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@MISC{oai:CiteSeerPSU:481302,
  author = {Paolo Ferragina and Giovanni Manzini},
  title = {Opportunistic Data Structures with Applications},
  month = sep # {~03},
  year = {2000},
  abstract = {In this paper we address the issue of compressing and indexing data.
	We devise a data structure whose space occupancy is a function of
	the entropy of the underlying data set. We call the data structure
	opportunistic since its space occupancy is decreased when the input
	is compressible and this space reduction is achieved at no significant
	slowdown in the query performance. More precisely, its space occupancy
	is optimal in an information-content sense because a text T [1, u]
	is stored using O(H k (T )) + o(1) bits per input symbol in the worst
	case, where H k (T ) is the kth order empirical entropy of T (the
	bound holds for any fixed k). Given an arbitrary string P [1; p],
	the opportunistic data structure allows one to search for the occ occurrences
	of P in T in O(p + occ log u) time (for any fixed > 0). If data are
	uncompressible we achieve the best space bound currently known [12];
	on compressible data our solution improves the succinct suffix array
	of [12] and the classical suffix tree and suffix array data structures
	either in space or in query time or both.},
  annote = {Paolo Ferragina (Universita di Pisa); Giovanni Manzini (Universita
	del Piemonte Orientale);},
  bdsk-url-1 = {http://citeseer.ist.psu.edu/481302.html;%20%20%20%20http://butirro.di.unipi.it/FM-index/FM-pages/../../Latex/focs00.ps},
  bibsource = {OAI-PMH server at cs1.ist.psu.edu},
  citeseer-references = {oai:CiteSeerPSU:227724; oai:CiteSeerPSU:371352; oai:CiteSeerPSU:76182;
	oai:CiteSeerPSU:104285; oai:CiteSeerPSU:226353; oai:CiteSeerPSU:370410;
	oai:CiteSeerPSU:460358; oai:CiteSeerPSU:16136; oai:CiteSeerPSU:506611;
	oai:CiteSeerPSU:1331; oai:CiteSeerPSU:688013; oai:CiteSeerPSU:456171;
	oai:CiteSeerPSU:161058; oai:CiteSeerPSU:174195},
  date-added = {2008-02-20 11:27:59 +0100},
  date-modified = {2008-02-20 11:27:59 +0100},
  language = {english},
  oai = {oai:CiteSeerPSU:481302},
  rights = {unrestricted},
  url = {http://citeseer.ist.psu.edu/481302.html; http://butirro.di.unipi.it/FM-index/FM-pages/../../Latex/focs00.ps}
}

@ARTICLE{journals/talg/FerraginaMMN07,
  author = {Paolo Ferragina and Giovanni Manzini and Veli M{\"a}kinen and Gonzalo
	Navarro},
  title = {Compressed representations of sequences and full-text indexes},
  journal = {ACM Transactions on Algorithms},
  year = {2007},
  volume = {3},
  number = {2},
  bdsk-url-1 = {http://doi.acm.org/10.1145/1240233.1240243},
  bibdate = {2007-10-23},
  bibsource = {DBLP, http://dblp.uni-trier.de/db/journals/talg/talg3.html#FerraginaMMN07},
  date-added = {2008-02-20 11:28:58 +0100},
  date-modified = {2008-02-20 11:28:58 +0100},
  url = {http://doi.acm.org/10.1145/1240233.1240243}
}

@MISC{genometools,
  author = {Gordon Gremme},
  title = {The \textsc{GenomeTools} genome analysis system},
  date-added = {2008-02-19 16:32:19 +0100},
  date-modified = {2008-02-19 16:45:15 +0100},
  note = {\url{http://genometools.org}},
  url = {http://genometools.org}
}

@INPROCEEDINGS{HAU:DOM:WIE:2008,
  author = {Haubold, Bernhard and Domazet-Loso, Mirjana and Wiehe, Thomas},
  title = {An Alignment-Free Distance Measure for Closely Related Genomes},
  booktitle = {RECOMB-CG ’08: Proceedings of the international workshop on Comparative
	Genomics},
  year = {2008},
  pages = {87-99},
  address = {Berlin, Heidelberg},
  publisher = {Springer-Verlag},
  doi = {http://dx.doi.org/10.1007/978-3-540-87989-3_7},
  file = {:/home/willrodt/Documents/Paper/HauDomWie2008.pdf:PDF},
  isbn = {978-3-540-87988-6},
  location = {Paris, France},
  owner = {willrodt},
  timestamp = {2011.05.10}
}

@ARTICLE{HAU:PFA:DOM:WIE:2009,
  author = {Haubold, B. and Pfaffelhuber, P. and Domazet-Loso, M. and Wiehe,
	T.},
  title = {Estimating Mutation Distances from Unaligned Genomes},
  journal = {J. Comput. Biol.},
  year = {2009},
  volume = {16},
  pages = {1487-1500},
  month = {"Oct"},
  file = {:/home/willrodt/Documents/Paper/HauPfaDomWie2009.pdf:PDF},
  owner = {willrodt},
  timestamp = {2011.05.10}
}

@ARTICLE{HAU:REE:PFA:2011,
  author = {Haubold, Bernhard and Reed, Floyd A. and Pfaffelhuber, Peter},
  title = {Alignment-free estimation of nucleotide diversity},
  journal = {Bioinformatics},
  year = {2011},
  volume = {27},
  pages = {449-455},
  number = {4},
  abstract = {Motivation: Sequencing capacity is currently growing more rapidly
	than CPU speed, leading to an analysis bottleneck in many genome
	projects. Alignment-free sequence analysis methods tend to be more
	efficient than their alignment-based counterparts. They may, therefore,
	be important in the long run for keeping sequence analysis abreast
	with sequencing.Results: We derive and implement an alignment-free
	estimator of the number of pairwise mismatches, . Our implementation
	of , pim, is based on an enhanced suffix array and inherits the superior
	time and memory efficiency of this data structure. Simulations demonstrate
	that is accurate if mutations are distributed randomly along the
	chromosome. While real data often deviates from this ideal, remains
	useful for identifying regions of low genetic diversity using a sliding
	window approach. We demonstrate this by applying it to the complete
	genomes of 37 strains of Drosophila melanogaster, and to the genomes
	of two closely related Drosophila species, D.simulans and D.sechellia.
	In both cases, we detect the diversity minimum and discuss its biological
	implications.Availability: pim is written in standard C and its sources
	can be downloaded from http://guanine.evolbio.mpg.de/pim/.Contact:
	haubold@evolbio.mpg.deSupplementary information: Supplementary data
	are available at Bioinformatics online.},
  doi = {10.1093/bioinformatics/btq689},
  eprint = {http://bioinformatics.oxfordjournals.org/content/27/4/449.full.pdf+html},
  file = {supplement:/home/willrodt/Documents/Paper/HauReePfa2011_supp.pdf:PDF;:/home/willrodt/Desktop/Paper/HauReePfa2011.pdf:PDF},
  owner = {willrodt},
  timestamp = {2012.01.26},
  url = {http://bioinformatics.oxfordjournals.org/content/27/4/449.abstract}
}

@MISC{gttestdata,
  title = {\textsc{GenomeTools} test data set},
  note = {\url{git://genometools.org/gttestdata.git}},
  bdsk-url-1 = {http://www.genometools.org/askgordon},
  date-added = {2008-02-19 01:42:22 +0100},
  date-modified = {2008-02-19 17:04:35 +0100},
  url = {git://genometools.org/gttestdata.git}
}

