Mechanisms of Gene Regulation: Boolean Network Models of the Lactose Operon in Escherichia coli

Mathematical Concepts and Methods in Modern Biology offers a quantitative framework for analyzing, predicting, and modulating the behavior of complex biological systems. The book presents important mathematical concepts, methods and tools in the context of essential questions raised in modern biology.Designed around the principles of project-based learning and problem-solving, the book considers biological topics such as neuronal networks, plant population growth, metabolic pathways, and phylogenetic tree reconstruction. The mathematical modeling tools brought to bear on these topics include Boolean and ordinary differential equations, projection matrices, agent-based modeling and several algebraic approaches. Heavy computation in some of the examples is eased by the use of freely available open-source software. Features self-contained chapters with real biological research examples using freely available computational tools Spans several mathematical techniques at basic to advanced levels Offers broad perspective on the uses of algebraic geometry/polynomial algebra in molecular systems biology Content: Front Matter , Pages i-iii Copyright , Page iv Contributors , Pages xi-xii Preface , Pages xiii-xxi Chapter 1 - Mechanisms of Gene Regulation: Boolean Network Models of the Lactose Operon in Escherichia coli , Pages 1-35 , Raina Robeva, Bessie Kirkwood, Robin Davies Chapter 2 - Bistability in the Lactose Operon of Escherichia coli : A Comparison of Differential Equation and Boolean Network Models , Pages 37-74 , Raina Robeva, Necmettin Yildirim Chapter 3 - Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering , Pages 75-103 , Brandilyn Stigler, Elena Dimitrova Chapter 4 - Global Dynamics Emerging from Local Interactions: Agent-Based Modeling for the Life Sciences , Pages 105-141 , David Gammack, Elsa Schaefer, Holly Gaff Chapter 5 - Agent-Based Models and Optimal Control in Biology: A Discrete Approach , Pages 143-178 , Reinhard Laubenbacher, Franziska Hinkelmann, Matt Oremland Chapter 6 - Neuronal Networks: A Discrete Model , Pages 179-211 , Winfried Just, Sungwoo Ahn, David Terman Chapter 7 - Predicting Population Growth: Modeling with Projection Matrices , Pages 213-238 , Janet Steven, James Kirkwood Chapter 8 - Metabolic Pathways Analysis: A Linear Algebraic Approach , Pages 239-266 , Terrell L. Hodge Chapter 9 - Identifying CpG Islands: Sliding Window and Hidden Markov Model Approaches , Pages 267-305 , Raina Robeva, Aaron Garrett, James Kirkwood, Robin Davies Chapter 10 - Phylogenetic Tree Reconstruction: Geometric Approaches , Pages 307-342 , David Haws, Terrell L. Hodge, Ruriko Yoshida Index , Pages 343-349

Mathematical Concepts and Methods in Modern Biology offers a quantitative framework for analyzing, predicting, and modulating the behavior of complex biological systems. The book presents important mathematical concepts, methods and tools in the context of essential questions raised in modern biology.

Designed around the principles of project-based learning and problem-solving, the book considers biological topics such as neuronal networks, plant population growth, metabolic pathways, and phylogenetic tree reconstruction. The mathematical modeling tools brought to bear on these topics include Boolean and ordinary differential equations, projection matrices, agent-based modeling and several algebraic approaches. Heavy computation in some of the examples is eased by the use of freely available open-source software.

• Features self-contained chapters with real biological research examples using freely available computational tools
• Spans several mathematical techniques at basic to advanced levels
• Offers broad perspective on the uses of algebraic geometry/polynomial algebra in molecular systems biology

Mathematical Concepts and Methods in Modern Biology offers a quantitative framework for analyzing, predicting, and modulating the behavior of complex biological systems. The book presents important mathematical concepts, methods and tools in the context of essential questions raised in modern biology. Designed around the principles of project-based learning and problem-solving, the book considers biological topics such as neuronal networks, plant population growth, metabolic pathways, and phylogenetic tree reconstruction. The mathematical modeling tools brought to bear on these topics include Boolean and ordinary differential equations, projection matrices, agent-based modeling and several algebraic approaches. Heavy computation in some of the examples is eased by the use of freely available open-source software. Features self-contained chapters with real biological research examples using freely available computational toolsSpans several mathematical techniques at basic to advanced levels Offers broad perspective on the uses of algebraic geometry/polynomial algebra in molecular systems biology Arising from current scientific publications and ongoing investigations by leading researchers, this book is an essential resource for anyone needing to better understand the interdisciplinary relationship between mathematics and biology. The book is organized by research topic of interest and introduces mathematical models and methods specifically to that topic -- Source other than Library of Congress