| 2006 | Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction. | Eun-Jong Hong, Toms Lozano-Prez |
| 2006 | Imputing Supertrees and Supernetworks from Quartets. | Barbara R. Holland, Glenn Conner, Katharina T. Huber, Vincent Moulton |
| 2006 | On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. | Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau |
| 2006 | Measures of Codon Bias in Yeast, the tRNA Pairing Index and Possible DNA Repair Mechanisms. | Markus T. Friberg, Pedro Gonnet, Yves Barral, Nicol N. Schraudolph, Gaston H. Gonnet |
| 2006 | Procrastination Leads to Efficient Filtration for Local Multiple Alignment. | Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna |
| 2006 | Segmentation with an Isochore Distribution. | Mikls Csrs, Ming-Te Cheng, Andreas Grimm, Amine Halawani, Perrine Landreau |
| 2006 | Linear-Time Haplotype Inference on Pedigrees Without Recombinations. | Bethany Man-Yee Chan, Joseph Wun-Tat Chan, Francis Y. L. Chin, Stanley P. Y. Fung, Ming-Yang Kao |
| 2006 | Improving the Layout of Oligonucleotide Microarrays: Pivot Partitioning. | Srgio A. de Carvalho, Sven Rahmann |
| 2006 | A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks. | Lukas Burger, Erik van Nimwegen |
| 2006 | Combinatorial Methods for Disease Association Search and Susceptibility Prediction. | Dumitru Brinza, Alexander Zelikovsky |
| 2006 | Decomposing Metabolomic Isotope Patterns. | Sebastian Bcker, Matthias C. Letzel, Zsuzsanna Liptk, Anton Pervukhin |
| 2006 | New Constructive Heuristics for DNA Sequencing by Hybridization. | Christian Blum, Mateu Ybar Valls |
| 2006 | A Unifying View of Genome Rearrangements. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression. | Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson |
| 2005 | A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem. | Gang Wu, Jia-Huai You, Guohui Lin |
| 2005 | A Faster Algorithm for Detecting Network Motifs. | Sebastian Wernicke |
| 2005 | Optimal Protein Threading by Cost-Splitting. | Philippe Veber, Nicola Yanev, Rumen Andonov, Vincent Poirriez |
| 2005 | Ortholog Clustering on a Multipartite Graph. | Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik |
| 2005 | Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds. | Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor |
| 2005 | Reconstructing Metabolic Networks Using Interval Analysis. | Warwick Tucker, Vincent Moulton |
| 2005 | Spectral Clustering Gene Ontology Terms to Group Genes by Function. | Nora Speer, Christian Spieth, Andreas Zell |
| 2005 | Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2005 | Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment. | Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai |
| 2005 | Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). | Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye |
| 2005 | Linear Time Algorithm for Parsing RNA Secondary Structure. | Baharak Rastegari, Anne Condon |