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  About site: http://www.cs.ucr.edu/~stelo/pattern.html

Title: Algorithms - Pattern Matching Pointers A collection of links for and to researchers in the subject.
Priority_Queues Electronic bibliography on priority queues (heaps). Links to downloadable reports, researchers' home pages, and software.

Problems_in_Analysis_of_Algorithms A list of open problems with updates and solutions.

Resources_for_the_Analysis_of_Algorithms Links to papers, conferences and other sites, maintained by Helmut Prodinger.

Self-stabilizing_Algorithms A project to create tools for developing and testing self-stabilizing algorithms.

Softpanorama_Virtual_Library Section on Algorithms and Data Structures. A compilation of links.

Sourcebank_-_Computer_Science_-_Algorithms A collection of source code for various topics.


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Pattern Matching Pointers (maintained by Stefano Lonardi)

Pattern Matching Pointers

Combinatorial Pattern Matching addresses issues of searchingand matching strings and more complicated patterns such as trees,regular expressions, graphs, point sets, and arrays. The goal is toderive non-trivial combinatorial properties for such structures andthen to exploit these properties in order to achieve improvedperformance for the corresponding computational problem.A steady flow of high-quality research on this subject has changeda sparse set of isolated results into a full-fledged area ofalgorithmics with important applications. This area is expected togrow even further due to the increasing demand for speed andefficiency that comes from molecular biology, but also fromareas such as information retrieval, patternrecognition, compiling, data compression, programanalysis and security.Disclaimer: The purpose of this page is to serveas an index to information relevant to Pattern Matching/ComputationalBiologist researchers. We prefer to point to information rather thanstore it locally. We include all submissions that seem appropriate.However, inclusion should not be interpreted as an endorsementof a contribution's accuracy or importance.

Contents

People page moved (not maintained anymore)CPM Presentation ArchiveConference announcementsResources: on-line bibliographies, journals, proceedings, software, newgroups.

Conferences

SIGACT News Theory CalendarSIAM Meetings and ConferencesPast events (1995-)CPM conferences

2008

Jan 4-8: PSB'08 (Big Island of Hawaii)Jan 14-17: APCB'08 (Kyoto, Japan)Jan 20-22: SODA'08 (San Francisco, CA)Mar 27-29: DCC'08 (Snowbird, UT)Mar 30- Apr 2: RECOMB'08 (Singapore)Apr 24-26: SDM'08 (Atlanta, GA)Jun 18-20: CPM'08 (Pisa, Italy)Jul 27-29: COCOON'08 (Dalian, China)Aug 25-29: CBS'08 (Stanford, CA)Jul 19-23: ISMB'08 (Toronto, Canada)Aug 24-27: KDD'08 (Las Vegas, NV)Sep 15-19: WABI 2008 (Karlsruhe, Germany)Sep 15-17: CIBCB'08 (Sun Valley, Idaho)Sep 15-17: ECCB'08 (Cagliari, Sardina Italy)Oct 8-10: BIBE 2008 (Athens, Greece)

