Bioinformatics For Agriculture High Throughput Approaches

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Bioinformatics for agriculture: High-throughput approaches

Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil
Bioinformatics for agriculture High throughput approaches Book PDF

Author : Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil
Publisher : Springer
Page : 0 pages
File Size : 54,6 Mb
Release : 2021-03-20
Category : Science
ISBN : 9813347902

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Bioinformatics for agriculture: High-throughput approaches by Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil Pdf

This book illustrates the importance and significance of bioinformatics in the field of agriculture. It first introduces the basic concepts of bioinformatics, such as homologous sequence and gene function analyses, determination of protein structures, and discusses machine learning applications for an in-depth understanding of the desired genes and proteins based on commonly used bioinformatics software and tools, e.g. BLAST, molecular modelling, molecular-docking and simulations, protein-protein and domain-domain interactions. The book also describes recent advances in the high-throughput analysis of whole genome and transcriptome using next-generation sequencing platforms, and functional proteome studies. It also examines the role of computational biology in understanding and improving the nutrient quality and yield of crops. Lastly, the book explores a comprehensive list of applications of bioinformatics to improve plant yield, biomass, and health, and the challenges involved.

Bioinformatics in Agriculture

Pradeep Sharma,Dinesh Yadav,R.K. Gaur
Bioinformatics in Agriculture Book PDF

Author : Pradeep Sharma,Dinesh Yadav,R.K. Gaur
Publisher : Academic Press
Page : 707 pages
File Size : 55,5 Mb
Release : 2022-04-28
Category : Technology & Engineering
ISBN : 9780323885997

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Bioinformatics in Agriculture by Pradeep Sharma,Dinesh Yadav,R.K. Gaur Pdf

Bioinformatics in Agriculture: Next Generation Sequencing Era is a comprehensive volume presenting an integrated research and development approach to the practical application of genomics to improve agricultural crops. Exploring both the theoretical and applied aspects of computational biology, and focusing on the innovation processes, the book highlights the increased productivity of a translational approach. Presented in four sections and including insights from experts from around the world, the book includes: Section I: Bioinformatics and Next Generation Sequencing Technologies; Section II: Omics Application; Section III: Data mining and Markers Discovery; Section IV: Artificial Intelligence and Agribots. Bioinformatics in Agriculture: Next Generation Sequencing Era explores deep sequencing, NGS, genomic, transcriptome analysis and multiplexing, highlighting practices forreducing time, cost, and effort for the analysis of gene as they are pooled, and sequenced. Readers will gain real-world information on computational biology, genomics, applied data mining, machine learning, and artificial intelligence. This book serves as a complete package for advanced undergraduate students, researchers, and scientists with an interest in bioinformatics. Discusses integral aspects of molecular biology and pivotal tool sfor molecular breeding Enables breeders to design cost-effective and efficient breeding strategies Provides examples ofinnovative genome-wide marker (SSR, SNP) discovery Explores both the theoretical and practical aspects of computational biology with focus on innovation processes Covers recent trends of bioinformatics and different tools and techniques

Bioinformatics for agriculture: High-throughput approaches

Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil
Bioinformatics for agriculture High throughput approaches Book PDF

Author : Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil
Publisher : Springer Nature
Page : 160 pages
File Size : 52,9 Mb
Release : 2021-03-19
Category : Science
ISBN : 9789813347915

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Bioinformatics for agriculture: High-throughput approaches by Atul Kumar Upadhyay,R Sowdhamini,Virupaksh U. Patil Pdf

This book illustrates the importance and significance of bioinformatics in the field of agriculture. It first introduces the basic concepts of bioinformatics, such as homologous sequence and gene function analyses, determination of protein structures, and discusses machine learning applications for an in-depth understanding of the desired genes and proteins based on commonly used bioinformatics software and tools, e.g. BLAST, molecular modelling, molecular-docking and simulations, protein-protein and domain-domain interactions. The book also describes recent advances in the high-throughput analysis of whole genome and transcriptome using next-generation sequencing platforms, and functional proteome studies. It also examines the role of computational biology in understanding and improving the nutrient quality and yield of crops. Lastly, the book explores a comprehensive list of applications of bioinformatics to improve plant yield, biomass, and health, and the challenges involved.

