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This detailed book explores techniques commonly used for research into drug repurposing, a well-known strategy to find alternative indications for drugs which have already undergone toxicology and pharma-kinetic studies but have failed later stages during the development, via computational methods. Thereby, it addresses the intense challenges of identifying the appropriate type of algorithm and relevant technical information for computational repurposing. Written for the highly successful Methods in Molecular Biology series, the authors of each chapter use their experience in the field to describe the implementation and successful use of a specific repurposing method thus providing lab-ready instruction. 
Authoritative and practical, Computational Methods for Drug Repurposing serves as an ideal guide to researchers interested in this vital area of drug development.

Computational Methods for Drug Repurposing

1. Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing

            E. Sila Ozdemir, Farideh Halakou, Ruth Nussinov, Attila Gursoy, and Ozlem Keskin

 

2. Performing an In Silico Repurposing of Existing Drugs by Combining Virtual Screening and Molecular Dynamics Simulation

            Farzin Sohraby, Milad Bagheri, and Hassan Aryapour

 

3. Repurposing Drugs Based on Evolutionary Relationships between Targets of Approved Drugs and Proteins of Interest

            Sohini Chakraborti, Gayatri Ramakrishnan, and Narayanaswamy Srinivasan

 

4. Drug Repositioning by Mining Adverse Event Data in ClinicalTrials.gov

            Eric Wen Su

 

5. Transcriptomic Data Mining and Repurposing for Computational Drug Discovery

            Yunguan Wang, Jaswanth Yella, and Anil G. Jegga

 

6. Network-Based Drug-Repositioning: Approaches, Resources, and Research Directions

            Salvatore Alaimo and Alfredo Pulvirenti

 

7. A Computational Bipartite-Graph-Based Drug Repurposing Method

            Si Zheng, Hetong Ma, Jiayang Wang, and Jiao Li

 

8. Implementation of a Pipeline Using Disease-Disease Associations for Computational Drug Repurposing

            Preethi Balasundaram, Rohini Kanagavelu, Nivya James, Sayoni Maiti, Shanthi Veerappapillai, and Ramanathan Karuppaswamy

 

9. An Application of Computational Drug Repurposing Based on Transcriptomic Signatures

            Evangelos Karatzas, George Kolios, and George M. Spyrou

 

10. Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity

            Kaitlyn Gayvert and Olivier Elemento

 

11. A Drug Repurposing Method Based on Drug-Drug Interaction Networks and Using Energy Model Layouts

            Mihai Udrescu and Lucre ia Udrescu

 

12. Integrating Biological Networks for Drug Target Prediction and Prioritization

            Xiao Ji, Johannes M. Freudenberg, and Pankaj Agarwal

 

13. Using Drug Expression Profiles and Machine Learning Approach for Drug Repurposing

            Kai Zhao and Hon-Cheong So

 

14. Computational Prediction of Drug-Target Interactions via Ensemble Learning

            Ali Ezzat, Min Wu, Xiaoli Li, and Chee-Keong Kwoh

 

15. A Machine-Learning-Based Drug Repurposing Approach Using Baseline Regularization

            Zhaobin Kuang, Yujia Bao, James Thomson, Michael Caldwell, Peggy Peissig, Ron Stewart, Rebecca Willett, and David Page

 

16. Machine Learning Approach for Predicting New Uses of Existing Drugs and Evaluation of Their Reliabilities

            Yutaka Fukuoka

 

17. A Drug-Target Network-Based Supervised Machine Learning Repurposing Method Allowing the Use of Multiple Heterogeneous Information Sources

            André C.A. Nascimento, Ricardo B.C. Prudencio, and Ivan G. Costa

 

18. Heter-LP: A Heterogeneous Label Propagation Method for Drug Repositioning

            Maryam Lotfi Shahreza, Nasser Ghadiri, and James Green

 

19. Tripartite Network-Based Repurposing Method Using Deep Learning to Compute Similarities for Drug-Target Prediction

            Nansu Zong, Rachael Sze Nga Wong, and Victoria Ngo