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@Article{Abouelhoda2004,
  Title                    = {Replacing suffix trees with enhanced suffix arrays},
  Author                   = {Mohamed Ibrahim Abouelhoda and Stefan Kurtz and Enno Ohlebusch},
  Journal                  = {Journal of Discrete Algorithms},
  Year                     = {2004},
  Number                   = {1},
  Pages                    = {53-86},
  Volume                   = {2},

  Doi                      = {10.1016/S1570-8667(03)00065-0},
  File                     = {Abouelhoda2004.pdf:jltsiren/Abouelhoda2004.pdf:PDF},
  Keywords                 = {suffix array, suffix tree, repeat analysis, genome comparison, pattern matching},
  Owner                    = {jltsiren},
  Timestamp                = {2009.04.30}
}

@InProceedings{Boucher2014,
  Title                    = {Variable-Order de {B}ruijn Graphs},
  Author                   = {Christina Boucher and others},
  Booktitle                = {Proc. 2015 IEEE Data Compression Conference (DCC 2015)},
  Year                     = {2015},
  Pages                    = {383-392},
  Publisher                = {IEEE},

  Doi                      = {10.1109/DCC.2015.70},
  File                     = {Boucher2014.pdf:jltsiren/Boucher2014.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.01.12}
}

@InProceedings{Bowe2012,
  Title                    = {Succinct de {B}ruijn Graphs},
  Author                   = {Alexander Bowe and Taku Onodera and Kunihiko Sadakane and Tetsuo Shibuya},
  Booktitle                = {Proc. 12th Workshop on Algorithms in Bioinformatics (WABI 2012)},
  Year                     = {2012},
  Pages                    = {225-235},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {7534},

  Doi                      = {10.1007/978-3-642-33122-0_18},
  File                     = {Bowe2012.pdf:jltsiren/Bowe2012.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2012.09.19}
}

@TechReport{Burrows1994,
  Title                    = {A block sorting lossless data compression algorithm},
  Author                   = {Burrows, Michael and Wheeler, David J.},
  Institution              = {Digital Equipment Corporation},
  Year                     = {1994},
  Number                   = {124},

  File                     = {Burrows1994.pdf:jltsiren/Burrows1994.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2009.04.29}
}

@InProceedings{Cazaux2014,
  Title                    = {From Indexing Data Structures to de Bruijn Graphs},
  Author                   = {Bastien Cazaux and Thierry Lecroq and Eric Rivals},
  Booktitle                = {Proc. 25th Annual Symposium on Combinatorial Pattern Matching (CPM 2014)},
  Year                     = {2014},
  Pages                    = {89-99},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {8486},

  Doi                      = {10.1007/978-3-319-07566-2_10},
  File                     = {Cazaux2014.pdf:jltsiren/Cazaux2014.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2014.06.24}
}

@Article{Church2015,
  Title                    = {Extending reference assembly models},
  Author                   = {Deanna M. Church and others},
  Journal                  = {Genome Biology},
  Year                     = {2015},
  Pages                    = {13},
  Volume                   = {16},

  Doi                      = {10.1186/s13059-015-0587-3},
  File                     = {Church2015.pdf:jltsiren/Church2015.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.10.01}
}

@Article{Danek2014,
  Title                    = {Indexing large genome collections on a {PC}},
  Author                   = {Agnieszka Danek and Sebastian Deorowicz and Szymon Grabowski},
  Journal                  = {PLOS ONE},
  Year                     = {2014},
  Number                   = {10},
  Pages                    = {e109384},
  Volume                   = {9},

  Doi                      = {10.1371/journal.pone.0109384},
  File                     = {Danek2014.pdf:jltsiren/Danek2014.pdf:PDF;Supplementary information:jltsiren/Danek2014-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2014.04.12}
}

@Article{Dilthey2015,
  Title                    = {Improved genome inference in the {MHC} using a population reference graph},
  Author                   = {Alexander Dilthey and others},
  Journal                  = {Nature Genetics},
  Year                     = {2015},
  Number                   = {6},
  Pages                    = {682-688},
  Volume                   = {47},

  Doi                      = {10.1038/ng.3257},
  File                     = {Dilthey2015.pdf:jltsiren/Dilthey2015.pdf:PDF;Supplementary information:jltsiren/Dilthey2015-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.10.01}
}

