Immune System Modeling And Analysis

Author : Ramit Mehr,Miles Davenport
Publisher : Frontiers Media SA
Page : 402 pages
File Size : 46,8 Mb
Release : 2015-04-22
Category : Electronic book
ISBN : 9782889195015

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Immune system modeling and analysis by Ramit Mehr,Miles Davenport Pdf

The rapid development of new methods for immunological data collection – from multicolor flow cytometry, through single-cell imaging, to deep sequencing – presents us now, for the first time, with the ability to analyze and compare large amounts of immunological data in health, aging and disease. The exponential growth of these datasets, however, challenges the theoretical immunology community to develop methods for data organization and analysis. Furthermore, the need to test hypotheses regarding immune function, and generate predictions regarding the outcomes of medical interventions, necessitates the development of mathematical and computational models covering processes on multiple scales, from the genetic and molecular to the cellular and system scales. The last few decades have seen the development of methods for presentation and analysis of clonal repertoires (those of T and B lymphocytes) and phenotypic (surface-marker based) repertoires of all lymphocyte types, and for modeling the intricate network of molecular and cellular interactions within the immune systems. This e-Book, which has first appeared as a ‘Frontiers in Immunology’ research topic, provides a comprehensive, online, open access snapshot of the current state of the art on immune system modeling and analysis.

Author : John A. Adam,Nicola Bellomo
Publisher : Springer Science & Business Media
Page : 357 pages
File Size : 55,9 Mb
Release : 2012-10-06
Category : Mathematics
ISBN : 9780817681197

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A Survey of Models for Tumor-Immune System Dynamics by John A. Adam,Nicola Bellomo Pdf

Mathematical Modeling and Immunology An enormous amount of human effort and economic resources has been directed in this century to the fight against cancer. The purpose, of course, has been to find strategies to overcome this hard, challenging and seemingly endless struggle. We can readily imagine that even greater efforts will be required in the next century. The hope is that ultimately humanity will be successful; success will have been achieved when it is possible to activate and control the immune system in its competition against neoplastic cells. Dealing with the above-mentioned problem requires the fullest pos sible cooperation among scientists working in different fields: biology, im munology, medicine, physics and, we believe, mathematics. Certainly, bi ologists and immunologists will make the greatest contribution to the re search. However, it is now increasingly recognized that mathematics and computer science may well able to make major contributions to such prob lems. We cannot expect mathematicians alone to solve fundamental prob lems in immunology and (in particular) cancer research, but valuable sup port, however modest, can be provided by mathematicians to the research aspirations of biologists and immunologists working in this field.

Author : Gennady Bocharov,Burkhard Ludewig,Andreas Meyerhans,Vitaly Volpert
Publisher : Frontiers Media SA
Page : 278 pages
File Size : 46,9 Mb
Release : 2020-02-24
Category : Electronic
ISBN : 9782889634613

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Mathematical Modeling of the Immune System in Homeostasis, Infection and Disease by Gennady Bocharov,Burkhard Ludewig,Andreas Meyerhans,Vitaly Volpert Pdf

The immune system provides the host organism with defense mechanisms against invading pathogens and tumor development and it plays an active role in tissue and organ regeneration. Deviations from the normal physiological functioning of the immune system can lead to the development of diseases with various pathologies including autoimmune diseases and cancer. Modern research in immunology is characterized by an unprecedented level of detail that has progressed towards viewing the immune system as numerous components that function together as a whole network. Currently, we are facing significant difficulties in analyzing the data being generated from high-throughput technologies for understanding immune system dynamics and functions, a problem known as the ‘curse of dimensionality’. As the mainstream research in mathematical immunology is based on low-resolution models, a fundamental question is how complex the mathematical models should be? To respond to this challenging issue, we advocate a hypothesis-driven approach to formulate and apply available mathematical modelling technologies for understanding the complexity of the immune system. Moreover, pure empirical analyses of immune system behavior and the system’s response to external perturbations can only produce a static description of the individual components of the immune system and the interactions between them. Shifting our view of the immune system from a static schematic perception to a dynamic multi-level system is a daunting task. It requires the development of appropriate mathematical methodologies for the holistic and quantitative analysis of multi-level molecular and cellular networks. Their coordinated behavior is dynamically controlled via distributed feedback and feedforward mechanisms which altogether orchestrate immune system functions. The molecular regulatory loops inherent to the immune system that mediate cellular behaviors, e.g. exhaustion, suppression, activation and tuning, can be analyzed using mathematical categories such as multi-stability, switches, ultra-sensitivity, distributed system, graph dynamics, or hierarchical control. GB is supported by the Russian Science Foundation (grant 18-11-00171). AM is also supported by grants from the Spanish Ministry of Economy, Industry and Competitiveness and FEDER grant no. SAF2016-75505-R, the “María de Maeztu” Programme for Units of Excellence in R&D (MDM-2014-0370) and the Russian Science Foundation (grant 18-11-00171).

Author : Jayajit Das,Ciriyam Jayaprakash
Publisher : CRC Press
Page : 355 pages
File Size : 40,7 Mb
Release : 2018-09-03
Category : Science
ISBN : 9781498717410

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Systems Immunology by Jayajit Das,Ciriyam Jayaprakash Pdf

"Taken together, the body of information contained in this book provides readers with a bird’s-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." –Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA New experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined. Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.

Author : Guri I. Marchuk
Publisher : Springer Science & Business Media
Page : 356 pages
File Size : 42,6 Mb
Release : 2013-04-17
Category : Mathematics
ISBN : 9789401587983

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Mathematical Modelling of Immune Response in Infectious Diseases by Guri I. Marchuk Pdf

Beginning his work on the monograph to be published in English, this author tried to present more or less general notions of the possibilities of mathematics in the new and rapidly developing science of infectious immunology, describing the processes of an organism's defence against antigen invasions. The results presented in this monograph are based on the construc tion and application of closed models of immune response to infections which makes it possible to approach problems of optimizing the treat ment of chronic and hypertoxic forms of diseases. The author, being a mathematician, had creative long-Iasting con tacts with immunologists, geneticist, biologists, and clinicians. As far back as 1976 it resulted in the organization of a special seminar in the Computing Center of Siberian Branch of the USSR Academy of Sci ences on mathematical models in immunology. The seminar attracted the attention of a wide circle of leading specialists in various fields of science. All these made it possible to approach, from a more or less united stand point, the construction of models of immune response, the mathematical description of the models, and interpretation of results.

Author : FILIPPO. CELADA CASTIGLIONE (FRANCO.),Franco Celada
Publisher : CRC Press
Page : 286 pages
File Size : 42,7 Mb
Release : 2020-12-18
Category : Electronic
ISBN : 0367738384

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Immune System Modelling and Simulation by FILIPPO. CELADA CASTIGLIONE (FRANCO.),Franco Celada Pdf

The book describes a computational model of the immune system reaction, C-ImmSim, built along the lines of the computer model known as the Celada-Seiden model (CS-model). The computational counterpart of the CS-model is called IMMSIM which stands for IMMune system SIMulator. IMMSIM was written in 1992 by the physicist Phil E. Seiden and the immunologist Franco Celada. This model was built around the idea of developing a computerized system to perform experiments similar in vivo experiments; a tool developed to help biologists testing theories and hypothesis about how the immune system works. C-ImmSim is best viewed as a collection of models in a single program. It incorporates the principal core facts of today's immunological knowledge, such as the diversity of specific elements, MHC restriction, clonal selection, thymic education of T cells, antigen processing and presentation (both the cytosolic and endocytic pathways are implemented), cell-cell cooperation, homeostasis of cells created by the bone marrow, hyper mutation of antibodies, maturation of the cellular and humoral response, and memory. Besides, an antigen can represent a bacterium, a virus, or an allergen or a tumor cell. C-ImmSim has been recently customized to simulate the HIV-1 infection. Moreover, it can simulate the immunotherapy for cancer. These features are all present in the code and people can choose to turn them on and off at compiling time. The book presents the basic model as well as the various customizations to implement the description of different diseases and the way they have been used in practice to produce new knowledge either from hypothesis or from lab-experiment data. In this respect, the book can be used as a practical guide to implement a computational model with which to study a specific disease and to try to address realistic clinical questions.

Author : Carlos Castillo-Chavez
Publisher : Springer Science & Business Media
Page : 416 pages
File Size : 47,9 Mb
Release : 2013-03-13
Category : Medical
ISBN : 9783642934544

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Mathematical and Statistical Approaches to AIDS Epidemiology by Carlos Castillo-Chavez Pdf

The 18 research articles of this volume discuss the major themes that have emerged from mathematical and statistical research in the epidemiology of HIV. The opening paper reviews important recent contributions. Five sections follow: Statistical Methodology and Forecasting, Infectivity and the HIV, Heterogeneity and HIV Transmission Dynamics, Social Dynamics and AIDS, and The Immune System and The HIV. In each, leading experts in AIDS epidemiology present the recent results. Some address the role of variable infectivity, heterogeneous mixing, and long periods of infectiousness in the dynamics of HIV; others concentrate on parameter estimation and short-term forecasting. The last section looks at the interaction between the HIV and the immune system.

