%{search_type} search results

• Association Study between Gene Expression and Multiple Relevant Phenotypes with Cluster Analysis.- Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae.- Chronic Rat Toxicity Prediction of Chemical Compounds Using Kernel Machines.- Simulating Evolution of Drosophila Melanogaster Ebony Mutants Using a Genetic Algorithm.- Microarray Biclustering: A Novel Memetic Approach Based on the PISA Platform.- F-score with Pareto Front Analysis for Multiclass Gene Selection.- A Hierarchical Classification Ant Colony Algorithm for Predicting Gene Ontology Terms.- Conquering the Needle-in-a-Haystack: How Correlated Input Variables Beneficially Alter the Fitness Landscape for Neural Networks.- Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease.- On the Efficiency of Local Search Methods for the Molecular Docking Problem.- A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems.- Guidelines to Select Machine Learning Scheme for Classification of Biomedical Datasets.- Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective.- Clustering Metagenome Short Reads Using Weighted Proteins.- A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony.- Validation of a Morphogenesis Model of Drosophila Early Development by a Multi-objective Evolutionary Optimization Algorithm.- Refining Genetic Algorithm Based Fuzzy Clustering through Supervised Learning for Unsupervised Cancer Classification.
• (source: Nielsen Book Data)

The ?eld of bioinformatics has two main objectives: the creation and main- nance of biological databases, and the discovery of knowledge from life sciences datainordertounravelthemysteriesofbiologicalfunction, leadingtonewdrugs andtherapiesforhumandisease.Life sciencesdatacomeinthe formofbiological sequences, structures, pathways, or literature. One major aspect of discovering biological knowledge is to search, predict, or model speci?c information in a given dataset in order to generate new interesting knowledge. Computer science methods such as evolutionary computation, machine learning, and data mining all have a great deal to o?er the ?eld of bioinformatics. The goal of the 7th - ropean Conference on Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics (EvoBIO 2009) was to bring together experts in these ?elds in order to discuss new and novel methods for tackling complex biological problems. The 7th EvoBIO conference was held in Tubing .. en, Germany during April 15-17, 2009 at the Eberhard-Karls-Universitat .. Tu ..bingen. EvoBIO 2009 was held jointly with the 12th European Conference on Genetic Programming (- roGP 2009), the 9th European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP 2009), and the Evo Workshops. C- lectively, the conferences and workshops are organized under the name Evo* (www.evostar.org).
(source: Nielsen Book Data)