@Article{Ferragina2009b,
  Title                    = {Compressing and indexing labeled trees, with applications},
  Author                   = {Ferragina, Paolo and Luccio, Fabrizio and Manzini, Giovanni and Muthukrishnan, S.},
  Journal                  = {Journal of the ACM},
  Year                     = {2009},
  Number                   = {1},
  Pages                    = {4},
  Volume                   = {57},

  Doi                      = {10.1145/1613676.1613680},
  File                     = {Ferragina2009b.pdf:jltsiren/Ferragina2009b.pdf:PDF},
  Keywords                 = {Burrows-Wheeler transform, labeled tree compression, labeled tree indexing, path searching, tree navigation, XML compression, XML indexing},
  Owner                    = {jltsiren},
  Timestamp                = {2009.11.18}
}

@Article{Ferragina2005a,
  Title                    = {Indexing compressed text},
  Author                   = {Ferragina, Paolo and Manzini, Giovanni},
  Journal                  = {Journal of the ACM},
  Year                     = {2005},
  Number                   = {4},
  Pages                    = {552-581},
  Volume                   = {52},

  Doi                      = {10.1145/1082036.1082039},
  File                     = {Ferragina2005a.pdf:jltsiren/Ferragina2005a.pdf:PDF},
  Keywords                 = {Burrows-Wheeler transform, full-text indexing, indexing data structure, Lempel-Ziv compressor, pattern searching, suffix tree, suffix array, text compression},
  Owner                    = {jltsiren},
  Timestamp                = {2009.04.30}
}

@Article{Fischer2009a,
  Title                    = {Faster entropy-bounded compressed suffix trees},
  Author                   = {Fischer, Johannes and Mäkinen, Veli and Navarro, Gonzalo},
  Journal                  = {Theoretical Computer Science},
  Year                     = {2009},
  Number                   = {51},
  Pages                    = {5354-5364},
  Volume                   = {410},

  Doi                      = {10.1016/j.tcs.2009.09.012},
  File                     = {Fischer2009a.pdf:jltsiren/Fischer2009a.pdf:PDF},
  Keywords                 = {suffix trees, compressed data structures, range minimum queries},
  Owner                    = {jltsiren},
  Timestamp                = {2010.03.10}
}

@Article{Gagie2012a,
  Title                    = {New algorithms on wavelet trees and applications to information retrieval},
  Author                   = {Travis Gagie and Gonzalo Navarro and Simon J. Puglisi},
  Journal                  = {Theoretical Computer Science},
  Year                     = {2012},
  Pages                    = {25-41},
  Volume                   = {426-427},

  Doi                      = {10.1016/j.tcs.2011.12.002},
  File                     = {Gagie2012a.pdf:jltsiren/Gagie2012a.pdf:PDF},
  Keywords                 = {information retrieval, document retrieval, data structures, 1D range queries, wavelet trees},
  Owner                    = {jltsiren},
  Timestamp                = {2016.04.18}
}

@InProceedings{Gagie2015,
  Title                    = {Document Counting in Compressed Space},
  Author                   = {Travis Gagie and others},
  Booktitle                = {Proc. 2015 IEEE Data Compression Conference (DCC 2015)},
  Year                     = {2015},
  Pages                    = {103-112},
  Publisher                = {IEEE},

  Doi                      = {10.1109/DCC.2015.55},
  File                     = {Gagie2015.pdf:jltsiren/Gagie2015.pdf:PDF;Full version:jltsiren/Gagie2015-full.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.01.08}
}

@Electronic{Garrison2014-2016,
  Title                    = {vg: the variation graph toolkit},
  Author                   = {Erik Garrison and others},
  Note                     = {\url{https://github.com/vgteam/vg}},
  Url                      = {https://github.com/vgteam/vg},
  Year                     = {2014--2016},

  Owner                    = {jltsiren},
  Timestamp                = {2016.04.18}
}

@InProceedings{Gog2014b,
  Title                    = {From Theory to Practice: Plug and Play with Succinct Data Structures},
  Author                   = {Simon Gog and Timo Beller and Alistair Moffat and Matthias Petri},
  Booktitle                = {Proc. 13th International Symposium on Experimental Algorithms (SEA 2014)},
  Year                     = {2014},
  Pages                    = {326-337},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {8504},

