| 2009 | Constructing Majority-Rule Supertrees. | Jianrong Dong, David Fernndez-Baca, Fred R. McMorris |
| 2009 | PMFastR: A New Approach to Multiple RNA Structure Alignment. | Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang |
| 2009 | Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks. | Phuong Dao, Alexander Schnhuth, Fereydoun Hormozdiari, Iman Hajirasouliha, Sleyman Cenk Sahinalp, Martin Ester |
| 2009 | biRNA: Fast RNA-RNA Binding Sites Prediction. | Hamidreza Chitsaz, Rolf Backofen, Sleyman Cenk Sahinalp |
| 2009 | Minimum Factorization Agreement of Spliced ESTs. | Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi |
| 2009 | Annotating Fragmentation Patterns. | Sebastian Bcker, Florian Rasche, Tamara Steijger |
| 2008 | A Faster Algorithm for RNA Co-folding. | Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir |
| 2008 | Genotype Sequence Segmentation: Handling Constraints and Noise. | Qi Zhang, Wei Wang, Leonard McMillan, Jan F. Prins, Fernando Pardo-Manuel de Villena, David Threadgill |
| 2008 | Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. | Xiuwei Zhang, Bernard M. E. Moret |
| 2008 | A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem. | Meng Zhang, William Arndt, Jijun Tang |
| 2008 | Read Mapping Algorithms for Single Molecule Sequencing Data. | Vladimir Yanovski, Stephen M. Rumble, Michael Brudno |
| 2008 | Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem. | Andrew Wei Xu, David Sankoff |
| 2008 | Multichromosomal Genome Median and Halving Problems. | Eric Tannier, Chunfang Zheng, David Sankoff |
| 2008 | Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices. | Seung-Jin Sul, Grant R. Brammer, Tiffani L. Williams |
| 2008 | Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. | Sagi Snir, Tamir Tuller |
| 2008 | Rapid Neighbour-Joining. | Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen |
| 2008 | Fast and Adaptive Variable Order Markov Chain Construction. | Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Dring, Knut Reinert, Martin Vingron |
| 2008 | The Relation between Indel Length and Functional Divergence: A Formal Study. | Raheleh Salari, Alexander Schnhuth, Fereydoun Hormozdiari, Artem Cherkasov, Sleyman Cenk Sahinalp |
| 2008 | Fast Bayesian Haplotype Inference Via Context Tree Weighting. | Pasi Rastas, Jussi Kollin, Mikko Koivisto |
| 2008 | Detecting Repeat Families in Incompletely Sequenced Genomes. | Jos Augusto Amgarten Quitzau, Jens Stoye |
| 2008 | Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles. | Nico Pfeifer, Oliver Kohlbacher |
| 2008 | Protein Decoy Generation Using Branch and Bound with Efficient Bounding. | Martin Paluszewski, Pawel Winter |
| 2008 | An Automated Combination of Kernels for Predicting Protein Subcellular Localization. | Cheng Soon Ong, Alexander Zien |
| 2008 | Hardness and Approximability of the Inverse Scope Problem. | Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhh |
| 2008 | An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. | Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan |