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Quantitative Biology

Author : Brian Munsky

Publisher : MIT Press

Page : 729 pages

File Size : 17,17 MB

Release : 2018-08-21

Category : Science

ISBN : 0262038080

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Book Description

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



Quantitative Biology

Author : Michael E. Wall

Publisher : CRC Press

Page : 406 pages

File Size : 36,53 MB

Release : 2012-08-25

Category : Science

ISBN : 1439827222

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Book Description

Quantitative methods are revolutionizing modern molecular and cellular biology. Groundbreaking technical advances are fueling the rapid expansion in our ability to observe, as seen in multidisciplinary studies that integrate theory, computation, experimental assays, and the control of microenvironments. Integrating new experimental and theoretical methods, Quantitative Biology: From Molecular to Cellular Systems gives both new and established researchers a solid foundation for starting work in this field. The book is organized into three sections: Fundamental Concepts covers bold ideas that inspire novel approaches in modern quantitative biology. It offers perspectives on evolutionary dynamics, system design principles, chance and memory, and information processing in biology. Methods describes recently developed or improved techniques that are transforming biological research. It covers experimental methods for studying single-molecule biochemistry, small-angle scattering from biomolecules, subcellular localization of proteins, and single-cell behavior. It also describes theoretical methods for synthetic biology and modeling random variations among cells. Molecular and Cellular Systems focuses on specific biological systems where modern quantitative biology methods are making an impact. It incorporates case studies of biological systems for which new concepts or methods are increasing our understanding. Examples include protein kinase at the molecular level, the genetic switch of phage lambda at the regulatory system level, and Escherichia coli chemotaxis at the cellular level. In short, Quantitative Biology presents practical tools for the observation, modeling, design, and manipulation of biological systems from the molecular to the cellular levels.



Biology by Numbers

Author : Richard F. Burton

Publisher : Cambridge University Press

Page : 260 pages

File Size : 29,27 MB

Release : 1998-02-26

Category : Mathematics

ISBN : 9780521576987

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Book Description

A practical undergraduate textbook for maths-shy biology students showing how basic maths reveals important insights.



Quantitative Conservation Biology

Author : William F. Morris

Publisher : Sinauer Associates Incorporated

Page : 480 pages

File Size : 12,8 MB

Release : 2002-01-01

Category : Science

ISBN : 9780878935468

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Book Description

The goal of this book is to provide practical, intelligible, and intuitive explanations of population modelling to empirical ecologists and conservation biologists. Modelling methods that do not require large amounts of data (typically unavailable for endangered species) are emphasised. As such, the book is appropriate for undergraduate and graduate students interested in quantitative conservation biology, managers charged with preserving endangered species, and, in short, for any conservation biologist or ecologist seeking to better understand the analysis and modelling of population data.



Quantitative Biology

Author : Michael E. Wall

Publisher : CRC Press

Page : 392 pages

File Size : 27,15 MB

Release : 2012-08-25

Category : Science

ISBN : 1439827230

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Book Description

Quantitative methods are revolutionizing modern molecular and cellular biology. Groundbreaking technical advances are fueling the rapid expansion in our ability to observe, as seen in multidisciplinary studies that integrate theory, computation, experimental assays, and the control of microenvironments. Integrating new experimental and theoretical



Quantitative Biology

Author : Akatsuki Kimura

Publisher : Springer Nature

Page : 130 pages

File Size : 17,54 MB

Release : 2022-01-04

Category : Science

ISBN : 9811650187

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Book Description

This textbook is for biologists, to conduct quantitative analysis and modeling of biological processes at molecular and cellular levels. Focusing on practical concepts and techniques for everyday research, this text will enable beginners, both students and established biologists, to take the first step in quantitative biology. It also provides step-by-step tutorials to run various sample programs in one’s personal computer using Excel and Python. This volume traces topics, starting with an introductory chapter, such as modeling, construction and execution of numerical models, and key concepts in quantitative biology: feedback regulations, fluctuations and randomness, and statistical analyses. It also provide sample codes with guidance to procedure programming for actual biological processes such as movement of the nucleus within a cell, cell-cycle regulation, stripe pattern formation of skins, and distribution of energy. Written by a leading research scientist who has a background in biology, studied quantitative approaches by himself, and teaches quantitative biology at several universities, this textbook broadens quantitative approaches for biologists who do not have a strong background in mathematics, physics, or computer programming, and helps them progress further in their research.