  Doi                      = {10.1007/978-3-319-07959-2_28},
  Owner                    = {jltsiren},
  Timestamp                = {2014.05.03}
}

@InProceedings{Grossi2003,
  Title                    = {High-order entropy-compressed text indexes},
  Author                   = {Grossi, Roberto and Gupta, Ankur and Vitter, Jeffrey Scott},
  Booktitle                = {Proc. fourteenth annual ACM-SIAM symposium on Discrete algorithms (SODA 2003)},
  Year                     = {2003},
  Pages                    = {841-850},
  Publisher                = {SIAM},

  File                     = {Grossi2003.pdf:jltsiren/Grossi2003.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2010.12.29}
}

@Article{Huang2013,
  Title                    = {Short read alignment with populations of genomes},
  Author                   = {Lin Huang and Victoria Popic and Serafim Batzoglou},
  Journal                  = {Bioinformatics},
  Year                     = {2013},
  Number                   = {13},
  Pages                    = {i361-i370},
  Volume                   = {29},

  Doi                      = {10.1093/bioinformatics/btt215},
  File                     = {Huang2013.pdf:jltsiren/Huang2013.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2013.06.24}
}

@InProceedings{Huang2010,
  Title                    = {Indexing Similar {DNA} Sequences},
  Author                   = {Huang, Songbo and others},
  Booktitle                = {Proc. The Sixth International Conference on Algorithmic Aspects in Information and Management (AAIM 2010)},
  Year                     = {2010},
  Pages                    = {180-190},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {6124},

  Doi                      = {10.1007/978-3-642-14355-7_19},
  File                     = {Huang2010.pdf:jltsiren/Huang2010.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2010.07.05}
}

@Article{Kim2015,
  Title                    = {{HISAT}: a fast spliced aligner with low memory requirements},
  Author                   = {Daehwan Kim and Ben Langmead and Steven L Salzberg},
  Journal                  = {Nature Methods},
  Year                     = {2015},
  Number                   = {4},
  Pages                    = {357-360},
  Volume                   = {12},

  Doi                      = {10.1038/nmeth.3317},
  File                     = {Kim2015.pdf:jltsiren/Kim2015.pdf:PDF;Supplementary Information:jltsiren/Kim2015-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.03.13}
}

@Electronic{Kim2015-2016,
  Title                    = {{HISAT2}},
  Author                   = {Daehwan Kim and others},
  Note                     = {\url{https://ccb.jhu.edu/software/hisat2/index.shtml}},
  Url                      = {https://ccb.jhu.edu/software/hisat2/index.shtml},
  Year                     = {2015--2016},

  Owner                    = {jltsiren},
  Timestamp                = {2016.04.19}
}

@Unpublished{Li2013,
  Title                    = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
  Author                   = {Heng Li},
  Note                     = {arXiv:1303.3997},
  Year                     = {2013},

  File                     = {Li2013.pdf:jltsiren/Li2013.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.03.26}
}

@Article{Li2009,
  Title                    = {Fast and accurate short read alignment with {B}urrows-{W}heeler transform},
  Author                   = {Heng Li and Richard Durbin},
  Journal                  = {Bioinformatics},
  Year                     = {2009},
  Number                   = {14},
  Pages                    = {1754-1760},
  Volume                   = {25},

  Doi                      = {10.1093/bioinformatics/btp324},
  File                     = {Li2009.pdf:jltsiren/Li2009.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2011.01.05}
}

@Article{Limasset2015,
  Title                    = {Read Mapping on de Bruijn graphs},
  Author                   = {Antoine Limasset and Bastien Cazaux and Eric Rivals and Pierre Peterlongo},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2016},
  Pages                    = {237},
  Volume                   = {17},

  Doi                      = {10.1186/s12859-016-1103-9},
  File                     = {Limasset2015.pdf:jltsiren/Limasset2015.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.04.19}
}

@InProceedings{Lin2014,
  Title                    = {Manifold de {B}ruijn Graphs},
  Author                   = {Yu Lin and Pavel A. Pevzner},
  Booktitle                = {Proc. 14th Workshop on Algorithms in Bioinformatics (WABI 2014)},
  Year                     = {2014},
  Pages                    = {296-310},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {8701},

