Bioinformatics Research and Development: First International Conference, BIRD 2007, Berlin, Germany, March 12-14, 2007. Proceedings

Nicole Radde, Lars Kaderali (auth.), Sepp Hochreiter, Roland Wagner (eds.)3540712321, 9783540712329

This volume contains the papers which were selected for oral presentation at the first Bioinformatics Research and Development (BIRD) conference held in Berlin, Germany during March 12-14, 2007. BIRD covers a wide range of topics related to bioinformatics like microarray data, genomics, single nucleotide polymorphism, sequence analysis, systems biology, medical applications, proteomics, information systems. The conference was very competitive. From about 140 submissions only 36 were selected by the Program Committee for oral presentation at BIRD and for publication in these proceedings. The acceptance rate was 1/4. The decisions of the Program Committee were guided by the recommendations of several reviewers for each paper. It should be mentioned that these proceedings have companion proceedings published by the Austrian Computer Society where selected poster presentations of the BIRD conference are included. The invited talk titled “From Flies to Human Disease” by Josef Penninger, one of the leading researcher in genetic experiments for investigating disease pathogenesis, was very inspiring and gave new insights into future bioinformatics challenges.

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Table of contents :
Front Matter….Pages –
Bayesian Inference of Gene Regulatory Networks Using Gene Expression Time Series Data….Pages 1-15
Biological Network Inference Using Redundancy Analysis….Pages 16-27
A Novel Graph Optimisation Algorithm for the Extraction of Gene Regulatory Networks from Temporal Microarray Data….Pages 28-37
Analysing Periodic Phenomena by Circular PCA….Pages 38-47
Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets….Pages 48-65
Mining Spatial Gene Expression Data for Association Rules….Pages 66-76
Individualized Predictions of Survival Time Distributions from Gene Expression Data Using a Bayesian MCMC Approach….Pages 77-89
Comparing Logic Regression Based Methods for Identifying SNP Interactions….Pages 90-103
Stochastical Analysis of Finite Point Sampling of 3D Chromatin Fiber in Interphase Cell Nuclei….Pages 104-118
Structural Screening of HIV-1 Protease/Inhibitor Docking by Non-parametric Binomial Distribution Test….Pages 119-130
satDNA Analyzer 1.2 as a Valuable Computing Tool for Evolutionary Analysis of Satellite-DNA Families: Revisiting Y-Linked Satellite-DNA Sequences of Rumex (Polygonaceae)….Pages 131-139
A Soft Hierarchical Algorithm for the Clustering of Multiple Bioactive Chemical Compounds….Pages 140-153
A Novel Method for Flux Distribution Computation in Metabolic Networks….Pages 154-167
Inverse Bifurcation Analysis of a Model for the Mammalian G 1 / S Regulatory Module….Pages 168-184
Weighted Cohesiveness for Identification of Functional Modules and Their Interconnectivity….Pages 185-198
Modelling and Simulation of the Genetic Phenomena of Additivity and Dominance via Gene Networks of Parallel Aggregation Processes….Pages 199-211
Protein Remote Homology Detection Based on Binary Profiles….Pages 212-223
Biological Sequences Encoding for Supervised Classification….Pages 224-238
Fast Search Algorithms for Position Specific Scoring Matrices….Pages 239-250
A Markovian Approach for the Segmentation of Chimpanzee Genome….Pages 251-262
Synthetic Protein Sequence Oversampling Method for Classification and Remote Homology Detection in Imbalanced Protein Data….Pages 263-277
Stem Kernels for RNA Sequence Analyses….Pages 278-291
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models….Pages 292-302
Patch Prediction of Protein Interaction Sites: Validation of a Scoring Function for an Online Server….Pages 303-313
Statistical Inference on Distinct RNA Stem-Loops in Genomic Sequences….Pages 314-327
Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions….Pages 328-342
Bayesian Inference for 2D Gel Electrophoresis Image Analysis….Pages 343-356
SimShiftDB: Chemical-Shift-Based Homology Modeling….Pages 357-370
Annotation of LC/ESI-MS Mass Signals….Pages 371-380
Stochastic Protein Folding Simulation in the d-Dimensional HP-Model….Pages 381-394
Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction….Pages 395-409
Joining Softassign and Dynamic Programming for the Contact Map Overlap Problem….Pages 410-423
An Evaluation of Text Retrieval Methods for Similarity Search of Multi-dimensional NMR-Spectra….Pages 424-438
Ontology-Based MEDLINE Document Classification….Pages 439-452
Integrating Mutations Data of the TP53 Human Gene in the Bioinformatics Network Environment….Pages 453-463
Efficient and Scalable Indexing Techniques for Biological Sequence Data….Pages 464-479
Back Matter….Pages –