High-Throughput Crop Phenotyping

Jianfeng Zhou,Henry T. Nguyen
High Throughput Crop Phenotyping Book PDF

Author : Jianfeng Zhou,Henry T. Nguyen
Publisher : Springer Nature
Page : 249 pages
File Size : 45,6 Mb
Release : 2021-07-17
Category : Science
ISBN : 9783030737344

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High-Throughput Crop Phenotyping by Jianfeng Zhou,Henry T. Nguyen Pdf

This book provides an overview of the innovations in crop phenotyping using emerging technologies, i.e., high-throughput crop phenotyping technology, including its concept, importance, breakthrough and applications in different crops and environments. Emerging technologies in sensing, machine vision and high-performance computing are changing the world beyond our imagination. They are also becoming the most powerful driver of the innovation in agriculture technology, including crop breeding, genetics and management. It includes the state of the art of technologies in high-throughput phenotyping, including advanced sensors, automation systems, ground-based or aerial robotic systems. It also discusses the emerging technologies of big data processing and analytics, such as advanced machine learning and deep learning technologies based on high-performance computing infrastructure. The applications cover different organ levels (root, shoot and seed) of different crops (grains, soybean, maize, potato) at different growth environments (open field and controlled environments). With the contribution of more than 20 world-leading researchers in high-throughput crop phenotyping, the authors hope this book provides readers the needed information to understand the concept, gain the insides and create the innovation of high-throughput phenotyping technology.

The Role of Bioinformatics in Agriculture

Santosh Kumar
The Role of Bioinformatics in Agriculture Book PDF

Author : Santosh Kumar
Publisher : CRC Press
Page : 492 pages
File Size : 51,8 Mb
Release : 2014-02-14
Category : Science
ISBN : 9781771880039

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The Role of Bioinformatics in Agriculture by Santosh Kumar Pdf

Advances in information technology and next generation sequencing have propelled the use of bioinformatics in agriculture, especially in the area of crop improvement. An extremely large amount of genomics data is available from plants and animals due to tremendous improvements in the field. This book acquaints readers with state-of-the-art sequencing technologies, recent developments in computing algorithms, and certain biological perspectives that influence development of bioinformatics tools by giving specific examples from model plant species. The challenge is now to make sense and use of this wealth of data.

Plant Bioinformatics

Khalid Rehman Hakeem,Adeel Malik,Fazilet Vardar-Sukan,Munir Ozturk
Plant Bioinformatics Book PDF

Author : Khalid Rehman Hakeem,Adeel Malik,Fazilet Vardar-Sukan,Munir Ozturk
Publisher : Springer
Page : 459 pages
File Size : 53,7 Mb
Release : 2017-11-21
Category : Science
ISBN : 9783319671567

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Plant Bioinformatics by Khalid Rehman Hakeem,Adeel Malik,Fazilet Vardar-Sukan,Munir Ozturk Pdf

This book: (i) introduces fundamental and applied bioinformatics research in the field of plant life sciences; (ii) enlightens the potential users towards the recent advances in the development and application of novel computational methods available for the analysis and integration of plant -omics data; (iii) highlights relevant databases, softwares, tools and web resources developed till date to make ease of access for researchers working to decipher plant responses towards stresses; and (iv) presents a critical cross-talks on the available high-throughput data in plant research. Therefore, in addition to being a reference for the professional researchers, it is also of great interest to students and their professors. Considering immense significance of plants for all lives on Earth, the major focus of research in plant biology has been to: (a) select plants that best fit the purposes of human, (b) develop crop plants superior in quality, quantity and farming practices when compared to natural (wild) plants, and (c) explore strategies to help plants to adapt biotic and abiotic/environmental stress factors. Accordingly the development of novel techniques and their applications have increased significantly in recent years. In particular, large amount of biological data have emerged from multi-omics approaches aimed at addressing numerous aspects of the plant systems under biotic or abiotic stresses. However, even though the field is evolving at a rapid pace, information on the cross-talks and/or critical digestion of research outcomes in the context of plant bioinformatics is scarce. “Plant Bioinformatics: Decoding the Phyta” is aimed to bridge this gap.

Bioinformatics for High Throughput Sequencing

Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay
Bioinformatics for High Throughput Sequencing Book PDF

Author : Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay
Publisher : Springer Science & Business Media
Page : 258 pages
File Size : 52,9 Mb
Release : 2011-10-26
Category : Science
ISBN : 9781461407829

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Bioinformatics for High Throughput Sequencing by Naiara Rodríguez-Ezpeleta,Michael Hackenberg,Ana M. Aransay Pdf

Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.

