bibtex entries
@InProceedings{GawryKuchSachStarSPIRE15,
author = {Gawrychowski, P. and Kucherov, G. and Sach, B. and Starikovskaia, T.},
title = {Computing the Longest Unbordered Substring},
OPTcrossref = {},
OPTkey = {},
booktitle = {Proc. of the 22nd International Symposium on String Processing and Information Retrieval (SPIRE), September 1-4, 2015, London, UK},
year = {2015},
editor = {Costas S. Iliopoulos and
Simon J. Puglisi and
Emine Yilmaz},
volume = {9309},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
pages = {246--257},
OPTmonth = {},
OPTaddress = {},
OPTorganization = {},
publisher = {Springer},
OPTannote = {}
}
@InProceedings{KucherovTsurSPIRE14,
author = {Kucherov, G. and Tsur, D.},
title = {Improved filters for the approximate suffix-prefix overlap problem},
OPTcrossref = {},
OPTkey = {},
booktitle = {Proc. of the 21st International Symposium on String Processing and Information Retrieval (SPIRE), Ouro Preto, Brazil (October 21-22, 2014)},
year = {2014},
editor = {Moura, E. and Crochemore, M.},
volume = {8799},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
pages = {139-148},
OPTmonth = {},
OPTaddress = {},
OPTorganization = {},
publisher = {Springer},
OPTannote = {}
}
@InProceedings{KucherovSalikhovTsurCPM14,
author = {Kucherov, G. and Salikhov, K. and Tsur, D.},
title = {Approximate String Matching using a Bidirectional Index},
booktitle = {Proceedings of the 25th Annual Symposium on Combinatorial Pattern Matching (CPM), June 16-18, 2014, Moscow (Russia)},
year = {2014},
editor = {Kulikov, A.S. and Kuznetsov, S.O. and Pevzner, P.},
volume = {8486},
series = {Lecture Notes in Computer Science},
pages = {222--231},
publisher = {Springer},
note = {full version at http://arxiv.org/abs/1310.1440}
}
@Article{SalikhovSacomotoKucherovBMCAMB14,
author = {Salikhov, K. and Sacomoto, G. and Kucherov, G.},
title = {Using cascading {B}loom filters to improve the memory usage for de {B}rujin graphs},
journal = {BMC Algorithms for Molecular Biology},
year = {2014},
volume = {9},
number = {1},
pages = {2},
OPTmonth = {},
OPTannote = {doi:10.1186/1748-7188-9-2},
URL = {http://www.almob.org/content/9/1/2},
ISSN = {1748-7188}
}
@PhdThesis{KucherovHabil00,
author = {Kucherov, G.},
title = {Patterns in words and trees},
school = {Henri Poincar\'e University of Nancy},
year = {2000},
OPTkey = {},
type = {Habilitation \`a diriger les recherches},
OPTaddress = {},
month = {December},
note = {in french},
OPTannote = {}
}
@InCollection{KolpakovKucherovLothaire04,
author = {Kolpakov, R. and Kucherov, G.},
title = {Identification of periodic structures in words},
booktitle = {Applied combinatorics on words},
pages = {430--477},
publisher = {Cambridge University Press},
year = {2005},
editor = {Berstel, J. and Perrin, D.},
volume = {Encyclopedia of Mathematics and its Applications, vol.~104},
series = {Lothaire books},
chapter = {8}
}
@InProceedings{KucherovSPIRE11,
author = {Kucherov, G.},
title = {On-line Construction of Position Heaps},
booktitle = {Proceedings of the 18th International Symposium on String Processing and Information Retrieval (SPIRE), Pisa, Italy (17 - 21 October, 2011)},
pages = {326--337},
year = {2011},
editor = {R.Grossi and F.Silvestri},
volume = {7024},
series = {Lecture Notes in Computer Science},
publisher = {Springer Verlag}
}
@Article{KucherovPinhasZiv-UkelsonJCB11,
author = {Kucherov, G. and Pinhas, T. and Ziv-Ukelson, M.},
title = {Regular Expression Constrained Sequence Alignment Revisited},
journal = {Journal of Computational Biology},
year = {2011},
volume = {18},
number = {5},
pages = {771-781},
month = {May}
}
@Article{NoeGirdeaKucherovABI10,
