Analysis of Biological Systems

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Publisher : World Scientific
ISBN 13 : 1783266899
Total Pages : 432 pages
Book Rating : 4.7/5 (832 download)

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Book Synopsis Analysis of Biological Systems by : Corrado Priami

Download or read book Analysis of Biological Systems written by Corrado Priami and published by World Scientific. This book was released on 2015-01-29 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling is fast becoming fundamental to understanding the processes that define biological systems. High-throughput technologies are producing increasing quantities of data that require an ever-expanding toolset for their effective analysis and interpretation. Analysis of high-throughput data in the context of a molecular interaction network is particularly informative as it has the potential to reveal the most relevant network modules with respect to a phenotype or biological process of interest. Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science. Contents:Algorithmic Systems BiologySetting the ContextSystems and ModelsStatic Modeling TechnologiesDynamic Modeling TechnologiesLanguage-based ModelingDynamic Modeling ProcessSimulationPerspectives and ConclusionsAppendix A: Basic MathAppendix B: Probability and StatisticsAppendix C: Semantics of Modeling Languages Readership: Graduate students in computer science, physics, mathematics or engineering or biology-related fields who want to better understand how to develop and use models of biological systems. Practitioners in systems biology who want to understand algorithmic modeling and algorithmic systems biology. Key Features:The book jointly deals with static (statistical) and dynamic (simulation) technologies making it a strong reference for who wants to approach real systems biology problemsThe content of the book is the result of more than ten years application of the material in university courses and to industrial-level problems in systems pharmacology and systems nutritionThere is no reference work available for the field of language-based modeling that is studied in depth in this bookKeywords:Modeling;Simulation;Network Analysis;Systems Biology;Systems Nutrition;Systems Pharmacology;Stochastic Models;Programming Biology;Multivariate Analysis

Biological Sequence Analysis

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Publisher :
ISBN 13 : 9780511337086
Total Pages : 0 pages
Book Rating : 4.3/5 (37 download)

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Book Synopsis Biological Sequence Analysis by : Richard Durbin

Download or read book Biological Sequence Analysis written by Richard Durbin and published by . This book was released on 1998 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents up-to-date computer methods for analysing DNA, RNA and protein sequences.

Analysis of biological processes

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Publisher : Springer
ISBN 13 : 9401773734
Total Pages : 166 pages
Book Rating : 4.4/5 (17 download)

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Book Synopsis Analysis of biological processes by : Alfonsas Juška

Download or read book Analysis of biological processes written by Alfonsas Juška and published by Springer. This book was released on 2015-12-04 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The main concern of the book is analysis of biological processes, the final stage of which is mathematical modeling, i.e. quantitative presentation of the processes in rigorous mathematical terms. It is designated for non-mathematicians. Mathematical models can be compared with experimental data thus verifying the validity of the models and finally of the initial assumptions and verbal descriptions of the processes. The models (usually in the form of mathematical equations) are achieved painlessly via the schemes summarising verbal description of what is known concerning the processes. To solve the equations computer software is used. The step-by-step analysis leads to quite sophisticated models some of them being original. The book helps the reader to develop more general approach to the problems. It may be useful for experienced readers as well.

Computational Methods for the Analysis of Genomic Data and Biological Processes

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Publisher : MDPI
ISBN 13 : 3039437712
Total Pages : 222 pages
Book Rating : 4.0/5 (394 download)

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Book Synopsis Computational Methods for the Analysis of Genomic Data and Biological Processes by : Francisco A. Gómez Vela

Download or read book Computational Methods for the Analysis of Genomic Data and Biological Processes written by Francisco A. Gómez Vela and published by MDPI. This book was released on 2021-02-05 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.

