Computational Methods for Processing and Analysis of Biological Pathways 1st Edition by Anastasios Bezerianos 3319538675 9783319538679

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ISBN-10 :  3319538675 

ISBN-13 :  9783319538679

Author:  Anastasios Bezerianos 

This work offers a guided walkthrough of one of the most promising research areas in modern life sciences, enabling a deeper understanding of involved concepts and methodologies via an interdisciplinary view, focusing on both well-established approaches and cutting-edge research. Highlighting what pathway analysis can offer to both the experimentalist and the modeler, the text opens with an introduction to a general methodology that outlines common workflows shared by several methods. This is followed by a review of pathway and sub-pathway based approaches for systems pharmacology. The work then presents an overview of pathway analysis methods developed to model the temporal aspects of drug- or disease-induced perturbations and extract relevant dynamic themes. The text concludes by discussing several state-of-the-art methods in pathway analysis, which address the important problem of identifying differentially expressed pathways and sub-pathways.

Computational Methods for Processing and Analysis of Biological Pathways 1st table of contents: 

1 Introduction
Abstract
1.1 Biological Networks
1.1.1 Properties
1.1.2 Categories of Biological Networks
1.2 Pathway Analysis
1.2.1 Methodology
1.2.2 Evolution of Pathway Analysis Methods
1.3 Systems Pharmacology
References
2 Networks and Pathways in Systems Pharmacology
Abstract
2.1 Introduction
2.2 Network- and Pathway/Sub-pathway-Based Characterization of Drugs Mechanism of Action
2.3 Identification of New Drug Targets and Polypharmacology Applications
2.3.1 Target Characterization and Identification Using Network Properties of Drug Targets
2.3.2 Identification of Drug Targets Based on Integrative Network Approaches
2.3.3 Network-Based Polypharmacology
2.4 Network-Based Drug Repositioning
2.4.1 Drug Repositioning Based on Molecular Profiles
2.4.2 Drug Repositioning Based on Phenotypic Profiles
2.5 Network-Based Side Effect Modeling and Prediction
2.5.1 Approaches Based on Chemical Structure
2.5.2 Approaches Based on Pathways/Sub-pathways
2.6 Current Challenges and Future Considerations
References
3 Time-Varying Methods for Pathway and Sub-pathway Analysis
Abstract
3.1 Introduction
3.2 Conversion of Pathway Databases to Graphs
3.3 Time-Varying Pathway and Sub-pathway Extraction
3.3.1 Linear Sub-pathway Extraction
3.3.2 Nonlinear Sub-pathway Extraction
3.4 Temporal Dynamics Scoring Schemes
3.4.1 Approach Followed in CHRONOS
3.4.2 Other Approaches
3.5 Synthetic and Biological Data Analysis Results
References
4 Identification of Differentially Expressed Pathways and Sub-pathways
Abstract
4.1 Introduction
4.2 Approaches Based on Gene Sets
4.3 Approaches Based on Pathway Topology
4.4 Conversion of Pathway Databases Information to Graphs
4.5 Gene and Pathway-Level Statistics of Differential Expression
4.5.1 Methods Using Experimental Data for Sub-pathway Identification
4.5.2 Methods Using Experimental Data for Evaluating the Statistical Significance of Sub-pathways
4.6 DEsubs: A Flexible Tool for Identification of Differentially Expressed Sub-pathways

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Tags: Computational Methods, Processing, Analysis, Biological Pathways, Anastasios Bezerianos