16. CPM 2005: Jeju Island, Korea

• Brona Brejová, Daniel G. Brown, Ian M. Harrower, Alejandro López-Ortiz, Tomás Vinar:
  Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. 1-10
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• Bin Ma, Kaizhong Zhang:
  On the Longest Common Rigid Subsequence Problem. 11-20
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• Moritz G. Maaß, Johannes Nowak:
  Text Indexing with Errors. 21-32
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• Dong Kyue Kim, Heejin Park:
  A New Compressed Suffix Tree Supporting Fast Search and Its Construction Algorithm Using Optimal Working Space. 33-44
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• Veli Mäkinen, Gonzalo Navarro:
  Succinct Suffix Arrays Based on Run-Length Encoding. 45-56
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• Joong Chae Na:
  Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets. 57-67
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• Peter Clifford, Raphaël Clifford, Costas S. Iliopoulos:
  Faster Algorithms for delta, gamma-Matching and Related Problems. 68-78
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• Zheng Liu, Xin Chen, James Borneman, Tao Jiang:
  A Fast Algorithm for Approximate String Matching on Gene Sequences. 79-90
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• Amihood Amir, Ohad Lipsky, Ely Porat, Julia Umanski:
  Approximate Matching in the L₁ Metric. 91-103
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• Luís M. S. Russo, Arlindo L. Oliveira:
  An Efficient Algorithm for Generating Super Condensed Neighborhoods. 104-115
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• Enno Ohlebusch, Mohamed Ibrahim Abouelhoda, Kathrin Hockel, Jan Stallkamp:
  The Median Problem for the Reversal Distance in Circular Bacterial Genomes. 116-127
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• Gad M. Landau, Laxmi Parida, Oren Weimann:
  Using PQ Trees for Comparative Genomics. 128-143
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• François Nicolas, Eric Rivals:
  Hardness of Optimal Spaced Seed Design. 144-155
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• Meng Zhang, Liang Hu, Qiang Li, Jiubin Ju:
  Weighted Directed Word Graph. 156-167
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• Shiri Dori, Gad M. Landau:
  Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets. 168-177
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• Sabrina Mantaci, Antonio Restivo, G. Rosone, Marinella Sciortino:
  An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Compression. 178-189
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• Behshad Behzadi, Fabrice Le Fessant:
  DNA Compression Challenge Revisited: A Dynamic Programming Approach. 190-200
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• Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson:
  On the Complexity of Sparse Exon Assembly. 201-218
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• Paul Horton, Wataru Fujibuchi:
  An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery. 219-228
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• Nadia Pisanti, Henry Soldano, Mathilde Carpentier:
  Incremental Inference of Relational Motifs with a Degenerate Alphabet. 229-240
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• Daniel Fredouille, Christopher H. Bryant:
  Speeding up Parsing of Biological Context-Free Grammars. 241-256
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• Kangmin Fan, William F. Smyth, R. J. Simpson:
  A New Periodicity Lemma. 257-265
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• Carmit Hazay, Moshe Lewenstein, Dekel Tsur:
  Two Dimensional Parameterized Matching. 266-279
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• Gen-Huey Chen, Jin-Ju Hong, Hsueh-I Lu:
  An Optimal Algorithm for Online Square Detection. 280-287
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• Frantisek Franek, Christopher G. Jennings, William F. Smyth:
  A Simple Fast Hybrid Pattern-Matching Algorithm. 288-297
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• Yo-Sub Han, Yajun Wang, Derick Wood:
  Prefix-Free Regular-Expression Matching. 298-309
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• Lucian Ilie, Roberto Solis-Oba, Sheng Yu:
  Reducing the Size of NFAs by Using Equivalences and Preorders. 310-321
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• Abdullah N. Arslan:
  Regular Expression Constrained Sequence Alignment. 322-333
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• Hélène Touzet:
  A Linear Tree Edit Distance Algorithm for Similar Ordered Trees. 334-345
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• Kazuhide Aikou, Yusuke Suzuki, Takayoshi Shoudai, Tomoyuki Uchida, Tetsuhiro Miyahara:
  A Polynomial Time Matching Algorithm of Ordered Tree Patterns Having Height-Constrained Variables. 346-357
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• Valentina Boeva, Julien Clément, Mireille Régnier, Mathias Vandenbogaert:
  Assessing the Significance of Sets of Words. 358-370
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• Tatsuya Akutsu, Daiji Fukagawa:
  Inferring a Graph from Path Frequency. 371-382
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• Ion I. Mandoiu, Dragos Trinca:
  Exact and Approximation Algorithms for DNA Tag Set Design. 383-393
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• David Fernández-Baca, Balaji Venkatachalam:
  Parametric Analysis for Ungapped Markov Models of Evolution. 394-405
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• Jijun Tang, Bernard M. E. Moret:
  Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. 406-416
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• Mary Ellen Bock, Guido Maria Cortelazzo, Carlo Ferrari, Concettina Guerra:
  Identifying Similar Surface Patches on Proteins Using a Spin-Image Surface Representation. 417-428
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• Sebastian Böcker, Hans-Michael Kaltenbach:
  Mass Spectra Alignments and Their Significance. 429-441
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