| 321 | -- | 322 | Ion I. Mandoiu, Yi Pan, Alexander Zelikovsky. Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications |
| 323 | -- | 331 | Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz. Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference |
| 332 | -- | 347 | Matthias Bernt, Daniel Merkle, Martin Middendorf. Solving the Preserving Reversal Median Problem |
| 348 | -- | 356 | Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier. Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution |
| 357 | -- | 367 | Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio. Reconstruction of 3D Structures From Protein Contact Maps |
| 368 | -- | 384 | George Lee, Carlos Rodriguez, Anant Madabhushi. Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies |
| 385 | -- | 400 | Hyuk Cho, Inderjit S. Dhillon. Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering |
| 401 | -- | 415 | Peng Wei, Wei Pan. Incorporating Gene Functions into Regression Analysis of DNA-Protein Binding Data and Gene Expression Data to Construct Transcriptional Networks |
| 416 | -- | 422 | Man-Wai Mak, Jian Guo, Sun-Yuan Kung. PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM |
| 423 | -- | 431 | Laura Elo, Sanna Filen, Riitta Lahesmaa, Tero Aittokallio. Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies |
| 432 | -- | 447 | Douglas Stott Parker Jr., Ruey-Lung Hsiao, Yi Xing, Alissa M. Resch, Christopher J. Lee. Solving the Problem of Trans-Genomic Query with Alignment Tables |
| 448 | -- | 460 | Zaher Dawy, Michel Sarkis, Joachim Hagenauer, Jakob C. Mueller. Fine-Scale Genetic Mapping Using Independent Component Analysis |
| 461 | -- | 471 | Michael D. Hendy, Sagi Snir. Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets |
| 472 | -- | 479 | Philippe Gambette, Daniel H. Huson. Improved Layout of Phylogenetic Networks |