| 2009 | A General Framework for Local Pairwise Alignment Statistics with Gaps. Pasi Rastas |
| 2009 | A Markov Classification Model for Metabolic Pathways. Timothy Hancock, Hiroshi Mamitsuka |
| 2009 | A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara |
| 2009 | A Simple, Practical and Complete Yelena Frid, Dan Gusfield |
| 2009 | A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy J. Warnow |
| 2009 | A Tree Based Method for the Rapid Screening of Chemical Fingerprints. Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen |
| 2009 | A Unifying View on Approximation and FPT of Agreement Forests. Chris Whidden, Norbert Zeh |
| 2009 | Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings Steven Salzberg, Tandy J. Warnow |
| 2009 | Aligning Biomolecular Networks Using Modular Graph Kernels. Fadi Towfic, M. Heather West Greenlee, Vasant G. Honavar |
| 2009 | Annotating Fragmentation Patterns. Sebastian Böcker, Florian Rasche, Tamara Steijger |
| 2009 | Back-Translation for Discovering Distant Protein Homologies. Marta Gîrdea, Laurent Noé, Gregory Kucherov |
| 2009 | Constructing Majority-Rule Supertrees. Jianrong Dong, David Fernández-Baca, Fred R. McMorris |
| 2009 | Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner |
| 2009 | Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael |
| 2009 | Exact Score Distribution Computation for Similarity Searches in Ontologies. Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Martin Vingron, Peter N. Robinson |
| 2009 | Fast Prediction of RNA-RNA Interaction. Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp |
| 2009 | FlexSnap: Flexible Non-sequential Protein Structure Alignment. Saeed Salem, Mohammed J. Zaki, Chris Bystroff |
| 2009 | Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. Fumei Lam, Dan Gusfield, Srinath Sridhar |
| 2009 | Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. Xiuwei Zhang, Bernard M. E. Moret |
| 2009 | K-Partite RNA Secondary Structures. Minghui Jiang, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser |
| 2009 | Large-Scale Neighbor-Joining with NINJA. Travis J. Wheeler |
| 2009 | Linear-Time Protein 3-D Structure Searching with Insertions and Deletions. Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane |
| 2009 | MADMX: A Novel Strategy for Maximal Dense Motif Extraction. Roberto Grossi, Andrea Pietracaprina, Nadia Pisanti, Geppino Pucci, Eli Upfal, Fabio Vandin |
| 2009 | Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli |
| 2009 | Minimum Factorization Agreement of Spliced ESTs. Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi |
| 2009 | On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices. Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio |
| 2009 | PMFastR: A New Approach to Multiple RNA Structure Alignment. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang |
| 2009 | Phylogenetic Comparative Assembly. Peter Husemann, Jens Stoye |
| 2009 | Predicting Gene Structures from Multiple RT-PCR Tests. Jakub Kovác, Tomás Vinar, Brona Brejová |
| 2009 | Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. Phuong Dao, Alexander Schönhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Süleyman Cenk Sahinalp, Martin Ester |
| 2009 | SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy. Pedro Feijão, João Meidanis |
| 2009 | Structural Alignment of RNA with Complex Pseudoknot Structure. Thomas K. F. Wong, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu |
| 2009 | Visualizing Phylogenetic Treespace Using Cartographic Projections. Kenneth Sundberg, Mark J. Clement, Quinn Snell |
| 2009 | biRNA: Fast RNA-RNA Binding Sites Prediction. Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp |
| 2009 | mpscan: Fast Localisation of Multiple Reads in Genomes. Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio |