Bioinformatik

This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors¿ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 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. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.

This book provides an overview of statistical concepts and basic methodology for the study of genetics of human traits and diseases. It attempts to provide a step-by-step description of problem identification, study design, methodology of data collection, data exploration, data summarization and visualization, and more advanced analytical methods for inferring genetic underpinnings of human phenotypes. The book provides codes in R programming language for implementation of most of the statistical methods described, which will enable practitioners to perform analysis of data on their own, without having to mold the data to fit the requirements of commercial statistical packages. Useful to anyone engaged in studies to understand and manage good health, the book is a useful guide for sustainable development of humankind. Primarily intended for practicing biologists especially those who carry out quantitative biological research, in particular, human geneticists, the book is also helpful in classroom teaching.

This book is about the dynamics of neural systems and should be suitable for those with a background in mathematics, physics, or engineering who want to see how their knowledge and skill sets can be applied in a neurobiological context. No prior knowledge of neuroscience is assumed, nor is advanced understanding of all aspects of applied mathematics! Rather, models and methods are introduced in the context of a typical neural phenomenon and a narrative developed that will allow the reader to test their understanding by tackling a set of mathematical problems at the end of each chapter. The emphasis is on mathematical- as opposed to computational-neuroscience, though stresses calculation above theorem and proof. The book presents necessary mathematical material in a digestible and compact form when required for specific topics. The book has nine chapters, progressing from the cell to the tissue, and an extensive set of references. It includes Markov chain models for ions,differential equations for single neuron models, idealised phenomenological models, phase oscillator networks, spiking networks, and integro-differential equations for large scale brain activity, with delays and stochasticity thrown in for good measure. One common methodological element that arises throughout the book is the use of techniques from nonsmooth dynamical systems to form tractable models and make explicit progress in calculating solutions for rhythmic neural behaviour, synchrony, waves, patterns, and their stability. This book was written for those with an interest in applied mathematics seeking to expand their horizons to cover the dynamics of neural systems. It is suitable for a Masters level course or for postgraduate researchers starting in the field of mathematical neuroscience.

This book includes contributions about mathematics, physics, philosophy of science, economics and finance and resulted from the Summer School "e;Complexity and Emergence: Ideas, Methods, with a Special Attention to Economics and Finance"e; held in Lake Como School of Advanced Studies, on 22-27 July 2018.The aim of the book is to provide useful instruments from the theory of complex systems, both on the theoretical level and the methodological ones, profiting from knowledge and insights from leading experts of different communities. It moves from the volume editors' conviction that to achieve progress in understanding socio-economical as well as ecological problems of our complex word such preparation is needed, together with a critical reconsideration of our basic scientific and economical approach.The potential readers are primarily master and doctorate students of mathematics, information sciences, theoretical physics and economics, as well as research workers in those areas, who want to enlarge their spectrum of knowledge towards the area of complexity and emergence. Since ideas and methods of the theory of complex systems also apply to other areas (from engineering and architecture to biology and medicine, e.g.), students and research workers from those areas will also profit from this book.

 This set of teaching notes provides extensive guidance for educators related to its sister title and contains numerous tools and questions to help educators provide didactics and evaluation of students in this essential area of biomedical informatics.  This is needed to understand the central topics of ontology, terminology and terminological systems in healthcare. Twenty-five years ago the notion that ontology would be essential to knowledge representation in healthcare was all but unknown. Almost all important terminologies and many ontologies are now in wide use and are growing in importance. With no general model of what a ontology and terminology should be, there are an increasing number of tools to support ontology / terminology development, implementation and maintenance. Steady progress since then has improved both ontology / terminology content and the technology and processes used to sustain that content. Terminology, Ontology and their Implementations: Teaching Guide and Notes provides extensive teaching materials to accompany Terminology, Ontology and their Implementations . It provides further definition of the topic and explains the use of reference terminologies needed to use them safely. It contains questions and explanations from each section of the textbook, making it easier to use the text in teaching Health Informatics students. The authors also provide supplementary information about the questions, their relevance and their relation to other concepts. This book augments Terminology, Ontology and their Implementations by assisting the understanding of terminology services and the architecture for terminological servers, and consequently serves as an essential tool for educators in their efforts to teach students in their study of health informatics.

This book presents a collection of high-quality research papers, presented at the Second International Symposium on Bioinformatics and Biomedicine (BioInfoMed¿2022). It offers a comprehensive look into some of the fastest growing fields of science, such as biomedicine, bioinformatics, artificial intelligence, and mathematical modeling. The different chapters of the work include both practical solutions and strictly scientific considerations expanding knowledge about the future bioinformatics and biomedical engineering challenges. We believe that the presented works will have a great impact not only on the development and the application of new methods for modeling, decision making and data mining in healthcare and biomedicine, but also it will provide a source of inspiration for researchers who can implement the proposed methods into their practice and scientific studies.

This third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help further their study in this field.

