and Jason Saliba and Cameron J. Grisdale and Lynzey Kujan and Shahil Pema and Jake Lever and Nicholas C. Spies and Andreea Chiorean and Damian T. Rieke and Kaitlin A. Clark and Payal Jani and Hideaki Takahashi and Peter Horak and Deborah I. Ritter and Xin Zhou and Benjamin J. Ainscough and Sean Delong and Mario Lamping and Alex R. Marr and Brian V. Li and Wan-Hsin Lin and Panieh Terraf and Yasser Salama and Katie M. Campbell and Kirsten M. Farncombe and Jianling Ji and Xiaonan Zhao and Xinjie Xu and Rashmi Kanagal-Shamanna and Kelsy C. Cotto and Zachary L. Skidmore and Jason R. Walker and Jinghui Zhang and Aleksandar Milosavljevic and Ronak Y. Patel and Rachel H. Giles and Raymond H. Kim and Lynn M. Schriml and Elaine R. Mardis and Steven J. M. Jones and Gordana Raca and Shruti Rao and Subha Madhavan and Alex H. Wagner and Obi L. Griffith and Malachi Griffith},
  title = {A community approach to the cancer-variant-interpretation bottleneck},
  journal = {Nature Cancer}
}

@article{Krysiak2022b,
  doi = {10.1093/nar/gkac979},
  url = {https://doi.org/10.1093/nar/gkac979},
  year = {2022},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {51},
  number = {D1},
  pages = {D1230--D1241},
  author = {Kilannin Krysiak and Arpad~M Danos and Jason Saliba and Joshua~F McMichael and Adam~C Coffman and Susanna Kiwala and Erica~K Barnell and Lana Sheta and Cameron~J Grisdale and Lynzey Kujan and Shahil Pema and Jake Lever and Sarah Ridd and Nicholas~C Spies and Veronica Andric and Andreea Chiorean and Damian~T Rieke and Kaitlin~A Clark and Caralyn Reisle and Ajay~C Venigalla and Mark Evans and Payal Jani and Hideaki Takahashi and Avila Suda and Peter Horak and Deborah~I Ritter and Xin Zhou and Benjamin~J Ainscough and Sean Delong and Chimene Kesserwan and Mario Lamping and Haolin Shen and Alex~R Marr and My~H Hoang and Kartik Singhal and Mariam Khanfar and Brian~V Li and Wan-Hsin Lin and Panieh Terraf and Laura~B Corson and Yasser Salama and Katie~M Campbell and Kirsten~M Farncombe and Jianling Ji and Xiaonan Zhao and Xinjie Xu and Rashmi Kanagal-Shamanna and Ian King and Kelsy~C Cotto and Zachary~L Skidmore and Jason~R Walker and Jinghui Zhang and Aleksandar Milosavljevic and Ronak~Y Patel and Rachel~H Giles and Raymond~H Kim and Lynn~M Schriml and Elaine~R Mardis and Steven J M Jones and Gordana Raca and Shruti Rao and Subha Madhavan and Alex~H Wagner and Malachi Griffith and Obi~L Griffith},
  title = {{CIViCdb} 2022: evolution of an open-access cancer variant interpretation knowledgebase},
  journal = {Nucleic Acids Research}
}

@article{Ley2008,
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}

@article{Li2017,
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}

@article{Mateo2018,
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}

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@Manual{rmarkdown2021,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2021},
  note = {R package version 2.10},
  url = {https://github.com/rstudio/rmarkdown},
}

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@Book{Xie2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
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  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{Xie2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}