Computational biology / bioinformatics Books

Book SynopsisThis book provides an up-to-date review of classic and advanced bioinformatics approaches and their utility in rice research. It summarizes databases and tools for analyzing DNA, proteins and gene expression profiles, mapping genetic variations, annotation of protein and RNA molecules, phylogenetic analysis, and pathway enrichment.In addition, it presents high-throughput technologies that are widely used to provide deep insights into the genetic architecture of important traits in the rice genome. The book subsequently discusses techniques for identifying RNA-protein, DNA-protein interactions, and molecular markers, including SNP and microsatellites, in the contexts of rice breeding and genetics.Lastly, it explores various tools that are used to identify and characterize non-coding RNA in rice and their potential role in rice research.Table of ContentsChapter 1_Introduction to Bioinformatics.- Chapter 2_Statistics for bioinformatics.- Chapter 3_ Introduction of the databases of rice.- Chapter 4_Brief insight into the evolutionary history and domestication of wild rice relatives.- Chapter 5_3000 Genome project- A brief insight.- Chapter 6_ Databases and bioinformatics tools for data mining .- Chapter 7_Sequence Alignment.- Chapter 8_Gene identification and structure Annotation.- Chapter 9_Phylogenetic Analysis.- Chapter 10_RNA Structure Prediction. -Chapter 11_Structural Proteomics.- Chapter 12_Gene ontology and pathway enrichment analysis.- Chapter 13_High throughput sequencing technologies.- Chapter 14_Mapping algorithms in high-throughput sequencing.- Chapter 15_DNA–Protein Interaction Analysis (ChIP-Seq).- Chapter 16_RNA–Protein Interaction Analysis.- Chapter 17_SNP Identification and Discovery.- Chapter 18_Microsatellite Markers from whole genome and Transcriptomic Sequences. - Chapter 19_Genome-wide association study.- Chapter 20_Expression Profiling and Discovery of microRNA.- Chapter 21_Computational approaches in identifying long non-coding RNA.- Chapter 22_circRNA in rice.- Chapter 23_ Metagenomics.- Chapter 24_RNA-Induced Gene Silencing.- Chapter 25_Single-cell RNA sequencing technologies.- Chapter 26_Recent Advancement in NGS Technologies.

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Book SynopsisThis textbook is for biologists, to conduct quantitative analysis and modeling of biological processes at molecular and cellular levels. Focusing on practical concepts and techniques for everyday research, this text will enable beginners, both students and established biologists, to take the first step in quantitative biology. It also provides step-by-step tutorials to run various sample programs in one’s personal computer using Excel and Python. This volume traces topics, starting with an introductory chapter, such as modeling, construction and execution of numerical models, and key concepts in quantitative biology: feedback regulations, fluctuations and randomness, and statistical analyses. It also provide sample codes with guidance to procedure programming for actual biological processes such as movement of the nucleus within a cell, cell-cycle regulation, stripe pattern formation of skins, and distribution of energy. Written by a leading research scientist who has a background in biology, studied quantitative approaches by himself, and teaches quantitative biology at several universities, this textbook broadens quantitative approaches for biologists who do not have a strong background in mathematics, physics, or computer programming, and helps them progress further in their research.Table of ContentsChapter 1: Introduction to Quantitative Biology.- Chapter 2: Architectonics of the Cell.- Chapter 3: Mechanics of the Cell.- Chapter 4: Implementing Toy Models in Microsoft Excel.- Chapter 5: Implementing Toy Models in Python.- Chapter 6: Differential Equations to Describe Temporal Changes.- Chapter 7: Diversity of the Cell.- Chapter 8: Randomness, diffusion, and probability.- Chapter 9: Self-Organization of the Cell.- Chapter 10: Modeling feedback regulations Chapter 11: Development of the Cell over Time (Perspectives).

