Computational Life Sciences: First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005, Proceedings, Volume 1

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Michael R. Berthold, Robert Glen, Kay Diederichs, Oliver Kohlbacher, Ingrid Fischer
Springer Science & Business Media, Sep 16, 2005 - Computers - 276 pages
The integration of knowledge in the life sciences is continuing apace with ev- increasingimportancebeing placedoncomputer-basedmethodsofdata capture, analysis, and knowledge representation. Today, our many di?erent sciences are providing us with a sea of information: it is the handling of this in?ux that is becoming a key discovery and regulatory question. The solutions to these problems will result in advancements to all of the involved sciences and will be highly in?uential both in the selection of the areas scientists seek to investigate and also on their success. For this to happen, it is crucial to establish an open and lively exchange between computer scientists, biologists, and chemists. To encourage precisely this type of exchange, crossing the borders of the sciences, we organized the 1st Symposium on Computational Life Science in Konstanz, Germany(September 25 27,2005). Themainobjectiveofthesymposiumwasto formbridges, bringingtogetherscientistsfromavarietyofdisciplinestoexchange ideas and research e?orts and to talk about the problems in areas of research that up until now have not been visible at an interdisciplinary level. Our conference program shows that the scienti?c mix worked out very well. From 49 submissions, 21 were selected for presentation at the symposium, c- ering areas ranging from high-level system biology to data analysis related to mass spec traces. As a supplement to the regularconference program, we dedicated one section to papers presentedinthe frameworkof a workshoponDistributed Data Mining in the Life Sciences (LifeDDM), organized by Giuseppe Di Fatta."
 

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Contents

Structural Protein Interactions Predict KinaseInhibitor Interactions in Upregulated Pancreas Tumour Genes Expression Data
1
Biochemical Pathway Analysis via Signature Mining
12
Recurrent Neurofuzzy Network Models for Reverse Engineering Gene Regulatory Interactions
24
Some Applications of Dummy Point Scatterers for Phasing in Macromolecular XRay Crystallography
35
A Structured Metadata Repository for Bioinformatic Databases
46
Robust Perron Cluster Analysis for Various Applications in Computational Life Science
57
Multiple Alignment of Protein Structures in Three Dimensions
67
Protein Annotation by Secondary Structure Based Alignments PASSTA
79
Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples
151
Detection of Protein Assemblies in Crystals
163
Molecular Similarity Searching Using COSMO Screening Charges COSMO3PP
175
Increasing Diversity in Insilico Screening with Target Flexibility
186
Multiple Semiflexible 3D Superposition of DrugSized Molecules
198
Efficiency Considerations in Solving Smoluchowski Equations for Rough Potentials
208
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization
217
Visual Analysis of Molecular Conformations by Means of a Dynamic Density Mixture Model
229

Multiple 3D Alignment of ProteinProtein Interfaces
91
Frequent Itemsets for Genomic Profiling
104
Gene Selection Through Sensitivity Analysis of Support Vector Machines
117
The Breakpoint Graph in Ciliates
128
An R Package for Analyzing SELDI Measurements Identifying Protein Biomarkers
140
Distributed BLAST in a Grid Computing Context
241
Parallel Tuning of Support Vector Machine Learning Parameters for Large and Unbalanced Data Sets
253
The Architecture of a Proteomic Network in the Yeast
265
Author Index
277
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