| 2011 | A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. Yann Ponty, Cédric Saule |
| 2011 | A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. Stefan Canzar, Mohammed El-Kebir |
| 2011 | A Practical Algorithm for Ancestral Rearrangement Reconstruction. Jakub Kovác, Brona Brejová, Tomás Vinar |
| 2011 | Algorithm for Identification of Piecewise Smooth Hybrid Systems: Application to Eukaryotic Cell Cycle Regulation. Vincent Noel, Sergei Vakulenko, Ovidiu Radulescu |
| 2011 | Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings Teresa M. Przytycka, Marie-France Sagot |
| 2011 | Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. Brona Brejová, Michal Burger, Tomás Vinar |
| 2011 | Boosting Binding Sites Prediction Using Gene's Positions. Mohamed Elati, Rim Fekih, Rémy Nicolle, Ivan Junier, Joan Hérisson, François Képès |
| 2011 | Bootstrapping Phylogenies Inferred from Rearrangement Data. Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2011 | Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno |
| 2011 | Constructing Large Conservative Supertrees. Jianrong Dong, David Fernández-Baca |
| 2011 | Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. Rob Gysel, Fumei Lam, Dan Gusfield |
| 2011 | Dynamic Programming Algorithms for Efficiently Computing Cosegmentations between Biological Images. Hang Xiao, Melvin Zhang, Axel Mosig, Hon Wai Leong |
| 2011 | Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values. Kristian Stevens, Bonnie Kirkpatrick |
| 2011 | Finding Driver Pathways in Cancer: Models and Algorithms. Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2011 | GASTS: Parsimony Scoring under Rearrangements. Andrew Wei Xu, Bernard M. E. Moret |
| 2011 | Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems. Hans-Michael Kaltenbach, Simona Constantinescu, Justin Feigelman, Jörg Stelling |
| 2011 | Indexing Finite Language Representation of Population Genotypes. Jouni Sirén, Niko Välimäki, Veli Mäkinen |
| 2011 | Learning Protein Functions from Bi-relational Graph of Proteins and Function Annotations. Jonathan Qiang Jiang |
| 2011 | Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. Rayan Chikhi, Dominique Lavenier |
| 2011 | Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky |
| 2011 | OMG! Orthologs in Multiple Genomes - Competing Graph-Theoretical Formulations. Chunfang Zheng, Krister M. Swenson, Eric Lyons, David Sankoff |
| 2011 | On a Conjecture about Compatibility of Multi-states Characters. Michel Habib, Thu-Hien To |
| 2011 | Parsimonious Reconstruction of Network Evolution. Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, Carl Kingsford |
| 2011 | PepCrawler: A Fast RRT-Like Algorithm for High-Resolution Refinement and Binding-Affinity Estimation of Peptide Inhibitors - (Abstract). Elad Donsky, Haim J. Wolfson |
| 2011 | Removing Noise from Gene Trees. Andrea Doroftei, Nadia El-Mabrouk |
| 2011 | Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. Kouichi Kimura, Asako Koike, Kenta Nakai |
| 2011 | Separating Metagenomic Short Reads into Genomes via Clustering - (Extended Abstract). Olga Tanaseichuk, James Borneman, Tao Jiang |
| 2011 | Speeding Up Bayesian HMM by the Four Russians Method. Md Pavel Mahmud, Alexander Schliep |
| 2011 | Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions - (Extended Abstract). Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh |
| 2011 | Towards a Practical O(n logn) Phylogeny Algorithm. Daniel G. Brown, Jakub Truszkowski |
| 2011 | Using Dominances for Solving the Protein Family Identification Problem. Noël Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov |