| 2007 | Incremental Discovery of Irredundant Motif Bases in Time | Alberto Apostolico, Claudia Tagliacollo |
| 2007 | A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence. | Rka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo D. Sontag, Alexander Zelikovsky, Kelly Westbrooks |
| 2006 | A Method to Design Standard HMMs with Desired Length Distribution for Biological Sequence Analysis. | Hongmei Zhu, Jiaxin Wang, Zehong Yang, Yixu Song |
| 2006 | Rapid | Jizhen Zhao, Russell L. Malmberg, Liming Cai |
| 2006 | Multiple Structure Alignment and Consensus Identification for Proteins. | Jieping Ye, Ivaylo Ilinkin, Ravi Janardan, Adam Isom |
| 2006 | Approximation Algorithms for Bi-clustering Problems. | Lusheng Wang, Yu Lin, Xiaowen Liu |
| 2006 | Alignment with Non-overlapping Inversions in | Augusto F. Vellozo, Carlos E. R. Alves, Alair Pereira do Lago |
| 2006 | Optimal Probing Patterns for Sequencing by Hybridization. | Dekel Tsur |
| 2006 | Accelerating the Computation of Elementary Modes Using Pattern Trees. | Marco Terzer, Jrg Stelling |
| 2006 | A Linear-Time Algorithm for Studying Genetic Variation. | Nikola Stojanovic, Piotr Berman |
| 2006 | Landscape Analysis for Protein-Folding Simulation in the H-P Model. | Kathleen Steinhfel, Alexandros Skaliotis, Andreas Alexander Albrecht |
| 2006 | Phylogenetic Network Inferences Through Efficient Haplotyping. | Yinglei Song, Chunmei Liu, Russell L. Malmberg, Liming Cai |
| 2006 | A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure. | Dandan Song, Zhidong Deng |
| 2006 | Accelerating Motif Discovery: Motif Matching on Parallel Hardware. | Geir Kjetil Sandve, Magnar Nedland, yvind B Syrstad, Lars Andreas Eidsheim, Osman Abul, Finn Drabls |
| 2006 | Flux-Based | Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter |
| 2006 | Integer Linear Programs for Discovering Approximate Gene Clusters. | Sven Rahmann, Gunnar W. Klau |
| 2006 | Segmenting Motifs in Protein-Protein Interface Surfaces. | Jeff M. Phillips, Johannes Rudolph, Pankaj K. Agarwal |
| 2006 | Gapped Permutation Patterns for Comparative Genomics. | Laxmi Parida |
| 2006 | Efficient Sampling of Transpositions and Inverted Transpositions for Bayesian MCMC. | Istvn Mikls, Timothy Brooks Paige, Pter Ligeti |
| 2006 | Efficient Model-Based Clustering for LC-MS Data. | Marta Luksza, Boguslaw Kluge, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin |
| 2006 | On the Complexity of the Crossing Contact Map Pattern Matching Problem. | Shuai Cheng Li, Ming Li |
| 2006 | How Many Transcripts Does It Take to Reconstruct the Splice Graph? | Paul A. Jenkins, Rune B. Lyngs, Jotun Hein |
| 2006 | Beaches of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems. | Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie |
| 2006 | Reducing Distortion in Phylogenetic Networks. | Daniel H. Huson, Mike A. Steel, Jim Whitfield |
| 2006 | Controlling Size When Aligning Multiple Genomic Sequences with Duplications. | Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller |