@phdthesis{PhD,
author = {Lu\'{i}s M. S. Russo},
title = {Enhanced Full-Text Self-Indexes based on {L}empel-{Z}iv Compression},
school = {Instituto Superior T\'{e}cnico},
year = {2007},
optkey = {},
opttype = {},
optaddress = {},
optmonth = {},
note = {Orientado por Arlindo Oliveira},
optannote = {},
ps = {phd/book.r.ps},
pdf = {phd/book.r.pdf},
http = {phd/index.html}
}
@mastersthesis{Diploma,
author = {Lu\'{i}s S. Russo},
title = {Algebra in a topos},
school = {CLC, Department of Mathematics, Instituto Superior T\'{e}cnico},
year = {2003},
optkey = {},
type = {Diploma thesis},
address = {1049-001 Lisboa, Portugal},
optmonth = {},
note = {Orientado por Pedro Resende},
optannote = {}
}
@article{MYDB:journals/jda/RussoOl07,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {Efficient Generation of Super Condensed Neighborhoods},
journal = {Journal of Discrete Algorithms},
year = {2007},
optkey = {},
volume = {5},
number = {3},
pages = {501--513},
month = {September},
optnote = {},
optannote = {},
publisher = {Elsevier Science Publishers},
ps = {jda07/paper.ps},
pdf = {jda07/paper.pdf},
http = {jda07/index.html},
doi = {http://dx.doi.org/10.1016/j.jda.2006.10.005}
}
@article{MYDB:journals/jir/RussoOl07,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {A Compressed Self-index Using a {Z}iv-{L}empel Dictionary.},
journal = {Journal of Information Retrieval},
year = {2008},
optkey = {},
optvolume = {5},
optnumber = {3},
optpages = {501--513},
optmonth = {September},
note = {Special issue SPIRE 2006},
annote = {(Aceite)},
optpublisher = {Elsevier Science Publishers},
ps = {jir07/paper.ps},
pdf = {jir07/paper.pdf},
http = {jir07/index.html},
doi = {http://dx.doi.org/10.1007/s10791-008-9050-3}
}
@article{a2031105,
author = {Russo, Lu\'{i}s M. S. and Navarro, Gonzalo and Oliveira, Arlindo L. and Morales, Pedro},
title = {Approximate String Matching with Compressed Indexes},
journal = {Algorithms},
volume = {2},
year = {2009},
number = {3},
pages = {1105--1136},
url = {http://www.mdpi.com/1999-4893/2/3/1105},
issn = {1999-4893},
doi = {10.3390/a2031105},
http = {http://www.mdpi.com/1999-4893/2/3/1105},
ps = {mdpi09/paper.ps},
pdf = {mdpi09/paper.pdf}
}
@article{DBLP:journals/bmcbi/FernandesFROF11,
author = {Francisco Fernandes and
Paulo G. S. da Fonseca and
Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira and
Ana T. Freitas},
title = {Efficient alignment of pyrosequencing reads for re-sequencing
applications},
journal = {BMC Bioinformatics},
volume = {12},
year = {2011},
pages = {163},
ee = {http://dx.doi.org/10.1186/1471-2105-12-163},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@article{RNOtalg11,
title = {Fully-Compressed Suffix Trees},
author = {{Lu\'{i}s S. Russo} and Gonzalo Navarro and Arlindo L. Oliveira},
journal = {ACM Transactions on Algorithms (TALG)},
volume = 7,
number = 4,
pages = {article 53},
note = {35 pages},
year = 2011
}
@article{LuisMS201230,
title = {Monge properties of sequence alignment},
journal = {Theoretical Computer Science},
volume = {423},
number = {0},
pages = {30 - 49},
year = {2012},
note = {},
issn = {0304-3975},
doi = {10.1016/j.tcs.2011.12.068},
url = {http://www.sciencedirect.com/science/article/pii/S0304397511010449},
author = {Lu\'{i}s M.S. and Russo}
}
@article{22551152,
author = {Vinga, Susana and Carvalho, Alexandra and Francisco, Alexandre and Russo, Lu\'{i}s and Almeida, Jonas},
title = {Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis},
journal = {Algorithms for Molecular Biology},
volume = {7},
year = {2012},
number = {1},
pages = {10},
url = {http://www.almob.org/content/7/1/10},
doi = {10.1186/1748-7188-7-10},
pubmedid = {22551152},
issn = {1748-7188}
}
@article{Navarro2012,
title = {Space-efficient data-analysis queries on grids},
journal = {Theoretical Computer Science},
volume = {1},
year = {2012},
issn = {0304-3975},
doi = {10.1016/j.tcs.2012.11.031},
url = {http://www.sciencedirect.com/science/article/pii/S0304397512010742},