Information Processing and Biological Systems

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Publisher : Springer Science & Business Media
ISBN 13 : 3642196217
Total Pages : 230 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis Information Processing and Biological Systems by : Samuli Niiranen

Download or read book Information Processing and Biological Systems written by Samuli Niiranen and published by Springer Science & Business Media. This book was released on 2011-03-10 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living beings require constant information processing for survival. In cells, information is being processed and propagated at various levels, from the gene regulatory network to chemical pathways, to the interaction with the environment. How this is achieved and how information is coded is still poorly understood. For example, what a cell interprets as information in the temporal level of an mRNA and what is interpreted as noise remains an open question. Recently, information theoretical methods and other tools, developed in the context of engineering and natural sciences, have been applied to study diverse biological processes. This book covers the latest findings on how information is processed in various biological processes, ranging from information processing and propagation in gene regulatory networks to information processing in natural language. An overview is presented of the state-of-the-art in information processing in biological systems and the opinion of current leaders in this research field on future research directions.

Quantitative Biology

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Publisher : MIT Press
ISBN 13 : 0262038080
Total Pages : 729 pages
Book Rating : 4.2/5 (62 download)

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Book Synopsis Quantitative Biology by : Brian Munsky

Download or read book Quantitative Biology written by Brian Munsky and published by MIT Press. This book was released on 2018-08-21 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber

Heat Transfer and Fluid Flow in Biological Processes

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Publisher : Academic Press
ISBN 13 : 0124079008
Total Pages : 428 pages
Book Rating : 4.1/5 (24 download)

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Book Synopsis Heat Transfer and Fluid Flow in Biological Processes by : Sid Becker

Download or read book Heat Transfer and Fluid Flow in Biological Processes written by Sid Becker and published by Academic Press. This book was released on 2014-12-31 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: Heat Transfer and Fluid Flow in Biological Processes covers emerging areas in fluid flow and heat transfer relevant to biosystems and medical technology. This book uses an interdisciplinary approach to provide a comprehensive prospective on biofluid mechanics and heat transfer advances and includes reviews of the most recent methods in modeling of flows in biological media, such as CFD. Written by internationally recognized researchers in the field, each chapter provides a strong introductory section that is useful to both readers currently in the field and readers interested in learning more about these areas. Heat Transfer and Fluid Flow in Biological Processes is an indispensable reference for professors, graduate students, professionals, and clinical researchers in the fields of biology, biomedical engineering, chemistry and medicine working on applications of fluid flow, heat transfer, and transport phenomena in biomedical technology. Provides a wide range of biological and clinical applications of fluid flow and heat transfer in biomedical technology Covers topics such as electrokinetic transport, electroporation of cells and tissue dialysis, inert solute transport (insulin), thermal ablation of cancerous tissue, respiratory therapies, and associated medical technologies Reviews the most recent advances in modeling techniques

Computational Methods for the Analysis of Genomic Data and Biological Processes

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Author :
Publisher :
ISBN 13 : 9783039437726
Total Pages : 222 pages
Book Rating : 4.4/5 (377 download)

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Book Synopsis Computational Methods for the Analysis of Genomic Data and Biological Processes by : Francisco A. Gómez Vela

Download or read book Computational Methods for the Analysis of Genomic Data and Biological Processes written by Francisco A. Gómez Vela and published by . This book was released on 2021 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.

Bioinformatics Methods in Clinical Research

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Publisher : Humana Press
ISBN 13 : 9781617796708
Total Pages : 0 pages
Book Rating : 4.7/5 (967 download)

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Book Synopsis Bioinformatics Methods in Clinical Research by : Rune Matthiesen

Download or read book Bioinformatics Methods in Clinical Research written by Rune Matthiesen and published by Humana Press. This book was released on 2012-02-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrated bioinformatics solutions have become increasingly valuable in past years, as technological advances have allowed researchers to consider the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes, and as the costs of such techniques have begun to lessen. In Bioinformatics Methods in Clinical Research, experts examine the latest developments impacting clinical omics, and describe in great detail the algorithms that are currently used in publicly available software tools. Chapters discuss statistics, algorithms, automated methods of data retrieval, and experimental consideration in genomics, transcriptomics, proteomics, and metabolomics. Composed in the highly successful Methods in Molecular BiologyTM series format, each chapter contains a brief introduction, provides practical examples illustrating methods, results, and conclusions from data mining strategies wherever possible, and includes a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Informative and ground-breaking, Bioinformatics Methods in Clinical Research establishes a much-needed bridge between theory and practice, making it an indispensable resource for bioinformatics researchers.

Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes

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Publisher : Academic Press
ISBN 13 : 0128117192
Total Pages : 454 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes by : Miguel Cerrolaza

Download or read book Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes written by Miguel Cerrolaza and published by Academic Press. This book was released on 2017-10-17 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes covers new and exciting modeling methods to help bioengineers tackle problems for which the Finite Element Method is not appropriate. The book covers a wide range of important subjects in the field of numerical methods applied to biomechanics, including bone biomechanics, tissue and cell mechanics, 3D printing, computer assisted surgery and fluid dynamics. Modeling strategies, technology and approaches are continuously evolving as the knowledge of biological processes increases. Both theory and applications are covered, making this an ideal book for researchers, students and R&D professionals. Provides non-conventional analysis methods for modeling Covers the Discrete Element Method (DEM), Particle Methods (PM), MessLess and MeshFree Methods (MLMF), Agent-Based Methods (ABM), Lattice-Boltzmann Methods (LBM) and Boundary Integral Methods (BIM) Includes contributions from several world renowned experts in their fields Compares pros and cons of each method to help you decide which method is most applicable to solving specific problems

Advanced Biological Processes for Wastewater Treatment

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Publisher : Springer
ISBN 13 : 3319588354
Total Pages : 299 pages
Book Rating : 4.3/5 (195 download)

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Book Synopsis Advanced Biological Processes for Wastewater Treatment by : Márcia Dezotti

Download or read book Advanced Biological Processes for Wastewater Treatment written by Márcia Dezotti and published by Springer. This book was released on 2017-09-12 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent developments in advanced biological treatment technologies that are attracting increasing attention or that have a high potential for large-scale application in the near future. It also explores the fundamental principles as well as the applicability of the engineered bioreactors in detail. It describes two of the emerging technologies: membrane bioreactors (MBR) and moving bed biofilm reactors (MBBR), both of which are finding increasing application worldwide thanks to their compactness and high efficiency. It also includes a chapter dedicated to aerobic granular sludge (AGS) technology, and discusses the main features and applications of this promising process, which can simultaneously remove organic matter, nitrogen and phosphorus and is considered a breakthrough in biological wastewater treatment. Given the importance of removing nitrogen compounds from wastewater, the latest advances in this area, including new processes for nitrogen removal (e.g. Anammox), are also reviewed. Developments in molecular biology techniques over the last twenty years provide insights into the complex microbial diversity found in biological treatment systems. The final chapter discusses these techniques in detail and presents the state-of-the-art in this field and the opportunities these techniques offer to improve process performance.

Molecular Biology of The Cell

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Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

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Book Synopsis Molecular Biology of The Cell by : Bruce Alberts

Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Statistical and Evolutionary Analysis of Biological Networks

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Publisher : World Scientific
ISBN 13 : 1848164335
Total Pages : 179 pages
Book Rating : 4.8/5 (481 download)

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Book Synopsis Statistical and Evolutionary Analysis of Biological Networks by : Michael P. H. Stumpf

Download or read book Statistical and Evolutionary Analysis of Biological Networks written by Michael P. H. Stumpf and published by World Scientific. This book was released on 2010 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community.