• Artificial Chemistries, Pre-biotic Evolution.- Chemical Organizations at Different Spatial Scales.- Formulating Membrane Dynamics with the Reaction of Surface Objects.- Multi-level Selectional Stalemate in a Simple Artificial Chemistry.- Simulation Model for Functionalized Vesicles: Lipid-Peptide Integration in Minimal Protocells.- Evolution.- Emergence of Genetic Coding: An Information-Theoretic Model.- Emergent Phenomena Only Belong to Biology.- Genotype Editing and the Evolution of Regulation and Memory.- Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms.- Simulation of the Evolution of Aging: Effects of Aggression and Kin-Recognition.- Ecosystems.- Artificial Ecosystem Selection for Evolutionary Optimisation.- Building Virtual Ecosystems from Artificial Chemistry.- Energy Flows and Maximum Power on an Evolutionary Ecological Network Model.- Entropy Production in Ecosystems.- Increasing Complexity Can Increase Stability in a Self-Regulating Ecosystem.- Niche Differentiation and Coexistence in a Multi-resource Ecosystem with Competition.- Variance in Water Temperature as a Factor in the Modelling of Starfish and Mussel Population Density and Diversity.- Morphodynamics, Development.- Cell Tracking: Genesis and Epigenesis in an Artificial Organism.- Developmental Neural Heterogeneity Through Coarse-Coding Regulation.- Re-examination of Swimming Motion of Virtually Evolved Creature Based on Fluid Dynamics.- Adaptive Behavior.- Adaptation to Sensory Delays.- Adapting to Your Body.- An Analysis of Behavioral Attractor Dynamics.- Artificial Emotions: Are We Ready for Them?.- Evolution of an Adaptive Sleep Response in Digital Organisms.- Where Did I Put My Glasses? Determining Trustfulness of Records in Episodic Memory by Means of an Associative Network.- Grounding Action-Selection in Event-Based Anticipation.- Learning and Evolution.- Aging in Artificial Learning Systems.- An Analysis of the Effects of Lifetime Learning on Population Fitness and Diversity in an NK Fitness Landscape.- Embodied Evolution and Learning: The Neglected Timing of Maturation.- Evolution and Learning in an Intrinsically Motivated Reinforcement Learning Robot.- Evolving Cultural Learning Parameters in an NK Fitness Landscape.- How Does Niche Construction Reverse the Baldwin Effect?.- Improving Search Efficiency in the Action Space of an Instance-Based Reinforcement Learning Technique for Multi-robot Systems.- Improving Agent Localisation Through Stereotypical Motion.- Neuroevolution of Agents Capable of Reactive and Deliberative Behaviours in Novel and Dynamic Environments.- On the Adaptive Disadvantage of Lamarckianism in Rapidly Changing Environments.- The Dynamics of Associative Learning in an Evolved Situated Agent.- Communication, Constitution of Meaning, Language.- Constructing the Basic Umwelt of Artificial Agents: An Information-Theoretic Approach.- Directed Evolution of Communication and Cooperation in Digital Organisms.- Evolution of Acoustic Communication Between Two Cooperating Robots.- Group Size Effects on the Emergence of Compositional Structures in Language.- Language Learning Dynamics: Coexistence and Selection of Grammars.- Multi-level Selection in the Emergence of Language Systematicity.- Protolanguages That Are Semi-holophrastic.- From the Outside-In: Embodied Attention in Toddlers.- Agency, Autopoiesis, Autonomy.- Autonomy: A Review and a Reappraisal.- Category Theoretical Distinction Between Autopoiesis and (M, R) Systems.- Measuring Autonomy by Multivariate Autoregressive Modelling.- Minimal Agency Detection of Embodied Agents.- Alife and Art.- Hermeneutic Resonance in Animats and Art.- Robotic Superstrings Installation: A-Life Science & Art.- Dynamics of Social Systems, Collective Behavior.- A Distributed Formation Algorithm to Organize Agents with No Coordinate Agreement.- A Multi-level Selection Model for the Emergence of Social Norms.- Evolution of Cooperation in a Population of Selfish Adaptive Agents.- Evolutionary Dilemmas in a Social Network.- Exogenous Fault Detection in a Collective Robotic Task.- From Artificial Societies to New Social Science Theory.- From Solitary to Collective Behaviours: Decision Making and Cooperation.- Individual Selection for Cooperative Group Formation.- Institutional Robotics.- Investigating the Evolution of Cooperative Behaviour in a Minimally Spatial Model.- Modeling Decentralized Organizational Change in Honeybee Societies.- Social Facilitation on the Development of Foraging Behaviors in a Population of Autonomous Robots.- Social Impact Theory Based Optimizer.- The Role of Collective Reproduction in Evolution.- Fear and the Behaviour of Virtual Flocking Animals.- Swarm and Ant Colony Systems.- Comparing ACO Algorithms for Solving the Bi-criteria Military Path-Finding Problem.- Decentralized Control and Interactive Design Methods for Large-Scale Heterogeneous Self-Organizing Swarms.- EcoPS - a Model of Group-Foraging with Particle Swarm Systems.- Efficient Multi-foraging in Swarm Robotics.- Modelling the Effects of Colony Age on the Foraging Behaviour of Harvester Ants.- Robotics and Autonomous Agents: Concepts and Applications.- A Mechanism to Self-Assemble Patterns with Autonomous Robots.- Binocular Vision-Based Robot Control with Active Hand-Eye Coordination.- Controlling an Anthropomimetic Robot: A Preliminary Investigation.- Evolution of Neural Networks for Active Control of Tethered Airfoils.- Feathered Flyer: Integrating Morphological Computation and Sensory Reflexes into a Physically Simulated Flapping-Wing Robot for Robust Flight Manoeuvre.- Guided Self-organisation for Autonomous Robot Development.- Near-Optimal Mobile Robot Recharging with the Rate-Maximizing Forager.- Neural Uncertainty and Sensorimotor Robustness.- Simulations of Simulations in Evolutionary Robotics.- Synthesizing Physically-Realistic Environmental Models from Robot Exploration.- The Evolution of Pain.- Evolutionary Computation.- A Computational Morphogenesis Approach to Simple Structure Development.- Program Evolvability Under Environmental Variations and Neutrality.- The Creativity Potential Within Evolutionary Algorithms.- The Problems with Counting Ancestors in a Simple Genetic Algorithm.- Networks, Cellular Automata, Complex Systems.- Asynchronous Graph-Rewriting Automata and Simulation of Synchronous Execution.- Catalysis by Self-Assembled Structures in Emergent Reaction Networks.- Community Detection in Complex Networks Using Collaborative Evolutionary Algorithms.- Detecting Non-trivial Computation in Complex Dynamics.- Evolution of One-Dimensional Cellular Automata by 1/f Noise.- Genotype Reuse More Important than Genotype Size in Evolvability of Embodied Neural Networks.- Information-Cloning of Scale-Free Networks.- MBEANN: Mutation-Based Evolving Artificial Neural Networks.- Measuring Entropy in Embodied Neural Agents with Homeostasic Units: A Link Between Complexity and Cybernetics.- Networks Regulating Networks: The Effects of Constraints on Topological Evolution.- Preliminary Investigations on the Evolvability of a Non spatial GasNet Model.- Semi-synchronous Activation in Scale-Free Boolean Networks.- Spatial Embedding and Complexity: The Small-World Is Not Enough.- The Application of the Idea of Extended Cellular Automata for Some Pedestrian Behaviors.- Transients of Active Tracking: A Stroll in Attractor Spaces.- Wavelet Network with Hybrid Algorithm to Linearize High Power Amplifiers.- Models and Methodologies.- A Behavior-Based Model of the Hydra, Phylum Cnidaria.- A Computational System for Investigating Chemotaxis-Based Cell Aggregation.- A Signal Based Approach to Artificial Agent Modeling.- Construction of Hypercycles in Typogenetics with Evolutionary Algorithms.- Designing a Methodology to Estimate Complexity of Protein Structures.- Designing for Surprise.- Evolving Virtual Neuronal Morphologies: A Case Study in Genetic L-Systems Programming.- Folding Protein-Like Structures with Open L-Systems.- Formal Model of Embodiment on Abstract Systems: From Hierarchy to Heterarchy.- Neuro-evolution Methods for Designing Emergent Specialization.- Neutral Emergence and Coarse Graining.- New Models for Old Questions: Evolutionary Robotics and the `A Not B' Error.- PLAZZMID: An Evolutionary Agent-Based Architecture Inspired by Bacteria and Bees.- Self-organizing Acoustic Categories in Sensor Arrays.- Self-organizing Systems Based on Bio-inspired Properties.- Stepwise Transition from Direct Encoding to Artificial Ontogeny in Neuroevolution.- Symbiosis, Synergy and Modularity: Introducing the Reciprocal Synergy Symbiosis Algorithm.- Turing Complete Catalytic Particle Computers.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the 9th European Conference on Artificial Life, ECAL 2007, held in Lisbon, Portugal. The 125 revised full papers cover morphogenesis and development, robotics and autonomous agents, evolutionary computation and theory, cellular automata, models of biological systems and their applications, ant colony and swarm systems, evolution of communication, simulation of social interactions, self-replication, artificial chemistry.
(source: Nielsen Book Data)