Author : Josep Bassaganya-Riera
Publisher : Academic Press
Page : 210 pages
File Size : 46,5 Mb
Release : 2015-10-21
Category : Medical
ISBN : 9780128037157

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Computational Immunology by Josep Bassaganya-Riera Pdf

Computational Immunology: Models and Tools encompasses the methodological framework and application of cutting-edge tools and techniques to study immunological processes at a systems level, along with the concept of multi-scale modeling. The book's emphasis is on selected cases studies and application of the most updated technologies in computational modeling, discussing topics such as computational modeling and its usage in immunological research, bioinformatics infrastructure, ODE based modeling, agent based modeling, and high performance computing, data analytics, and multiscale modeling. There are also modeling exercises using recent tools and models which lead the readers to a thorough comprehension and applicability. The book is a valuable resource for immunologists, computational biologists, bioinformaticians, biotechnologists, and computer scientists, as well as all those who wish to broaden their knowledge in systems modeling. Offers case studies with different levels of complexity Provides a detailed view on cutting-edge tools for modeling that are useful to experimentalists with limited computational skills Explores the usage of simulation for hypothesis generation, helping the reader to understand the most valuable points on experimental setting

Author : Namrata Tomar
Publisher : Humana
Page : 409 pages
File Size : 44,6 Mb
Release : 2021-03-26
Category : Medical
ISBN : 1071603914

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Immunoinformatics by Namrata Tomar Pdf

This book covers a wide range of diverse immunoinformatics research topics, involving tools and databases of potential epitope prediction, HLA gene analysis, MHC characterizing, in silico vaccine design, mathematical modeling of host-pathogen interactions, and network analysis of immune system data. In that way, this fully updated volume explores the enormous value of computational tools and models in immunology research. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of key insights and detailed implementation advice to encourage successful results in the lab. Authoritative and practical, Immunoinformatics, Third Edition serves as an ideal guide for scientists working at the intersection of bioinformatics, mathematical modelling, and statistics for the study of immune systems biology.

Author : Ole Lund,Morten Nielsen,Claus Lundegaard,Can Kesmir,Søren Brunak
Publisher : MIT Press
Page : 335 pages
File Size : 46,9 Mb
Release : 2024-02-06
Category : Computers
ISBN : 9780262551120

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Immunological Bioinformatics by Ole Lund,Morten Nielsen,Claus Lundegaard,Can Kesmir,Søren Brunak Pdf

Using bioinformatics methods to generate a systems-level view of the immune system; description of the main biological concepts and the new data-driven algorithms. Despite the fact that advanced bioinformatics methodologies have not been used as extensively in immunology as in other subdisciplines within biology, research in immunological bioinformatics has already developed models of components of the immune system that can be combined and that may help develop therapies, vaccines, and diagnostic tools for such diseases as AIDS, malaria, and cancer. In a broader perspective, specialized bioinformatics methods in immunology make possible for the first time a systems-level understanding of the immune system. The traditional approaches to immunology are reductionist, avoiding complexity but providing detailed knowledge of a single event, cell, or molecular entity. Today, a variety of experimental bioinformatics techniques connected to the sequencing of the human genome provides a sound scientific basis for a comprehensive description of the complex immunological processes. This book offers a description of bioinformatics techniques as they are applied to immunology, including a succinct account of the main biological concepts for students and researchers with backgrounds in mathematics, statistics, and computer science as well as explanations of the new data-driven algorithms in the context of biological data that will be useful for immunologists, biologists, and biochemists working on vaccine design. In each chapter the authors show interesting biological insights gained from the bioinformatics approach. The book concludes by explaining how all the methods presented in the book can be integrated to identify immunogenic regions in microorganisms and host genomes.