author = {Gonzalo Navarro and Yakov Nekrich and Lu\'{i}s M.S. Russo}
}
@unpublished{DBLP:journals/corr/abs-1106-4649,
author = {Gonzalo Navarro and
Lu\'{i}s M. S. Russo},
title = {Space-Efficient Data-Analysis Queries on Grids},
journal = {CoRR},
volume = {abs/1106.4649},
year = 2011,
ee = {http://arxiv.org/abs/1106.4649},
bibsource = {DBLP, http://dblp.uni-trier.de},
note = {Submitted to Theoretical Computer Science}
}
@unpublished{2012arXiv1207.4598R,
author = {{Russo}, Lu\'{i}s~M.~S. and {Francisco}, Alexandre~P.},
title = {{Quick HyperVolume}},
journal = {ArXiv e-prints},
archiveprefix = {arXiv},
eprint = {1207.4598},
primaryclass = {cs.DS},
keywords = {Computer Science - Data Structures and Algorithms, Computer Science - Discrete Mathematics, Computer Science - Neural and Evolutionary Computing},
year = 2012,
month = jul,
adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1207.4598R},
note = {Submitted to IEEE Transactions on Evolutionary Computation},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@inproceedings{DBLP:conf/isaac/NavarroR11,
author = {Gonzalo Navarro and
Lu\'{i}s M. S. Russo},
title = {Space-Efficient Data-Analysis Queries on Grids},
booktitle = {22nd International Symposium on Algorithms and Computation, ISAAC},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
volume = {7074},
isbn = {978-3-642-25590-8},
year = {2011},
pages = {323-332},
ee = {http://dx.doi.org/10.1007/978-3-642-25591-5_34},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@inproceedings{Rspire11,
author = {German Tischler and Lu\'{i}s M. S. Russo},
title = {Succinct Gapped Suffix Arrays},
booktitle = {Proc. 18th International Symposium on String Processing and Information Retrieval (SPIRE)},
year = {2011},
series = {LNCS},
publisher = {Springer},
ps = {spire2011/camera.ps},
pdf = {spire2011/camera.pdf},
http = {spire2011/index.html}
}
@inproceedings{JorgeCosta2_2011,
author = {Jorge Costa and
Gabriel Pereira Lopes and
Lu\'{i}s Gomes and
Lu\'{i}s M. S. Russo},
title = {Managing and Querying a Bilingual Lexicon with Suffix Trees},
booktitle = {Proceedings of the 15th Portuguese Conference
on Artificial Intelligence (EPIA)},
year = {2011},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
ps = {epia2011/camera.ps},
pdf = {epia2011/camera.pdf}
}
@inproceedings{costa2011mapping,
author = { Costa and Ana Teresa Freitas and Lu\'{i}s M. S. Russo },
title = { Exploring Efficient Data Structures and Algorithms for Mapping RNA-Seq Reads },
booktitle = { Proceedings of InForum 2011 },
publisher = { Universidade de Coimbra },
year = { 2011 },
month = { 09 }
}
@inproceedings{JorgeCosta_3_2011,
author = {Jorge Costa and
Gabriel Pereira Lopes and
Lu\'{i}s Gomes and
Lu\'{i}s M. S. Russo},
title = {Representing a bilingual lexicon with Suffix Trees},
booktitle = {Proceedings of the 2011 ACM Symposium on Applied Computing
(SAC), TaiChung, Taiwan, March 21 - 24, 2011},
year = {2011},
publisher = {ACM},
pages = {1164-1165},
ee = {http://doi.acm.org/10.1145/1982185.1982440},
bibsource = {DBLP, http://dblp.uni-trier.de},
ps = {sac2011/camera.ps},
pdf = {sac2011/camera.pdf}
}
@inproceedings{Rspire10,
author = {Lu\'{i}s M. S. Russo},
title = {Multiplication Algorithms for Monge Matrices},
booktitle = {Proc. 17th International Symposium on String Processing and Information Retrieval (SPIRE)},
year = {2010},
series = {LNCS},
publisher = {Springer},
ps = {spire2010/camera.ps},
pdf = {spire2010/camera.pdf},
http = {spire2010/index.html}
}
@inproceedings{RNOcpm10,
author = {Lu\'{i}s M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira},
title = {Parallel and Distributed Compressed Indexes},
booktitle = {Proc. 21st Annual Symposium on Combinatorial Pattern Matching (CPM)},
year = {2010},
pages = {348--360},
series = {LNCS},
publisher = {Springer},
ee = {http://dx.doi.org/10.1007/978-3-642-13509-5_31},
ps = {cpm2010/camera.ps},
pdf = {cpm2010/camera.pdf},
http = {cpm2010/abstract.html}
}
@inproceedings{RNOspire08.5,
author = {Lu\'{i}s M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira},
