paper.bib

@article{ucsc2002,
author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler,  and David}, 
title = {The Human Genome Browser at UCSC},
volume = {12}, 
number = {6}, 
pages = {996-1006}, 
year = {2002}, 
doi = {10.1101/gr.229102}, 
abstract ={As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided athttp://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.}, 
URL = {http://genome.cshlp.org/content/12/6/996.abstract}, 
eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html}, 
journal = {Genome Research} 
}


@article{ensembl2018,
author = {Zerbino, Daniel R and Achuthan, Premanand and Akanni, Wasiu and Amode, M Ridwan and Barrell, Daniel and Bhai, Jyothish and Billis, Konstantinos and Cummins, Carla and Gall, Astrid and Girón, Carlos García and Gil, Laurent and Gordon, Leo and Haggerty, Leanne and Haskell, Erin and Hourlier, Thibaut and Izuogu, Osagie G and Janacek, Sophie H and Juettemann, Thomas and To, Jimmy Kiang and Laird, Matthew R and Lavidas, Ilias and Liu, Zhicheng and Loveland, Jane E and Maurel, Thomas and McLaren, William and Moore, Benjamin and Mudge, Jonathan and Murphy, Daniel N and Newman, Victoria and Nuhn, Michael and Ogeh, Denye and Ong, Chuang Kee and Parker, Anne and Patricio, Mateus and Riat, Harpreet Singh and Schuilenburg, Helen and Sheppard, Dan and Sparrow, Helen and Taylor, Kieron and Thormann, Anja and Vullo, Alessandro and Walts, Brandon and Zadissa, Amonida and Frankish, Adam and Hunt, Sarah E and Kostadima, Myrto and Langridge, Nicholas and Martin, Fergal J and Muffato, Matthieu and Perry, Emily and Ruffier, Magali and Staines, Dan M and Trevanion, Stephen J and Aken, Bronwen L and Cunningham, Fiona and Yates, Andrew and Flicek, Paul},
title = {Ensembl 2018},
journal = {Nucleic Acids Research},
volume = {46},
number = {D1},
pages = {D754-D761},
year = {2018},
doi = {10.1093/nar/gkx1098},
URL = {http://dx.doi.org/10.1093/nar/gkx1098}
}

@misc{MANIFESTO,
  author        = {Pjotr Prins},
  title         = {The Small Tools Manifesto for Bioinformatics},
  year          = {2014},
  doi           = {10.5281/zenodo.11321},
  url           = {http://dx.doi.org/10.5281/zenodo.11321}
 }