book.bib

@article{Hundal2016,
  doi = {10.1186/s13073-016-0264-5},
  url = {https://doi.org/10.1186/s13073-016-0264-5},
  year = {2016},
  month = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {8},
  number = {1},
  author = {Jasreet Hundal and Beatriz M. Carreno and Allegra A. Petti and Gerald P. Linette and Obi L. Griffith and Elaine R. Mardis and Malachi Griffith},
  title = {{pVAC}-Seq: A genome-guided in silico approach to identifying tumor neoantigens},
  journal = {Genome Medicine}
}

@article{Hundal2018,
  doi = {10.1038/s41588-018-0283-9},
  url = {https://doi.org/10.1038/s41588-018-0283-9},
  year = {2018},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {51},
  number = {1},
  pages = {175--179},
  author = {Jasreet Hundal and Susanna Kiwala and Yang-Yang Feng and Connor J. Liu and Ramaswamy Govindan and William C. Chapman and Ravindra Uppaluri and S. Joshua Swamidass and Obi L. Griffith and Elaine R. Mardis and Malachi Griffith},
  title = {Accounting for proximal variants improves neoantigen prediction},
  journal = {Nature Genetics}
}

@article{Hundal2020,
  doi = {10.1158/2326-6066.cir-19-0401},
  url = {https://doi.org/10.1158/2326-6066.cir-19-0401},
  year = {2020},
  month = mar,
  publisher = {American Association for Cancer Research ({AACR})},
  volume = {8},
  number = {3},
  pages = {409--420},
  author = {Jasreet Hundal and Susanna Kiwala and Joshua McMichael and Christopher A. Miller and Huiming Xia and Alexander T. Wollam and Connor J. Liu and Sidi Zhao and Yang-Yang Feng and Aaron P. Graubert and Amber Z. Wollam and Jonas Neichin and Megan Neveau and Jason Walker and William E. Gillanders and Elaine R. Mardis and Obi L. Griffith and Malachi Griffith},
  title = {{pVACtools}: A Computational Toolkit to Identify and Visualize Cancer Neoantigens},
  journal = {Cancer Immunology Research}
}

@article{Keskin2018,
  doi = {10.1038/s41586-018-0792-9},
  url = {https://doi.org/10.1038/s41586-018-0792-9},
  year = {2018},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {565},
  number = {7738},
  pages = {234--239},
  author = {Derin B. Keskin and Annabelle J. Anandappa and Jing Sun and Itay Tirosh and Nathan D. Mathewson and Shuqiang Li and Giacomo Oliveira and Anita Giobbie-Hurder and Kristen Felt and Evisa Gjini and Sachet A. Shukla and Zhuting Hu and Letitia Li and Phuong M. Le and Rosa L. Alles{\o}e and Alyssa R. Richman and Monika S. Kowalczyk and Sara Abdelrahman and Jack E. Geduldig and Sarah Charbonneau and Kristine Pelton and J. Bryan Iorgulescu and Liudmila Elagina and Wandi Zhang and Oriol Olive and Christine McCluskey and Lars R. Olsen and Jonathan Stevens and William J. Lane and Andres M. Salazar and Heather Daley and Patrick Y. Wen and E. Antonio Chiocca and Maegan Harden and Niall J. Lennon and Stacey Gabriel and Gad Getz and Eric S. Lander and Aviv Regev and Jerome Ritz and Donna Neuberg and Scott J. Rodig and Keith L. Ligon and Mario L. Suv{\`{a}} and Kai W. Wucherpfennig and Nir Hacohen and Edward F. Fritsch and Kenneth J. Livak and Patrick A. Ott and Catherine J. Wu and David A. Reardon},
  title = {Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial},
  journal = {Nature}
}

@article{Xia2023,
  doi = {10.1126/sciimmunol.abg2200},
  url = {https://doi.org/10.1126/sciimmunol.abg2200},
  year = {2023},
  month = apr,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {8},
  number = {82},
  author = {Huiming Xia and Joshua McMichael and Michelle Becker-Hapak and Onyinyechi C. Onyeador and Rico Buchli and Ethan McClain and Patrick Pence and Suangson Supabphol and Megan M. Richters and Anamika Basu and Cody A. Ramirez and Cristina Puig-Saus and Kelsy C. Cotto and Sharon L. Freshour and Jasreet Hundal and Susanna Kiwala and S. Peter Goedegebuure and Tanner M. Johanns and Gavin P. Dunn and Antoni Ribas and Christopher A. Miller and William E. Gillanders and Todd A. Fehniger and Obi L. Griffith and Malachi Griffith},
  title = {Computational prediction of {MHC} anchor locations guides neoantigen identification and prioritization},
  journal = {Science Immunology}
}