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Book SynopsisThis textbook covers all the essential elements of pharmacokinetics, from basics to applications. It describes authoritative equations and methods on pharmacokinetic evaluation procedures with their importance. Each chapter of the book is supplemented with numerous illustrations and figures for easy understanding of the subject. The book presents mathematical techniques, step- by-step descriptive equations, and applicable statistical analysis methods for the easy understanding of the topic. Further, it covers the preclinical applications and methods of pharmacokinetic aspects. The book also contains mathematical problems and questions related to pharmacokinetics for students. Special emphasis is on recent pharmacokinetic methods and their applications for managing clinical data and biostatistical approaches based on the current literature. This book is primarily meant for researchers and students from academic institutions and to R&D professionals.Table of ContentsChapter 1: Fundamentals of Pharmacokinetics.- Chapter 2: Drug absorption.- Chapter 3: The extent of drug absorption: bioavailability, clearance, bioequivalence, and protein-binding.- Chapter 4: Pharmacokinetic models and drug distribution.- Chapter 5: Drug metabolism .- Chapter 6: Drug elimination and nonlinear kinetics.- Chapter 7: Pharmacokinetic drug-drug interactions.- Chapter 8: Pharmacokinetic applications.- Chapter 9: Pharmacokinetic sample collection and processing.- Chapter 10: Important bio-analytical instrumental techniques in pharmacokinetics.- Chapter 11: Statistics in pharmacokinetics.- Chapter 12: Pharmacokinetic software and tools.- Chapter 13: Pharmacokinetic laboratory-based experiments.- Chapter 14: Pharmacokinetic numerical problems with solutions.- Chapter 15: Questions, and questions & answers for practice.

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Book SynopsisThis textbook covers all the essential elements of pharmacokinetics, from basics to applications. It describes authoritative equations and methods on pharmacokinetic evaluation procedures with their importance. Each chapter of the book is supplemented with numerous illustrations and figures for easy understanding of the subject. The book presents mathematical techniques, step- by-step descriptive equations, and applicable statistical analysis methods for the easy understanding of the topic. Further, it covers the preclinical applications and methods of pharmacokinetic aspects. The book also contains mathematical problems and questions related to pharmacokinetics for students. Special emphasis is on recent pharmacokinetic methods and their applications for managing clinical data and biostatistical approaches based on the current literature. This book is primarily meant for researchers and students from academic institutions and to R&D professionals.Table of ContentsChapter 1: Fundamentals of Pharmacokinetics.- Chapter 2: Drug absorption.- Chapter 3: The extent of drug absorption: bioavailability, clearance, bioequivalence, and protein-binding.- Chapter 4: Pharmacokinetic models and drug distribution.- Chapter 5: Drug metabolism .- Chapter 6: Drug elimination and nonlinear kinetics.- Chapter 7: Pharmacokinetic drug-drug interactions.- Chapter 8: Pharmacokinetic applications.- Chapter 9: Pharmacokinetic sample collection and processing.- Chapter 10: Important bio-analytical instrumental techniques in pharmacokinetics.- Chapter 11: Statistics in pharmacokinetics.- Chapter 12: Pharmacokinetic software and tools.- Chapter 13: Pharmacokinetic laboratory-based experiments.- Chapter 14: Pharmacokinetic numerical problems with solutions.- Chapter 15: Questions, and questions & answers for practice.

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Book SynopsisThis handbook covers tested and proven DNA forensic testing methodologies, forensic bioinformatics techniques, case studies and current forensic legal framework for investigation of variety of crimes and provides a clinching evidence for speedy justice. DNA testing is widely used for forensic purposes and is changing the paradigm of (crime) investigation. The book contains chapters on usage of ultramodern DNA collection kits, presents era evidence collection and preservation, high-end DNA sample analysis in laboratory, DNA legislation, expert evidences, challenging and successful case studies, data generation and application of AI and IoT techniques for DNA data analysis, DNA databanks and training manpower to facilitate timely reporting to the requesting agencies. This handbook equips and enables police, investigators and crime analysis laboratories with knowhow of high-end tools, procedures and techniques to link or exclude a criminal to a crime. It is expected that this will be used by first responders, police, forensic analysts, judiciaries, evidence handlers and students and scholars of criminology and forensic sciences worldwide. The intention to write this handbook is to make DNA technology and its importance reach every common man and professional for correctly using it as a tool as and when required. This is quite evident that awareness of DNA technology has increased at a reasonable pace. Courts and investigating agencies are convinced and confident with its accuracy, reliability and unmatched peace delivered by various techniques of DNA fingerprinting and DNA profiling.Table of ContentsThe Master Molecule in Witness Box (With some Case Studies) Collection, Preservation, retention, safety and Handling of DNA Evidences Chain of Custody – Dos and Don’ts Extraction and Analysis of DNA Samples in Laboratory Handling Mixed DNA Samples with the help of Forensic Bioinformatics Maintaining Standards and Calibration of DNA Testing Equipment DNA Based Identification in Mass Disaster Cases Using DNA Technologies in Sexual Offenses DNA Legislations – Challenges and Opportunities Developing DNA Databases and revolutionizing the Forensic Investigation Modernization of Police DNA Forensics Wing DNA Forensic Trainings for Police and Law enforcement Agencies Next Generation Technologies – Forensic Bioinformatics, LIMS, RFID, Biometrics, AI and IOT in modernising Crime Laboratories. Rapid DNA Identification and Best Practices