title = {Indexed Hierarchical Approximate String Matching},
booktitle = {Proc. 15th International Symposium on String Processing and Information Retrieval (SPIRE)},
year = {2008},
series = {LNCS},
publisher = {Springer},
ps = {spire08/paper.ps},
pdf = {spire08/paper.pdf},
http = {spire08/index.html}
}
@inproceedings{RNOcpm08.2,
title = {{D}ynamic {F}ully-{C}ompressed {S}uffix {T}rees},
author = {Lu\'{i}s M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira},
booktitle = {Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM 2008)},
series = {LNCS},
year = 2008,
note = {},
ps = {cpm08/paper.ps},
pdf = {cpm08/paper.pdf},
http = {cpm08/index.html}
}
@inproceedings{NRdcc08.3,
author = {Gonzalo Navarro and Lu\'{i}s M. S. Russo},
title = {Re-Pair Achieves High-Order Entropy},
booktitle = {Proc. 18th IEEE Data Compression Conference (DCC'08)},
year = {2008},
pages = {537},
note = {Poster.},
ps = {dcc08/poster.ps},
pdf = {dcc08/poster.pdf},
http = {dcc08/index.html},
poster = {dcc08/a0poster.pdf}
}
@inproceedings{RNOlatin08,
title = {Fully-{C}ompressed {S}uffix {T}rees},
author = {Lu\'{i}s M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira},
booktitle = {{Proc. 8th Latin American Symposium on Theoretical Informatics (LATIN)}},
year = 2008,
series = {LNCS 4957},
pages = {362--373},
ps = {latin08/paper.ps},
pdf = {latin08/paper.pdf},
http = {latin08/index.html},
doi = {http://dx.doi.org/10.1007/978-3-540-78773-0_32}
}
@inproceedings{DBLP:conf/spire/RussoNO07,
author = {Lu\'{i}s M. S. Russo and
Gonzalo Navarro and
Arlindo L. Oliveira},
title = {Approximate String Matching with {L}empel-{Z}iv Compressed Indexes},
booktitle = {SPIRE},
year = {2007},
pages = {264-275},
ee = {abstract://dx.doi.org/10.1007/978-3-540-75530-2_24},
crossref = {DBLP:conf/spire/2007},
bibsource = {DBLP, abstract://dblp.uni-trier.de},
ps = {spire07/paper.ps},
pdf = {spire07/paper.pdf},
http = {spire07/index.html},
doi = {http://dx.doi.org/10.1007/978-3-540-75530-2_24}
}
@proceedings{DBLP:conf/spire/2007,
editor = {Nivio {Z}iviani and
Ricardo A. Baeza-Yates},
title = {String Processing and Information Retrieval, 14th International
Symposium, SPIRE 2007, Santiago, Chile, October 29-31, 2007,
Proceedings},
booktitle = {SPIRE},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
volume = {4726},
year = {2007},
isbn = {978-3-540-75529-6},
bibsource = {DBLP, abstract://dblp.uni-trier.de}
}
@inproceedings{DBLP:conf/spire/RussoO06,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {A Compressed Self-index Using a {Z}iv-{L}empel Dictionary.},
booktitle = {SPIRE},
year = {2006},
pages = {163-180},
ee = {abstract://dx.doi.org/10.1007/11880561_14},
crossref = {DBLP:conf/spire/2006},
bibsource = {DBLP, abstract://dblp.uni-trier.de},
ps = {spire06/clean_paper.ps},
pdf = {spire06/clean_paper.pdf},
http = {spire06/index.html},
doi = {http://dx.doi.org/10.1007/11880561_14}
}
@proceedings{DBLP:conf/spire/2006,
editor = {Fabio Crestani and
Paolo Ferragina and
Mark Sanderson},
title = {String Processing and Information Retrieval, 13th International
Conference, SPIRE 2006, Glasgow, UK, October 11-13, 2006,
Proceedings},
booktitle = {SPIRE},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
volume = {4209},
year = {2006},
isbn = {3-540-45774-7},
bibsource = {DBLP, abstract://dblp.uni-trier.de}
}
@inproceedings{DBLP:conf/spire/RussoO05,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {Faster Generation of Super Condensed Neighbourhoods Using
Finite Automata.},
booktitle = {SPIRE},
year = {2005},
pages = {246-255},
ee = {abstract://dx.doi.org/10.1007/11575832_28},
crossref = {DBLP:conf/spire/2005},
bibsource = {DBLP, abstract://dblp.uni-trier.de},
ps = {spire05/clean_paper.ps},
pdf = {spire05/clean_paper.pdf},
http = {spire05/index.html},
doi = {http://dx.doi.org/10.1007/11575832_28}
}
@proceedings{DBLP:conf/spire/2005,
editor = {Mariano P. Consens and
Gonzalo Navarro},
title = {String Processing and Information Retrieval, 12th International