@article{Ott2017,
  doi = {10.1038/nature22991},
  url = {https://doi.org/10.1038/nature22991},
  year = {2017},
  month = jul,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {547},
  number = {7662},
  pages = {217--221},
  author = {Patrick A. Ott and Zhuting Hu and Derin B. Keskin and Sachet A. Shukla and Jing Sun and David J. Bozym and Wandi Zhang and Adrienne Luoma and Anita Giobbie-Hurder and Lauren Peter and Christina Chen and Oriol Olive and Todd A. Carter and Shuqiang Li and David J. Lieb and Thomas Eisenhaure and Evisa Gjini and Jonathan Stevens and William J. Lane and Indu Javeri and Kaliappanadar Nellaiappan and Andres M. Salazar and Heather Daley and Michael Seaman and Elizabeth I. Buchbinder and Charles H. Yoon and Maegan Harden and Niall Lennon and Stacey Gabriel and Scott J. Rodig and Dan H. Barouch and Jon C. Aster and Gad Getz and Kai Wucherpfennig and Donna Neuberg and Jerome Ritz and Eric S. Lander and Edward F. Fritsch and Nir Hacohen and Catherine J. Wu},
  title = {An immunogenic personal neoantigen vaccine for patients with melanoma},
  journal = {Nature}
}

@article{Hilf2018,
  doi = {10.1038/s41586-018-0810-y},
  url = {https://doi.org/10.1038/s41586-018-0810-y},
  year = {2018},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {565},
  number = {7738},
  pages = {240--245},
  author = {Norbert Hilf and Sabrina Kuttruff-Coqui and Katrin Frenzel and Valesca Bukur and Stefan Stevanovi{\'{c}} and C{\'{e}}cile Gouttefangeas and Michael Platten and Ghazaleh Tabatabai and Valerie Dutoit and Sjoerd H. van der Burg and Per thor Straten and Francisco Mart{\'{\i}}nez-Ricarte and Berta Ponsati and Hideho Okada and Ulrik Lassen and Arie Admon and Christian H. Ottensmeier and Alexander Ulges and Sebastian Kreiter and Andreas von Deimling and Marco Skardelly and Denis Migliorini and Judith R. Kroep and Manja Idorn and Jordi Rodon and Jordi Pir{\'{o}} and Hans S. Poulsen and Bracha Shraibman and Katy McCann and Regina Mendrzyk and Martin L\"{o}wer and Monika Stieglbauer and Cedrik M. Britten and David Capper and Marij J. P. Welters and Juan Sahuquillo and Katharina Kiesel and Evelyna Derhovanessian and Elisa Rusch and Lukas Bunse and Colette Song and Sandra Heesch and Claudia Wagner and Alexandra Kemmer-Br\"{u}ck and J\"{o}rg Ludwig and John C. Castle and Oliver Schoor and Arbel D. Tadmor and Edward Green and Jens Fritsche and Miriam Meyer and Nina Pawlowski and Sonja Dorner and Franziska Hoffgaard and Bernhard R\"{o}ssler and Dominik Maurer and Toni Weinschenk and Carsten Reinhardt and Christoph Huber and Hans-Georg Rammensee and Harpreet Singh-Jasuja and Ugur Sahin and Pierre-Yves Dietrich and Wolfgang Wick},
  title = {Actively personalized vaccination trial for newly diagnosed glioblastoma},
  journal = {Nature}
}

@article{Brown2014,
  doi = {10.1101/gr.165985.113},
  url = {https://doi.org/10.1101/gr.165985.113},
  year = {2014},
  month = apr,
  publisher = {Cold Spring Harbor Laboratory},
  volume = {24},
  number = {5},
  pages = {743--750},
  author = {Scott D. Brown and Rene L. Warren and Ewan A. Gibb and Spencer D. Martin and John J. Spinelli and Brad H. Nelson and Robert A. Holt},
  title = {Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival},
  journal = {Genome Research}
}

@article{Rizvi2015,
  doi = {10.1126/science.aaa1348},
  url = {https://doi.org/10.1126/science.aaa1348},
  year = {2015},
  month = apr,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {348},
  number = {6230},
  pages = {124--128},
  author = {Naiyer A. Rizvi and Matthew D. Hellmann and Alexandra Snyder and Pia Kvistborg and Vladimir Makarov and Jonathan J. Havel and William Lee and Jianda Yuan and Phillip Wong and Teresa S. Ho and Martin L. Miller and Natasha Rekhtman and Andre L. Moreira and Fawzia Ibrahim and Cameron Bruggeman and Billel Gasmi and Roberta Zappasodi and Yuka Maeda and Chris Sander and Edward B. Garon and Taha Merghoub and Jedd D. Wolchok and Ton N. Schumacher and Timothy A. Chan},
  title = {Mutational landscape determines sensitivity to {PD}-1 blockade in non{\textendash}small cell lung cancer},
  journal = {Science}
}

