Practical Applications of Computational Biology and Bioinformatics, 12th International Conference

Name: Practical Applications of Computational Biology and Bioinformatics, 12th International Conference
Brand: Springer
Price: 149.79 EUR
Availability: OnlineOnly

Florentino Fdez-Riverola Mohd Saberi Mohamad Miguel Rocha Juan F. De Paz Pascual González(Editor)

Springer (Publisher)

1st Edition

Published on 16. August 2018

XIII, 226 pages

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978-3-319-98702-6 (ISBN)

€149.79incl. 7% vat

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Content

Intro
Preface
Organization
General Co-chairs
Program Committee
PACBB 2018 Sponsors
Contents
A Hybrid of Simple Constrained Artificial Bee Colony Algorithm and Flux Balance Analysis for Enhancing Lactate and Succinate in Escherichia Coli
Abstract
1 Introduction
2 Materials and Methods
2.1 Dataset
2.2 A Hybrid of Simple Constrained Artificial Bee Colony Algorithm and Flux Balance Analysis
3 Results and Discussion
4 Conclusion
Acknowledgement
References
Parameter Estimation of Essential Amino Acids in Arabidopsis thaliana Using Hybrid of Bees Algorithm and Harmony Search
Abstract
1 Introduction
2 Materials and Methods
2.1 Datasets and Experimental Setup
2.2 A Hybrid Bees Algorithm and Harmony Search (BAHS)
2.2.1 Initiate Population with Random Solutions
2.2.2 Neighbourhood Search
2.2.3 Initiate Harmony Memory
2.2.4 Generate New Harmony
2.2.5 Update HM
2.2.6 Termination
3 Results and Discussion
4 Conclusion
Acknowledgements
References
In Silico Modeling and Simulation Approach for Apoptosis Caspase Pathways
Abstract
1 Introduction
2 Materials and Methods
2.1 The in Silico Modeling and Simulation of Cellular Signal Transduction
2.2 The Caspase Signaling Model
3 Results and Discussion
3.1 From Modeling to Simulation of Caspase Signaling Pathways
3.2 In Silico Studies of the Caspases Signaling Pathway
4 Conclusions
References
Molecular Dynamic Simulations Suggest that P152R Mutation Within MeCP2 Can Lead to Higher DNA Binding Affinity and Loss of Selective Binding to Methylated DNA
Abstract
1 Introduction
2 Materials and Methods
2.1 Initial Complex Structure and PDB Editing
2.2 Force Field Parameters and Partial Atomic Charges
2.3 MD Preparation and Analysis
3 Results
3.1 Structural Fit
3.2 Contact Surface
3.3 Binding Energy
4 Conclusions
Acknowledgments
References
Impact of Genealogical Features in Transthyretin Familial Amyloid Polyneuropathy Age of Onset Prediction
1 Introduction
2 Regression Algorithms
2.1 Regression Algorithms (State of the Art Approaches)
2.2 Methods Which Incorporate Feature Selection
3 Methodology and Experimental Context
3.1 Approach and Regression Algorithms Used
3.2 Modeling Schema and Experiments Setup
4 Results and Discussion
5 Conclusions and Future Work
References
Feature Selection and Polydispersity Characterization for QSPR Modelling: Predicting a Tensile Property
Abstract
1 Introduction
2 Feature Selection in QSPR for Polymeric Informatics
3 Proposed Methodology and Experimental Results
4 Conclusions
Acknowledgments
References
Methods of Creating Knowledge Graph by Linking Biological Databases
1 Introduction
2 Linked Data Projects
2.1 Bio2RDF
2.2 Linked Life Data (LLD)
2.3 Linking Open Drug Data (LODD)
2.4 The Knowledge Base of Biomedicine (KaBOB)
2.5 Neurocommons
3 Methods of Inferring Relationships in Knowledge Graphs
3.1 Observable Features
3.2 Latent Features
3.3 Markov Random Fields
4 Comparison Between Different Approaches
5 Conclusion
References
QSAR Modelling for Drug Discovery: Predicting the Activity of LRRK2 Inhibitors for Parkinson's Disease Using Cheminformatics Approaches
Abstract
1 Introduction
2 Materials and Methods
3 Conclusions
Acknowledgments
References
Improving the Use of Deep Convolutional Neural Networks for the Prediction of Molecular Properties
1 Introduction
2 Deep Learning in Cheminformatics
3 Proposed Model
4 Experiments
4.1 Data
4.2 Experimental Design
4.3 Implementation