Resources

BibliographiesDatabases & LogicProgramming Bibliographymaintained by Michael LeyA Collection of Computer Science Bibliographies (Canadian Mirror)more than one million of CS BibTeX referencesSequence Alignment, Analysis and Comparison: a bibliography1,760 entries by William H. E. DayMathSciNetAMS bibliography on-lineNetworked Computer Science Technical Reports Library(NCSTRL)Computer Science Research Paper Search EngineYahoo-style search engine for CS papersResearchIndexover 7 millions pages and 5 millions citationsACM Computing Research Repository(CoRR)IEEE bibliographies on-lineBenno's Computer Science Bio-Digesta regular survey of some CS journals for articles related to the field of Computational BiologyA bibliography on stringologyby T. LecroqThe Hypertext Bibliography Projectby David M. JonesA bibliography on computational gene recognitionby Wentian Li Groups and link collectionsTheoretical Computer Science On The Webmaintained by Suresh VenkatPattern Matching & Data Mining Research Group Homepagemaintained by Mika Klemettinen and Jaak ViloHuman Genome Most Used Linkshosted at LANLComplexity Related Linksmaintained by Bruce EdmondsACM SIGACTSpecial Interest Group on Algorithms and Computation TheoryTheoretical Computer Science GenealogyTCS: virtual address booklists URLs of 1105 theoretical computer scientists around the worldA compendium of NP optimization problemsmaintained by P. Crescenzi and V. KannKnowledge Discovery Nuggets Directory:Data Mining and Knowledge Discovery InformationThe Bioinformatics ResourcesThe Rewriting Pagemaintained by Nachum Dershowitz and Laurent VigneronAmos' WWW links pagemaintained by Amos Bairoch BooksPattern Matching AlgoritmsAlberto Apostolico, Zvi Galil, eds.Bioinformatics: The Machine Learning Approach Pierre Baldi, Søren BrunakBioinformatics: A Practical Guide to the Analysis of Genes and ProteinsAndreas Baxevanis, B.F.Francis Ouellette (Eds.)Computational Molecular Biology: An IntroductionPeter Clote, Rolf BackofenText AlgorithmsMaxime Crochemore, Wojciech RytterJewels of StringologyMaxime Crochemore, Wojciech RytterBiological Sequence Analysis: Probabilistic Models of Proteins and Nucleic AcidsRichard Durbin (Editor), S. Eddy, A. Krogh, G. MitchisonInformation Retrieval Data Structures & AlgorithmsBill Frakes, Ricardo Baeza-Yates (eds.)Developing Bioinformatics Computer SkillsCynthia Gibas, Per JambeckHandbook of Algorithms and Data StructuresGaston H. Gonnet, Ricardo Baeza-YatesCombinatorics on WordsM. LothaireAlgebraic Combinatorics on WordsM. LothaireApplied Combinatorics on WordsM. LothaireAlgorithms on Strings, Trees and SequencesDan GusfieldRewriting Solving ProvingClaude Kirchner, Helene KirchnerBioinformatics: Sequence and Genome AnalysisDavid MountIntroduction to Computational Molecular BiologyJoão Meidanis & João Carlos SetubalPattern Discovery in Bioinformatics: Theory & AlgorithmsLaxmi ParidaComputational Molecular Biology: An Algorithmic ApproachPavel A. PevznerFlexible Pattern Matching in StringsGonzalo Navarro and Mathieu Raffinot Computational Methods in Molecular BiologySteven Salzberg, David Searls, Simon Kasif (eds.)String SearchingAlgorithmsGraham A. StephenPattern Discovery in Biomolecular DataJason Wang, Bruce A. Shapiro, Dennis Shasha (eds.)Introduction To Computational BiologyMichael Waterman JournalsTheory Calendar - Journal CallsACM: Digital LibraryLOTS of papers on lineACM Transactions on Algorithms (TALG)papers on lineIEEE OPeRA (Online Periodicals and Research Area)LOTS of papers on lineIEEE conference proceedings on-lineAlgorithmicapapers on lineBMC Bioinformaticspapers on lineBioinformatics (formerly CABIOS)papers on lineChicago Journal of Theoretical Computer Sciencepapers on lineCombinatorics, Probability and Computingpapers on lineComplexitypapers on lineData Mining and Knowledge Discoveryabstracts on lineDiscrete Applied Mathematicsabstracts on lineDiscrete Mathematics and Theoretical Computer Sciencepapers on