"Bioinformatics: Principles and Applications" provides an authoritative and accessible exploration of the theoretical foundations and practical implementations driving today’s computational biology landscape. Aimed at rendering vast, diverse life-sciences datasets both interpretable and actionable, this volume underscores the field’s rapid evolution and the imperative for continual methodological innovation. The advent of next-generation sequencing has unleashed an unprecedented flood of fully sequenced genomes—from humans and model organisms to plants, animals, and microorganisms—now housed in public repositories. While this high-throughput “omics” revolution opens new avenues for comparative and translational research, it also poses significant analytical and computational challenges. This book guides readers through algorithmic strategies, database architectures, and statistical frameworks essential for decoding complex biological information at scale. Authored by internationally recognized experts, each chapter blends rigorous theory with real-world examples and case studies. Readers will find clear explanations of core techniques—sequence alignment, genome assembly, variant calling, transcriptomics, proteomics, and systems-level modelling— alongside insights into emerging trends, such as single-cell analysis, machine learning applications, and cloud-native pipelines. The result is a comprehensive resource that serves both as a structured textbook for students and a practical reference for researchers, software developers, policy-makers, and informed members of the public. The authors extend their heartfelt gratitude to colleagues across multiple institutions whose constructive feedback and collaboration enriched this work. Sincere thanks are also due to International Books & Periodical Supply Service for their unwavering support throughout the editorial and publication process.
Dr. Satendra Singh is currently working as an Associate Professor in the Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh. Completed his Graduation in Pharmaceutical Sciences from Uttar Pradesh Technical University, Lucknow, he completed his M. Tech. in Information Technology (Bioinformatics) from Indian Institute of Information Technology, Allahabad (IIITA) and Ph.D. in Bioinformatics from Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj (SHUATS). He has qualified GATE in 2003, 2004 and 2006. His main area of research interests includes genome analysis, drug designing, chemoinformatics molecular dynamics and Agriculture Bioinformatics. Having teaching and research experience of more than 20 years, Dr. Singh has published around 85 research and review papers in national and international peer reviewed journals. He has surprvised a number of Ph.D., M.Sc., M. Tech. thesis and B. Tech. research projects in the field of Bioinformatics. He is the recipient of several awards, including Excellence in Teaching award, Young Scientist Awards, Best research paper award and Best oral presentation award, etc. He has edited 03 book on Bioinformatics and various aspects of life sciences. Dr. Singh is having lifetime memberships of several National and International professional societies.
Dr. Konda Aravind Kumar is a Scientist (Senior Scale) at the ICAR–Indian Institute of Pulses Research, Kanpur, bringing over 20 years of research experience in molecular biology, computational and functional genomics, and agricultural biotechnology. He holds a Ph.D. in Plant Sciences from the University of Hyderabad—an Institute of Eminence—with doctoral research conducted at the ICAR–Indian Institute of Oilseeds Research, Hyderabad. He earned his M.Sc. in Biotechnology from M.S. University of Baroda and B.Sc. in Biotechnology, Zoology, and Chemistry from Osmania University, Hyderabad. A recipient of fellowships from DBT, CSIR, ICMR, and ICAR, Dr. Kumar qualified for the Agricultural Research Service (ARS) and has been recognized with the SERB Early Career Research Award, Distinguished Scientist Award (SBBS), Best Team Award (IIPR), and multiple best presentation honors. He serves on academic and selection committees under the Ministry of Education and CSJM University, Kanpur. Dr. Kumar’s research spans genome sequencing, stress biology, and transgenic innovations in pulse crops. He has decoded insecticidal bacterial strains, biocontrol fungi, and the legume Vigna marina, uncovering agriculturally significant plasmids with insecticidal, glyphosate-degrading, and heavy metal resistance genes. In chickpea and pigeonpea, he has identified key gene families and novel defense-related genes including WRKY TF, Car_Chit-15, CcBBI, and Cc-SSCP-1, supported by 3D protein modeling and co-expression network analysis. His innovations include tissue-specific multigene vectors, pod-specific promoters, and genotype-independent transformation protocols. He has published extensively in peer-reviewed journals and compiled technical manuals on molecular biology and biosafety. Currently, he leads competitive research grants funded by DBT, DST–SERB, and ICAR, focused on genome editing, effector gene characterization, and climate resilience—advancing translational biotechnology for sustainable agriculture and global food security.
Dr. Dhirendra Kumar is presently working as an Associate Professor (Animal Genetics and Breeding) at CoVAS, Kishanganj, BASU, Patna. Dr. Dhirendra is a recipient of Best Ph.D. Thesis Award, Appreciation Award (2), Distinguished Scientist Award, Excellence in Teaching Award, Young Scientist Award (2) and Life Science Leadership Award. He has also served as an Organizing Secretary of International Conference (1), Joint Organizing Secretary of International Conference (1) and Co-Organizing Secretary of National Conference/Symposium (4). He has been the Principal Investigator of Network Project of NBAGR-ICAR on Characterization of Poonchi Chicken. He also acted as a Co-Principal Investigator under Network Projects of ICAR for Characterization of Sheep as well as Goat. He has been the co-project leader of the project “Capacity building/Training of Women Self Help Group members from Umeed as Community Paravets”. He has published more than 65 research and review articles in reputed national and international scientific journals. He has also contributed in scientific fields by means of books (12), popular articles, conference proceeding papers, short communications, chapters in books, manuals, edited publications, etc.