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Book SynopsisThis book gathers outstanding research papers presented at the 2nd International Conference on Frontiers in Computing and Systems (COMSYS 2021), organized by Department of Electronics and Communication Engineering and Department of Information Technology, North-Eastern Hill University, Shillong, Meghalaya, India held during September 29–October 1, 2021. The book presents the latest research and results in various fields of machine learning, computational intelligence, VLSI, networks and systems, computational biology, and security, making it a rich source of reference material for academia and industry alike.Table of ContentsExperimental Face Recognition System using Deep Learning Approaches.- MultiNet: A Diffusion based Approach to Assign Directionality in Protein Interactions using a Consensus of Eight Protein Interaction Datasets.- An Irrigation Support System Using Regressor Assembly.- Does Random Hopping Ensure More Pandal Visits than Planned Pandal Hopping?.- Consensus-based Identification and Comparative Analysis of Structural Variants and their Influence on 3D Genome Structure using Long- and Short-read Sequencing Technologies in Polish Families.- On the Performance of Convolutional Neural Networks with Resizing and Padding.- Analysis of Vegetation Health of the Sundarbans Region using Remote Sensing Methods.- You Reap What You Sow - Revisiting Intra-class Variations and Seed Selection in Temporal Ensembling for Image Classification.- Light U-Net: Network Architecture for Outdoor Scene Semantic Segmentation.- Framework of Intelligent Transportation System: A Survey.

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Book SynopsisThis book presents the latest research findings on the laterality of fish and other animals. It describes all aspects of lateral asymmetry, including ecology, morphology, behaviour, dynamics of lefty and righty morphs, genetics and evolution, through field observations, experiments and modeling. Lateral asymmetry in scale-eating cichlids gives a simple and beautiful example of negative frequency-dependent selection and resulting oscillation of lefty and righty morph frequencies. Lateral dimorphism is found not only in scale-eaters but in all orders of fish, shrimps and cuttlefish. Lateral asymmetry interacts between species through "cross-predation." Contrary to fish, lateral asymmetry in snails acts as, in most cases, positive frequency-dependent selection and provides deep insights into speciation. Especially, snakes eating righty snails facilitate speciation of lefty snails.As a collaboration work of field ecologists and theoretical biologists, this book covers a variety of topics on lateral asymmetry, which are consistently related to predation. The topics include behavioral ecology, population dynamics, physiology, evolution, genetics, development, learning and neuroscience, statistics, with the subjects of fish, shrimp, prawn, and crayfish, crab, cuttlefish, and snake and snail. Chapters cover new research results such as cuttlefish laterality dynamics, interaction between laterality of snails and snakes, evolution of laterality genetic system, and statistical analysis of laterality oscillation. Readers will appreciate the simplicity and beauty of lateral asymmetry and its profound impact on ecology and evolution.Table of ContentsChapter 1. Laterality of Fish – Anti-symmetry in Fish Populations Maintained by the Interspecific Interaction.- Chapter 2. Universality of laterality among fish and invertebrates in aquatic communities.- Chapter 3.Predominance of Cross Predation or Parallel Predation in Fish.- Chapter 4.Behavioral laterality in the scale-eating cichlid fish: detailed movement, development, and neuronal mechanisms.- Chapter 5.Models of Lateral Asymmetry Dynamics:Realistic Oscillations by Time Delay andFrequency Dependence.- Chapter 6.Mathematical models of predators and prey with laterality.- Chapter 7.Statistical Analysis of Lateral Asymmetry:Detect Antisymmetry and Oscillation fromUnequal-Interval Binomial Data.- Chapter 8.Models of Genetic System of LateralAsymmetry: Population Dynamics DriveEvolution of Genetic System.- Chapter 9.Mechanisms Underlying Variations in the Dentition Asymmetry of Asian Snail-Eating Snakes.- Chapter 10.Single-gene speciation, balanced polymorphism, and antagonistic coevolution in left-right asymmetry of land snails.