• Shotgun Protein Sequencing.- Locality Kernels for Protein Classification.- When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features.- Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.- Bringing Folding Pathways into Strand Pairing Prediction.- A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage.- Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies.- Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity.- Haplotype Inference Via Hierarchical Genotype Parsing.- Seeded Tree Alignment and Planar Tanglegram Layout.- Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion.- An ?(n 2/logn) Speed-Up of
• Heuristics for the Gene-Duplication Problem.- Incremental Discovery of Irredundant Motif Bases in Time O(
• (source: Nielsen Book Data)

The refereed proceedings from the 7th International Workshop on Algorithms in Bioinformatics are provided in this volume. Papers address current issues in algorithms in bioinformatics, ranging from mathematical tools to experimental studies of approximation algorithms to significant computational analyses. Biological problems examined include genetic mapping, sequence alignment and analysis, phylogeny, comparative genomics, and protein structure.
(source: Nielsen Book Data)

• Identifying Regulatory Sites Using Neighborhood Species.- Genetic Programming and Other Machine Learning Approaches to Predict Median Oral Lethal Dose (LD50) and Plasma Protein Binding Levels (%PPB) of Drugs.- Hypothesis Testing with Classifier Systems for Rule-Based Risk Prediction.- Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data.- One-Versus-One and One-Versus-All Multiclass SVM-RFE for Gene Selection in Cancer Classification.- Understanding Signal Sequences with Machine Learning.- Targeting Differentially Co-regulated Genes by Multiobjective and Multimodal Optimization.- Modeling Genetic Networks: Comparison of Static and Dynamic Models.- A Genetic Embedded Approach for Gene Selection and Classification of Microarray Data.- Modeling the Shoot Apical Meristem in A. thaliana: Parameter Estimation for Spatial Pattern Formation.- Evolutionary Search for Improved Path Diagrams.- Simplifying Amino Acid Alphabets Using a Genetic Algorithm and Sequence Alignment.- Towards Evolutionary Network Reconstruction Tools for Systems Biology.- A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites.- Bio-mimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks.- Tuning ReliefF for Genome-Wide Genetic Analysis.- Dinucleotide Step Parameterization of Pre-miRNAs Using Multi-objective Evolutionary Algorithms.- Amino Acid Features for Prediction of Protein-Protein Interface Residues with Support Vector Machines.- Predicting HIV Protease-Cleavable Peptides by Discrete Support Vector Machines.- Inverse Protein Folding on 2D Off-Lattice Model: Initial Results and Perspectives.- Virtual Error: A New Measure for Evolutionary Biclustering.- Characterising DNA/RNA Signals with Crisp Hypermotifs: A Case Study on Core Promoters.- Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes.- The Role of a Priori Information in the Minimization of Contact Potentials by Means of Estimation of Distribution Algorithms.- Classification of Cell Fates with Support Vector Machine Learning.- Reconstructing Linear Gene Regulatory Networks.- Individual-Based Modeling of Bacterial Foraging with Quorum Sensing in a Time-Varying Environment.- Substitution Matrix Optimisation for Peptide Classification.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the 5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2007, held in Valencia, Spain, April 2007. Coverage brings together experts in computer science with experts in bioinformatics and the biological sciences. It presents contributions on fundamental and theoretical issues along with papers dealing with different applications areas.
(source: Nielsen Book Data)

