@article{bazzini2014identification,
  title={Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation},
  author={Bazzini, Ariel A and Johnstone, Timothy G and Christiano, Romain and Mackowiak, Sebastian D and Obermayer, Benedikt and Fleming, Elizabeth S and Vejnar, Charles E and Lee, Miler T and Rajewsky, Nikolaus and Walther, Tobias C and others},
  journal={The EMBO journal},
  volume={33},
  number={9},
  pages={981--993},
  year={2014},
  publisher={John Wiley \& Sons, Ltd}
}

@article{chung2015use,
  title={The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis},
  author={Chung, Betty Y and Hardcastle, Thomas J and Jones, Joshua D and Irigoyen, Nerea and Firth, Andrew E and Baulcombe, David C and Brierley, Ian},
  journal={Rna},
  volume={21},
  number={10},
  pages={1731--1745},
  year={2015},
  publisher={Cold Spring Harbor Lab}
}

@article{ingolia2009genome,
  title={Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling},
  author={Ingolia, Nicholas T and Ghaemmaghami, Sina and Newman, John RS and Weissman, Jonathan S},
  journal={science},
  volume={324},
  number={5924},
  pages={218--223},
  year={2009},
  publisher={American Association for the Advancement of Science}
}

@article{ingolia2014ribosome,
  title={Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes},
  author={Ingolia, Nicholas T and Brar, Gloria A and Stern-Ginossar, Noam and Harris, Michael S and Talhouarne, Ga{\"e}lle JS and Jackson, Sarah E and Wills, Mark R and Weissman, Jonathan S},
  journal={Cell reports},
  volume={8},
  number={5},
  pages={1365--1379},
  year={2014},
  publisher={Elsevier}
}

@article{lauria2018ribowaltz,
  title={riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data},
  author={Lauria, Fabio and Tebaldi, Toma and Bernab{\`o}, Paola and Groen, Ewout JN and Gillingwater, Thomas H and Viero, Gabriella},
  journal={PLoS computational biology},
  volume={14},
  number={8},
  pages={e1006169},
  year={2018},
  publisher={Public Library of Science}
}

@article{mohammad2019systematically,
  title={A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution},
  author={Mohammad, Fuad and Green, Rachel and Buskirk, Allen R},
  journal={Elife},
  volume={8},
  pages={e42591},
  year={2019},
  publisher={eLife Sciences Publications Limited}
}

@article{popa2016riboprofiling,
  title={RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing},
  author={Popa, Alexandra and Lebrigand, Kevin and Paquet, Agnes and Nottet, Nicolas and Robbe-Sermesant, Karine and Waldmann, Rainer and Barbry, Pascal},
  journal={F1000Research},
  volume={5},
  year={2016},
  publisher={Faculty of 1000 Ltd}
}

@article{risso2014normalization,
  title={Normalization of RNA-seq data using factor analysis of control genes or samples},
  author={Risso, Davide and Ngai, John and Speed, Terence P and Dudoit, Sandrine},
  journal={Nature biotechnology},
  volume={32},
  number={9},
  pages={896},
  year={2014},
  publisher={Nature Publishing Group}
}

@mastersthesis{tjeldnes2018atlas,
  title={An Atlas of the Human uORFome and its Regulation across Tissues},
  author={Tjeldnes, H{\aa}kon},
  year={2018},
  school={The University of Bergen}
}
