Problems and Solutions in Biological Sequence Analysis

Problems and Solutions in Biological Sequence Analysis

Author: Mark Borodovsky

Publisher: Cambridge University Press

Published: 2006-09-04

Total Pages: 15

ISBN-13: 1139458124

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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.


Levels of Organization in the Biological Sciences

Levels of Organization in the Biological Sciences

Author: Daniel S. Brooks

Publisher: MIT Press

Published: 2021-08-24

Total Pages: 337

ISBN-13: 0262045338

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Scientific philosophers examine the nature and significance of levels of organization, a core structural principle in the biological sciences. This volume examines the idea of levels of organization as a distinct object of investigation, considering its merits as a core organizational principle for the scientific image of the natural world. It approaches levels of organization--roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity--in terms of its roles in scientific reasoning as a dynamic, open-ended idea capable of performing multiple overlapping functions in distinct empirical settings. The contributors--scientific philosophers with longstanding ties to the biological sciences--discuss topics including the philosophical and scientific contexts for an inquiry into levels; whether the concept can actually deliver on its organizational promises; the role of levels in the development and evolution of complex systems; conditional independence and downward causation; and the extension of the concept into the sociocultural realm. Taken together, the contributions embrace the diverse usages of the term as aspects of the big picture of levels of organization. Contributors Jan Baedke, Robert W. Batterman, Daniel S. Brooks, James DiFrisco, Markus I. Eronen, Carl Gillett, Sara Green, James Griesemer, Alan C. Love, Angela Potochnik, Thomas Reydon, Ilya Tëmkin, Jon Umerez, William C. Wimsatt, James Woodward


Evolutionary Causation

Evolutionary Causation

Author: Tobias Uller

Publisher: MIT Press

Published: 2019-09-03

Total Pages: 361

ISBN-13: 0262039923

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A comprehensive treatment of the concept of causation in evolutionary biology that makes clear its central role in both historical and contemporary debates. Most scientific explanations are causal. This is certainly the case in evolutionary biology, which seeks to explain the diversity of life and the adaptive fit between organisms and their surroundings. The nature of causation in evolutionary biology, however, is contentious. How causation is understood shapes the structure of evolutionary theory, and historical and contemporary debates in evolutionary biology have revolved around the nature of causation. Despite its centrality, and differing views on the subject, the major conceptual issues regarding the nature of causation in evolutionary biology are rarely addressed. This volume fills the gap, bringing together biologists and philosophers to offer a comprehensive, interdisciplinary treatment of evolutionary causation. Contributors first address biological motivations for rethinking evolutionary causation, considering the ways in which development, extra-genetic inheritance, and niche construction challenge notions of cause and process in evolution, and describing how alternative representations of evolutionary causation can shed light on a range of evolutionary problems. Contributors then analyze evolutionary causation from a philosophical perspective, considering such topics as causal entanglement, the commingling of organism and environment, and the relationship between causation and information. Contributors John A. Baker, Lynn Chiu, David I. Dayan, Renée A. Duckworth, Marcus W Feldman, Susan A. Foster, Melissa A. Graham, Heikki Helanterä, Kevin N. Laland, Armin P. Moczek, John Odling-Smee, Jun Otsuka, Massimo Pigliucci, Arnaud Pocheville, Arlin Stoltzfus, Karola Stotz, Sonia E. Sultan, Christoph Thies, Tobias Uller, Denis M. Walsh, Richard A. Watson


Electromagnetic Fields in Biological Systems

Electromagnetic Fields in Biological Systems

Author: James C. Lin

Publisher: CRC Press

Published: 2016-04-19

Total Pages: 460

ISBN-13: 1000218694

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Spanning static fields to terahertz waves, this volume explores the range of consequences electromagnetic fields have on the human body. Topics discussed include essential interactions and field coupling phenomena; electric field interactions in cells, focusing on ultrashort, pulsed high-intensity fields; dosimetry or coupling of ELF fields into biological systems; and the historical developments and recent trends in numerical dosimetry. It also discusses mobile communication devices and the dosimetry of RF radiation into the human body, exposure and dosimetry associated with MRI and spectroscopy, and available data on the interaction of terahertz radiation with biological tissues, cells, organelles, and molecules.


Biological Computation

Biological Computation

Author: Ehud Lamm

Publisher: CRC Press

Published: 2011-05-25

Total Pages: 332

ISBN-13: 1420087967

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The area of biologically inspired computing, or biological computation, involves the development of new, biologically based techniques for solving difficult computational problems. A unified overview of computer science ideas inspired by biology, Biological Computation presents the most fundamental and significant concepts in this area. In the book


Skin

Skin

Author: P. F. Millington

Publisher: Cambridge University Press

Published: 1983-05-05

Total Pages: 250

ISBN-13: 9780521241229

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First published in 1983 this book provides a review of the fundamentals of the biology and mechanics of human skin. The major theme is the interaction between and dependence of the integrity of skin on, cell turnover, nutrition, control mechanisms and disease. Mechanical, thermal and electrical properties are presented separately in a way that should allow the mathematically inexperienced reader to understand the principles but with sufficient detail to permit development of more advanced ideas. Discussion of environmental effects on skin includes cosmetics, solar radiation and clinical treatments. An account of methods of wound closure and of the recent attempts to find a substitute for skin completes an overview of this fascinating tissue.


Dynamics of Biological Systems

Dynamics of Biological Systems

Author: Michael Small

Publisher: CRC Press

Published: 2011-08-25

Total Pages: 286

ISBN-13: 1439853363

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From the spontaneous rapid firing of cortical neurons to the spatial diffusion of disease epidemics, biological systems exhibit rich dynamic behaviour over a vast range of time and space scales. Unifying many of these diverse phenomena, Dynamics of Biological Systems provides the computational and mathematical platform from which to understand the underlying processes of the phenomena. Through an extensive tour of various biological systems, the text introduces computational methods for simulating spatial diffusion processes in excitable media, such as the human heart, as well as mathematical tools for dealing with systems of nonlinear ordinary and partial differential equations, such as neuronal activation and disease diffusion. The mathematical models and computer simulations offer insight into the dynamics of temporal and spatial biological systems, including cardiac pacemakers, artificial electrical defibrillation, pandemics, pattern formation, flocking behaviour, the interaction of autonomous agents, and hierarchical and structured network topologies. Tools from complex systems and complex networks are also presented for dealing with real phenomenological systems. With exercises and projects in each chapter, this classroom-tested text shows students how to apply a variety of mathematical and computational techniques to model and analyze the temporal and spatial phenomena of biological systems. MATLAB® implementations of algorithms and case studies are available on the author’s website.