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Book SynopsisThis book presents a collection of selected papers presented at the 22nd FAI International Conference on Mathematical, Computational Intelligence and Engineering Approaches to Healthcare, Business and Tourism Analytics (FAI-ICMCIE 2020), held at American College, Madurai, India, from 20–22 December 2020. This book discusses advanced mathematical concepts and computational intelligence approaches for: medical diagnostic approach in cardiac diseases, nano topology in medical diseases, stability of indicators in assessing business development, AI-guided paradigmatic competence in science and spirituality integration, neural network-TOPSIS analytics in hotel service quality, itinerary planning destination ranking tourism analytics, molecular modeling and docking simulation for unraveling medicinal properties, value-oriented approach on commercial banks security, Brownian motion in shares of the bank, internet of things linking to social media and e-commerce, and more, which are discussed by using fuzzy analytics, nano-topology, statistical, TOPSIS and neural network tools.Table of ContentsA Study on Medical Diagnostic Approach to Investigate Cardiac Diseases.- Economic and Mathematical Methods for Classifying the Stability of Indicators in Assessing Business Development.- Nano Topological Reductions of Attributes in Medical Diagnosis.- AI-Guided Paradigmatic Competence to Embrace Future Trends and Research: A Science-Spirituality Contribution.- Itinerary Planning Destination Ranking Tourism Analytics System.- Generalized Unitary Convolution, Ramanujan Sums and Applications.- A Class of the Extended Multi-Index Bessel-Maitland Functions and It’s Properties.- A Numerical Study on Atangana-Baleanu and Caputo-Fabrizio Fractional Derivatives for MHD Flow Past an Impulsively Started Vertical Plate with Ramped Temperature and Concentration with Viscous Dissipation.- Sufficient Conditions of q-Starlikeness and q-Convexity Associated with Basic Hypergeometric Function.- A New Computing Techniques on Digital Nano Topology.- A New Notion of Mappings in Nano Topology.

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Book SynopsisThis book helps the reader make use of the mathematical models of biological phenomena starting from the basics of programming and computer simulation. Computer simulations based on a mathematical model enable us to find a novel biological mechanism and predict an unknown biological phenomenon. Mathematical biology could further expand the progress of modern life sciences. Although many biologists are interested in mathematical biology, they do not have experience in mathematics and computer science. An educational course that combines biology, mathematics, and computer science is very rare to date. Published books for mathematical biology usually explain the theories of established mathematical models, but they do not provide a practical explanation for how to solve the differential equations included in the models, or to establish such a model that fits with a phenomenon of interest. MATLAB is an ideal programming platform for the beginners of computer science. This book starts from the very basics about how to write a programming code for MATLAB (or Octave), explains how to solve ordinary and partial differential equations, and how to apply mathematical models to various biological phenomena such as diabetes, infectious diseases, and heartbeats. Some of them are original models, newly developed for this book. Because MATLAB codes are embedded and explained throughout the book, it will be easy to catch up with the text. In the final chapter, the book focuses on the mathematical model of the proneural wave, a phenomenon that guarantees the sequential differentiation of neurons in the brain. This model was published as a paper from the author’s lab (Sato et al., PNAS 113, E5153, 2016), and was intensively explained in the book chapter “Notch Signaling in Embryology and Cancer”, published by Springer in 2020. This book provides the reader who has a biological background with invaluable opportunities to learn and practice mathematical biology.Table of Contents1. Preparation.- 2. Introduction to MATLAB programming .- 3. Simulating time variations in life phenomena.- 4. Simulating temporal and spatial changes in biological phenomena.

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Book SynopsisThis book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it is a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and the Web. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly concern mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.Trade Review"This is a comprehensive introduction to a powerful and important new technique that is transforming our understanding of gene regulation. This volume contains everything you need to know to become an expert in CAGE, from library construction to bioinformatic analysis of the voluminous data sets."—Gene E. Robinson, University of IllinoisTable of ContentsBrief Historical Perspective on Transcriptional Regulation. Preparation of CAGE Libraries: An Enabling Experimental Protocol. Ditags and PET-Technologies for Transcript Identification and Review Use of Ditags with Emphasis on Gene Identification. From Sequencing Output to CAGE Tags: A Chapter on the Extraction of CAGE Tags from the Raw Output of the Sequencing Machine. Using CAGE Data for Quantitative Expression. Compare CAGE Expression to Microarrays and qPCR. Identification of Isoforms. Promoter Analysis Databases. Construction and Tutorial of the CAGE Analysis Viewer and Genome Viewer. Transcriptional Network Analysis Using CAGE. Biological Examples of Alternative TSS/Promoters. Challenges in CAGE Analysis.

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