Dr. Pramod Kumar Yadav is working as an Associate Professor in the Department of Computational Biology and Bioinformatics at Sam Higginbotom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj (U.P.), India. He has graduated in Pharmacy from C.C.S. University, Meerut, India and post-graduated in Bioinformatics from Indian Institute of Information Technology (IIIT), Allahabad, India. He has qualified GATE-2003 and 2004 respectively and got scholarship from MHRD (2004-06), New Delhi. Dr. Yadav has an experience of 19 years in teaching and research in the field of Bioinformatics. He has published 40 research papers in reputed international and national journals. He has edited one book and contributed 05 chapters in several books. He is editor/reviewer of several international journals published by Springer, Elsevier, Oxford Univ. Press, Wiley, Bentham, etc. Dr. Yadav has supervised/co-supervised 05 Ph.D., 11 M.Tech. and 07 M.Sc. students in their thesis work. Moreover, he has delivered several invited lectures on various topics in International/ National Conferences/Seminars. His areas of research interest include drug target identification, molecular modelling, docking, structure based drug design, molecular dynamics simulation, in silico epitope prediction and NGS data analysis.
Dr. Richa Arora is currently working as an Assistant Professor (Veterinary Biochemistry) at CoVAS, Kishanganj, BASU, Patna. She holds a M.V.Sc. and Ph.D. degree in Animal Biotechnology from ICAR–Indian Veterinary Research Institute, Bareilly. She is a recipient of fellowships from ICAR in her Post-graduation and IVRI institute fellowship in her Doctoral programme. She has also qualified DBT-JRF and earned DST International travel grant to attend conference at Canada. Dr. Richa has also received Best Ph.D. Thesis Award, Appreciation Award (2), Young Scientist Award (1) and Dr. M.N. Kulkarni best research paper presentation award. She has also served as a Course Director of International online training on Bioinformatics (1), technical coordinator of different training programs (2) and participated in various Conference/Symposium/Seminar (3). Her main area of research interests are next generation sequencing, viral gene oncotherapy, tumor biology, biomarkers for canine mammary tumor diagnosis, molecular biology, etc. She has published approximately 18 research and review articles in reputed national and international scientific journals. She has also made contributions to scientific subjects through book chapters, popular articles, short communications, manuals, etc.
1. Introduction to Genome Sequencing .......................................................1 Richa Arora, Komal, Arpit Tyagi, Waseem Akram Malla and Ashwini R. Chaple
2. Primer Designing for Gene Amplification ............................................15 Ashwini R. Chaple, Mayur M. Visputel and Richa Arora, Dhirendra Kumar and Satendra Singh
3. A Step-by-Step Guide to RNA-Seq Data Analysis ...............................21 Waseem Akram Malla, Kuldeep Singh, Richa Arora and Ravikumar Gandham
4. Crispr Bioinformatics ............................................................................33 Amir Kumar Samal and Nitish Singh Kharayat
5. Discovery, Mechanisms and Applications of RNA Interference (RNAi) in Crop Improvement and Agriculture .................45 Shailesh Kumar, Gurudayal Ram Guru, Upasna Srivastava, Prateek Paul, Atul Singh and Satendra Singh
6. Murraya koenigii: Bioinformatics Analysis of Phytochemical Constituents with Medicinal Properties ................................................63 Anamika Singh, Shailesh Kumar, Ritesh Kumar, Shivani Singh Kamin Alexander and Satendra Singh
7. Exploring the Nutritional and Therapeutic Value with Genome Assembly of Salvia hispanica ................................................85 Aliya Fatima, Shavez Ali, Ranjana and Satendra Singh
8. Piper nigrum: Exploring Phytochemicals and Medicinal Properties .............................................................................................111 Ritesh Kumar, Rajat Kumar Vimal, Akhilesh Bind, Alka Sagar and Satendra Singh
9. Insight into Moringa oleifera Phytochemical Constituents Focusing Medicinal and Related Properties Using Bioinformatics Approaches .................................................................129 Satendra Singh, Akriti Srivastava, Rama Nath Shukla, Ajay Kumar Singh and Neerja Katiyar
10. Bioinformatics Perspective on microRNA (miRNA) and Gene Regulation in Oilseed Crops ......................................................169 Shivani Singh, Srishti Jaiswal, Sharad Kumar jaiswal, Avanish Kumar and Satendra Singh
11. Plant-derived Natural Products as PPARγ Modulators ......................195 Ganesh Prasad Mishra, Satendra Singh and Pramod Kumar Yadav
12. Genome-Wide Identification and Characterization of Anti-microbial Protein in Legumes: Implications for Combating Antimicrobial Resistance .................................................227 Satish Kumar, Ashish Udgata, Alok Pandey, Raj Kumar Mishra, Satendra Singh and Aravind Kumar Konda
13. Emerging Role of Artificial Intelligence (AI) in Bioinformatics ........265 Narendra Kumar Gupta, Sharad Kumar Jaiswal and Satendra Singh
14. Recent Advancements in Bioinformatics for the Treatment of Glaucoma .......................................................................283 Sumit Kumar Rai, Manvi Rawat, Arun Bhatt, Pramod Kumar Yadav, Vinay Kumar Singh and Satendra Singh
15. Bioinformatics Tools and Techniques in Human Genomics Research and Healthcare ....................................................319 Vinay Kumar Singh and Satendra Singh