• Sequence Analysis.- Automated Methods of Predicting the Function of Biological Sequences Using GO and Rough Set.- C-Based Design Methodology for FPGA Implementation of ClustalW MSA.- A Two-Phase ANN Method for Genome-Wide Detection of Hormone Response Elements.- An Expert Knowledge-Guided Mutation Operator for Genome-Wide Genetic Analysis Using Genetic Programming.- cDNA-Derived Amino Acid Sequence from Rat Brain A2aR Possesses Conserved Motifs PMNYM of TM 5 Domain, Which May Be Involved in Dimerization of A2aR.- Strong GC and AT Skew Correlation in Chicken Genome.- Comparative Analysis of a Hierarchical Bayesian Method for Quantitative Trait Loci Analysis for the Arabidopsis Thaliana.- Prediction of Protein Structure, Interaction and Localization.- Using Decision Templates to Predict Subcellular Localization of Protein.- Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction.- Using Fuzzy Support Vector Machine Network to Predict Low Homology Protein Structural Classes.- SVM-BetaPred: Prediction of Right-Handed ss-Helix Fold from Protein Sequence Using SVM.- Protein Fold Recognition Based Upon the Amino Acid Occurrence.- Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties.- Dynamic Outlier Exclusion Training Algorithm for Sequence Based Predictions in Proteins Using Neural Network.- Bioinformatics on ?-Barrel Membrane Proteins: Sequence and Structural Analysis, Discrimination and Prediction.- Estimation of Evolutionary Average Hydrophobicity Profile from a Family of Protein Sequences.- Gene Expression Analysis.- APMA Database for Affymetrix Target Sequences Mapping, Quality Assessment and Expression Data Mining.- Ensemble of Dissimilarity Based Classifiers for Cancerous Samples Classification.- Gene Expression Analysis of Leukemia Samples Using Visual Interpretation of Small Ensembles: A Case Study.- Ant-MST: An Ant-Based Minimum Spanning Tree for Gene Expression Data Clustering.- Integrating Gene Expression Data from Microarrays Using the Self-Organising Map and the Gene Ontology.- Order Preserving Clustering by Finding Frequent Orders in Gene Expression Data.- Correlation-Based Relevancy and Redundancy Measures for Efficient Gene Selection.- SVM-RFE with Relevancy and Redundancy Criteria for Gene Selection.- In Silico Expression Profiles of Human Endogenous Retroviruses.- Pathway Analysis.- A Framework for Path Analysis in Gene Regulatory Networks.- Transcriptional Gene Regulatory Network Reconstruction Through Cross Platform Gene Network Fusion.- Reconstruction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates.- Validation of Gene Regulatory Networks from Protein-Protein Interaction Data: Application to Cell-Cycle Regulation.- Medical Informatics.- Rough Sets and Fuzzy Sets Theory Applied to the Sequential Medical Diagnosis.- In silico Identification of Putative Drug Targets in Pseudomonas aeruginosa Through Metabolic Pathway Analysis.- Understanding Prediction Systems for HLA-Binding Peptides and T-Cell Epitope Identification.- Predicting Binding Peptides with Simultaneous Optimization of Entropy and Evolutionary Distance.- Bioimaging.- 3D Automated Nuclear Morphometric Analysis Using Active Meshes.- Time-Frequency Method Based Activation Detection in Functional MRI Time-Series.- High Performance Classification of Two Imagery Tasks in the Cue-Based Brain Computer Interface.- Human Brain Anatomical Connectivity Analysis Using Sequential Sampling and Resampling.- Classification of CT Brain Images of Head Trauma.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the International Workshop on Pattern Recognition in Bioinformatics, PRIB 2007, held in Singapore in October 2007. The 38 revised full papers presented were carefully reviewed and selected from 125 submissions. The papers discuss the applications of pattern recognition methods in the field of bioinformatics to solve problems in life sciences.
(source: Nielsen Book Data)

