| 2011 | Speeding Up Bayesian HMM by the Four Russians Method. | Md Pavel Mahmud, Alexander Schliep |
| 2011 | Bootstrapping Phylogenies Inferred from Rearrangement Data. | Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2011 | A Practical Algorithm for Ancestral Rearrangement Reconstruction. | Jakub Kovc, Brona Brejov, Toms Vinar |
| 2011 | Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. | Kouichi Kimura, Asako Koike, Kenta Nakai |
| 2011 | Graph-Based Decomposition of Biochemical Reaction Networks into Monotone Subsystems. | Hans-Michael Kaltenbach, Simona Constantinescu, Justin Feigelman, Jrg Stelling |
| 2011 | Learning Protein Functions from Bi-relational Graph of Proteins and Function Annotations. | Jonathan Qiang Jiang |
| 2011 | On a Conjecture about Compatibility of Multi-states Characters. | Michel Habib, Thu-Hien To |
| 2011 | Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. | Rob Gysel, Fumei Lam, Dan Gusfield |
| 2011 | Boosting Binding Sites Prediction Using Gene's Positions. | Mohamed Elati, Rim Fekih, Rmy Nicolle, Ivan Junier, Joan Hrisson, Franois Kps |
| 2011 | Removing Noise from Gene Trees. | Andrea Doroftei, Nadia El-Mabrouk |
| 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 | Constructing Large Conservative Supertrees. | Jianrong Dong, David Fernndez-Baca |
| 2011 | Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions - (Extended Abstract). | Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh |
| 2011 | Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. | Rayan Chikhi, Dominique Lavenier |
| 2011 | A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. | Stefan Canzar, Mohammed El-Kebir |
| 2011 | Towards a Practical O(n logn) Phylogeny Algorithm. | Daniel G. Brown, Jakub Truszkowski |
| 2011 | Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. | Brona Brejov, Michal Burger, Toms Vinar |
| 2010 | An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation. | Louxin Zhang, Yun Cui |
| 2010 | Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant's Approach. | Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson |
| 2010 | Quantifying the Strength of Natural Selection of a Motif Sequence. | Chen-Hsiang Yeang |
| 2010 | Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. | Corinna Theis, Stefan Janssen, Robert Giegerich |
| 2010 | An Experimental Study of Quartets MaxCut and Other Supertree Methods. | M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow |
| 2010 | Listing All Sorting Reversals in Quadratic Time. | Krister M. Swenson, Ghada Badr, David Sankoff |
| 2010 | Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. | Kristian Stevens, Dan Gusfield |
| 2010 | Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties. | Alexander Schnhuth, Raheleh Salari, Sleyman Cenk Sahinalp |