  Doi                      = {10.1007/978-3-662-44753-6_22},
  File                     = {Lin2014.pdf:jltsiren/Lin2014.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.04.13}
}

@Unpublished{Liu2016,
  Title                    = {{deBGA}: read alignment with de {B}ruijn Graph-based seed and extension},
  Author                   = {Bo Liu and Hongzhe Guo and Michael Brudno and Yadong Wang},
  Note                     = {Accepted to Bioinformatics},
  Year                     = {2016},

  Doi                      = {10.1093/bioinformatics/btw371},
  File                     = {Liu2016.pdf:jltsiren/Liu2016.pdf:PDF;Supplementary material:jltsiren/Liu2016-supplement.docx:Word 2007+},
  Owner                    = {jltsiren},
  Timestamp                = {2016.07.11}
}

@Unpublished{Maciuca2016,
  Title                    = {A natural encoding of genetic variation in a {B}urrows-{W}heeler Transform to enable mapping and genome inference},
  Author                   = {Sorina Maciuca and Carlos del Ojo Elias and Gil McVean and Zamin Iqbal},
  Note                     = {bioRxiv},
  Year                     = {2016},

  Doi                      = {10.1101/059170},
  File                     = {Maciuca2016.pdf:jltsiren/Maciuca2016.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.06.16}
}

@Article{Maekinen2005,
  Title                    = {Succinct suffix arrays based on run-length encoding},
  Author                   = {Mäkinen, Veli and Navarro, Gonzalo},
  Journal                  = {Nordic Journal of Computing},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {40-66},
  Volume                   = {12},

  File                     = {Maekinen2005.ps:jltsiren/Maekinen2005.ps:PostScript},
  Keywords                 = {compressed full-text self-indexes, empirical k-th order entropy, indexed string matching, text retrieval, Burrows-Wheeler transform, suffix arrays, run-length compression},
  Owner                    = {jltsiren},
  Timestamp                = {2007.12.03}
}

@Article{Maekinen2010,
  Title                    = {Storage and Retrieval of Highly Repetitive Sequence Collections},
  Author                   = {Mäkinen, Veli and Navarro, Gonzalo and Sirén, Jouni and Välimäki, Niko},
  Journal                  = {Journal of Computational Biology},
  Year                     = {2010},
  Number                   = {3},
  Pages                    = {281-308},
  Volume                   = {17},

  Doi                      = {10.1089/cmb.2009.0169},
  File                     = {Maekinen2010.pdf:jltsiren/Maekinen2010.pdf:PDF},
  Keywords                 = {comparative genomics, compressed data structures, full-text indexing, suffix tree},
  Owner                    = {jltsiren},
  Timestamp                = {2010.04.14}
}

@Article{Manber1993,
  Title                    = {Suffix Arrays: A New Method for On-Line String Searches},
  Author                   = {Udi Manber and Gene Myers},
  Journal                  = {SIAM Journal on Computing},
  Year                     = {1993},
  Number                   = {5},
  Pages                    = {935-948},
  Volume                   = {22},

  Doi                      = {10.1137/0222058},
  File                     = {Manber1993.pdf:jltsiren/Manber1993.pdf:PDF},
  Keywords                 = {string searching, string matching, pattern matching, suffix trees, algorithms, text indexing, inverted indices},
  Owner                    = {jltsiren},
  Timestamp                = {2011.03.02}
}

@Article{Marcus2014,
  Title                    = {{SplitMEM}: a graphical algorithm for pan-genome analysis with suffix skips},
  Author                   = {Shoshana Marcus and Hayan Lee and Michael C. Schatz},
  Journal                  = {Bioinformatics},
  Year                     = {2014},
  Number                   = {24},
  Pages                    = {3476-3483},
  Volume                   = {30},

  Doi                      = {10.1093/bioinformatics/btu756},
  File                     = {Marcus2014.pdf:jltsiren/Marcus2014.pdf:PDF;Supplementary material:jltsiren/Marcus2014-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.10.01}
}

@Unpublished{Marschall2016,
  Title                    = {Computational Pan-Genomics: Status, Promises and Challenges},
  Author                   = {Tobias Marschall and others},
  Note                     = {BioRxiv},
  Year                     = {2016},