lineElectronic Journal of Combinatoricspapers on lineEuropean Journal of Combinatoricsabstracts on lineGenome Researchpapers on lineGenome Biologypapers on lineJournal of ACMpapers on lineJournal of Algorithmspapers on lineJournal of Bioinformatics and Computational BiologyNEWJournal of Computational Biologyrecent papers onlineJournal of Complexityabstracts on lineJournal of Molecular Biologypapers on lineJournal of Experimental Algorithmicspapers on lineJournal of Universal Computer Sciencepapers on lineJournal of Graph Algorithms and Applicationspapers on lineIEEE Transactions on Information TheoryIEEE Transactions on Knowledge and Data EngineeringInformation and Computation (or here)abstract on lineInformaticaabstract on lineInformation Processing Letterspapers on lineInternational Journal of Bioinformatics Research and Applicationspapers on lineInternational Journal of Data Mining and Bioinformaticspapers on lineLecture Notes in Computer Sciencepapers on lineNucleic Acid Researchpapers on lineNordic Journal on Computingabstracts on lineSIAM Journal on Computingpapers on lineSIGACT News Onlinepapers on lineTheoretical Computer Sciencepapers on lineIEEE/ACM Transactions on Computational Biology and Bioinformaticspapers on lineThe Computer Journalpapers on line ProceedingsBio-Informatics and Biomedical Engineering (BIBE)papers on line (2001)Bio-Informatics and Biomedical Engineering (BIBE)papers on line (2003)Bio-Informatics and Biomedical Engineering (BIBE)papers on line (2004)BIOKDDpapers on line (2001)BIOKDDpapers on line (2002)IEEE Computer Society Bioinformatics Conference (CSB)papers on line (2003)IEEE Computer Society Bioinformatics Conference (CSB)papers on line (2002)Combinatorial Pattern Matching (CPM)papers on line (2007)Combinatorial Pattern Matching (CPM)papers on line (2005)Combinatorial Pattern Matching (CPM)papers on line (2004)Combinatorial Pattern Matching (CPM)papers on line (2003)Combinatorial Pattern Matching (CPM)papers on line (2002)Combinatorial Pattern Matching (CPM)papers on line (2001)Combinatorial Pattern Matching (CPM)papers on line (2000)Combinatorial Pattern Matching (CPM)papers on line (1999)Compression and Complexity of Sequences (SEQUENCES)papers on line (1997)Computational System Bioinformatics (CSB)papers on line (2003-)Data Compression Conference (DCC)papers on line (1991-)European Conference on Computational Biology (ECCB)papers on line (2002)European Conference on Computational Biology (ECCB)papers on line (2003)European Conference on Computational Biology (ECCB)papers on line (2004)Foundations of Computer Science (FOCS)papers on line (1996-)Genome Informaticspapers on line (1996-)Intelligent Systems for Molecular Biology (ISMB)papers on line (2004)Intelligent Systems for Molecular Biology (ISMB)papers on line (2003)Intelligent Systems for Molecular Biology (ISMB)papers on line (2002)Intelligent Systems for Molecular Biology (ISMB)papers on line (2001)Intelligent systems for Molecular Biology (ISMB)papers on line (2000)Pacific Symposium on Biocomputing (PSB)papers on line (1996-)Principles of Programming Languages (POPL)papers on line (1987-)Research in Computational Molecular Biology (RECOMB)papers on line (1997-2004)Research in Computational Molecular Biology (RECOMB)papers on line (2008)Research in Computational Molecular Biology (RECOMB)papers on line (2005)Research in Computational Molecular Biology (RECOMB)papers on line (2006)String Processing and Information Retrieval Symposium (SPIRE)papers on line (1998)String Processing and Information Retrieval Symposium (SPIRE)papers on line (1999)String Processing and Information Retrieval Symposium (SPIRE)papers on line (2000)String Processing and Information Retrieval Symposium (SPIRE)papers on line (2001)String Processing and Information Retrieval Symposium (SPIRE)papers on line (2004)Symposium on Discrete Algorithms (SODA)papers on line (1997-)Symposium on Theory of Computing (STOC)papers on line (1985-)Algorithms in