Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks -- Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks -- Towards an Integrated Protein-Protein Interaction Network -- The Factor Graph Network Model for Biological Systems -- Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution -- Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model -- Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis -- Keynote -- A Regulatory Network Controlling Drosophila Development -- Keynote -- Yeast Cells as a Discovery Platform for Neurodegenerative Disease -- RIBRA–An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem -- Avoiding Local Optima in Single Particle Reconstruction -- A High-Throughput Approach for Associating microRNAs with Their Activity Conditions -- RNA-RNA Interaction Prediction and Antisense RNA Target Search -- Consensus Folding of Unaligned RNA Sequences Revisited -- Keynote -- Discovery and Annotation of Genetic Modules -- Efficient q-Gram Filters for Finding All ?-Matches over a Given Length -- A Polynomial Time Solvable Formulation of Multiple Sequence Alignment -- A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters -- Reconstruction of Reticulate Networks from Gene Trees -- A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction -- Constructing a Smallest Refining Galled Phylogenetic Network -- Keynote -- Mapping Molecular Landscapes Inside Cells -- Information Theoretic Approaches to Whole Genome Phylogenies -- Maximum Likelihood of Evolutionary Trees Is Hard -- Graph Theoretical Insights into Evolution of Multidomain Proteins -- Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry -- A Hidden Markov Model Based Scoring Function for Mass Spectrometry Database Search -- EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning -- Keynote -- Biology as Information -- Using Multiple Alignments to Improve Gene Prediction -- Learning Interpretable SVMs for Biological Sequence Classification -- Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition -- Rapid Protein Side-Chain Packing via Tree Decomposition -- Recognition of Binding Patterns Common to a Set of Protein Structures -- Predicting Protein-Peptide Binding Affinity by Learning Peptide-Peptide Distance Functions -- Keynote -- Amino Acid Sequence Control of the Folding of the Parallel ?-Helix, the Simplest ?-Sheet Fold -- A Practical Approach to Significance Assessment in Alignment with Gaps -- Alignment of Optical Maps -- Keynote -- Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology -- Modeling the Combinatorial Functions of Multiple Transcription Factors -- Predicting Transcription Factor Binding Sites Using Structural Knowledge -- Motif Discovery Through Predictive Modeling of Gene Regulation -- HAPLOFREQ – Estimating Haplotype Frequencies Efficiently -- Improved Recombination Lower Bounds for Haplotype Data -- A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem -- Keynote -- Human Genome Sequence Variation and the Inherited Basis of Common Disease -- Stability of Rearrangement Measures in the Comparison of Genome Sequences -- On Sorting by Translocations.