author = {No{\'e}, L. and G{\^\i}rdea, M. and Kucherov, G.},
title = {Designing efficient spaced seeds for {SOLiD} read mapping},
journal = {Advances in Bioinformatics},
year = {2010},
note = {http://www.hindawi.com/journals/abi/aip.708501.html}
}
@Article{GirdeaNoeKucherovAMB10,
author = {G{\^\i}rdea, M. and No{\'e}, L. and Kucherov, G.},
title = {Back-translation for discovering distant protein homologies in the presence of frameshift mutations},
journal = {Algorithms for Molecular Biology},
year = {2010},
volume = {5:6},
month = {Jan}
}
@Article{KolpakovKucherovOchemIPL10,
author = {Kolpakov, R. and Kucherov, G. and Ochem, P.},
title = {On maximal repetitions of arbitrary exponent},
journal = {Information Processing Letters},
year = {2010},
volume = {110},
number = {7},
pages = {252--256},
month = {March}
}
@InProceedings{GirdeaNoeKucherovWABI09,
author = {G\^{\i}rdea, M. and No{\'e}, L. and Kucherov, G.},
title = {Back-translation for discovering distant protein homologies},
booktitle = {Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI), Philadelphia (USA), September 12-13, 2009},
OPTcrossref = {},
OPTkey = {},
pages = {108-120},
year = {2009},
OPTeditor = {},
volume = {5724},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {Springer Verlag}
}
@Article{RoytbergEtAlTCBB09,
author = {Roytberg, M. and Gambin, A. and No{\'e}, L. and Lasota, S. and Furletova, E. and Szczurek, E. and Kucherov, G.},
title = {On Subset Seeds for Protein Alignment},
journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
year = {2009},
OPTkey = {},
volume = {6},
number = {3},
pages = {483--494},
month = {July-September},
doi = {10.1109/TCBB.2009.4},
OPTannote = {}
}
@ARTICLE{PeterlongoEtAlBMCBioinformatics08,
author = {Peterlongo, P. and No{\'e}, L. and Lavenier, D. and Nguyen, V. H. and Kucherov, G. and Giraud, M.},
inria = {Sequoia},
labo = {dans},
journal = {BMC Bioinformatics},
year = {2008},
volume = {9:534},
title = {Optimal neighborhood indexing for protein similarity search}
}
@Article{GrzebelusEtAlBMCGenomics07,
author = {Grzebelus, D. and Lasota, L. and Gambin, T. and Kucherov, G. and Gambin, A.},
title = {Diversity and structure of {PIF}/{H}arbinger-like elements in the genome of {\em {M}edicago truncatula}},
journal = {BMC Genomics},
year = {2007},
OPTkey = {},
volume = {8},
number = {409},
OPTpages = {},
month = {9 November},
doi = {10.1186/1471-2164-8-409},
url = {http://www.biomedcentral.com/1471-2164/8/409/}
}
@Article{KucherovNoeRoytberg06,
author = {Kucherov, G. and No{\'e}, L. and Roytberg, M.},
title = {A Unifying Framework for Seed Sensitivity and its Application to Subset Seeds},
journal = {Journal of Bioinformatics and Computational Biology},
year = {2006},
volume = {4},
number = {2},
pages = {553-570},
month = {April}
}
@Article{NoeKucherovNAR05,
author = {No{\'e}, L. and Kucherov, G.},
title = {YASS: enhancing the sensitivity of DNA similarity search},
journal = {Nucleic Acid Research},
year = {2005},
OPTkey = {},
volume = {33},
OPTnumber = {},
pages = {W540-W543},
OPTmonth = {},
OPTannote = {}
}
@Article{KucherovNoeRoytbergJCBB05,
author = {Kucherov, G. and No{\'e}, L. and Roytberg, M.},
title = {Multi-seed lossless filtration},
journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
year = {2005},
OPTkey = {},
volume = {2},
number = {1},
pages = {51--61},
month = {January-March},
OPTnote = {},
OPTannote = {}
}
@Article{DuvalEtAlTCS2004,
author = {Duval, Jean-Pierre and Kolpakov, Roman and Kucherov,
Gregory and Lecroq, Thierry and Lefebvre, Arnaud},
title = {Linear-time computation of local periods},
journal = {Theoretical Computer Science},
volume = {326},
number = {1--3},
pages = {229--240},
day = {20},
month = {Oct},