Conference, SPIRE 2005, Buenos Aires, Argentina, November
2-4, 2005, Proceedings},
booktitle = {SPIRE},
publisher = {Springer},
series = {Lecture Notes in Computer Science},
volume = {3772},
year = {2005},
isbn = {3-540-29740-5},
bibsource = {DBLP, abstract://dblp.uni-trier.de}
}
@inproceedings{DBLP:conf/cpm/RussoO05,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {An Efficient Algorithm for Generating Super Condensed Neighborhoods.},
booktitle = {CPM},
year = {2005},
pages = {104-115},
ee = {abstract://dx.doi.org/10.1007/11496656_10},
crossref = {DBLP:conf/cpm/2005},
bibsource = {DBLP, abstract://dblp.uni-trier.de},
ps = {cpm05/cpm05.ps},
pdf = {cpm05/cpm05.pdf},
http = {cpm05/index.html},
doi = {http://dx.doi.org/10.1007/11496656_10}
}
@proceedings{DBLP:conf/cpm/2005,
editor = {Alberto Apostolico and
Maxime Crochemore and
Kunsoo Park},
title = {Combinatorial Pattern Matching, 16th Annual Symposium, CPM
2005, Jeju Island, Korea, June 19-22, 2005, Proceedings},
booktitle = {CPM},
publisher = {Springer},
series = {LNCS},
volume = {3537},
year = {2005},
isbn = {3-540-26201-6},
bibsource = {DBLP, abstract://dblp.uni-trier.de}
}
@techreport{tecilzi,
author = {Lu\'{i}s M. S. Russo and
Arlindo L. Oliveira},
title = {A Compressed Self-Index using a {Z}iv-{L}empel Dictionary},
institution = {INESC-ID},
year = {2006},
optkey = {},
opttype = {},
number = {6/2006},
optaddress = {},
month = {March},
optnote = {},
optannote = {}
}
@incollection{pit,
author = {Lu\'{i}s M. S. Russo},
title = {O Teorema de {P}it\'{a}goras},
booktitle = {Semin\'{a}rio Diagonal},
optcrossref = {},
optkey = {},
pages = {77--84},
publisher = {Proceedings IST},
year = {2001},
editor = {Boavida, J. P. and Cannas da Silva, A. and Cruz-Filipe and L., Fachada and J. and Resende, P.},
optvolume = {},
optnumber = {},
series = {IST 2000-01},
opttype = {},
optchapter = {},
address = {1049-001 Lisboa, Portugal},
optedition = {},
optmonth = {},
optnote = {},
optannote = {},
pdf = {ist00/proc2001.pdf},
http = {ist00/abstract/index.html}
}
@misc{nips2012,
optkey = {},
author = {Lu\'{i}s M. S. Russo, Ana T. Freitas, Arlindo L. Oliveira},
title = {Transparent Hidden {M}arkov Models},
howpublished = {Neural Information Processing Systems},
optmonth = {},
year = {2012},
note = {Poster},
optannote = {}
}
@misc{TapFr,
author = {Francisco Fernandes and Paulo G. S. Fonseca and Lu\'{i}s M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas},
title = {TAPYR - An efficient high-throughput sequence aligner for re-sequencing applications.},
howpublished = {Paris, France. GDR CNRS 3003 Bioinformatique Mol\'{e}culaire},
year = {2012},
note = {Poster}
}
@misc{TapBl,
author = {Francisco Fernandes and Paulo G. S. Fonseca and Lu\'{i}s M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas},
title = {TAPYR - An efficient high-throughput sequence aligner for re-sequencing applications.},
howpublished = {Brussels, Belgium. Poster at SeqAhead Scientific Meeting - BMBS COST Action BM1006},
year = {2011},
note = {Poster}
}
@misc{TapBr,
author = {Francisco Fernandes and Paulo G. S. Fonseca and Lu\'{i}s M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas},
title = {TAPYR - An efficient high-throughput sequence aligner for re-sequencing applications.},
howpublished = {Florianopolis, Brazil. Poster at X-Meeting 2011},
year = {2011},
note = {Poster}
}
@misc{TapXa,
author = {Francisco Fernandes and Paulo G. S. Fonseca and Luis M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas},
title = {An efficient data representation for large scale genome re-sequencing},
howpublished = {13th International Meeting on Human Genome Variation and Complex Genome Analysis},
year = {2012},
note = {Poster}
}
@misc{PTap,
author = {Miguel Coimbra and Francisco Fernandes and Lu\'{i}s M. S. Russo and Ana T. Freitas},
title = {Parallel Efficient Aligner of Pyrosequencing Reads},
howpublished = {COST Action SeqAhead Workshop},
year = {2013},
note = {Poster}
}
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