  Doi                      = {http://dx.doi.org/10.1101/043430},
  File                     = {Marschall2016.pdf:jltsiren/Marschall2016.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.04.19}
}

@Article{Na2015,
  Title                    = {{FM}-index of alignment: A compressed index for similar strings},
  Author                   = {Joong Chae Na and others},
  Journal                  = {Theoretical Computer Science},
  Year                     = {2016},
  Pages                    = {159-170},
  Volume                   = {638},

  Doi                      = {10.1016/j.tcs.2015.08.008},
  File                     = {Na2015.pdf:jltsiren/Na2015.pdf:PDF},
  Keywords                 = {indexes for similar strings, FM-indexes, suffix arrays, alignments, backward search},
  Owner                    = {jltsiren},
  Timestamp                = {2015.08.18}
}

@Unpublished{Na2016,
  Title                    = {{FM}-index of Alignment with Gaps},
  Author                   = {Joong Chae Na and others},
  Note                     = {arXiv:1606.03897},
  Year                     = {2016},

  File                     = {Na2016.pdf:jltsiren/Na2016.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.06.14}
}

@Unpublished{Novak2016,
  Title                    = {A Graph Extension of the Positional {B}urrows-{W}heeler Transform and its Applications},
  Author                   = {Adam M. Novak and Erik Garrison and Benedict Paten},
  Note                     = {bioRxiv},
  Year                     = {2016},

  Doi                      = {10.1101/051409},
  File                     = {Novak2016.pdf:jltsiren/Novak2016.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.05.03}
}

@InProceedings{Ohlebusch2010a,
  Title                    = {Computing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes},
  Author                   = {Enno Ohlebusch and Simon Gog and Adrian Kügel},
  Booktitle                = {Proc. 17th Symposium on String Processing and Information Retrieval (SPIRE 2010)},
  Year                     = {2010},
  Pages                    = {347-358},
  Publisher                = {Springer},
  Series                   = {LNCS},
  Volume                   = {6393},

  Doi                      = {10.1007/978-3-642-16321-0_36},
  File                     = {Ohlebusch2010a.pdf:jltsiren/Ohlebusch2010a.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.05.05}
}

@InProceedings{Okanohara2007,
  Title                    = {Practical Entropy-Compressed Rank/Select Dictionary},
  Author                   = {Okanohara, Daisuke and Sadakane, Kunihiko},
  Booktitle                = {Proc. Ninth Workshop on Algorithm Engineering and Experiments (ALENEX 2007)},
  Year                     = {2007},
  Pages                    = {60-70},
  Publisher                = {SIAM},

  File                     = {Okanohara2007.pdf:jltsiren/Okanohara2007.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2010.07.05}
}

@Unpublished{Paten2014,
  Title                    = {Mapping to a Reference Genome Structure},
  Author                   = {Benedict Paten and Adam Novak and David Haussler},
  Note                     = {arXiv:1404.5010},
  Year                     = {2014},

  File                     = {Paten2014.pdf:jltsiren/Paten2014.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.10.01}
}

@Article{Pell2012,
  Title                    = {Scaling metagenome sequence assembly with probabilistic de {B}ruijn graphs},
  Author                   = {Jason Pell and others},
  Journal                  = {Proc. National Academy of Sciences of the United States of America},
  Year                     = {2012},
  Number                   = {33},
  Pages                    = {13272–13277},
  Volume                   = {109},

  Doi                      = {10.1073/pnas.1121464109},
  File                     = {Pell2012.pdf:jltsiren/Pell2012.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2016.06.23}
}

@Article{Roedland2013,
  Title                    = {Compact representation of k-mer de {B}ruijn graphs for genome read assembly},
  Author                   = {Einar Andreas Rødland},
  Journal                  = {BMC Bioinformatics},
  Year                     = {2013},
  Pages                    = {313},
  Volume                   = {14},

  Doi                      = {10.1186/1471-2105-14-313},
  File                     = {Roedland2013.pdf:jltsiren/Roedland2013.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2014.02.10}
}

@Article{Sadakane2007,
  Title                    = {Compressed Suffix Trees with Full Functionality},
  Author                   = {Kunihiko Sadakane},
  Journal                  = {Theory of Computing Systems},
  Year                     = {2007},
  Number                   = {4},
  Pages                    = {589-607},
  Volume                   = {41},

