17. CPM 2006: Barcelona, Spain

• Amihood Amir:
  Asynchronous Pattern Matching. 1-10
  Electronic Edition (link) BibTeX
• Eran Halperin:
  SNP and Haplotype Analysis - Algorithms and Applications. 11-11
  Electronic Edition (link) BibTeX
• Levon Lloyd, Andrew Mehler, Steven Skiena:
  Identifying Co-referential Names Across Large Corpora. 12-23
  Electronic Edition (link) BibTeX

Data Structures

• Jérémy Barbay, Alexander Golynski, J. Ian Munro, S. Srinivasa Rao:
  Adaptive Searching in Succinctly Encoded Binary Relations and Tree-Structured Documents. 24-35
  Electronic Edition (link) BibTeX
• Johannes Fischer, Volker Heun:
  Theoretical and Practical Improvements on the RMQ-Problem, with Applications to LCA and LCE. 36-48
  Electronic Edition (link) BibTeX

Indexing Data Structures

• Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong:
  A Linear Size Index for Approximate Pattern Matching. 49-59
  Electronic Edition (link) BibTeX
• Shunsuke Inenaga, Masayuki Takeda:
  On-Line Linear-Time Construction of Word Suffix Trees. 60-71
  Electronic Edition (link) BibTeX
• Pang Ko, Srinivas Aluru:
  Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. 72-83
  Electronic Edition (link) BibTeX
• Tetsuo Shibuya:
  Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures. 84-93
  Electronic Edition (link) BibTeX

Probabilistic and Algebraic Techniques

• Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar:
  New Bounds for Motif Finding in Strong Instances. 94-105
  Electronic Edition (link) BibTeX
• Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri:
  Fingerprint Clustering with Bounded Number of Missing Values. 106-116
  Electronic Edition (link) BibTeX
• Olivier Bodini, Eric Rivals:
  Tiling an Interval of the Discrete Line. 117-128
  Electronic Edition (link) BibTeX
• Eric Blais, Mathieu Blanchette:
  Common Substrings in Random Strings. 129-140
  Electronic Edition (link) BibTeX

Applications in Molecular Biology I

• Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter:
  On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem. 141-152
  Electronic Edition (link) BibTeX
• Sven Rahmann:
  Subsequence Combinatorics and Applications to Microarray Production, DNA Sequencing and Chaining Algorithms. 153-164
  Electronic Edition (link) BibTeX
• Sylvain Guillemot, François Nicolas:
  Solving the Maximum Agreement SubTree and the Maximum Compatible Tree Problems on Many Bounded Degree Trees. 165-176
  Electronic Edition (link) BibTeX
• Behshad Behzadi, Martin Vingron:
  An Improved Algorithm for the Macro-evolutionary Phylogeny Problem. 177-187
  Electronic Edition (link) BibTeX

String Matching I

• Amihood Amir, Eran Chencinski, Costas S. Iliopoulos, Tsvi Kopelowitz, Hui Zhang:
  Property Matching and Weighted Matching. 188-199
  Electronic Edition (link) BibTeX
• Amihood Amir, Eran Chencinski:
  Faster Two Dimensional Scaled Matching. 200-210
  Electronic Edition (link) BibTeX

Applications in Molecular Biology II

• Marcin Kubica, Romeo Rizzi, Stéphane Vialette, Tomasz Walen:
  Approximation of RNA Multiple Structural Alignment. 211-222
  Electronic Edition (link) BibTeX
• Patricia A. Evans:
  Finding Common RNA Pseudoknot Structures in Polynomial Time. 223-232
  Electronic Edition (link) BibTeX
• Carl Kingsford, Elena Zaslavsky, Mona Singh:
  A Compact Mathematical Programming Formulation for DNA Motif Finding. 233-245
  Electronic Edition (link) BibTeX
• Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann:
  Local Alignment of RNA Sequences with Arbitrary Scoring Schemes. 246-257
  Electronic Edition (link) BibTeX

Applications in Molecular Biology III

• Michal Ozery-Flato, Ron Shamir:
  An O(n^3/2sqrt(log n)) Algorithm for Sorting by Reciprocal Translocations. 258-269
  Electronic Edition (link) BibTeX
• Alexandre Tiskin:
  Longest Common Subsequences in Permutations and Maximum Cliques in Circle Graphs. 270-281
  Electronic Edition (link) BibTeX

Data Compression

• Haim Kaplan, Shir Landau, Elad Verbin:
  A Simpler Analysis of Burrows-Wheeler Based Compression. 282-293
  Electronic Edition (link) BibTeX
• Rodrigo González, Gonzalo Navarro:
  Statistical Encoding of Succinct Data Structures. 294-305
  Electronic Edition (link) BibTeX
• Veli Mäkinen, Gonzalo Navarro:
  Dynamic Entropy-Compressed Sequences and Full-Text Indexes. 306-317
  Electronic Edition (link) BibTeX
• Diego Arroyuelo, Gonzalo Navarro, Kunihiko Sadakane:
  Reducing the Space Requirement of LZ-Index. 318-329
  Electronic Edition (link) BibTeX

String Matching II

• Gerth Stølting Brodal, Kanela Kaligosi, Irit Katriel, Martin Kutz:
  Faster Algorithms for Computing Longest Common Increasing Subsequences. 330-341
  Electronic Edition (link) BibTeX
• Roman Kolpakov, Mathieu Raffinot:
  New Algorithms for Text Fingerprinting. 342-353
  Electronic Edition (link) BibTeX
• Leena Salmela, Jorma Tarhio:
  Sublinear Algorithms for Parameterized Matching. 354-364
  Electronic Edition (link) BibTeX
• Amihood Amir, Costas S. Iliopoulos, Oren Kapah, Ely Porat:
  Approximate Matching in Weighted Sequences. 365-376
  Electronic Edition (link) BibTeX

Dynamic Programming

• Jesper Jansson, Zeshan Peng:
  Algorithms for Finding a Most Similar Subforest. 377-388
  Electronic Edition (link) BibTeX
• Yun Sheng Chung, Chin Lung Lu, Chuan Yi Tang:
  Efficient Algorithms for Regular Expression Constrained Sequence Alignment. 389-400
  Electronic Edition (link) BibTeX
• Aude Liefooghe, Hélène Touzet, Jean-Stéphane Varré:
  Large Scale Matching for Position Weight Matrices. 401-412
  Electronic Edition (link) BibTeX