Research in Computational Molecular Biology

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 FastDatabase 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.