This volume provides protocols and methods on techniques to study plant gametogenesis. Chapters are divided into four sections covering omics, cytological, molecular approaches, plant transformation, genome editing, bioinformatics, and data analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Plant Gametogenesis: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

This highly interdisciplinary book, covering more than six fields, from philosophy and sciences all the way up to the humanities and with contributions from eminent authors, addresses the interplay between content and context, reductionism and holism and their meeting point: the notion of emergence. Much of today's science is reductionist (bottom-up); in other words, behaviour on one level is explained by reducing it to components on a lower level. Chemistry is reduced to atoms, ecosystems are explained in terms of DNA and proteins, etc. This approach fails quickly since we can't cannot extrapolate to the properties of atoms solely from Schrodinger's equation, nor figure out protein folding from an amino acid sequence or obtain the phenotype of an organism from its genotype. An alternative approach to this is holism (top-down). Consider an ecosystem or an organism as a whole: seek patterns on the same scale. Model a galaxy not as 400 billion-point masses (stars) but as an object in its own right with its own properties (spiral, elliptic). Or a hurricane as a structured form of moist air and water vapour. Reductionism is largely about content, whereas holistic models are more attuned to context. Reductionism (content) and holism (context) are not opposing philosophies - in fact, they work best in tandem. Join us on a journey to understand the multifaceted dialectic concerning this duo and how they shape the foundations of sciences and humanities, our thoughts and, the very nature of reality itself.

This volume explores the latest technological advances and covers all facets of systems medicine with respect to precision medicine. The chapters in this book are organized into four parts. Part One highlights the recent achievements in proteomics for biomarkers identification, integration of omics and phenotypic data for precision medicine, and medicine-guided treatment of drug-induced Stevens-Johnson syndrome. Part Two covers systems-based computational approaches for pharmaceutical research and drug development, the principle of optimizing systemic exposure of drugs, and Animal Rule for drug repurposing. Part Three looks at computational tools and methodologies of network biology, quantitative systems toxicology, and modeling and stimulating patient response variabilities. Part Four talks about how systems medicine can address unmet medical and health needs, and identify educational needs. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and thorough, Systems Medicine: Methods and Protocols is a valuable resource for the scientific community that will help researchers work together toward the further advancement of achieving the goal of promoting global health.Chapter 8 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com

¿This book comprises selected papers of the 26th International Conference on Difference Equations and Applications, ICDEA 2021, held virtually at the University of Sarajevo, Bosnia and Herzegovina, in July 2021.The book includes the latest and significant research and achievements in difference equations, discrete dynamical systems, and their applications in various scientific disciplines.The book is interesting for Ph.D. students and researchers who want to keep up to date with the latest research, developments, and achievements in difference equations, discrete dynamical systems, and their applications, the real-world problems.

This book is devoted to the Little Bustard, a medium sized Paleartic steppe bird whose distribution ranges from the Iberian Peninsula to Central Asia. At present, the European population is suffering a severe decline mainly due to agricultural intensification, although its status and concerns in non-European countries are relatively unknown. In spite of this dramatic situation, the Little Bustard is an interesting model species for topics as varied as phylogeny, life history evolution and demographic traits, sexual selection and lekking behavior, habitat selection, intra- and interspecific relationships, or interaction with farming and other anthropogenic disturbances. This book provides an updated, interdisciplinary, and worldwide review of the most recent information of this crucial species in the Palearctic steppe-bird community, from specific biological aspects and traits to research-focused management. Some of the most prominent scientists from different fields (systematics, breeding ecology, behavior, competence, predation, population dynamics, farming, conservation) update and synthesize the existing information on a singular, threatened and vulnerable species.

This book constitutes the Third 3D Head and Neck Tumor Segmentation in PET/CT Challenge, HECKTOR 2022, which was held in conjunction with the 25th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2022, on September 22, 2022.The 22 contributions presented, as well as an overview paper, were carefully reviewed and selected from 24 submissions. This challenge aims to evaluate and compare the current state-of-the-art methods for automatic head and neck tumor segmentation. In the context of this challenge, a dataset of 883 delineated PET/CT images was made available for training.

This volume details current and new computational methodologies to study peptides. Chapters guide readers through antimicrobial peptides, foldability, amyloid sheet formation, membrane-active peptides, organized peptide assemblies, protein-peptide interfaces, prediction of peptide-MHC complexes, advanced free energy simulations for peptide binding, and methods for high throughput peptide or miniprotein design. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, software, and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Peptides Science: Methods and Protocols aims to provide concepts, methods, and guidelines to help both novices and experienced workers benefit from today's new opportunities and challenges.

This book broadly covers the given spectrum of disciplines in Computational Life Sciences, transforming it into a strong helping hand for teachers, students, practitioners and researchers. In Life Sciences, problem-solving and data analysis often depend on biological expertise combined with technical skills in order to generate, manage and efficiently analyse big data. These technical skills can easily be enhanced by good theoretical foundations, developed from well-chosen practical examples and inspiring new strategies. This is the innovative approach of Computational Life Sciences-Data Engineering and Data Mining for Life Sciences: We present basic concepts, advanced topics and emerging technologies, introduce algorithm design and programming principles, address data mining and knowledge discovery as well as applications arising from real projects. Chapters are largely independent and often flanked by illustrative examples and practical advise.