Bioinformatics: 5th International Workshop (WABI)papers on line (2005)Algorithms in Bioinformatics: 4th International Workshop (WABI)papers on line (2004)Algorithms in Bioinformatics: 3rd International Workshop (WABI)papers on line (2003) SoftwareExact string matching algorithms in Javaby Christian Charras - Thierry LecroqInformation Retrieval ProjectsPERLthe "information extraction" languageThe LEDA LibraryLibrary of Efficient Datatypes and AlgorithmsThe Stony Brook Algorithm RepositoryGLIMPSE and AGREPA tool to search entire file systemsHARVESTInformation Discovery and Access SystemAGREP for DOS, OS/2 and Windows 95/NT(not yet GLIMPSE)GAISA General-Purposed Information Discovery System Handbook of Algorithms and Data StructuresSource codeInformation Retrieval Data Structures & AlgorithmsSource codeFIRE & SPAREC++ implementations of algorithms for finite automata, transducers, pattern matching of keywords and regular expressions{Codepage}listing of programming resources on the webAlgorithms Archivemaintained by Florian SchintkeIllustrated Pattern Matching in JavaSAMSequence Alignment and Modeling SystemIsearchsoftware for indexing and searching text documentsLPM and PAISLEI IDELaleh's pattern matcher system for Win32 systemsIcon Programming Language homepageSNOBOL4 and SPITBOL Programming Languagesstrmat packageexact string matching and suffix treesXPARAL: Graphical Computation of Parameterized AlignmentsGraph Template LibraryGPLstring matching algorithm animationSmaanrgrepfast and flexible online pattern matchingAlgorithm Archiveby Scott Gasch (work in progress)grappepattern matching with wildcardsBoyer-Moore appletby Dieter BühlerAho-Corasick appletby Dieter BühlerNaive, KMP, and BM pattern matching algorithms appletby Masayuki TakedaMulti : Efficient Multi-Suffix-Tree String Dictionaryby Stefan EdelkampCompact Affix Trees appletby Moritz G. MaaßSuffix Trees appletby Moritz G. MaaßSuffix Trees appletby Craig Nevill-ManningTree Structures for Algorithmic Problems on Stringssuffix trees, suffix arrays softwareELANa language where (equational) pattern matching plays a fundamental roleRewriting Calculus resourcesa calculus based on pattern matchingA Library for Computational Biology ProgramsA C++ regular expressions librarySary: a suffix array library and toolsSufary: a suffix array libraryBoost LibraryTemplate C++ Library: contains Graph Library and RegEx++ LibraryCCP - a compact and fast algorithm for Regular Expression Searchby J.-M. Champarnaud, F. Coulon, T. ParanthoenANSI C implementation of a Suffix Treeby Dotan Tsadok, Shlomo Yona, Offer KayeSuffix Arraysby M. Douglas McIlroyC Library to search over compressed textsby Paolo Ferragina, Alessandro Tommasi, Giovanni ManziniLinear-time and Lightweight Suffix Arrays constructionby Juha Kärkkäinen PERL module String:Approxby Jarkko HietaniemiTRE: regexp matching libraryby Ville LaurikariRegular expression (regex/grep) string matchingby Nic RoetsYet another suffix tree implementationMREPStandem repeatsYASSlocal aligmentSTR Librarya fast C++ string class with RegExpPizza&Chili CorpusCompressed Indexes and their TestbedsTompattern matching compiler for Java or CNews Groups and Mailing ListsTheory-Edgetheoretical computer science on Egroupscomp.compressiondata compressioncomp.compression.researchdata compression researchcomp.theory.info-retrievaltheory of information retrievalcomp.theorytheoretical computer sciencecomp.texttext processingcomp.infosystems.harvestinformation systems harvestIf you have questions, complains, errata, or you would like to be included in this page, please send a message to stelo@cs.ucr.edu_uacct = "UA-664697-1";urchinTracker();
 

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http://www.cs.ucr.edu/~stelo/pattern.html

Pattern Matching Pointers 2008 August

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A collection of links for and to researchers in the subject.

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