OMICs-based Techniques for Global Food Security

Sajid Fiaz,Channapatna S. Prakash
OMICs based Techniques for Global Food Security Book PDF

Author : Sajid Fiaz,Channapatna S. Prakash
Publisher : John Wiley & Sons
Page : 324 pages
File Size : 41,7 Mb
Release : 2024-06-04
Category : Technology & Engineering
ISBN : 9781394209125

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OMICs-based Techniques for Global Food Security by Sajid Fiaz,Channapatna S. Prakash Pdf

Forward-thinking resource discussing how to integrate OMICs and novel genome editing technologies for sustainable crop production OMICS-based Techniques for Global Food Security provides an in-depth understanding of the mechanisms of OMICs techniques for crop improvement, details how OMICs techniques can contribute to identifying genes and traits with economic benefits, and explains how to develop crop plants with improved yield, quality, and resistance to stresses through genome editing technologies, providing evidence on the developments of climate resilient crops via applications of genome editing techniques throughout. The text covers the application of OMICs in crop plants, the integration of bioinformatics and multi-OMICs for precision breeding, de-novo domestication, CRISPR/Cas system for crop improvement, hybrid seed production, transgene free breeding, regulation for genome edit crops, bioinformatics and genome editing, and other topics related OMICs and genome editing. The text also includes a chapter on the global regulations for genome edited crops, and explains how these regulations influence novel plant breeding techniques in their adopted countries. Written by two highly qualified academics, OMICs-based Techniques for Global Food Security covers sample topics such as: Crops genome sequencing and their application for crop improvement, and functional characterization of cereals genome The role of OMICs based technologies in plant sciences and utilization of different multi-OMICs approaches for crop improvement Genomic database and genetic resource of cereals, speed breeding for rapid crop improvement, and evolution of genome editing technologies CRISPR system discovery, history, and future perspective, and CRISPR/Cas system for biotic and abiotic stress resistance in cereals Providing a collection of recent literature focusing on developments and applications of OMICs based technologies for crop improvement, OMICs-based Techniques for Global Food Security is an important read for plant breeders, molecular biologists, researchers, postdoctoral fellows, and students in disciplines for developing crops with high yield and nutritional potential.

Essentials of Bioinformatics, Volume III

Khalid Rehman Hakeem,Noor Ahmad Shaik,Babajan Banaganapalli,Ramu Elango
Essentials of Bioinformatics Volume III Book PDF

Author : Khalid Rehman Hakeem,Noor Ahmad Shaik,Babajan Banaganapalli,Ramu Elango
Publisher : Springer Nature
Page : 218 pages
File Size : 47,5 Mb
Release : 2019-11-01
Category : Science
ISBN : 9783030193188

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Essentials of Bioinformatics, Volume III by Khalid Rehman Hakeem,Noor Ahmad Shaik,Babajan Banaganapalli,Ramu Elango Pdf

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it will mostly focus on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. The third volume is titled In Silico Life Sciences: Agriculture. It focuses on plant genetic, genomic, transcriptomic, proteomic and metabolomics data. Using examples of new crop diseases-emergence, crop productivity and biotic/abiotic stress tolerance, this book illustrates how bioinformatics can be an integral components of modern day plant science research.

Bioinformatics in Rice Research

Manoj Kumar Gupta,Lambodar Behera
Bioinformatics in Rice Research Book PDF

Author : Manoj Kumar Gupta,Lambodar Behera
Publisher : Springer Nature
Page : 609 pages
File Size : 51,6 Mb
Release : 2021-09-24
Category : Science
ISBN : 9789811639937

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Bioinformatics in Rice Research by Manoj Kumar Gupta,Lambodar Behera Pdf

This 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.

Beginners Guide to Bioinformatics for High Throughput Sequencing

Eric Lee,Tin Wee Tan
Beginners Guide to Bioinformatics for High Throughput Sequencing Book PDF

Author : Eric Lee,Tin Wee Tan
Publisher : World Scientific Publishing Company
Page : 0 pages
File Size : 49,8 Mb
Release : 2019
Category : Bioinformatics
ISBN : 9813230517

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Beginners Guide to Bioinformatics for High Throughput Sequencing by Eric Lee,Tin Wee Tan Pdf

Biologists find computing bewildering; yet they are expected to be able to process the voluminous data available from the machines they buy and the datasets that has accumulated in genomic databanks worldwide. It is now increasingly difficult for them to avoid dealing with large volumes of data, that goes beyond just doing manual programming. Most books in this realm are full of equations and complex code but this book gives a much gentler entry point particularly for biologists, with code snippets users can use to cut and paste, and run on their Linux or MacOSX operating system or cloud instance. It also provides a step by step installation instructions which they can easily follow. Those who are in the field of genome sequencing and already familiar with the procedures of analysis, may also find this book useful in closing some knowledge gaps. High throughput sequencing requires high throughput and high performance computing. This book provides a gentle entry to high throughput sequencing by dealing with simple skills which the average biologist is increasingly required to master. You will find this book a breeze to read, and some suggestions in this book maybe new to you, something you might want to try out.

