Soft Computing for Biological Systems

1. Front Matter

   Pages i-xii

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2. Current Scenario on Application of Computational Tools in Biological Systems

   • Hemant J. Purohit, Hitesh Tikariha, Vipin Chandra Kalia

   Pages 1-12

3. Diagnostic Prediction Based on Gene Expression Profiles and Artificial Neural Networks

   • Eugene Lin, Shih-Jen Tsai

   Pages 13-22

4. Soft Computing Approaches to Extract Biologically Significant Gene Network Modules

   • Swarup Roy, Hazel Nicolette Manners, Monica Jha, Pietro H. Guzzi, Jugal K. Kalita

   Pages 23-37

5. A Hybridization of Artificial Bee Colony with Swarming Approach of Bacterial Foraging Optimization for Multiple Sequence Alignment

   • R. Ranjani Rani, D. Ramyachitra

   Pages 39-65

6. Construction of Gene Networks Using Expression Profiles

   • Harun Pirim

   Pages 67-89

7. Bioinformatics Tools for Shotgun Metagenomic Data Analysis

   • Rajesh Ramavadh Pal, Ravi Prabhakar More, Hemant J. Purohit

   Pages 91-110

8. Protein-protein Interactions: Basics, Characteristics, and Predictions

   • Angshuman Bagchi

   Pages 111-120

9. Machine Learning Framework: Predicting Protein Structural Features

   • Pramod Kumar, Vandana Mishra, Subarna Roy

   Pages 121-141

10. Drug Transporters as Therapeutic Targets: Computational Models, Challenges, and Future Perspective

    • Deepak Singla, Ritika Bishnoi, Sandeep Kumar Dhanda, Shailendra Asthana

    Pages 143-168

11. Module-Based Knowledge Discovery for Multiple-Cytosine-Variant Methylation Profile

    • Saurav Mallik, Ujjwal Maulik

    Pages 169-186

12. Outlook of Various Soft Computing Data Preprocessing Techniques to Study the Pest Population Dynamics in Integrated Pest Management

    • M. Pratheepa, J. Cruz Antony

    Pages 187-200

13. Genomics for Oral Cancer Biomarker Research

    • Kavitha Prasad, Roopa S. Rao, Rupali C. Mane

    Pages 201-223

14. Soft Computing Methods and Tools for Bacteria DNA Barcoding Data Analysis

    • Ravi Prabhakar More, Hemant J. Purohit

    Pages 225-240

15. Fish DNA Barcoding: A Comprehensive Survey of Bioinformatics Tools and Databases

    • Rupali C. Mane, Ganesh Hegde, Ravi Prabhakar More, Rajesh Ramavadh Pal, Hemant J. Purohit

    Pages 241-251

16. Microbes and Mountains: The Mid-Domain Effect on Mt. Fuji, Japan

    • Dharmesh Singh

    Pages 253-263

17. Integration of Soft Computing Approach in Plant Biology and Its Applications in Agriculture

    • Archana Kumari, Minu Kesheri, Rajeshwar P. Sinha, Swarna Kanchan

    Pages 265-281

18. Future Perspectives of Computational Biology: Demanding Shifts in Analytical Thinking to Unfold Biological Complexities

    • Hemant J. Purohit, Hitesh Tikariha, Vipin Chandra Kalia

    Pages 283-293

19. Back Matter

    Pages 295-300

    PDF

This book explains how the biological systems and their functions are driven by genetic information stored in the DNA, and their expression driven by different factors. The soft computing approach recognizes the different patterns in DNA sequence and try to assign the biological relevance with available information.The book also focuses on using the soft-computing approach to predict protein-protein interactions, gene expression and networks. The insights from these studies can be used in metagenomic data analysis and predicting artificial neural networks.

