% Encoding: UTF-8

@Article{friedlander2011mirdeep2,
  author    = {Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
  title     = {miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
  journal   = {Nucleic acids research},
  year      = {2011},
  volume    = {40},
  number    = {1},
  pages     = {37--52},
  publisher = {Oxford University Press},
  doi={10.1093/nar/gkr688},
  url={https://doi.org/10.1093/nar/gkr688}
}

@Article{martin2011cutadapt,
  author  = {Martin, Marcel},
  title   = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
  journal = {EMBnet. journal},
  year    = {2011},
  volume  = {17},
  number  = {1},
  pages   = {pp--10},
  doi={10.14806/ej.17.1.200},
  url={http://dx.doi.org/10.14806/ej.17.1.200}
}

@Article{pantano2009seqbuster,
  author    = {Pantano, Lorena and Estivill, Xavier and Mart{\'\i}, Eul{\`a}lia},
  title     = {SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells},
  journal   = {Nucleic acids research},
  year      = {2009},
  volume    = {38},
  number    = {5},
  pages     = {e34--e34},
  publisher = {Oxford University Press},
  doi={10.1093/nar/gkp1127},
  url={https://doi.org/10.1093/nar/gkp1127}
}

@Article{kozomara2013mirbase,
  author    = {Kozomara, Ana and Griffiths-Jones, Sam},
  title     = {miRBase: annotating high confidence microRNAs using deep sequencing data},
  journal   = {Nucleic acids research},
  year      = {2013},
  volume    = {42},
  number    = {D1},
  pages     = {D68--D73},
  publisher = {Oxford University Press},
  doi={10.1093/nar/gkt1181},
  url={https://doi.org/10.1093/nar/gkt1181}
}

@Article{betel2008microrna,
  author    = {Betel, Doron and Wilson, Manda and Gabow, Aaron and Marks, Debora S and Sander, Chris},
  title     = {The microRNA. org resource: targets and expression},
  journal   = {Nucleic acids research},
  year      = {2008},
  volume    = {36},
  number    = {suppl\_1},
  pages     = {D149--D153},
  publisher = {Oxford University Press},
  doi={10.1093/nar/gkm995},
  url={https://doi.org/10.1093/nar/gkm995}
}

@article{wu2010fast,
  title={Fast and SNP-tolerant detection of complex variants and splicing in short reads},
  author={Wu, Thomas D and Nacu, Serban},
  journal={Bioinformatics},
  volume={26},
  number={7},
  pages={873--881},
  year={2010},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btq057},
  url={https://doi.org/10.1093/bioinformatics/btq057}
}

@Article{uren2012site,
  author    = {Uren, Philip J and Bahrami-Samani, Emad and Burns, Suzanne C and Qiao, Mei and Karginov, Fedor V and Hodges, Emily and Hannon, Gregory J and Sanford, Jeremy R and Penalva, Luiz OF and Smith, Andrew D},
  title     = {Site identification in high-throughput RNA--protein interaction data},
  journal   = {Bioinformatics},
  year      = {2012},
  volume    = {28},
  number    = {23},
  pages     = {3013--3020},
  publisher = {Oxford University Press},
  doi={10.1093/bioinformatics/bts569},
  url={https://doi.org/10.1093/bioinformatics/bts569}
}

@Misc{rice2000emboss,
  author    = {Rice, Peter and Longden, Ian and Bleasby, Alan},
  title     = {EMBOSS: the European molecular biology open software suite},
  year      = {2000},
  publisher = {Elsevier Current Trends},
  doi={10.1016/S0168-9525(00)02024-2},
  url={https://doi.org/10.1016/S0168-9525(00)02024-2}
}

@Article{li2009fast,
  author    = {Li, Heng and Durbin, Richard},
  title     = {Fast and accurate short read alignment with Burrows--Wheeler transform},
  journal   = {Bioinformatics},
  year      = {2009},
  volume    = {25},
  number    = {14},
  pages     = {1754--1760},
  publisher = {Oxford University Press},
  doi={},
  url={}
}

@Article{altschul1990basic,
  author    = {Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J},
  title     = {Basic local alignment search tool},
  journal   = {Journal of molecular biology},
  year      = {1990},
  volume    = {215},
  number    = {3},
  pages     = {403--410},
  publisher = {Elsevier},
  doi={10.1016/S0022-2836(05)80360-2},
  url={https://doi.org/10.1016/S0022-2836(05)80360-2}
}

@Article{li2009sequence,
  author    = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
  title     = {The sequence alignment/map format and SAMtools},
  journal   = {Bioinformatics},
  year      = {2009},
  volume    = {25},
  number    = {16},
  pages     = {2078--2079},
  publisher = {Oxford University Press},
  doi={10.1093/bioinformatics/btp352},
  url={https://doi.org/10.1093/bioinformatics/btp352}
}

@Article{quinlan2010bedtools,
  author    = {Quinlan, Aaron R and Hall, Ira M},
  title     = {BEDTools: a flexible suite of utilities for comparing genomic features},
  journal   = {Bioinformatics},
  year      = {2010},
  volume    = {26},
  number    = {6},
  pages     = {841--842},
  publisher = {Oxford University Press},
  doi={10.1093/bioinformatics/btq033},
  url={https://doi.org/10.1093/bioinformatics/btq033}
}

@Article{lechner2011proteinortho,
  author    = {Lechner, Marcus and Findei{\ss}, Sven and Steiner, Lydia and Marz, Manja and Stadler, Peter F and Prohaska, Sonja J},
  title     = {Proteinortho: detection of (co-) orthologs in large-scale analysis},
  journal   = {BMC bioinformatics},
  year      = {2011},
  volume    = {12},
  number    = {1},
  pages     = {124},
  publisher = {BioMed Central},
  doi={10.1186/1471-2105-12-124},
  url={https://doi.org/10.1186/1471-2105-12-124}
}
@article{zhang2017transcriptome,
  title={Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti},
  author={Zhang, Xiufeng and Aksoy, Emre and Girke, Thomas and Raikhel, Alexander S and Karginov, Fedor V},
  journal={Proceedings of the National Academy of Sciences},
  volume={114},
  number={10},
  pages={E1895--E1903},
  year={2017},
  publisher={National Acad Sciences},
  doi={10.1073/pnas.1701474114},
  url={https://doi.org/10.1073/pnas.1701474114}
}
@article{amsel2017evaluation,
  title={Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum},
  author={Amsel, Daniel and Vilcinskas, Andreas and Billion, Andr{\'e}},
  journal={BMC bioinformatics},
  volume={18},
  number={1},
  pages={359},
  year={2017},
  publisher={BioMed Central},
  doi={10.1186/s12859-017-1772-z},
  url={https://doi.org/10.1186/s12859-017-1772-z}
}

@Comment{jabref-meta: databaseType:bibtex;}