year = {2004}
}
@Article{NoeKucherovBMC04,
author = {No{\'e}, L.and Kucherov, G.},
title = {Improved hit criteria for {DNA} local alignment},
journal = {BMC Bioinformatics},
year = {2004},
OPTkey = {},
volume = {5},
number = {149},
OPTpages = {},
month = {14 October},
note = {},
OPTannote = {}
}
@InProceedings{KucherovNoePontyBIBE04,
author = {Kucherov, Gregory and Noe, Laurent and Ponty, Yann},
title = {Estimating seed sensitivity on homogeneous alignments},
booktitle = {Proceedings of the IEEE 4th Symposium on Bioinformatics and Bioengineering (BIBE 2004), May 19-21, 2004, Taichung (Taiwan)},
OPTcrossref = {},
OPTkey = {},
pages = {387--394},
year = {2004},
OPTeditor = {},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {IEEE Computer Society Press},
OPTannote = {}
}
@Article{KolpakovBanaKucherovNAR03,
author = {Kolpakov, Roman and Bana, Ghizlane and Kucherov, Gregory},
title = {{\tt mreps}: efficient and flexible detection of tandem
repeats in {DNA}},
journal = {Nucleic Acid Research},
year = {2003},
OPTkey = {},
volume = {31},
number = {13},
pages = {3672-3678},
month = {July 1}
}
@Article{CsurosNoeKucherovTiG07,
author = {Cs\H{u}r\"os, M. and Noé, L. and Kucherov, G.},
title = {Reconsidering the significance of genomic word frequencies},
journal = {Trends in Genetics},
year = {2007},
OPTkey = {},
volume = {23},
number = {11},
pages = {543--546},
doi = {10.1016/j.tig.2007.07.008},
url = {http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4R0CPJM-1&_user=10&_coverDate=11%2F30%2F2007&_rdoc=5&_fmt=summary&_orig=browse&_srch=doc-info(%23toc%235183%232007%23999769988%23673507%23FLA%23display%23Volume)&_cdi=5183&_sort=d&_docanchor=&_ct=10&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a3fb8ee5a874f6ab2b63d923b746e352},
month = {November},
OPTannote = {}
}
@ARTICLE{CabocheEtAlBMC09,
title = {Structural pattern matching of nonribosomal peptides},
author = {Caboche, S. and Pupin, M. and Lecl{\`e}re, V. and Jacques, Ph. and Kucherov, G.},
journal = {BMC Structural Biology},
year = {2009},
month = {March 18},
volume = {9:15},
doi = {10.1186/1472-6807-9-15},
url = {http://www.biomedcentral.com/1472-6807/9/15}
}
@ARTICLE{CabocheEtAlNAR07,
title = {{NORINE}: a database of nonribosomal peptides},
author = {Caboche, S. and Pupin, M. and Lecl{\`e}re, V. and Fontaine, A. and Jacques, Ph. and Kucherov, G.},
journal = {Nucleic Acids Research},
year = {2007},
month = {October 2},
doi = {10.1093/nar/gkm792},
url = {http://nar.oxfordjournals.org/cgi/content/abstract/gkm792?ijkey=QQrD7uHNr8uBJp4&keytype=ref}
}
@Article{KolpakovKucherovTCS09,
author = {Kolpakov, R. and Kucherov, G.},
title = {Searching for gapped palindromes},
journal = {Theoretical Computer Science},
year = {2009},
OPTkey = {},
volume = {410},
number = {51},
pages = {5299-5382},
month = {28 November},
OPTannote = {}
}
@InProceedings{KolpakovKucherovCPM08,
author = {Kolpakov, R. and Kucherov, G.},
title = {Searching for gapped palindromes},
booktitle = {Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM), June 18-20, 2008, Pisa (Italy)},
OPTcrossref = {},
OPTkey = {},
pages = {18--30},
year = {2008},
OPTeditor = {},
volume = {5029},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {Springer Verlag},
isbn = {978-3-540-69066-5},
doi = {10.1007/978-3-540-69068-9_5},
url = {http://www.springerlink.com/content/v45825l304h45533/}
}
@Article{KolpakovKucherovTCS03,
author = {Kolpakov, Roman and Kucherov, Gregory},
title = {Finding approximate repetitions under {H}amming distance},
journal = {Theoretical Computer Science},
year = {2003},
OPTkey = {},
volume = {303},
number = {1},
pages = {135-156},
month = {June},
OPTannote = {}
}