• computation
• bioinformatics
• gene expression
• neural networks
• machine learning
• diagnostic prediction

• Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India

  Hemant J. Purohit

• Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology (IGIB) Delhi University Campus, Delhi, India

  Vipin Chandra Kalia

• ADBS, Lab 18, Neural Stem Cell Program, TIFR-National Centre for Biological Sciences, Bangalore, India

  Ravi Prabhakar More

Dr. Vipin Chandra Kalia is an Emeritus scientist and Ex-Chief Scientist at Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, Delhi. He obtained his M.Sc. and Ph.D. degrees in Genetics from the Indian Agricultural Research Institute, New Delhi. He has been elected as: (1) Fellow of the Association of Microbiologists of India (FAMI), (2) Fellow of the National Academy of Sciences (FNASc), and (3) Fellow of National Academy of agricultural Sciences (FNAAS). His main areas of research are microbial biodiversity, genomics and evolution, bioenergy, biopolymers, antimicrobials, quorum sensing, and quorum quenching. He has published 101 papers in scientific journals such as (1) Nature Biotechnology, (2) Biotechnology Advances, (3) Trends in Biotechnology, (4) Critical Reviews in Microbiology, (5) Bioresource Technology, (6) International Journal of Hydrogen Energy, (7) PLoS ONE, (8) BMC Genomics, (9) Gene, and (10) Annual Review of Microbiology.His Google scholar citations are 4219 (as on 31st Aug 2017),  and he has an h index of 36 and an i10 index of 76. He has edited 3 books: Quorum sensing versus quorum quenching: A battle with no end in sight (2015, Springer India), Microbial Factories Vol 1 and 2 (2015). He is presently the editor in chief of the Indian Journal of Microbiology and Editor of (1) PLoS ONE, (2)Journal of Microbiology & Biotechnology (Korea), (3) Applied Biochemistry & Biotechnology (USA), (4) International Scholarly Research Notices (Energy), (5) Dataset Papers in Science (Microbiology), and (6) Journal of Molecular and Genetic Medicine. He is a life member of the following scientific societies: (1) Society of Biological Chemists of India (2) Society for Plant Biochemistry and Biotechnology, India; (3) Association of Microbiologists of India; (4) Indian Science Congress Association; (5) BioEnergy Society of India, and (6) the Biotech Research Society of India (BRSI). He is also a member of the American Society for Microbiology.



Dr Hemant J. Purohit is Chief Scientist, Head Environmental Biotechnology & Genomics Division. He completed his PhD from Nagpur University in 1986. He has been involved in Designing a strategy for capturing microbial diversity and exploration  by interfacing culturable and DNA fingerprinting tools; Developing genomics based monitoring tools for EIA and bio-remediation process; Study of stress dependent microbial response using dynamic gene expression and its application in bioprocess optimization; Developing better insights into microbial capacities for utilization of organics through genome sequence analysis etc. He has been project coordinator for a number of high value projects. He has 225 publications to his credit. His Google scholar citations is 4843 (as on August 2017), and he has an h-index of 38 and i10-index of 113. He has supervised 25 PhD students and more than 100 students for their projects / dissertations. He is a highly distinguished scientist. He is a recipient of a number of prestigious awards, including Fogarty International Exchange Program Fellowship (NINDS, NIH, Bethesda); Commonwealth Fellowship (Department of Biochemistry, Hull University, UK), Department of Biochemistry, University of Hull, UK; CSIR Research Fellowships (JRF and SRF) etc.



Dr. Ravi Prabhakar More is a Bioinformatician in the Accelerator program for Discovery in Brain disorders using Stem cells (ADBS) program at the prestigious TIFR-National Centre for Biological Sciences, Bangalore, India. His current research interest is the genetic analysis of individuals from mental illness families using the whole genome and exome sequence analysis. He completed his PhD in Bioinformatics from CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India. He is the author of twelve research articles that have been published in well reputed peer-reviewed international journals. He has developed QR encrypted signature-based matK-QR Classifier software for plant species identification using matK gene sequences and published in BMC BioDataMining journal. For taxonomic classification of 16S rRNA sequences based on QR code encrypted signatures, he has developed a DNA BarID software tool, which is published in Journal of Computational Biology. He is the recipient of the award for outstanding project personnel in CSIR-NEERI, Nagpur India. He has analyzed metagenomes of CETP and Rumen Microbial Fibrolytic Enzymes in Indian Crossbred Cattle metagenome analysis, which was carried out to understand the taxonomic and metabolic potential using various tools and databases. On these work, four research articles are published in different journals viz. Bioresource Technology, AMB Express Journal. He was International Intern at NIBB Institute, Japan and developed combined supervised approach (Naïve Bayesian and homology) for detecting horizontal gene transfer (HGT) events in the microbial community. He did DNA Barcoding studies with respect to construction and analysis of phylogenetic trees of insect pests and published his work in well-reputed journals. He has attended a number of international conferences and published posters on different topics.

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