• QNet: A Tool for Querying Protein Interaction Networks.- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology.- Reconstructing the Topology of Protein Complexes.- Network Legos: Building Blocks of Cellular Wiring Diagrams.- An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments.- A Feature-Based Approach to Modeling Protein-DNA Interactions.- Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking.- Nucleosome Occupancy Information Improves de novo Motif Discovery.- Framework for Identifying Common Aberrations in DNA Copy Number Data.- Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models.- GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data.- Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions.- Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding.- Reconstructing the Phylogeny of Mobile Elements.- Beyond Galled Trees - Decomposition and Computation of Galled Networks.- Variational Upper Bounds for Probabilistic Phylogenetic Models.- Heuristics for the Gene-Duplication Problem: A ?(n) Speed-Up for the Local Search.- Support Vector Training of Protein Alignment Models.- Tools for Simulating and Analyzing RNA Folding Kinetics.- Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences.- Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data.- Multivariate Segmentation in the Analysis of Transcription Tiling Array Data.- A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements.- Rearrangements in Genomes with Centromeres Part I: Translocations.- Identification of Deletion Polymorphisms from Haplotypes.- Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation.- Minimizing and Learning Energy Functions for Side-Chain Prediction.- Protein Conformational Flexibility Analysis with Noisy Data.- Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules.- Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments.- Improved Ranking Functions for Protein and Modification-Site Identifications.- Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions.- A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data.- Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms.- An Efficient and Accurate Graph-Based Approach to Detect Population Substructure.- RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints.- Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007, held in Oakland, CA, USA in April 2007. The 37 revised full papers address all current issues in algorithmic, theoretical, and experimental bioinformatics.
(source: Nielsen Book Data)

This book constitutes the refereed proceedings of the Second International Workshop on Biologically Inspired Approaches to Advanced Information Technology, BioADIT 2006, held in Osaka, Japan, in January 2006. The 30 full papers presented together with the abstracts of 3 invited talks were carefully reviewed and selected for inclusion in the book. The contributions range from basic research in biology and in information technology, to more application-oriented developments in software and in hardware. The papers are organized in topical sections on robotics, networking, biological systems, self-organization, evolutionary computation, and modeling and imaging.
(source: Nielsen Book Data)

This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003. The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.
(source: Nielsen Book Data)

This book presents a selection of revised full papers accepted for presentation at the First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000, held in Montpellier, France, in May 2000. The 13 papers included in the book were selected after two rounds of reviewing and revision from a total of 67 submissions. Among the topics addressed are algorithms, comparative genomics, evolution, phylogeny, databases, knowledge processing, genome anotation, graph theory, combinatorial mathematics, macromolecular structures, RNA and proteins, metabolic pathways and regulatory networks, and statistics and classification.
(source: Nielsen Book Data)

• Molecular computing : from conformational pattern recognition to complex processing networks / M. Conrad and K.-P. Zauner
• A look at the visual modeling of plants using L-systems / P. Prusinkiewicz
• Bioinformatics and cheminformatics in the drug discovery cycle / H. Lim
• New developments in linking of biological databases and computer-generation of annotation : SWISS-PROT and its computer-annotated supplement TREMBL / R. Apweiler ... [et al.]
• EpoDB : an erythropoiesis gene expression database in progress / F. Salas ... [et al.]
• Recent advances in molecular distance geometry / T. Havel, S. Hyberts and I. Najfeld
• Three models of gene regulation in E. coli / J. Collado-Vides, A. Huerta and K. Klose
• A new method to develop highly specific models for regulatory DNA-regions / K. Frech, K. Quandt and T. Werner
• Towards an object-oriented framework for the modeling of integrated metabolic processes / G. Breuel and E. Gilles
• TRRD and COMPEL databases on transcription linked to TRANSFAC as tools for analysis and recognition of regulatory sequences / A. Kel ... [et al.]
• Integrating heterogeneous datasets in genomic mapping : radiation hybrids, YACs, genes and STS markers over the entire human chromosome X / A. Grigoriev, H. Lehrach and J. Kumlien
• A clustering approach to generalized tree alignment with application to alu repeats / B. Schwikowski and M. Vingron
• Simple folding model for HP lattice proteins / E. Bornberg-Bauer
• Fast protein fold recognition and accurate sequence-structure alignment / R. Zimmer and R. Thiele
• Carbohydrates : second-class citizens in biomedicine and bioinformatics? / C.-W. von der Lieth, E. Lang and T. Kozár
• Structural constraints and neutrality in RNA / U. Göbel, C. Forst and P. Schuster
• A systematic approach to finding new lead structures having biological activity / C. Schwab ... [et al.]
• Visualization and analysis of the complete yeast genome / A. Kaps ... [et al.]
• Virtual reality modeling for structural biology / J. Sühnel
• Evolutionary grammars : a grammatical model for genome evolution / J. Dassow and V. Mitrana
• From DNA recombination to DNA computing, via formal languages / G. Păun and A. Salomaa.