4.4 Experimental Results
5 Discussion and Conclusion
References
An Analysis of Symmetric Words in Human DNA: Adjacent vs Non-adjacent Word Distances
1 Introduction
2 Methods
3 Results and Discussion
4 Conclusions
References
A Bioinformatics Protocol for Quickly Creating Large-Scale Phylogenetic Trees
Abstract
1 Introduction
2 Materials and Methods
3 Results and Discussion
4 Conclusions
Acknowledgements
References
Deep Learning Analysis of Binding Behavior of Virus Displayed Peptides to AuNPs
1 Introduction
2 Self-Assembly Experiment
3 Binding Pattern Analysis
3.1 Deep Learning
4 Experiment
5 Conclusion and Future Work
References
Compression of Amino Acid Sequences
1 Introduction
2 Method
2.1 Context Models
2.2 Substitutional Tolerant Context Models
2.3 Cooperation
2.4 Implementation
3 Dataset
4 Results
5 Conclusions
References
NET-ASAR: A Tool for DNA Sequence Search Based on Data Compression
1 Introduction
2 Method
2.1 Description
2.2 Implementation
3 Results
3.1 Synthetic Data
3.2 Application to Ancient DNA
4 Conclusions
References
Can an Integrative SNP Approach Substitute Standard Identification in Comprehensive Case/Control Analyses?
1 Background
2 Materials and Methods
2.1 Data
2.2 Advanced Analysis Approach
2.3 Novel Integrative Analysis
3 Results
3.1 Quantitative Results
3.2 Runtimes
4 Discussion
5 Conclusions
References
Simple Pattern-only Heuristics Lead to Fast Subgraph Matching Strategies on Very Large Networks
1 Introduction
2 An Annotated Overview of Subgraph Isomorphism Algorithms
3 Results
4 Conclusion
References
In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum
Abstract
1 Introduction
2 Methods
3 Results and Discussion
4 Conclusions
Acknowledgements
References
EvoPPI: A Web Application to Compare Protein-Protein Interactions (PPIs) from Different Databases and Species
Abstract
1 Introduction
2 Materials and Methods
3 Results and Discussion
4 Conclusions
Acknowledgements
References
A Review on Metabolomics Data Analysis for Cancer Applications
1 Introduction
2 Univariate Analysis
3 Unsupervised Multivariate Analysis
4 Supervised Multivariate Analysis
5 Case Studies
6 Conclusions
References
A Framework for the Automatic Combination and Evaluation of Gene Selection Methods
1 Introduction
2 Related Work
3 Proposed Framework
4 Experiments
5 Discussion
6 Conclusion
References
Parallel Cellular Automaton Tumor Growth Model
1 Introduction
2 Tumor Growth Model
2.1 Seams Adjustment During Simulation
3 Model Implementations and Measurements
4 Conclusion and Future Work
References
MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis
1 Introduction
2 Methods
2.1 Installation, Development and Overview of the Pipeline
2.2 Simulation of Metagenomics and Metatranscriptomics Datasets for Validation
3 Results and Discussion
4 Conclusions and Future Perspectives
References
Metabolite Integration Pipeline for the Improvement of Human Metabolic Models
1 Introduction
2 Materials and Methods
3 Results and Discussion
4 Conclusions and Future Work
References
A Genetic Programming Approach Applied to Feature Selection from Medical Data
1 Introduction
2 An Approach for Rule Induction
2.1 Fitness Functions
2.2 Genetic Operators
3 Results on Clinical Data
3.1 Assessing Accuracy and Comparing with Other Methods
4 Conclusions
References
A DNA Sequence Corpus for Compression Benchmark
1 Introduction
2 The DNA Sequence Corpus
3 Compression Benchmark
4 Conclusions
References
17a-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools
Abstract
1 Introduction
2 Methods
2.1 Experimental Design
2.2 Endo- and Exometabolome Extraction
2.3 1H-NMR Spectroscopy
2.4 Bioinformatic Analysis
3 Results and Discussion
3.1 Identification of Xenobiotic in Complex Matrices
4 Conclusion
Acknowledgements
References
Author Index

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Practical Applications of Computational Biology and Bioinformatics, 12th International Conference

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