| 2008 | A Branch-and-Bound Method for the Multichromosomal Reversal Median Problem. Meng Zhang, William Arndt, Jijun Tang |
| 2008 | A Faster Algorithm for RNA Co-folding. Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir |
| 2008 | A Local Move Set for Protein Folding in Triangular Lattice Models. Hans-Joachim Böckenhauer, Abu Zafer M. Dayem Ullah, Leonidas Kapsokalivas, Kathleen Steinhöfel |
| 2008 | Algorithms in Bioinformatics, 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings Keith A. Crandall, Jens Lagergren |
| 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 |
| 2008 | An Automated Combination of Kernels for Predicting Protein Subcellular Localization. Cheng Soon Ong, Alexander Zien |
| 2008 | An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem. Rumen Andonov, Nicola Yanev, Noël Malod-Dognin |
| 2008 | Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. Xiuwei Zhang, Bernard M. E. Moret |
| 2008 | Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. Inke Herms, Sven Rahmann |
| 2008 | Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. Serdar Bozdag, Timothy J. Close, Stefano Lonardi |
| 2008 | Constructing Phylogenetic Supernetworks from Quartets. Stefan Grünewald, Andreas Spillner, Kristoffer Forslund, Vincent Moulton |
| 2008 | Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem. Andrew Wei Xu, David Sankoff |
| 2008 | Detecting Repeat Families in Incompletely Sequenced Genomes. José Augusto Amgarten Quitzau, Jens Stoye |
| 2008 | Efficient Genome Wide Tagging by Reduction to SAT. Arthur Choi, Noah Zaitlen, Buhm Han, Knot Pipatsrisawat, Adnan Darwiche, Eleazar Eskin |
| 2008 | Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices. Seung-Jin Sul, Grant R. Brammer, Tiffani L. Williams |
| 2008 | Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Fábio Viduani Martinez, Marie-France Sagot, Leen Stougie |
| 2008 | Exact Transcriptome Reconstruction from Short Sequence Reads. Vincent Lacroix, Michael Sammeth, Roderic Guigó, Anne Bergeron |
| 2008 | Fast Bayesian Haplotype Inference Via Context Tree Weighting. Pasi Rastas, Jussi Kollin, Mikko Koivisto |
| 2008 | Fast Target Set Reduction for Large-Scale Protein Function Prediction: A Multi-class Multi-label Machine Learning Approach. Thomas Lingner, Peter Meinicke |
| 2008 | Fast and Adaptive Variable Order Markov Chain Construction. Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Döring, Knut Reinert, Martin Vingron |
| 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 | Hardness and Approximability of the Inverse Scope Problem. Zoran Nikoloski, Sergio Grimbs, Joachim Selbig, Oliver Ebenhöh |
| 2008 | Minimum Common String Partition Parameterized. Peter Damaschke |
| 2008 | Multichromosomal Genome Median and Halving Problems. Eric Tannier, Chunfang Zheng, David Sankoff |
| 2008 | Multiple Instance Learning Allows MHC Class II Epitope Predictions Across Alleles. Nico Pfeifer, Oliver Kohlbacher |
| 2008 | NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem. Glenn Hickey, Paz Carmi, Anil Maheshwari, Norbert Zeh |
| 2008 | Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. Sagi Snir, Tamir Tuller |
| 2008 | Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments. Florian Battke, Carsten Müller-Tidow, Hubert Serve, Kay Nieselt |
| 2008 | Protein Decoy Generation Using Branch and Bound with Efficient Bounding. Martin Paluszewski, Pawel Winter |
| 2008 | Rapid Neighbour-Joining. Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen |
| 2008 | Read Mapping Algorithms for Single Molecule Sequencing Data. Vladimir Yanovski, Stephen M. Rumble, Michael Brudno |
| 2008 | Summarizing Multiple Gene Trees Using Cluster Networks. Daniel H. Huson, Regula Rupp |
| 2008 | The Relation between Indel Length and Functional Divergence: A Formal Study. Raheleh Salari, Alexander Schönhuth, Fereydoun Hormozdiari, Artem Cherkasov, Süleyman Cenk Sahinalp |