This book is the first comprehensive compilation describing the importance of sandalwood in national and international markets, genetic resources, molecular markers, whole genome sequencing, and pathway genes involved in oil biosynthesis, aroma and fragrance. Application of various ¿omics¿ approaches in delineating genome architecture and annotation of genes is highlighted. This book comprises 10 chapters covered over 200 pages authored by the researchers involved in sandalwood genomics.The sandalwood, Santalum album is known for its unique fragrance and finest wood available for carving. Also, sandalwood is intertwined with Indian culture and it is the second most valuable and expensive tree in the world.

This book offers a gripping introduction to the fastest growing field of biology with easy-to-follow examples and a well-prepared appendix for the reader to cook up and experience everything right away.The book gets the reader started with the basics, such as how to easily find sequence information and then analyze it. In further chapters, the authors go into the various analysis options from RNA, DNA and proteins to entire metabolic pathways. Exciting examples from biology are chosen in each chapter to illustrate the analysis. Each chapter concludes with an exercise section that immediately puts what has been learned to use.The subject of this book is a must for any biology student, whether undergraduate or graduate, as bioinformatics is now unearthing amazing insights into the molecular basis of all living things. Computer science students and other students from related sciences will get a good introduction to bioinformatics, as biology and current topics (e.g. AI)are systematically introduced step by step alongside the software.Discover the key to life together with the authors and learn to understand the language of life. This book is a translation of the original German 2nd edition Bioinformatik by Thomas Dandekar and Meik Kunz, published by Springer-Verlag GmbH Germany, part of Springer Nature in 2021. The translation was done with the help of artificial intelligence (machine translation by the service DeepL.com). A subsequent human revision was done primarily in terms of content, so that the book will read stylistically differently from a conventional translation. Springer Nature works continuously to further the development of tools for the production of books and on the related technologies to support the authors.

This book brings together what is currently known in terms of basic research in the field of long noncoding RNAs (lncRNAs) and builds on this to delve more deeply in the specific roles that lncRNAs are playing during inflammation. The book provides readers with basic knowledge on lncRNAs: from understanding the complexity of the transcriptome, conservation, structure and the tools used to investigate these aspects, to how we use this information to study lncRNAs in a specific biological context. The volume covers the emerging roles of lncRNAs in the initial stages of inflammation as well as their roles in specific inflammatory diseases including arthritis, lupus, diabetes and cardiovascular disease. The book also shows the emerging interest in using lncRNAs as a therapeutic target and how this could impact our ability to diagnose and treat inflammatory diseases in the future.

This book helps readers easily learn basic model checking by presenting examples, exercises and case studies. The toolset mCRL2 provides a language to specify the behaviour of distributed systems, in particular where there is concurrency with inter-process communication. This language allows us to analyse a distributed system with respect to its functional requirements. For example, biological cells, supply chain management systems, patient support platforms, and communication protocols.The underlying technique is based on verifying requirements through model checking. The book explains the syntax of mCRL2 and offers modelling tips and tricks.

This textbook is aimed at students of non-specialist courses with computer science components. Special emphasis is placed on the so-called life sciences, such as medical technology, rescue engineering, biotechnology, environmental engineering or process engineering. The textbook is suitable for readers in study and practice who want to get an introduction to computer science. The special feature of this book is the problem-based approach, as well as the exercises designed according to different taxonomy levels.

Living organisms are distinguished by their chemical basis. Thus, knowledge of the properties of the elements and the interactions of the resulting compounds is a prerequisite for understanding biology.Chemistry answers the questions of why, among the more than 100 elements of the periodic table (PSE), carbon and not silicon is the dominant element in biology and why precious metals, such as gold and silver, do not play a role. The PSE provides information about why phosphoric acid and not sulfuric acid acts as a bridge in polynucleic acids and why DNA had to evolve from RNA. At the same time, only chemistry makes clear why D-glucose is so central in building biopolymers such as cellulose and glycogen, and why the citrate cycle is logically self-contained and without alternative. Biochemistry is also a synthesis chemistry that differs from "man-made" synthesis chemistry "only" in terms of the framework conditions. Individuals are selected from the multitude of elements of the PSE and the almost infinite number of chemical compounds. The selection is based on the environmental conditions on Earth, such as moderate temperatures, preferably atmospheric pressure, solvent water and as primary reaction partner oxygen.The hypothesis is developed that the guiding principle of modern biology, the theory of evolution, has its roots in the underlying chemistry. This turns Darwinism from its biological head to its chemical feet. For example, the effect of phenols as radical scavengers is a priori chemical, before biological phenomena could evolve from it as differences in distinction in colored flowering plants. The book develops a completely new, chemistry-centered view of "animate nature" and challenges a changed, biologically oriented didactics of chemistry in schools and universities.