11. WABI 2011: Saarbrücken, Germany

• Brona Brejová, Michal Burger, Tomás Vinar:
  Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. 1-13
  
• Daniel G. Brown, Jakub Truszkowski:
  Towards a Practical O(n logn) Phylogeny Algorithm. 14-25
  
• Stefan Canzar, Mohammed El-Kebir:
  A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. 26-38
  
• Rayan Chikhi, Dominique Lavenier:
  Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. 39-48
  
• Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh:
  Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions - (Extended Abstract). 49-60
  
• Jianrong Dong, David Fernández-Baca:
  Constructing Large Conservative Supertrees. 61-72
  
• Elad Donsky, Haim J. Wolfson:
  PepCrawler: A Fast RRT-Like Algorithm for High-Resolution Refinement and Binding-Affinity Estimation of Peptide Inhibitors - (Abstract). 73-75
  
• Andrea Doroftei, Nadia El-Mabrouk:
  Removing Noise from Gene Trees. 76-91
  
• Mohamed Elati, Rim Fekih, Rémy Nicolle, Ivan Junier, Joan Hérisson, François Képès:
  Boosting Binding Sites Prediction Using Gene's Positions. 92-103
  
• Rob Gysel, Fumei Lam, Dan Gusfield:
  Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. 104-115
  
• Michel Habib, Thu-Hien To:
  On a Conjecture about Compatibility of Multi-states Characters. 116-127
  
• Jonathan Qiang Jiang:
  Learning Protein Functions from Bi-relational Graph of Proteins and Function Annotations. 128-138
  
• Hans-Michael Kaltenbach, Simona Constantinescu, Justin Feigelman, Jörg Stelling:
  Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems. 139-150
  
• Kouichi Kimura, Asako Koike, Kenta Nakai:
  Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. 151-162
  
• Jakub Kovác, Brona Brejová, Tomás Vinar:
  A Practical Algorithm for Ancestral Rearrangement Reconstruction. 163-174
  
• Yu Lin, Vaibhav Rajan, Bernard M. E. Moret:
  Bootstrapping Phylogenies Inferred from Rearrangement Data. 175-187
  
• Md Pavel Mahmud, Alexander Schliep:
  Speeding Up Bayesian HMM by the Four Russians Method. 188-200
  
• Noël Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov:
  Using Dominances for Solving the Protein Family Identification Problem. 201-212
  
• Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky:
  Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. 213-224
  
• Vincent Noel, Sergei Vakulenko, Ovidiu Radulescu:
  Algorithm for Identification of Piecewise Smooth Hybrid Systems: Application to Eukaryotic Cell Cycle Regulation. 225-236
  
• Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford:
  Parsimonious Reconstruction of Network Evolution. 237-249
  
• Yann Ponty, Cédric Saule:
  A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. 250-269
  
• Jouni Sirén, Niko Välimäki, Veli Mäkinen:
  Indexing Finite Language Representation of Population Genotypes. 270-281
  
• Kristian Stevens, Bonnie Kirkpatrick:
  Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values. 282-297
  
• Olga Tanaseichuk, James Borneman, Tao Jiang:
  Separating Metagenomic Short Reads into Genomes via Clustering - (Extended Abstract). 298-313
  
• Fabio Vandin, Eli Upfal, Benjamin J. Raphael:
  Finding Driver Pathways in Cancer: Models and Algorithms. 314-325
  
• Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno:
  Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. 326-338
  
• Hang Xiao, Melvin Zhang, Axel Mosig, Hon Wai Leong:
  Dynamic Programming Algorithms for Efficiently Computing Cosegmentations between Biological Images. 339-350
  
• Andrew Wei Xu, Bernard M. E. Moret:
  GASTS: Parsimony Scoring under Rearrangements. 351-363
  
• Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff:
  OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. 364-375
  

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