This book constitutes the strictly refereed post-workshop proceedings of the German Conference on Bioinformatics, GCB'96, held in Leipzig, Germany, in September/October 1996. The volume presents 18 revised full papers together with three invited papers; these contributions were selected after a second round of reviewing from the 91 conference presentations. The book addresses current issues in computational biology and biologically inspired computing. The papers are organized in sections on biological and metabolic pathways, sequence analysis, molecular modeling, visualization, and formal languages, and DNA.
(source: Nielsen Book Data)

• Identifying Regulatory Sites Using Neighborhood Species.- Genetic Programming and Other Machine Learning Approaches to Predict Median Oral Lethal Dose (LD50) and Plasma Protein Binding Levels (%PPB) of Drugs.- Hypothesis Testing with Classifier Systems for Rule-Based Risk Prediction.- Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data.- One-Versus-One and One-Versus-All Multiclass SVM-RFE for Gene Selection in Cancer Classification.- Understanding Signal Sequences with Machine Learning.- Targeting Differentially Co-regulated Genes by Multiobjective and Multimodal Optimization.- Modeling Genetic Networks: Comparison of Static and Dynamic Models.- A Genetic Embedded Approach for Gene Selection and Classification of Microarray Data.- Modeling the Shoot Apical Meristem in A. thaliana: Parameter Estimation for Spatial Pattern Formation.- Evolutionary Search for Improved Path Diagrams.- Simplifying Amino Acid Alphabets Using a Genetic Algorithm and Sequence Alignment.- Towards Evolutionary Network Reconstruction Tools for Systems Biology.- A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites.- Bio-mimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks.- Tuning ReliefF for Genome-Wide Genetic Analysis.- Dinucleotide Step Parameterization of Pre-miRNAs Using Multi-objective Evolutionary Algorithms.- Amino Acid Features for Prediction of Protein-Protein Interface Residues with Support Vector Machines.- Predicting HIV Protease-Cleavable Peptides by Discrete Support Vector Machines.- Inverse Protein Folding on 2D Off-Lattice Model: Initial Results and Perspectives.- Virtual Error: A New Measure for Evolutionary Biclustering.- Characterising DNA/RNA Signals with Crisp Hypermotifs: A Case Study on Core Promoters.- Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes.- The Role of a Priori Information in the Minimization of Contact Potentials by Means of Estimation of Distribution Algorithms.- Classification of Cell Fates with Support Vector Machine Learning.- Reconstructing Linear Gene Regulatory Networks.- Individual-Based Modeling of Bacterial Foraging with Quorum Sensing in a Time-Varying Environment.- Substitution Matrix Optimisation for Peptide Classification.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the 5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2007, held in Valencia, Spain, April 2007. Coverage brings together experts in computer science with experts in bioinformatics and the biological sciences. It presents contributions on fundamental and theoretical issues along with papers dealing with different applications areas.
(source: Nielsen Book Data)

• Not All Scale Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Emulation.- Probabilistic Paths for Protein Complex Inference.- Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting.- A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells.- Identification and Evaluation of Functional Modules in Gene Co-expression Networks.- A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast.- A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ion-Trap Mass Spectrometry.- De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis.- Alignment of Mass Spectrometry Data by Clique Finding and Optimization.
• (source: Nielsen Book Data)

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2006 satellite events: the Second Annual Workshop on Systems Biology, RSB 2006, and the First Biennial Workshop on Computational Proteomics, RCP 2006, held in San Diego, CA, USA in December 2006. The papers cover various aspects of systems biology and explore the use of computational mass spectrometry in various proteomic applications.
(source: Nielsen Book Data)

• An Interactive Map of Regulatory Networks of Pseudomonas aeruginosa Genome.- The Pathalyzer: A Tool for Analysis of Signal Transduction Pathways.- Decomposition of Overlapping Protein Complexes: A Graph Theoretical Method for Analyzing Static and Dynamic Protein Associations.- Comparison of Protein-Protein Interaction Confidence Assignment Schemes.- Characterization of the Effects of TF Binding Site Variations on Gene Expression Towards Predicting the Functional Outcomes of Regulatory SNPs.- Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes.- Improvement of Computing Times in Boolean Networks Using Chi-square Tests.- Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements.- Causal Inference of Regulator-Target Pairs by Gene Mapping of Expression Phenotypes.- Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels.- Improved Duplication Models for Proteome Network Evolution.- Application of Expectation Maximization Clustering to Transcription Factor Binding Positions for cDNA Microarray Analysis.- Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data.- Topological Robustness of the Protein-Protein Interaction Networks.- A Bayesian Approach for Integrating Transcription Regulation and Gene Expression: Application to Saccharomyces Cerevisiae Cell Cycle Data.- Probabilistic in Silico Prediction of Protein-Peptide Interactions.- Improved Pattern-Driven Algorithms for Motif Finding in DNA Sequences.- Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties.- An Interaction-Dependent Model for Transcription Factor Binding.- Computational Characterization and Identification of Core Promoters of MicroRNA Genes in C. elegans, H. sapiens and A. thaliana.- A Comprehensive Kinetic Model of the Exocytotic Process: Evaluation of the Reaction Mechanism.
• (source: Nielsen Book Data)

