@article{kang2018,
	title = {miRTrace reveals the organismal origins of microRNA sequencing data},
	author = {Kang, Wenjing and Eldfjell, Yrin and Fromm, Bastian and Estivill, Xavier and Biryukova, Inna and {Friedländer}, Marc R.},
	year = {2018},
	month = {12},
	journal = {Genome Biology},
	volume = {19},
	number = {1},
	doi = {10.1186/s13059-018-1588-9},
	url = {http://dx.doi.org/10.1186/s13059-018-1588-9},
	langid = {en}
}

@misc{umu2022,
	title = {Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine},
	author = {Umu, {Sinan U{\u{g}}ur} and Paynter, Vanessa M. and Trondsen, {Håvard} and Buschmann, Tilo and Rounge, Trine B. and Peterson, Kevin J. and Fromm, Bastian},
	year = {2022},
	month = {11},
	url = {http://dx.doi.org/10.1101/2022.11.23.517654}
}

@article{johnson2016,
	title = {Improved Placement of Multi-mapping Small RNAs},
	author = {Johnson, Nathan R and Yeoh, Jonathan M and Coruh, Ceyda and Axtell, Michael J},
	year = {2016},
	month = {07},
	journal = {G3 Genes|Genomes|Genetics},
	pages = {2103--2111},
	volume = {6},
	number = {7},
	doi = {10.1534/g3.116.030452},
	url = {http://dx.doi.org/10.1534/g3.116.030452},
	langid = {en}
}

@article{shahid2014,
	title = {Identification and annotation of small RNA genes using ShortStack},
	author = {Shahid, Saima and Axtell, Michael J.},
	year = {2014},
	month = {05},
	journal = {Methods},
	pages = {20--27},
	volume = {67},
	number = {1},
	doi = {10.1016/j.ymeth.2013.10.004},
	url = {http://dx.doi.org/10.1016/j.ymeth.2013.10.004},
	langid = {en}
}

@article{axtell2013a,
	title = {ShortStack: Comprehensive annotation and quantification of small RNA genes},
	author = {Axtell, Michael J.},
	year = {2013},
	month = {04},
	journal = {RNA},
	pages = {740--751},
	volume = {19},
	number = {6},
	doi = {10.1261/rna.035279.112},
	url = {http://dx.doi.org/10.1261/rna.035279.112},
	langid = {en}
}

@article{shahid2014,
	title = {Identification and annotation of small RNA genes using ShortStack},
	author = {Shahid, Saima and Axtell, Michael J.},
	year = {2014},
	month = {05},
	journal = {Methods},
	pages = {20--27},
	volume = {67},
	number = {1},
	doi = {10.1016/j.ymeth.2013.10.004},
	url = {http://dx.doi.org/10.1016/j.ymeth.2013.10.004}
}

@article{johnson2016a,
	title = {Improved Placement of Multi-mapping Small RNAs},
	author = {Johnson, Nathan R and Yeoh, Jonathan M and Coruh, Ceyda and Axtell, Michael J},
	year = {2016},
	month = {07},
	journal = {G3 Genes|Genomes|Genetics},
	pages = {2103--2111},
	volume = {6},
	number = {7},
	doi = {10.1534/g3.116.030452},
	url = {http://dx.doi.org/10.1534/g3.116.030452},
	langid = {en}
}

@article{altschul1990,
	title = {Basic local alignment search tool},
	author = {Altschul, Stephen F. and Gish, Warren and Miller, Webb and Myers, Eugene W. and Lipman, David J.},
	year = {1990},
	month = {10},
	journal = {Journal of Molecular Biology},
	pages = {403--410},
	volume = {215},
	number = {3},
	doi = {10.1016/s0022-2836(05)80360-2},
	url = {http://dx.doi.org/10.1016/s0022-2836(05)80360-2},
	langid = {en}
}

@article{friedländer2011,
	title = {miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
	author = {{Friedländer}, Marc R. and Mackowiak, Sebastian D. and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
	year = {2011},
	month = {09},
	date = {2011-09-10},
	journal = {Nucleic Acids Research},
	pages = {37--52},
	volume = {40},
	number = {1},
	doi = {10.1093/nar/gkr688},
	url = {http://dx.doi.org/10.1093/nar/gkr688},
	langid = {en}
}