| 2008 | Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach. | Thomas Lingner, Peter Meinicke |
| 2008 | Exact Transcriptome Reconstruction from Short Sequence Reads. | Vincent Lacroix, Michael Sammeth, Roderic Guig, Anne Bergeron |
| 2008 | Summarizing Multiple Gene Trees Using Cluster Networks. | Daniel H. Huson, Regula Rupp |
| 2008 | NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem. | Glenn Hickey, Paz Carmi, Anil Maheshwari, Norbert Zeh |
| 2008 | Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. | Inke Herms, Sven Rahmann |
| 2008 | Constructing Phylogenetic Supernetworks from Quartets. | Stefan Grnewald, Andreas Spillner, Kristoffer Forslund, Vincent Moulton |
| 2008 | Minimum Common String Partition Parameterized. | Peter Damaschke |
| 2008 | Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. | Ludovic Cottret, Paulo Vieira Milreu, Vicente Acua, Alberto Marchetti-Spaccamela, Fbio Viduani Martinez, Marie-France Sagot, Leen Stougie |
| 2008 | Efficient Genome Wide Tagging by Reduction to SAT. | Arthur Choi, Noah Zaitlen, Buhm Han, Knot Pipatsrisawat, Adnan Darwiche, Eleazar Eskin |
| 2008 | Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. | Serdar Bozdag, Timothy J. Close, Stefano Lonardi |
| 2008 | A Local Move Set for Protein Folding in Triangular Lattice Models. | Hans-Joachim Bckenhauer, Abu Zafer M. Dayem Ullah, Leonidas Kapsokalivas, Kathleen Steinhfel |
| 2008 | Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments. | Florian Battke, Carsten Mller-Tidow, Hubert Serve, Kay Nieselt |
| 2008 | An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem. | Rumen Andonov, Nicola Yanev, Nol Malod-Dognin |
| 2007 | Alignment-Free Local Structural Search by Writhe Decomposition. | Degui Zhi, Maxim Shatsky, Steven E. Brenner |
| 2007 | Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping Data. | Yonghui Wu, Prasanna Bhat, Timothy J. Close, Stefano Lonardi |
| 2007 | Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment. | Xueyi Wang, Jack Snoeyink |
| 2007 | Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps. | Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio |
| 2007 | When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features. | Roy Varshavsky, Menachem Fromer, Amit Man, Michal Linial |
| 2007 | Locality Kernels for Protein Classification. | Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski |
| 2007 | On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. | Rastislav Srmek, Brona Brejov, Toms Vinar |
| 2007 | Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach. | Alexander Schliep, Roland Krause |
| 2007 | Haplotype Inference Via Hierarchical Genotype Parsing. | Pasi Rastas, Esko Ukkonen |
| 2007 | Shotgun Protein Sequencing. | Pavel A. Pevzner |
| 2007 | Using Protein Domains to Improve the Accuracy of | Mihaela Pertea, Steven Salzberg |
| 2007 | Informative Motifs in Protein Family Alignments. | Hatice Gulcin Ozer, William C. Ray |