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Bayesian Mixture Models For Metagenomic Community Profiling
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Book Synopsis Pattern Recognition in Bioinformatics by : Marco Loog
Download or read book Pattern Recognition in Bioinformatics written by Marco Loog and published by Springer. This book was released on 2011-10-29 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 6th International Conference on Pattern Recognition in Bioinformatics, PRIB 2011, held in Delft, The Netherlands, in November 2011. The 29 revised full papers presented were carefully reviewed and selected from 35 submissions. The papers cover the wide range of possible applications of bioinformatics in pattern recognition: novel algorithms to handle traditional pattern recognition problems such as (bi)clustering, classification and feature selection; applications of (novel) pattern recognition techniques to infer and analyze biological networks and studies on specific problems such as biological image analysis and the relation between sequence and structure. They are organized in the following topical sections: clustering, biomarker selection and classification, network inference and analysis, image analysis, and sequence, structure, and interactions.
Book Synopsis Multi-omics Profiling of Unique Niches to Reveal the Microbial and Metabolite Composition by : Roshan Kumar
Download or read book Multi-omics Profiling of Unique Niches to Reveal the Microbial and Metabolite Composition written by Roshan Kumar and published by Frontiers Media SA. This book was released on 2022-09-29 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Insect Communities: Diversity Patterns and their Driving Forces by : Ai-Bing Zhang
Download or read book Insect Communities: Diversity Patterns and their Driving Forces written by Ai-Bing Zhang and published by Frontiers Media SA. This book was released on 2023-03-17 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Statistical Analysis of Microbiome Data by : Somnath Datta
Download or read book Statistical Analysis of Microbiome Data written by Somnath Datta and published by Springer Nature. This book was released on 2021-10-27 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.
Book Synopsis Microbiome and Machine Learning, Volume II by : Erik Bongcam-Rudloff
Download or read book Microbiome and Machine Learning, Volume II written by Erik Bongcam-Rudloff and published by Frontiers Media SA. This book was released on 2024-10-24 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the success of Microbiome and Machine Learning, which collected research results and perspectives of researchers working in the field of machine learning (ML) applied to the analysis of microbiome data, we are launching the second volume to collate any new findings in the field to further our understanding and encourage the participation of experts worldwide in the discussion. The success of ML algorithms in the field is substantially due to their capacity to process high-dimensional data and deal with uncertainty and noise. However, to maximize the combinatory potential of these emerging fields (microbiome and ML), researchers have to deal with some aspects that are complex and inherently related to microbiome data. Microbiome data are convoluted, noisy and highly variable, and non-standard analytical methodologies are required to unlock their clinical and scientific potential. Therefore, although a wide range of statistical modelling and ML methods are available, their application is only sometimes optimal when dealing with microbiome data.
Book Synopsis Metagenomics for Microbiology by : Jacques Izard
Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. - Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies - Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose - Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.
Book Synopsis Computational Intelligence Methods for Bioinformatics and Biostatistics by : Claudia Angelini
Download or read book Computational Intelligence Methods for Bioinformatics and Biostatistics written by Claudia Angelini and published by Springer. This book was released on 2016-07-30 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-conference proceedings of the 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2015, held in Naples, Italy, in September, 2015. The 21 revised full papers presented were carefully reviewed and selected from 24 submissions. They present problems concerning computational techniques in bioinformatics, systems biology and medical informatics discussing cutting edge methodologies and accelerate life science discoveries, as well as novel challenges with an high impact on molecular biology and translational medicine.
Book Synopsis Constrained Clustering by : Sugato Basu
Download or read book Constrained Clustering written by Sugato Basu and published by CRC Press. This book was released on 2008-08-18 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the initial work on constrained clustering, there have been numerous advances in methods, applications, and our understanding of the theoretical properties of constraints and constrained clustering algorithms. Bringing these developments together, Constrained Clustering: Advances in Algorithms, Theory, and Applications presents an extensive collection of the latest innovations in clustering data analysis methods that use background knowledge encoded as constraints. Algorithms The first five chapters of this volume investigate advances in the use of instance-level, pairwise constraints for partitional and hierarchical clustering. The book then explores other types of constraints for clustering, including cluster size balancing, minimum cluster size,and cluster-level relational constraints. Theory It also describes variations of the traditional clustering under constraints problem as well as approximation algorithms with helpful performance guarantees. Applications The book ends by applying clustering with constraints to relational data, privacy-preserving data publishing, and video surveillance data. It discusses an interactive visual clustering approach, a distance metric learning approach, existential constraints, and automatically generated constraints. With contributions from industrial researchers and leading academic experts who pioneered the field, this volume delivers thorough coverage of the capabilities and limitations of constrained clustering methods as well as introduces new types of constraints and clustering algorithms.