@article{Schumacher2015,
  doi = {10.1126/science.aaa4971},
  url = {https://doi.org/10.1126/science.aaa4971},
  year = {2015},
  month = apr,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {348},
  number = {6230},
  pages = {69--74},
  author = {Ton N. Schumacher and Robert D. Schreiber},
  title = {Neoantigens in cancer immunotherapy},
  journal = {Science}
}

@article{Richters2019,
  doi = {10.1186/s13073-019-0666-2},
  url = {https://doi.org/10.1186/s13073-019-0666-2},
  year = {2019},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {11},
  number = {1},
  author = {Megan M. Richters and Huiming Xia and Katie M. Campbell and William E. Gillanders and Obi L. Griffith and Malachi Griffith},
  title = {Best practices for bioinformatic characterization of neoantigens for clinical utility},
  journal = {Genome Medicine}
}

@article{McLaren2016,
  doi = {10.1186/s13059-016-0974-4},
  url = {https://doi.org/10.1186/s13059-016-0974-4},
  year = {2016},
  month = jun,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {17},
  number = {1},
  author = {William McLaren and Laurent Gil and Sarah E. Hunt and Harpreet Singh Riat and Graham R. S. Ritchie and Anja Thormann and Paul Flicek and Fiona Cunningham},
  title = {The Ensembl Variant Effect Predictor},
  journal = {Genome Biology}
}

@article{Haas2019,
  doi = {10.1186/s13059-019-1842-9},
  url = {https://doi.org/10.1186/s13059-019-1842-9},
  year = {2019},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {20},
  number = {1},
  author = {Brian J. Haas and Alexander Dobin and Bo Li and Nicolas Stransky and Nathalie Pochet and Aviv Regev},
  title = {Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods},
  journal = {Genome Biology}
}

@article{Murphy2016,
  doi = {10.1101/080903},
  url = {https://doi.org/10.1101/080903},
  year = {2016},
  month = oct,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Charlie Murphy and Olivier Elemento},
  title = {{AGFusion}: annotate and visualize gene fusions}
}

@article{Uhrig2021,
  doi = {10.1101/gr.257246.119},
  url = {https://doi.org/10.1101/gr.257246.119},
  year = {2021},
  month = jan,
  publisher = {Cold Spring Harbor Laboratory},
  volume = {31},
  number = {3},
  pages = {448--460},
  author = {Sebastian Uhrig and Julia Ellermann and Tatjana Walther and Pauline Burkhardt and Martina Fr\"{o}hlich and Barbara Hutter and Umut H. Toprak and Olaf Neumann and Albrecht Stenzinger and Claudia Scholl and Stefan Fr\"{o}hling and Benedikt Brors},
  title = {Accurate and efficient detection of gene fusions from {RNA} sequencing data},
  journal = {Genome Research}
}

@article{Szolek2014,
  doi = {10.1093/bioinformatics/btu548},
  url = {https://doi.org/10.1093/bioinformatics/btu548},
  year = {2014},
  month = aug,
  publisher = {Oxford University Press ({OUP})},
  volume = {30},
  number = {23},
  pages = {3310--3316},
  author = {Andr{\'{a}}s Szolek and Benjamin Schubert and Christopher Mohr and Marc Sturm and Magdalena Feldhahn and Oliver Kohlbacher},
  title = {{OptiType}: precision {HLA} typing from next-generation sequencing data},
  journal = {Bioinformatics}
}

@incollection{Bai2018,
  doi = {10.1007/978-1-4939-8546-3_13},
  url = {https://doi.org/10.1007/978-1-4939-8546-3_13},
  year = {2018},
  publisher = {Springer New York},
  pages = {193--201},
  author = {Yu Bai and David Wang and Wen Fury},
  title = {{PHLAT}: Inference of High-Resolution {HLA} Types from {RNA} and Whole Exome Sequencing},
  booktitle = {Methods in Molecular Biology}
}