  Doi                      = {10.1007/s00224-006-1198-x},
  File                     = {Sadakane2007.pdf:jltsiren/Sadakane2007.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2009.09.09}
}

@Article{Sadakane2007a,
  Title                    = {Succinct data structures for flexible text retrieval systems},
  Author                   = {Kunihiko Sadakane},
  Journal                  = {Journal of Discrete Algorithms},
  Year                     = {2007},
  Number                   = {1},
  Pages                    = {12-22},
  Volume                   = {5},

  Doi                      = {10.1016/j.jda.2006.03.011},
  File                     = {Sadakane2007a.pdf:jltsiren/Sadakane2007a.pdf:PDF},
  Keywords                 = {information retrieval, Tf*idf, succinct data structures, succinct trees, inverted files},
  Owner                    = {jltsiren},
  Timestamp                = {2013.05.22}
}

@Article{Schneeberger2009,
  Title                    = {Simultaneous alignment of short reads against multiple genomes},
  Author                   = {Korbinian Schneeberger and others},
  Journal                  = {Genome Biology},
  Year                     = {2009},
  Number                   = {9},
  Pages                    = {R98},
  Volume                   = {10},

  Doi                      = {10.1186/gb-2009-10-9-r98},
  File                     = {Schneeberger2009.pdf:jltsiren/Schneeberger2009.pdf:PDF;Supplementary information:jltsiren/Schneeberger2009-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.07.01}
}

@Article{Siren2014,
  Title                    = {Indexing Graphs for Path Queries with Applications in Genome Research},
  Author                   = {Jouni Sirén and Niko Välimäki and Veli Mäkinen},
  Journal                  = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  Year                     = {2014},
  Number                   = {2},
  Pages                    = {375-388},
  Volume                   = {11},

  Doi                      = {10.1109/TCBB.2013.2297101},
  File                     = {Siren2014.pdf:jltsiren/Siren2014.pdf:PDF},
  Keywords                 = {pan-genome indexing, graph indexing, read alignment, variation calling, extended Burrows-Wheeler transform},
  Owner                    = {jltsiren},
  Timestamp                = {2014.03.09}
}

@Article{Thachuk2013,
  Title                    = {Indexing hypertext},
  Author                   = {Chris Thachuk},
  Journal                  = {Journal of Discrete Algorithms},
  Year                     = {2013},
  Pages                    = {113-122},
  Volume                   = {18},

  Doi                      = {10.1016/j.jda.2012.10.001},
  File                     = {Thachuk2013.pdf:jltsiren/Thachuk2013.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.07.17}
}

@Article{1000GP2015,
  Title                    = {A global reference for human genetic variation},
  Author                   = {{The 1000 Genomes Project Consortium}},
  Journal                  = {Nature},
  Year                     = {2015},
  Pages                    = {68-64},
  Volume                   = {526},

  Doi                      = {10.1038/nature15393},
  File                     = {1000GP2015.pdf:jltsiren/1000GP2015.pdf:PDF;Supplementary information:jltsiren/1000GP2015-supplement.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2015.10.08}
}

@Article{Wandelt2013,
  Title                    = {{RCSI}: Scalable similarity search in thousand(s) of genomes},
  Author                   = {Sebastian Wandelt and Johannes Starlinger and Marc Bux and Ulf Leser},
  Journal                  = {Proc. VLDB Endowment},
  Year                     = {2013},
  Number                   = {13},
  Pages                    = {1534-1545},
  Volume                   = {6},

  File                     = {Wandelt2013.pdf:jltsiren/Wandelt2013.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2014.01.15}
}

@InProceedings{Weiner1973,
  Title                    = {Linear pattern matching algorithms},
  Author                   = {Weiner, Peter},
  Booktitle                = {Proc. 14th Annual IEEE Symposium on Switching and Automata Theory (FOCS 1973)},
  Year                     = {1973},
  Pages                    = {1-11},
  Publisher                = {IEEE},

  Doi                      = {10.1109/SWAT.1973.13},
  File                     = {Weiner1973.pdf:jltsiren/Weiner1973.pdf:PDF},
  Owner                    = {jltsiren},
  Timestamp                = {2011.03.02}
}

