| 2009 | Large-Scale Neighbor-Joining with NINJA. | Travis J. Wheeler |
| 2009 | Aligning Biomolecular Networks Using Modular Graph Kernels. | Fadi Towfic, M. Heather West Greenlee, Vasant G. Honavar |
| 2009 | A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. | M. Shel Swenson, Franois Barbanon, C. Randal Linder, Tandy J. Warnow |
| 2009 | Visualizing Phylogenetic Treespace Using Cartographic Projections. | Kenneth Sundberg, Mark J. Clement, Quinn Snell |
| 2009 | Linear-Time Protein 3-D Structure Searching with Insertions and Deletions. | Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane |
| 2009 | Exact Score Distribution Computation for Similarity Searches in Ontologies. | Marcel H. Schulz, Sebastian Khler, Sebastian Bauer, Martin Vingron, Peter N. Robinson |
| 2009 | A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. | Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara |
| 2009 | FlexSnap: Flexible Non-sequential Protein Structure Alignment. | Saeed Salem, Mohammed J. Zaki, Chris Bystroff |
| 2009 | Fast Prediction of RNA-RNA Interaction. | Raheleh Salari, Rolf Backofen, Sleyman Cenk Sahinalp |
| 2009 | mpscan: Fast Localisation of Multiple Reads in Genomes. | Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio |
| 2009 | A General Framework for Local Pairwise Alignment Statistics with Gaps. | Pasi Rastas |
| 2009 | Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. | Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner |
| 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 | Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. | Fumei Lam, Dan Gusfield, Srinath Sridhar |
| 2009 | A Tree Based Method for the Rapid Screening of Chemical Fingerprints. | Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen |
| 2009 | Predicting Gene Structures from Multiple RT-PCR Tests. | Jakub Kovc, Toms Vinar, Brona Brejov |
| 2009 | Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. | Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael |
| 2009 | K-Partite RNA Secondary Structures. | Minghui Jiang, Pedro J. Tejada, Ramoni O. Lasisi, Shanhong Cheng, D. Scott Fechser |
| 2009 | Phylogenetic Comparative Assembly. | Peter Husemann, Jens Stoye |
| 2009 | Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction. | Matthew Hansen, Logan Everett, Larry N. Singh, Sridhar Hannenhalli |
| 2009 | A Markov Classification Model for Metabolic Pathways. | Timothy Hancock, Hiroshi Mamitsuka |
| 2009 | MADMX: A Novel Strategy for Maximal Dense Motif Extraction. | Roberto Grossi, Andrea Pietracaprina, Nadia Pisanti, Geppino Pucci, Eli Upfal, Fabio Vandin |
| 2009 | Back-Translation for Discovering Distant Protein Homologies. | Marta Grdea, Laurent No, Gregory Kucherov |
| 2009 | A Simple, Practical and Complete | Yelena Frid, Dan Gusfield |
| 2009 | SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy. | Pedro Feijo, Joo Meidanis |