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.
(source: Nielsen Book Data)

• QNet: A Tool for Querying Protein Interaction Networks.- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology.- Reconstructing the Topology of Protein Complexes.- Network Legos: Building Blocks of Cellular Wiring Diagrams.- An Efficient Method for Dynamic Analysis of Gene Regulatory Networks and in silico Gene Perturbation Experiments.- A Feature-Based Approach to Modeling Protein-DNA Interactions.- Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking.- Nucleosome Occupancy Information Improves de novo Motif Discovery.- Framework for Identifying Common Aberrations in DNA Copy Number Data.- Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models.- GIMscan: A New Statistical Method for Analyzing Whole-Genome Array CGH Data.- Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions.- Shift-Invariant Adaptive Double Threading: Learning MHC II - Peptide Binding.- Reconstructing the Phylogeny of Mobile Elements.- Beyond Galled Trees - Decomposition and Computation of Galled Networks.- Variational Upper Bounds for Probabilistic Phylogenetic Models.- Heuristics for the Gene-Duplication Problem: A ?(n) Speed-Up for the Local Search.- Support Vector Training of Protein Alignment Models.- Tools for Simulating and Analyzing RNA Folding Kinetics.- Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences.- Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data.- Multivariate Segmentation in the Analysis of Transcription Tiling Array Data.- A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements.- Rearrangements in Genomes with Centromeres Part I: Translocations.- Identification of Deletion Polymorphisms from Haplotypes.- Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation.- Minimizing and Learning Energy Functions for Side-Chain Prediction.- Protein Conformational Flexibility Analysis with Noisy Data.- Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules.- Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments.- Improved Ranking Functions for Protein and Modification-Site Identifications.- Peptide Retention Time Prediction Yields Improved Tandem Mass Spectrum Identification for Diverse Chromatography Conditions.- A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry Data.- Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms.- An Efficient and Accurate Graph-Based Approach to Detect Population Substructure.- RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints.- Comparative Analysis of Spatial Patterns of Gene Expression in Drosophila melanogaster Imaginal Discs.
• (source: Nielsen Book Data)

This book constitutes the refereed proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2007, held in Oakland, CA, USA in April 2007. The 37 revised full papers address all current issues in algorithmic, theoretical, and experimental bioinformatics.
(source: Nielsen Book Data)

• Property-Driven Statistics of Biological Networks.- On the Computational Power of Brane Calculi.- Analysis of Signalling Pathways Using Continuous Time Markov Chains.- Machine Learning Biochemical Networks from Temporal Logic Properties.- Qualitative Petri Net Modelling of Genetic Networks.- Simulating Bacterial Transcription and Translation in a Stochastic ? Calculus.- Automated Abstraction Methodology for Genetic Regulatory Networks.- P Systems, a New Computational Modelling Tool for Systems Biology.- Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation.- Multiple Representations of Biological Processes.
• (source: Nielsen Book Data)

The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.
(source: Nielsen Book Data)

• Trend-Based Analysis of a Population Model of the AKAP Scaffold Protein / Oana Andrei and Muffy Calder
• Quasi Product Form Approximation for Markov Models of Reaction Networks / Alessio Angius, András Horváth and Verena Wolf
• Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study / Ezio Bartocci, Pietro Liò, Emanuela Merelli and Nicola Paoletti
• On Approximative Reachability Analysis of Biochemical Dynamical Systems / L. Brim, J. Fabriková, S. Dražan and D. Šafránek
• Minimal Reaction Systems / Andrzej Ehrenfeucht, Jetty Kleijn, Maciej Koutny and Grzegorz Rozenberg
• Complex Functional Rates in Rule-Based Languages for Biochemistry / Cristian Versari and Gianluigi Zavattaro
• Probabilistic Model Checking of the PDGF Signaling Pathway / Qixia Yuan, Panuwat Trairatphisan, Jun Pang, Sjouke Mauw and Monique Wiesinger, et al.
• Self-assembly Models of Variable Resolution / Andrzej Mizera, Eugen Czeizler and Ion Petre
• Metabolic Constraints on the Evolution of Genetic Codes: Did Multiple Preaerobic' Ecosystem Transitions Entrain Richer Dialects via Serial Endosymbiosis? / Rodrick Wallace.

