
@article{AMBROS01032003,
author = {AMBROS, VICTOR and BARTEL, BONNIE and BARTEL, DAVID P. and BURGE, CHRISTOPHER B. and CARRINGTON, JAMES C. and CHEN, XUEMEI and DREYFUSS, GIDEON and EDDY, SEAN R and GRIFFITHS-JONES, SAM and MARSHALL, MHAIRI and MATZKE, MARJORI and RUVKUN, GARY and TUSCHL, THOMAS},
title = {A uniform system for microRNA annotation},
volume = {9},
number = {3},
pages = {277-279},
year = {2003},
doi = {10.1261/rna.2183803},
abstract ={MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for the identification and annotation of new miRNAs from diverse organisms, particularly so that miRNAs can be reliably distinguished from other RNAs such as small interfering RNAs. We describe specific criteria for the experimental verification of miRNAs, and conventions for naming miRNAs and miRNA genes. Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families.},
URL = {http://rnajournal.cshlp.org/content/9/3/277.abstract},
eprint = {http://rnajournal.cshlp.org/content/9/3/277.full.pdf+html},
journal = {RNA}
}

@article{meyers2008criteria,
  title={Criteria for annotation of plant MicroRNAs},
  author={Meyers, Blake C and Axtell, Michael J and Bartel, Bonnie and Bartel, David P and Baulcombe, David and Bowman, John L and Cao, Xiaofeng and Carrington, James C and Chen, Xuemei and Green, Pamela J and others},
  journal={The Plant Cell},
  volume={20},
  number={12},
  pages={3186--3190},
  year={2008},
  publisher={Am Soc Plant Biol}
}

@article{Griffiths-Jones01012004,
author = {Griffiths-Jones, Sam},
title = {The microRNA Registry},
volume = {32},
number = {suppl 1},
pages = {D109-D111},
year = {2004},
doi = {10.1093/nar/gkh023},
abstract ={The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for download. Release 2.0 of the database contains 506 miRNA entries from six organisms.},
URL = {http://nar.oxfordjournals.org/content/32/suppl_1/D109.abstract},
eprint = {http://nar.oxfordjournals.org/content/32/suppl_1/D109.full.pdf+html},
journal = {Nucleic Acids Research}
}

@article{Griffiths-Jones01012006,
author = {Griffiths-Jones, Sam and Grocock, Russell J. and van Dongen, Stijn and Bateman, Alex and Enright, Anton J.},
title = {miRBase: microRNA sequences, targets and gene nomenclature},
volume = {34},
number = {suppl 1},
pages = {D140-D144},
year = {2006},
doi = {10.1093/nar/gkj112},
abstract ={The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA sequence data and annotation. miRBase Targets is a comprehensive new database of predicted miRNA target genes. miRBase is available at http://microrna.sanger.ac.uk/.},
URL = {http://nar.oxfordjournals.org/content/34/suppl_1/D140.abstract},
eprint = {http://nar.oxfordjournals.org/content/34/suppl_1/D140.full.pdf+html},
journal = {Nucleic Acids Research}
}

@article{Griffiths-Jones01012008,
author = {Griffiths-Jones, Sam and Saini, Harpreet Kaur and van Dongen, Stijn and Enright, Anton J.},
title = {miRBase: tools for microRNA genomics},
volume = {36},
number = {suppl 1},
pages = {D154-D158},
year = {2008},
doi = {10.1093/nar/gkm952},
abstract ={miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs are mapped to their genomic coordinates. Clusters of miRNA sequences in the genome are highlighted, and can be defined and retrieved with any inter-miRNA distance. The overlap of miRNA sequences with annotated transcripts, both protein- and non-coding, are described. Finally, graphical views of the locations of a wide range of genomic features in model organisms allow for the first time the prediction of the likely boundaries of many miRNA primary transcripts. miRBase is available at http://microrna.sanger.ac.uk/.},
URL = {http://nar.oxfordjournals.org/content/36/suppl_1/D154.abstract},
eprint = {http://nar.oxfordjournals.org/content/36/suppl_1/D154.full.pdf+html},
journal = {Nucleic Acids Research}
}

@article{Kozomara01012011,
author = {Kozomara, Ana and Griffiths-Jones, Sam},
title = {miRBase: integrating microRNA annotation and deep-sequencing data},
volume = {39},
number = {suppl 1},
pages = {D152-D157},
year = {2011},
doi = {10.1093/nar/gkq1027},
abstract ={miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15 000 microRNA gene loci in over 140 species, and over 17 000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.},
URL = {http://nar.oxfordjournals.org/content/39/suppl_1/D152.abstract},
eprint = {http://nar.oxfordjournals.org/content/39/suppl_1/D152.full.pdf+html},
journal = {Nucleic Acids Research}
}

@article{Kozomara01012014,
author = {Kozomara, Ana and Griffiths-Jones, Sam},
title = {miRBase: annotating high confidence microRNAs using deep sequencing data},
volume = {42},
number = {D1},
pages = {D68-D73},
year = {2014},
doi = {10.1093/nar/gkt1181},
abstract ={We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.},
URL = {http://nar.oxfordjournals.org/content/42/D1/D68.abstract},
eprint = {http://nar.oxfordjournals.org/content/42/D1/D68.full.pdf+html},
journal = {Nucleic Acids Research}
}

@Manual{bibtex,
  title = {bibtex: bibtex parser},
  author = {Romain Francois},
  year = {2014},
  note = {R package version 0.4.0},
  url = {http://CRAN.R-project.org/package=bibtex}
}

@Manual{knitr1,
  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  author = {Yihui Xie},
  year = {2015},
  note = {R package version 1.11},
  url = {http://yihui.name/knitr/}
}

@Book{knitr2,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.name/knitr/}
}

@InCollection{knitr3,
  booktitle = {Implementing Reproducible Computational Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595}
}

@Manual{knitcitations,
  title = {knitcitations: Citations for 'Knitr' Markdown Files},
  author = {Carl Boettiger},
  year = {2015},
  note = {R package version 1.0.7},
  url = {http://CRAN.R-project.org/package=knitcitations}
}

@Manual{rsqlitecite,
    title = {RSQLite: SQLite Interface for R},
    author = {Hadley Wickham and David A. James and Seth Falcon},
    year = {2014},
    note = {R package version 1.0.0},
    url = {http://CRAN.R-project.org/package=RSQLite}
}

@Manual{annotdbicite,
    title = {AnnotationDbi: Annotation Database Interface},
    author = {Pages H, Carlson M, Falcon S and Li N},
    year = {2016},
    note = {R package version 1.32.3},
    url = {https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html}
}

@Manual{toolscite,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2015},
    url = {https://www.R-project.org/}
 }

@Manual{mirbaseversionscite,
    title = {miRBaseVersions.db: Collection of mature miRNA names of 21 different miRBase release
versions},
    author = {Stefan J. Haunsberger},
    year = {2016},
    note = {R package version 0.99.0},
  }
