Bioinformatics: Sequences, Structures, Phylogeny

1. Front Matter

   Pages i-ix

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2. Intellectual Property Rights and Bioinformatics: An Introduction

   • Shilpa, Umang Gupta

   Pages 1-14

3. Next-Generation Sequencing: Technology, Advancements, and Applications

   • Gourja Bansal, Kiran Narta, Manoj Ramesh Teltumbade

   Pages 15-46

4. Sequence Alignment

   • Benu Atri, Olivier Lichtarge

   Pages 47-69

5. Understanding Genomic Variations in the Context of Health and Disease: Annotation, Interpretation, and Challenges

   • Ankita Narang, Aniket Bhattacharya, Mitali Mukerji, Debasis Dash

   Pages 71-95

6. Metagenomics: Focusing on the Haystack

   • Indu Khatri, Meenakshi Anurag

   Pages 97-113

7. Computational Epigenomics and Its Application in Regulatory Genomics

   • Shalu Jhanwar

   Pages 115-139

8. Data Mining to Detect Common, Unique, and Polymorphic Simple Sequence Repeats

   • Aditi Kapil, C. K. Jha, Asheesh Shanker

   Pages 141-154

9. R-Programming for Genome-Wide Data Analysis

   • Arunima Shilpi, Shraddha Dubey

   Pages 155-171

10. Computational Approaches to Studying Molecular Phylogenetics

    • Benu Atri, Olivier Lichtarge

    Pages 173-190

11. Structural Bioinformatics: Life Through The 3D Glasses

    • Ankita Punetha, Payel Sarkar, Siddharth Nimkar, Himanshu Sharma, Yoganand KNR, Siranjeevi Nagaraj

    Pages 191-253

12. A Survey of the Structural Parameters Used for Computational Prediction of Protein Folding Process

    • Gulshan Khalique, Tambi Richa

    Pages 255-270

13. Quality Assessment of Protein Tertiary Structures: Past, Present, and Future

    • Ankita Singh, Rahul Kaushik, B. Jayaram

    Pages 271-288

14. Predicting Protein Function Using Homology-Based Methods

    • Swati Sinha, Birgit Eisenhaber, Andrew M. Lynn

    Pages 289-305

15. Drug Discovery: An In Silico Approach

    • Sukriti Goyal, Salma Jamal, Abhinav Grover, Asheesh Shanker

    Pages 307-328

16. Advanced In Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus

    • Mehak Dangi, Rinku Kumari, Bharat Singh, Anil Kumar Chhillar

    Pages 329-357

17. Machine Learning: What, Why, and How?

    • Salma Jamal, Sukriti Goyal, Abhinav Grover, Asheesh Shanker

    Pages 359-374

18. Command-Line Tools in Linux for Handling Large Data Files

    • Deepti Mishra, Garima Khandelwal

    Pages 375-392

19. Back Matter

    Pages 393-402

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This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

• Bioinformatics
• Sequence and Phylogenetic Analysis
• Structural Bioinformatics
• Drug Discovery
• Machine Learning
• Biodiversity informatics
• Protein Structure

• Department of Bioinformatics, Central University of South Bihar, Gaya, India

  Asheesh Shanker

Dr. Asheesh Shanker is Associate Professor and Coordinator of the Bioinformatics Programme at the Centre for Biological Sciences, Central University of South Bihar, India. Prior to that he served as an Assistant/Associate Professor (2004-2015) at the Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India, and he has a decade of teaching and research experience. His research focuses on data mining, database and server development, evolutionary analysis, computational genomics, and structure analysis. He is a recipient of prestigious Indo-Swiss Joint Research Programme fellowship from the University of Lausanne, Switzerland. He has been a convener/organizing secretary for several national bioinformatics workshops, served as a member of organizing committee of International conferences, and delivered invited talks. He is also a reviewer for a number of peer-reviewed journals. He has published more than 50 research articles in leading national and international journals and authored/co-authored 3 books in the field of bioinformatics, which are popular among students.

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