@InProceedings{KolpakovKucherovSPIRE00,
author = {Kolpakov, Roman and Kucherov, Gregory},
title = {Finding Repeats With Fixed Gap},
booktitle = {Proceedings of the 7th International Symposium on String Processing and Information Retrieval (SPIRE), A Coru{\~n}a, Spain (27 - 29 Septembre, 2000)},
OPTcrossref = {},
OPTkey = {},
pages = {162--168},
year = {2000},
OPTeditor = {},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
OPTaddress = {},
month = {September},
OPTorganization = {},
publisher = {IEEE},
OPTannote = {}
}
@InProceedings{KolpakovKucherovFOCS99,
author = {Kolpakov, Roman and Kucherov, Gregory},
title = {Finding Maximal Repetitions in a Word in Linear Time},
booktitle = {Proceedings of the 1999 Symposium on Foundations of Computer Science (FOCS'99), New York (USA)},
OPTcrossref = {},
OPTkey = {},
pages = {596--604},
year = {1999},
OPTeditor = {},
OPTvolume = {},
OPTnumber = {},
OPTseries = {},
address = {New-York},
month = {October 17-19},
OPTorganization = {},
publisher = {IEEE Computer Society},
OPTannote = {}
}
@ARTICLE{KucherovRusiTCS97,
AUTHOR = {Kucherov, G. and Rusinowitch, M.},
TITLE = {Matching a Set of Strings with Variable Length Don't Cares},
JOURNAL = {Theoretical Computer Science},
YEAR = {1997},
VOLUME = {178},
NUMBER = {},
PAGES = {129--154}
}
@InProceedings{CohenEtAlMFCS06,
author = {Cohen, J. and Fomin, F. and Heggernes, P. and Kratsch, D. and Kucherov, G.},
title = {Optimal Linear Arrangement of Interval Graphs},
booktitle = {Proceedings of the 31st International Symposium on
Mathematical Foundations of Computer Science (MFCS 2006), High Tatras (Slovakia), August 28 - September 1, 2006},
pages = {267-279},
year = {2006},
OPTeditor = {},
volume = {4162},
url = {http://www.springerlink.com/content/wrk8346657167528/?p=a1f283d79ac14affb4d165501b84e569&pi=23},
pdf = {},
doi = {http://dx.doi.org/10.1007/11821069},
series = {Lecture Notes in Computer Science},
publisher = {Springer Verlag}
}
@InProceedings{BouvelGrebinskiKucherovWG05,
author = {Bouvel, M. and Grebinski, V. and Kucherov, G.},
title = {Combinatorial search on graphs motivated by bioinformatics applicaitons: a brief survey},
booktitle = {Proceedings of the 31st International Workshop on
Graph-Theoretic Concepts in Computer Science (WG), Metz (France), June 23-25, 2005},
OPTcrossref = {},
OPTkey = {},
pages = {16--27},
year = {2005},
editor = {Kratsch, D.},
volume = {3787},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {Springer Verlag}
}
@InProceedings{GrebKuchSODA99,
author = {Grebinski, Vladimir and Kucherov, Gregory},
title = {Reconstructing Set Partitions},
booktitle = {Proceedings of the 10th ACM-SIAM Symposium on Discrete Algorithms (SODA'99), Baltimore, Maryland, January 17-19, 1999},
pages = {915--916},
year = {1999},
publisher = {ACM, SIAM}
}
@INPROCEEDINGS{GrebKuchISTCS97,
AUTHOR = {Grebinski, Vladimir and Kucherov, Gregory},
TITLE = {Optimal Query Bounds for Reconstructing a Hamiltonian Cycle in Complete Graphs},
BOOKTITLE = {Proceedings of the 5th Israeli Symposium on Theory of Computing and Systems (ISTCS'97)},
YEAR = {1997},
PUBLISHER = {IEEE Press},
MONTH = {June},
PAGES = {166--173},
NOTE = {complete version in \cite{GrebKuchDAM98}}
}
@Article{KucherovOchemRaoEJC03,
author = {Kucherov, Gregory and Ochem, Pascal and Rao, Micha\"el},
title = {How many square occurrences must a binary sequence contain},
journal = {Electronic Journal of Combinatorics},
year = {2003},
OPTkey = {},
volume = {10},
number = {1},
pages = {11pp},
OPTmonth = {},
note = {{\tt http://www.combinatorics.org/}},
OPTannote = {}
}
@InProceedings{KolpakovKucherovFCT99,
author = {Kolpakov, Roman and Kucherov, Gregory},
title = {On Maximal Repetitions in Words},