Book Synopsis Statistical and Computational Methods for Microbiome Multi-Omics Data by : Himel Mallick
Download or read book Statistical and Computational Methods for Microbiome Multi-Omics Data written by Himel Mallick and published by Frontiers Media SA. This book was released on 2020-11-19 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Functional Metagenomics: Tools and Applications by : Trevor C. Charles
Download or read book Functional Metagenomics: Tools and Applications written by Trevor C. Charles and published by Springer. This book was released on 2017-10-09 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
Book Synopsis Computational Methods for Microbiome Analysis by : Joao Carlos Setubal
Download or read book Computational Methods for Microbiome Analysis written by Joao Carlos Setubal and published by Frontiers Media SA. This book was released on 2021-02-02 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Next Generation Sequencing by : Jerzy Kulski
Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.
Book Synopsis Environmental Metagenomics, Water Quality and Suggested Remediation Measures of Polluted Waters: A Combined Approach by : Inderjeet Tyagi
Download or read book Environmental Metagenomics, Water Quality and Suggested Remediation Measures of Polluted Waters: A Combined Approach written by Inderjeet Tyagi and published by Elsevier. This book was released on 2024-03-26 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental Metagenomics, Water Quality and Suggested Remediation Measures of Polluted Waters: A Combined Approach is a reference handbook for scientists, engineers and early-career researchers seeking guidance in the areas of water quality, and remediation studies. The comprehensive book, which includes case studies and applications from a range of contributors in the field, offers an essential resource in the science of water quality assessment. - Includes a range of applications and case studies in wetland, riverine, drinking, and groundwater metagenomics, along with approaches for the remediation of pollutants from wastewater - Offers the latest updates on environmental metagenomics and its correlation with water environments, remediation measures, and SDGs - Provides key contributions from global researchers in the fields of water chemistry, environmental science, engineering, and public health
Book Synopsis Statistical Analysis of Microbiome Data with R by : Yinglin Xia
Download or read book Statistical Analysis of Microbiome Data with R written by Yinglin Xia and published by Springer. This book was released on 2018-10-06 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.
Book Synopsis Microbial Environmental Genomics (MEG) by : Francis Martin
Download or read book Microbial Environmental Genomics (MEG) written by Francis Martin and published by Springer Nature. This book was released on 2022-12-15 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.
Book Synopsis Optimal Design of Experiments by : Peter Goos
Download or read book Optimal Design of Experiments written by Peter Goos and published by John Wiley & Sons. This book was released on 2011-06-28 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This is an engaging and informative book on the modern practice of experimental design. The authors' writing style is entertaining, the consulting dialogs are extremely enjoyable, and the technical material is presented brilliantly but not overwhelmingly. The book is a joy to read. Everyone who practices or teaches DOE should read this book." - Douglas C. Montgomery, Regents Professor, Department of Industrial Engineering, Arizona State University "It's been said: 'Design for the experiment, don't experiment for the design.' This book ably demonstrates this notion by showing how tailor-made, optimal designs can be effectively employed to meet a client's actual needs. It should be required reading for anyone interested in using the design of experiments in industrial settings." —Christopher J. Nachtsheim, Frank A Donaldson Chair in Operations Management, Carlson School of Management, University of Minnesota This book demonstrates the utility of the computer-aided optimal design approach using real industrial examples. These examples address questions such as the following: How can I do screening inexpensively if I have dozens of factors to investigate? What can I do if I have day-to-day variability and I can only perform 3 runs a day? How can I do RSM cost effectively if I have categorical factors? How can I design and analyze experiments when there is a factor that can only be changed a few times over the study? How can I include both ingredients in a mixture and processing factors in the same study? How can I design an experiment if there are many factor combinations that are impossible to run? How can I make sure that a time trend due to warming up of equipment does not affect the conclusions from a study? How can I take into account batch information in when designing experiments involving multiple batches? How can I add runs to a botched experiment to resolve ambiguities? While answering these questions the book also shows how to evaluate and compare designs. This allows researchers to make sensible trade-offs between the cost of experimentation and the amount of information they obtain.
Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis
Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