Author : Gregory R. Bock,Jamie A. Goode
Publisher : John Wiley & Sons
Page : 272 pages
File Size : 41,8 Mb
Release : 2004-03-05
Category : Medical
ISBN : 9780470090756

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Immunoinformatics by Gregory R. Bock,Jamie A. Goode Pdf

The astounding diversity of the immune system and the complexity of its regulatory pathways makes immunology a combinatorial science. Computational analysis has therefore become an essential element of immunology research and this has led to the creation of the emerging field of immunoinformatics. This book is the first to feature thorough coverage of this new field. Immunoinformatics facilitates the understanding of immune function by modelling the interactions among immunological components. Biological research provides ever deeper insights into the complexity of living organisms while computer science provides an effective means to store and analyse large volumes of complex data. Combining the two fields increases the efficiency of biological research and offers the potential for major advances in the study of biological systems. This book encompasses key developments in immunoinformatics, including immunological databases, sequence analysis, structure modelling, mathematical modelling of the immune system, simulation of laboratory experiments, statistical support for immunological experimentation and immunogenomics. The difficulties in effective application of bioinformatic tools in immunology arise at both ends of the spectrum: most immunologists have only a limited comprehension of sophisticated data analysis and applicability and limitations, while the average computer scientist lacks knowledge of the depth and complexity of biological data. The purpose of this book, therefore, is to present contributions from a multidisciplinary team of biologists and computer scientists to explore the issues related to better understanding of immune function and, in particular, to help apply new computer science methods to immunological research. Related Novartis Foundation symposia: 247 In Silico Simulation of Biological Processes Chair: Denis Noble 252 Generation and effector functions of regulatory lymphocytes Chair: Jean-François Bach

Author : Bruce Alberts
Publisher : Unknown
Page : 0 pages
File Size : 46,9 Mb
Release : 2002
Category : Cytology
ISBN : 0815332181

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Molecular Biology of The Cell by Bruce Alberts Pdf

Author : Dipankar Dasgupta,Taylor & Francis Group,Fernando Nino
Publisher : Auerbach Publications
Page : 296 pages
File Size : 47,7 Mb
Release : 2019-08-30
Category : Electronic
ISBN : 0367386909

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Immunological Computation by Dipankar Dasgupta,Taylor & Francis Group,Fernando Nino Pdf

Clearly, nature has been very effective in creating organisms that are capable of protecting themselves against a wide variety of pathogens such as bacteria, fungi, and parasites. The powerful information-processing capabilities of the immune system, such as feature extraction, pattern recognition, learning, memory, and its distributive nature provide rich metaphors that researchers are finding very useful for the development of computational models. While some of these models are designed to give us a better understanding of the immune system, other models are being developed to solve complex real-world problems such as anomaly detection, pattern recognition, data analysis (clustering), function optimization, and computer security. Immunological Computation: Theory and Applications is devoted to discussing different immunological mechanisms and their relation to information processing and problem solving. This unique volume presents a compendium of up-to-date work related to immunity-based techniques. After presenting the general abstractions of immune elements and processes used in computational models, it then-- Reviews standard procedures, representations, and matching rules that are used in all immunological computation models Covers the details of one of the earliest and most well-known immune algorithms, based on the negative selection (NS) process that occurs in the thymus Examines promising immune models, including those based on danger theory, cytokine network models, and MHC-based models The text goes further to describe a wide variety of applications, which include computer security, the detection and analysis of anomalies and faults, robotics, and data mining among others. To enhance understanding of this emerging field of study, each chapter includes a summary, review questions, and exercis

Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Page : 570 pages
File Size : 45,5 Mb
Release : 2011-12-30
Category : Science
ISBN : 9780309219396

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The Science and Applications of Synthetic and Systems Biology by Institute of Medicine,Board on Global Health,Forum on Microbial Threats Pdf

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Author : Gyan Bhanot,Shiyi Chen,Philip Seiden
Publisher : World Scientific
Page : 336 pages
File Size : 51,7 Mb
Release : 1997
Category : Computers
ISBN : 9810231962

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Some New Directions in Science on Computers by Gyan Bhanot,Shiyi Chen,Philip Seiden Pdf

Computers are used in today's technological world as a powerful tool to simulate many complex phenomena in various fields. This book is an introduction to some of these exciting developments. All the articles are written by experts in their respective fields. Each article teaches by example and the book contains case studies in fields as diverse as physics, biology, fluid dynamics, astrophysics, device modeling and weather simulation. This book should be of interest to a new researcher as an introduction to an exciting arena of computer applications. It should also benefit expert scientists, providing methods that may apply to their own problems or open up new research possibilities with unlimited promise.