9. WABI 2009: Philadelphia, PA, USA

• Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi:
  Minimum Factorization Agreement of Spliced ESTs. 1-12
  
• Sebastian Böcker, Florian Rasche, Tamara Steijger:
  Annotating Fragmentation Patterns. 13-24
  
• Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp:
  biRNA: Fast RNA-RNA Binding Sites Prediction. 25-36
  
• Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester:
  Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. 37-48
  
• Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang:
  PMFastR: A New Approach to Multiple RNA Structure Alignment. 49-61
  
• Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio:
  On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices. 62-72
  
• Jianrong Dong, David Fernández-Baca, Fred R. McMorris:
  Constructing Majority-Rule Supertrees. 73-84
  
• Pedro Feijão, João Meidanis:
  SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy. 85-96
  
• Yelena Frid, Dan Gusfield:
  A Simple, Practical and Complete O(\fracn³ logn)O(\frac{n^3}{ \log n})-Time Algorithm for RNA Folding Using the Four-Russians Speedup. 97-107
  
• Marta Gîrdea, Laurent Noé, Gregory Kucherov:
  Back-Translation for Discovering Distant Protein Homologies. 108-120
  
• Timothy Hancock, Hiroshi Mamitsuka:
  A Markov Classification Model for Metabolic Pathways. 121-132
  
• Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli:
  Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. 133-144
  
• Peter Husemann, Jens Stoye:
  Phylogenetic Comparative Assembly. 145-156
  
• Minghui Jiang, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser:
  K-Partite RNA Secondary Structures. 157-168
  
• Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael:
  Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. 169-180
  
• Jakub Kovác, Tomás Vinar, Brona Brejová:
  Predicting Gene Structures from Multiple RT-PCR Tests. 181-193
  
• Thomas Greve Kristensen, Jesper Nielsen, Christian N. S. Pedersen:
  A Tree Based Method for the Rapid Screening of Chemical Fingerprints. 194-205
  
• Fumei Lam, Dan Gusfield, Srinath Sridhar:
  Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. 206-219
  
• Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner:
  Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. 220-232
  
• Pasi Rastas:
  A General Framework for Local Pairwise Alignment Statistics with Gaps. 233-245
  
• Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio:
  mpscan: Fast Localisation of Multiple Reads in Genomes. 246-260
  
• Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp:
  Fast Prediction of RNA-RNA Interaction. 261-272
  
• Saeed Salem, Mohammed J. Zaki, Chris Bystroff:
  FlexSnap: Flexible Non-sequential Protein Structure Alignment. 273-285
  
• Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
  A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. 286-297
  
• Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Martin Vingron, Peter N. Robinson:
  homepages/84/1721 journals/jiis/BarbanconM07 conf/fqas/BarbanconM04 conf/bibe/NakhlehMBPD03 conf/ideas/BarbanconM02 Exact Score Distribution Computation for Similarity Searches in Ontologies. 298-309
  
• Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane:
  Linear-Time Protein 3-D Structure Searching with Insertions and Deletions. 310-320
  
• Kenneth Sundberg, Mark J. Clement, Quinn Snell:
  Visualizing Phylogenetic Treespace Using Cartographic Projections. 321-332
  
• M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy Warnow:
  A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. 333-344
  
• Fadi Towfic, M. Heather West Greenlee, Vasant Honavar:
  Aligning Biomolecular Networks Using Modular Graph Kernels. 345-361
  
• Roberto Grossi, Andrea Pietracaprina, Nadia Pisanti, Geppino Pucci, Eli Upfal, Fabio Vandin:
  MADMX: A Novel Strategy for Maximal Dense Motif Extraction. 362-374
  
• Travis J. Wheeler:
  Large-Scale Neighbor-Joining with NINJA. 375-389
  
• Chris Whidden, Norbert Zeh:
  A Unifying View on Approximation and FPT of Agreement Forests. 390-402
  
• Thomas K. F. Wong, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu:
  Structural Alignment of RNA with Complex Pseudoknot Structure. 403-414
  
• Xiuwei Zhang, Bernard M. E. Moret:
  Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. 415-428
  

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