Quantitative Imaging in Cell Biology

Author :

Publisher : Academic Press

Page : 609 pages

File Size : 25,70 MB

Release : 2014-06-25

Category : Science

ISBN : 0124202012

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Book Description

This new volume, number 123, of Methods in Cell Biology looks at methods for quantitative imaging in cell biology. It covers both theoretical and practical aspects of using optical fluorescence microscopy and image analysis techniques for quantitative applications. The introductory chapters cover fundamental concepts and techniques important for obtaining accurate and precise quantitative data from imaging systems. These chapters address how choice of microscope, fluorophores, and digital detector impact the quality of quantitative data, and include step-by-step protocols for capturing and analyzing quantitative images. Common quantitative applications, including co-localization, ratiometric imaging, and counting molecules, are covered in detail. Practical chapters cover topics critical to getting the most out of your imaging system, from microscope maintenance to creating standardized samples for measuring resolution. Later chapters cover recent advances in quantitative imaging techniques, including super-resolution and light sheet microscopy. With cutting-edge material, this comprehensive collection is intended to guide researchers for years to come. Covers sections on model systems and functional studies, imaging-based approaches and emerging studies Chapters are written by experts in the field Cutting-edge material



Quantitative Bioimaging

Author : Raimund J. Ober

Publisher : CRC Press

Page : 693 pages

File Size : 37,18 MB

Release : 2020-12-15

Category : Medical

ISBN : 0429892128

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Book Description

Quantitative bioimaging is a broad interdisciplinary field that exploits tools from biology, chemistry, optics, and statistical data analysis for the design and implementation of investigations of biological processes. Instead of adopting the traditional approach of focusing on just one of the component disciplines, this textbook provides a unique introduction to quantitative bioimaging that presents all of the disciplines in an integrated manner. The wide range of topics covered include basic concepts in molecular and cellular biology, relevant aspects of antibody technology, instrumentation and experimental design in fluorescence microscopy, introductory geometrical optics and diffraction theory, and parameter estimation and information theory for the analysis of stochastic data. Key Features: Comprises four parts, the first of which provides an overview of the topics that are developed from fundamental principles to more advanced levels in the other parts. Presents in the second part an in-depth introduction to the relevant background in molecular and cellular biology and in physical chemistry, which should be particularly useful for students without a formal background in these subjects. Provides in the third part a detailed treatment of microscopy techniques and optics, again starting from basic principles. Introduces in the fourth part modern statistical approaches to the determination of parameters of interest from microscopy data, in particular data generated by single molecule microscopy experiments. Uses two topics related to protein trafficking (transferrin trafficking and FcRn-mediated antibody trafficking) throughout the text to motivate and illustrate microscopy techniques. An online appendix providing the background and derivations for various mathematical results presented or used in the text is available at http://www.routledge.com/9781138598980.



Systems Biology of Cell Signaling

Author : James Ferrell

Publisher : Garland Science

Page : 285 pages

File Size : 21,38 MB

Release : 2021-09-28

Category : Science

ISBN : 1000430731

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Book Description

How can we understand the complexity of genes, RNAs, and proteins and the associated regulatory networks? One approach is to look for recurring types of dynamical behavior. Mathematical models prove to be useful, especially models coming from theories of biochemical reactions such as ordinary differential equation models. Clever, careful experiments test these models and their basis in specific theories. This textbook aims to provide advanced students with the tools and insights needed to carry out studies of signal transduction drawing on modeling, theory, and experimentation. Early chapters summarize the basic building blocks of signaling systems: binding/dissociation, synthesis/destruction, and activation/inactivation. Subsequent chapters introduce various basic circuit devices: amplifiers, stabilizers, pulse generators, switches, stochastic spike generators, and oscillators. All chapters consistently use approaches and concepts from chemical kinetics and nonlinear dynamics, including rate-balance analysis, phase plane analysis, nullclines, linear stability analysis, stable nodes, saddles, unstable nodes, stable and unstable spirals, and bifurcations. This textbook seeks to provide quantitatively inclined biologists and biologically inclined physicists with the tools and insights needed to apply modeling and theory to interesting biological processes. Key Features: Full-color illustration program with diagrams to help illuminate the concepts Enables the reader to apply modeling and theory to the biological processes Further Reading for each chapter High-quality figures available for instructors to download



An Introduction to Systems Biology

Author : Uri Alon

Publisher : CRC Press

Page : 324 pages

File Size : 30,6 MB

Release : 2006-07-07

Category : Mathematics

ISBN : 1584886420

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Book Description

Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.