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SPECIAL SECTION on Bioinformatics Research and Applications

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications
Ion I. Mandoiu, Yi Pan, Alexander Zelikovsky

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz

Solving the Preserving Reversal Median Problem
Matthias Bernt, Daniel Merkle, Martin Middendorf

Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution
Marília D.V. Braga, Marie-France Sagot, Celine Scornavacca, Eric Tannier

Reconstruction of 3D Structures from Protein Contact Maps
Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio

Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene and Protein Expression Studies
George Lee, Carlos Rodriguez, Anant Madabhushi

Papers

Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
Hyuk Cho, Inderjit S. Dhillon

Incorporating Gene Functions into Regression Analysis of DNA-Protein Binding Data and Gene Expression Data to Construct Transcriptional Networks
Peng Wei, Wei Pan

PairProSVM: Protein Subcellular Localization Based on Local Pairwise Profile Alignment and SVM
Man-Wai Mak, Jian Guo, Sun-Yuan Kung

Reproducibility-Optimized Test Statistic for Ranking Genes in Microarray Studies
Laura L. Elo, Sanna Filén, Riitta Lahesmaa, Tero Aittokallio

Solving the Problem of Trans-Genomic Query with Alignment Tables
Douglass Stott Parker, Ruey-Lung Hsiao, Yi Xing, Alissa M. Resch, Christopher J. Lee

Fine-Scale Genetic Mapping Using Independent Component Analysis
Zaher Dawy, Michel Sarkis, Joachim Hagenauer, Jakob C. Mueller

Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets
Michael D. Hendy, Sagi Snir

Improved Layout of Phylogenetic Networks
Philippe Gambette, Daniel H. Huson

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