@article{Vita2018,
  doi = {10.1093/nar/gky1006},
  url = {https://doi.org/10.1093/nar/gky1006},
  year = {2018},
  month = oct,
  publisher = {Oxford University Press ({OUP})},
  volume = {47},
  number = {D1},
  pages = {D339--D343},
  author = {Randi Vita and Swapnil Mahajan and James A Overton and Sandeep Kumar Dhanda and Sheridan Martini and Jason R Cantrell and Daniel K Wheeler and Alessandro Sette and Bjoern Peters},
  title = {The Immune Epitope Database ({IEDB}): 2018 update},
  journal = {Nucleic Acids Research}
}

@article{Jurtz2017,
  doi = {10.1101/149518},
  url = {https://doi.org/10.1101/149518},
  year = {2017},
  month = jun,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Vanessa Jurtz and Sinu Paul and Massimo Andreatta and Paolo Marcatili and Bjoern Peters and Morten Nielsen},
  title = {{NetMHCpan} 4.0: Improved peptide-{MHC} class I interaction predictions integrating eluted ligand and peptide binding affinity data}
}

@article{ODonnell2018,
  doi = {10.1016/j.cels.2018.05.014},
  url = {https://doi.org/10.1016/j.cels.2018.05.014},
  year = {2018},
  month = jul,
  publisher = {Elsevier {BV}},
  volume = {7},
  number = {1},
  pages = {129--132.e4},
  author = {Timothy J. O{\textquotesingle}Donnell and Alex Rubinsteyn and Maria Bonsack and Angelika B. Riemer and Uri Laserson and Jeff Hammerbacher},
  title = {{MHCflurry}: Open-Source Class I {MHC} Binding Affinity Prediction},
  journal = {Cell Systems}
}

@article{Shao2020,
  doi = {10.1158/2326-6066.cir-19-0464},
  url = {https://doi.org/10.1158/2326-6066.cir-19-0464},
  year = {2020},
  month = mar,
  publisher = {American Association for Cancer Research ({AACR})},
  volume = {8},
  number = {3},
  pages = {396--408},
  author = {Xiaoshan M. Shao and Rohit Bhattacharya and Justin Huang and I.K. Ashok Sivakumar and Collin Tokheim and Lily Zheng and Dylan Hirsch and Benjamin Kaminow and Ashton Omdahl and Maria Bonsack and Angelika B. Riemer and Victor E. Velculescu and Valsamo Anagnostou and Kymberleigh A. Pagel and Rachel Karchin},
  title = {High-Throughput Prediction of {MHC} Class I and {II} Neoantigens with {MHCnuggets}},
  journal = {Cancer Immunology Research}
}

@article{Rasmussen2016,
  doi = {10.4049/jimmunol.1600582},
  url = {https://doi.org/10.4049/jimmunol.1600582},
  year = {2016},
  month = aug,
  publisher = {The American Association of Immunologists},
  volume = {197},
  number = {4},
  pages = {1517--1524},
  author = {Michael Rasmussen and Emilio Fenoy and Mikkel Harndahl and Anne Bregnballe Kristensen and Ida Kallehauge Nielsen and Morten Nielsen and S{\o}ren Buus},
  title = {Pan-Specific Prediction of Peptide{\textendash}{MHC} Class I Complex Stability,  a Correlate of T Cell Immunogenicity},
  journal = {The Journal of Immunology}
}

@article{Nielsen2005,
  doi = {10.1007/s00251-005-0781-7},
  url = {https://doi.org/10.1007/s00251-005-0781-7},
  year = {2005},
  month = mar,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {57},
  number = {1-2},
  pages = {33--41},
  author = {Morten Nielsen and Claus Lundegaard and Ole Lund and Can Ke{\c{s}}mir},
  title = {The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage},
  journal = {Immunogenetics}
}

@article{Rubinsteyn2017,
  doi = {10.1101/142919},
  url = {https://doi.org/10.1101/142919},
  year = {2017},
  month = may,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Alexander Rubinsteyn and Isaac Hodes and Julia Kodysh and Jeffrey Hammerbacher},
  title = {Vaxrank: A computational tool for designing personalized cancer vaccines}
}

@article{Altschul1990,
  doi = {10.1016/s0022-2836(05)80360-2},
  url = {https://doi.org/10.1016/s0022-2836(05)80360-2},
  year = {1990},
  month = oct,
  publisher = {Elsevier {BV}},
  volume = {215},
  number = {3},
  pages = {403--410},
  author = {Stephen F. Altschul and Warren Gish and Webb Miller and Eugene W. Myers and David J. Lipman},
  title = {Basic local alignment search tool},
  journal = {Journal of Molecular Biology}
}

@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},
}

@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},
  year = {2018},
  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},
}