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This, the 14th Transactions on Computational Systems Biology volume, guest edited by Ion Petre and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions, initially presented at the CompMod workshop, which took place in Aachen, Germany, in September 2011. The papers, written from different points of view and following various approaches, cover a wide range of topics within the field of modeling and analysis of biological systems. In addition, two regular submissions deal with models of self-assembling systems and metabolic constraints on the evolution of genetic codes.

• Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene
• Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway
• Impulse-Based Dynamic Simulation of Deformable Biological Structures
• Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach
• Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis
• Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities
• Cultural Epigenetics: On the Heritability of Complex Diseases
• Refining Dynamics of Gene Regulatory Networks in a Stochastic [pi]-Calculus Framework.

• Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene
• Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway
• Impulse-Based Dynamic Simulation of Deformable Biological Structures
• Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach
• Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis
• Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities
• Cultural Epigenetics: On the Heritability of Complex Diseases
• Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework.

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This, the 13th Transactions on Computational Systems Biology volume, guest edited by Ralph-Johan Back, Ion Petre, and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions initially presented at the CompMod workshop, which took place in Eindhoven, The Netherlands, in November 2009. From different points of view and following various approaches, the papers cover a wide range of topics in systems biology, addressing the dynamics and the computational principles of this emerging field.

• Invited Talks.- Association Analysis Techniques for Bioinformatics Problems.- Analyzing and Interrogating Biological Networks (Abstract).- From Architecture to Function (and Back) in Bio-networks.- A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants.- Assembly of Large Genomes from Paired Short Reads.- Amino Acid Classification and Hash Seeds for Homology Search.- Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads.- Gene Networks Viewed through Two Models.- Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper.- The 2-Interval Pattern Matching Problems and Its Application to ncRNA Scanning.- Refereed Papers.- RNA Pseudoknot Folding through Inference and Identification Using TAGRNA.- Comparing Bacterial Genomes by Searching Their Common Intervals.- Generalized Binary Tanglegrams: Algorithms and Applications.- Three-Dimensional Multimodality Modelling by Integration of High-Resolution Interindividual Atlases and Functional MALDI-IMS Data.- Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding.- A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets.- Computational Protocol for Screening GPI-anchored Proteins.- Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors.- An Agent-Based Model of Solid Tumor Progression.- Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma.- Selection of Multiple SNPs in Case-Control Association Study Using a Discretized Network Flow Approach.- Biclustering Expression Data Based on Expanding Localized Substructures.- Constrained Fisher Scores Derived from Interaction Profile Hidden Markov Models Improve Protein to Protein Interaction Prediction.- Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding.- The Impact of Gene Selection on Imbalanced Microarray Expression Data.- Spatial Information and Boolean Genetic Regulatory Networks.- Modeling of Genetic Regulatory Network in Stochastic ?-Calculus.- fMRI Activation Detection by MultiScale Hidden Markov Model.- cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models.- A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments.- A Fitness Distance Correlation Measure for Evolutionary Trees.- Alignment and Analysis of Closely Related Genomes.- Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements.- Multiple Sequence Alignment System for Pyrosequencing Reads.- A Bayesian Approach to High-Throughput Biological Model Generation.- Parallel Selection of Informative Genes for Classification.- Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways.- GridSPiM: A Framework for Simple Locality and Containment in the Stochastic ?-Calculus.- Mutual Information Based Extrinsic Similarity for Microarray Analysis.- Graph Spectral Approach for Identifying Protein Domains.
• (source: Nielsen Book Data)

This volume presents the proceedings of the First International Conference on Bioinformatics and Computational Biology (BICoB 2009). This conference was supported by the International Society for Computers and Applications (ISCA) and Springer. Computational techniques have already enabled unprecedented advances in modern biology and medicine. This continues to be a vibrant research area with broadening of computational techniques and new emerging challenges. The Bioinformatics and Computational Biology (BICoB) conference has the goal of promoting the advancement of computing techniques and their application to life sciences. The topics of interest include (and are not limited to): - Genome analysis: genome assembly; genome and chromosome annotation, gene ?nding; alternative splicing; EST analysis and comparative genomics - Sequence analysis: multiple sequence alignment; sequence search and cl- tering; function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences - Phylogenetics: phylogeny estimation; models of evolution; comparative b- logical methods; population genetics - StructuralBioinformatics:structurematching, prediction, analysisandc- parison; methods and tools for docking; protein design - Analysis of high-throughput biological data: microarrays (nucleic acid, p- tein, array CGH, genome tiling, and other arrays); EST; SAGE; MPSS; proteomics; mass spectrometry - Geneticsandpopulationanalysis:linkageanalysis; associationanalysis; p- ulation simulation; haplotyping; marker discovery; genotype calling - Systems biology: systems approaches to molecular biology; multiscale m- eling; pathways; gene networks BICoB is interested in all areas of computing with an impact on life sciences including (but not limited to) algorithms, databases, languages, systems, and high-performance computing.
(source: Nielsen Book Data)