Bioinformatics

David Edwards,Jason Stajich,David Hansen
Bioinformatics Book PDF

Author : David Edwards,Jason Stajich,David Hansen
Publisher : Springer Science & Business Media
Page : 450 pages
File Size : 45,7 Mb
Release : 2009-09-03
Category : Science
ISBN : 9780387927381

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Bioinformatics by David Edwards,Jason Stajich,David Hansen Pdf

Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

OMICS

Debmalya Barh,Vasudeo Zambare,Vasco Azevedo
OMICS Book PDF

Author : Debmalya Barh,Vasudeo Zambare,Vasco Azevedo
Publisher : CRC Press
Page : 721 pages
File Size : 55,6 Mb
Release : 2013-03-26
Category : Medical
ISBN : 9781466562813

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OMICS by Debmalya Barh,Vasudeo Zambare,Vasco Azevedo Pdf

With the advent of new technologies and acquired knowledge, the number of fields in omics and their applications in diverse areas are rapidly increasing in the postgenomics era. Such emerging fields—including pharmacogenomics, toxicogenomics, regulomics, spliceomics, metagenomics, and environomics—present budding solutions to combat global challenges in biomedicine, agriculture, and the environment. OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences provides valuable insights into the applications of modern omics technologies to real-world problems in the life sciences. Filling a gap in the literature, it offers a broad, multidisciplinary view of current and emerging applications of omics in a single volume. Written by highly experienced active researchers, each chapter describes a particular area of omics and the associated technologies and applications. Topics covered include: Proteomics, epigenomics, and pharmacogenomics Toxicogenomics and the assessment of environmental pollutants Applications of plant metabolomics Nutrigenomics and its therapeutic applications Microalgal omics and omics approaches in biofuel production Next-generation sequencing and omics technology for transgenic plant analysis Omics approaches in crop improvement Engineering dark-operative chlorophyll synthesis Computational regulomics Omics techniques for the analysis of RNA splicing New fields, including metagenomics, glycomics, and miRNA Breast cancer biomarkers for early detection Environomics strategies for environmental sustainability This timely book explores a wide range of omics application areas in the biomedical, agricultural, and environmental sciences. Throughout, it highlights working solutions as well as open problems and future challenges. Demonstrating the diversity of omics, it introduces readers to state-of-the-art developments and trends in omics-driven research.

Essentials of Bioinformatics, Volume I

Noor Ahmad Shaik,Khalid Rehman Hakeem,Babajan Banaganapalli,Ramu Elango
Essentials of Bioinformatics Volume I Book PDF

Author : Noor Ahmad Shaik,Khalid Rehman Hakeem,Babajan Banaganapalli,Ramu Elango
Publisher : Springer
Page : 405 pages
File Size : 44,5 Mb
Release : 2019-03-27
Category : Science
ISBN : 9783030026349

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Essentials of Bioinformatics, Volume I by Noor Ahmad Shaik,Khalid Rehman Hakeem,Babajan Banaganapalli,Ramu Elango Pdf

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it mostly focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Unlike other bioinformatics books which are mostly theoretical, this book provides practical examples for the readers on state-of-the-art open source tools to solve biological problems. Flow charts of experiments, graphical illustrations, and mock data are included for quick reference. Volume I is therefore an ideal companion for students and early stage professionals wishing to master this blooming field.

Applications of Bioinformatics in Rice Research

Manoj Kumar Gupta,Lambodar Behera
Applications of Bioinformatics in Rice Research Book PDF

Author : Manoj Kumar Gupta,Lambodar Behera
Publisher : Springer Nature
Page : 363 pages
File Size : 49,8 Mb
Release : 2021-09-24
Category : Science
ISBN : 9789811639975

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Applications of Bioinformatics in Rice Research by Manoj Kumar Gupta,Lambodar Behera Pdf

This book summarizes the advanced computational methods for mapping high-density linkages and quantitative trait loci in the rice genome. It also discusses the tools for analyzing metabolomics, identifying complex polyploidy genomes, and decoding the extrachromosomal genome in rice. Further, the book highlights the application of CRISPR-Cas technology and methods for understanding the evolutionary development and the de novo evolution of genes in rice. Lastly, it discusses the role of artificial intelligence and machine learning in rice research and computational tools to analyze plant-pathogen co-evolution in rice crops.