booktitle = {Proceedings of the 12-th International Symposium on
Fundamentals of Computation Theory (FCT'99), 1999, Iasi (Romania)},
OPTcrossref = {},
OPTkey = {},
pages = {374 -- 385},
year = {1999},
editor = {G.Ciobanu and Gh.P{\v a}un},
volume = {1684},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
month = {August 30 - September 3},
OPTorganization = {},
publisher = {Springer Verlag},
OPTannote = {}
}
@InProceedings{KucherovRusiPSI99,
author = {Kucherov, Gregory and Rusinowitch, Micha{\"e}l},
title = {Patterns in words vs patterns in trees: a brief survey and some new results},
booktitle = {Proceedings of the Andrei Ershov 3rd International Conference ``Perspectives of System Informatics'' (6 - 9 July 1999, Novosibirsk, Akademgorodok, Russia)},
OPTcrossref = {},
OPTkey = {},
pages = {280-293},
year = {1999},
OPTeditor = {},
volume = {1755},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {Springer Verlag},
OPTannote = {}
}
@Article{KolpakovKucherovTaranTCS99,
author = {Kolpakov, Roman and Kucherov, Gregory and Tarannikov, Yuri},
title = {On repetition-free binary words of minimal density},
journal = {Theoretical Computer Science},
year = {1999},
OPTkey = {},
volume = {218},
number = {1},
pages = {143-160},
OPTmonth = {},
OPTnote = {},
OPTannote = {}
}
@INPROCEEDINGS{KucherovRusiCTRS94,
AUTHOR = {Kucherov, G. and Rusinowitch, M.},
TITLE = {Complexity of testing ground reducibility for linear word rewriting systems with variables},
BOOKTITLE = {Proceedings 4th International Workshop on Conditional and Typed Term Rewriting Systems, Jerusalem (Israel)},
SERIES = {Lecture Notes in Computer Science},
VOLUME = 968,
PUBLISHER = {Springer Verlag},
YEAR = 1995,
PAGES = {262--275}
}
@ARTICLE{KucherovRusiIPL95,
AUTHOR = {G. Kucherov and M. Rusinowitch},
TITLE = {Undecidability of Ground Reducibility for Word Rewriting Systems with Variables},
JOURNAL = {Information Processing Letters},
YEAR = {1995},
VOLUME = {53},
PAGES = {209--215}
}
@Article{PlaistedKucherovIPL99,
author = {Plaisted, D. and Kucherov, G.},
title = {The complexity of some complementation problems},
journal = {Information Processing Letters},
year = {1999},
OPTkey = {},
volume = {71},
OPTnumber = {},
pages = {159-165},
OPTmonth = {},
OPTnote = {},
OPTannote = {}
}
@INBOOK{HofHubKuchCSLI97,
AUTHOR = {Hofbauer, D. and Huber, M. and Kucherov, G.},
CHAPTER = {15},
PAGES = {235--247},
TITLE = {How to get rid of projection rules in context-free tree grammars},
PUBLISHER = {Center for the Study of Language and Information (CSLI), Stanford and The European Association for Logic, Language and Information (FoLLI)},
YEAR = {1998},
VOLUME = {},
BOOKTITLE = {The Tbilisi Symposium on Logic, Language and Computation: Selected Papers},
SERIES = {Studies in Logic, Language and Information},
ADDRESS = {},
EDITION = {},
NOTE = {}
}
@InProceedings{HofbauerHuberKucherovCAAP94,
author = {Hofbauer, D. and Huber, M. and Kucherov, G.},
title = {Some Results on Top-context-free Tree Languages},
booktitle = {Proceedings of the 19th International Colloquium on Trees in Algebra and Programming (CAAP'94)},
OPTcrossref = {},
OPTkey = {},
pages = {157--171},
year = {1994},
OPTeditor = {},
volume = {787},
OPTnumber = {},
series = {Lecture Notes in Computer Science},
OPTaddress = {},
OPTmonth = {},
OPTorganization = {},
publisher = {Springer Verlag},
OPTnote = {},
OPTannote = {}
}
@ARTICLE{KucherovTajineIC95,
AUTHOR = {Kucherov, G. and Tajine, M.},
TITLE = {Decidability of Regularity and Related Properties of
Ground Normal Form Languages},
JOURNAL = "Information and Computation",
YEAR = {1995},
VOLUME = {118},
NUMBER = {1},
MONTH = {April},
PAGES = {91--100}
}