Stochastic Processes in Cell Biology

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Publisher : Springer Nature
ISBN 13 : 3030725154
Total Pages : 773 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis Stochastic Processes in Cell Biology by : Paul C. Bressloff

Download or read book Stochastic Processes in Cell Biology written by Paul C. Bressloff and published by Springer Nature. This book was released on 2022-01-04 with total page 773 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book develops the theory of continuous and discrete stochastic processes within the context of cell biology. In the second edition the material has been significantly expanded, particularly within the context of nonequilibrium and self-organizing systems. Given the amount of additional material, the book has been divided into two volumes, with volume I mainly covering molecular processes and volume II focusing on cellular processes. A wide range of biological topics are covered in the new edition, including stochastic ion channels and excitable systems, molecular motors, stochastic gene networks, genetic switches and oscillators, epigenetics, normal and anomalous diffusion in complex cellular environments, stochastically-gated diffusion, active intracellular transport, signal transduction, cell sensing, bacterial chemotaxis, intracellular pattern formation, cell polarization, cell mechanics, biological polymers and membranes, nuclear structure and dynamics, biological condensates, molecular aggregation and nucleation, cellular length control, cell mitosis, cell motility, cell adhesion, cytoneme-based morphogenesis, bacterial growth, and quorum sensing. The book also provides a pedagogical introduction to the theory of stochastic and nonequilibrium processes – Fokker Planck equations, stochastic differential equations, stochastic calculus, master equations and jump Markov processes, birth-death processes, Poisson processes, first passage time problems, stochastic hybrid systems, queuing and renewal theory, narrow capture and escape, extreme statistics, search processes and stochastic resetting, exclusion processes, WKB methods, large deviation theory, path integrals, martingales and branching processes, numerical methods, linear response theory, phase separation, fluctuation-dissipation theorems, age-structured models, and statistical field theory. This text is primarily aimed at graduate students and researchers working in mathematical biology, statistical and biological physicists, and applied mathematicians interested in stochastic modeling. Applied probabilists should also find it of interest. It provides significant background material in applied mathematics and statistical physics, and introduces concepts in stochastic and nonequilibrium processes via motivating biological applications. The book is highly illustrated and contains a large number of examples and exercises that further develop the models and ideas in the body of the text. It is based on a course that the author has taught at the University of Utah for many years.

Problems and Solutions in Biological Sequence Analysis

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Publisher : Cambridge University Press
ISBN 13 : 1139458124
Total Pages : 15 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Problems and Solutions in Biological Sequence Analysis by : Mark Borodovsky

Download or read book Problems and Solutions in Biological Sequence Analysis written by Mark Borodovsky and published by Cambridge University Press. This book was released on 2006-09-04 with total page 15 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis, by Durbin et al. (Cambridge, 1998), widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in Biological Sequence Analysis as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as Biological Sequence Analysis and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever MSc degree program in Bioinformatics was held.

Evolution of Translational Omics

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Publisher : National Academies Press
ISBN 13 : 0309224187
Total Pages : 354 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis Evolution of Translational Omics by : Institute of Medicine

Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Mathematical and Experimental Modeling of Physical and Biological Processes

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Publisher : CRC Press
ISBN 13 : 9781420073386
Total Pages : 298 pages
Book Rating : 4.0/5 (733 download)

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Book Synopsis Mathematical and Experimental Modeling of Physical and Biological Processes by : H.T. Banks

Download or read book Mathematical and Experimental Modeling of Physical and Biological Processes written by H.T. Banks and published by CRC Press. This book was released on 2009-01-12 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Through several case study problems from industrial and scientific research laboratory applications, Mathematical and Experimental Modeling of Physical and Biological Processes provides students with a fundamental understanding of how mathematics is applied to problems in science and engineering. For each case study problem, the authors discuss why a model is needed and what goals can be achieved with the model. Exploring what mathematics can reveal about applications, the book focuses on the design of appropriate experiments to validate the development of mathematical models. It guides students through the modeling process, from empirical observations and formalization of properties to model analysis and interpretation of results. The authors also describe the hardware and software tools used to design the experiments so faculty/students can duplicate them. Integrating real-world applications into the traditional mathematics curriculum, this textbook deals with the formulation and analysis of mathematical models in science and engineering. It gives students an appreciation of the use of mathematics and encourages them to further study the applied topics. Real experimental data for projects can be downloaded from CRC Press Online.