Limit search to available items
Book Cover
E-book

Title Discrete and topological models in molecular biology / Nataša Jonoska, Masahico Saito, editors
Published Heidelberg : Springer, 2014
Table of Contents
pt. I Discrete and Graph-Theoretic Models for Data Analysis 
 Perspectives in Computational Genome Analysis / Giuditta Franco3
 The Sequence Reconstruction Problem / Zoran Nikoloski23
 Extracting Coevolving Characters from a Tree of Species / Alessandra Carbone45
 When and How the Perfect Phylogeny Model Explains Evolution / Teresa M. Przytycka67
 An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques / Mark Daley85
 Simplicial Models and Topological Inference in Biological Systems / Radmila Sazdanovic109
pt. II Molecular Arrangements and Structures 
 Combinatorial Insights into RNA Secondary Structure / Svetlana Poznanovic145
 Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis / Ileana Streinu167
 Modeling Autonomous Supramolecular Assembly / Meera Sitharam197
 The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach / Reidun Twarock217
 Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs / Akie Hashimoto241
pt. III Gene Rearrangements 
 Programmed Genome Processing in Ciliates / Laura F. Landweber273
 The Algebra of Gene Assembly in Ciliates / Hendrik Jan Hoogeboom289
 Invariants of Graphs Modeling Nucleotide Rearrangements / Karin Valencia309
pt. IV Topological Models and Spatial DNA Embeddings 
 Introduction to DNA Topology / Robert G. Scharein327
 Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations / Dorothy Buck347
 Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links / Kenneth L. Baker363
 Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination / Mariel Vazquez387
pt. V Dynamics and Kinetics of Molecular Interactions 
 Understanding DNA Looping Through Cre-Recombination Kinetics / Stephen D. Levene405
 The QSSA in Chemical Kinetics: As Taught and as Practiced / Gheorghe Craciun419
 Algebraic Models and Their Use in Systems Biology / Alan Veliz-Cuba443
 Deconstructing Complex Nonlinear Models in System Design Space / Jason G. Lomnitz475
 IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology / Katarzyna A. Rejniak507
Online access available from:
Springer eBooks    View Resource Record  

Copies

Description 1 online resource (480 pages)
Series Natural Computing Series
Natural computing series.
Contents Part I. Discrete and Graph-Theoretic Models for Data Analysis -- Perspectives in Computational Genome Analysis / Giuditta Franco -- The Sequence Reconstruction Problem / Angela Angeleska, Sabrina Kleessen and Zoran Nikoloski -- Extracting Coevolving Characters from a Tree of Species / Alessandra Carbone -- When and How the Perfect Phylogeny Model Explains Evolution / Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi and Teresa M. Przytycka -- An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques / Mark Daley -- Simplicial Models and Topological Inference in Biological Systems / Vidit Nanda and Radmila Sazdanović -- Part II. Molecular Arrangements and Structures -- Combinatorial Insights into RNA Secondary Structure / Christine Heitsch and Svetlana Poznanović -- Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis / Naomi Fox and Ileana Streinu -- Modeling Autonomous Supramolecular Assembly / Meera Sitharam -- The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach / Paolo Cermelli, Giuliana Indelicato and Reidun Twarock -- Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs / Joanna Ellis-Monaghan, Greta Pangborn, Laura Beaudin, David Miller, Nick Bruno and Akie Hashimoto -- Part III. Gene Rearrangements -- Programmed Genome Processing in Ciliates / Aaron David Goldman, Elizabeth M. Stein, John R. Bracht and Laura F. Landweber -- The Algebra of Gene Assembly in Ciliates / Robert Brijder and Hendrik Jan Hoogeboom -- Invariants of Graphs Modeling Nucleotide Rearrangements / Egor Dolzhenko and Karin Valencia -- Part IV. Topological Models and Spatial DNA Embeddings -- Introduction to DNA Topology / Isabel K. Darcy, Stephen D. Levene and Robert G. Scharein -- Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations / Dorothy Buck -- Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links / Kenneth L. Baker -- Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination / Kai Ishihara, Koya Shimokawa and Mariel Vazquez -- Part V. Dynamics and Kinetics of Molecular Interactions -- Understanding DNA Looping Through Cre-Recombination Kinetics / Massa J. Shoura and Stephen D. Levene -- The QSSA in Chemical Kinetics: As Taught and as Practiced / Casian Pantea, Ankur Gupta, James B. Rawlings and Gheorghe Craciun -- Algebraic Models and Their Use in Systems Biology / Reinhard Laubenbacher, Franziska Hinkelmann, David Murrugarra and Alan Veliz-Cuba -- Deconstructing Complex Nonlinear Models in System Design Space / Michael A. Savageau and Jason G. Lomnitz -- IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology / Katarzyna A. Rejniak
Perspectives in Computational Genome Analysis -- The Sequence Reconstruction Problem -- Extracting Coevolving Characters from a Tree of Species -- When and How the Perfect Phylogeny Model Explains Evolution -- An Invitation to the Study of Brain Networks with Some Statistical Analysis of Thresholding Techniques -- Simplicial Models and Topological Inference in Biological Systems -- Combinatorial Insights into RNA Secondary Structure -- Redundant and Critical Noncovalent Interactions in Protein Rigid Cluster Analysis -- Modeling Autonomous Supramolecular Assembly -- The Role of Symmetry in Conformational Changes of Viral Capsids: A Mathematical Approach -- Minimal Tile and Bond-Edge Types for Self-Assembling DNA Graphs -- Programmed Genome Processing in Ciliates -- The Algebra of Gene Assembly in Ciliates -- Invariants of Graphs Modeling Nucleotide Rearrangements -- Introduction to DNA Topology -- Reactions Mediated by Topoisomerases and Other Enzymes: Modelling Localised DNA Transformations -- Site-Specific Recombination on Unknot and Unlink Substrates Producing Two-Bridge Links -- Site-Specific Recombination Modeled as a Band Surgery: Applications to Xer Recombination -- Understanding DNA Looping Through Cre-Recombination Kinetics -- The QSSA in Chemical Kinetics: As taught and as Practiced -- Algebraic Models and Their Use in Systems Biology -- Deconstructing Complex Nonlinear Models in System Design Space -- IBCell Morphocharts: A Computational Model for Linking Cell Molecular Activity with Emerging Tissue Morphology
Summary Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics in domains such as algebra, combinatorics, and graph and knot theories can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology
Bibliography Includes bibliographical references at the end of each chapters
Notes Print version record
Subject Computational biology.
Biomathematics.
Computer science -- Mathematics.
Computational Biology.
Models, Theoretical.
Form Electronic book
Author Jonoska, Nataša, 1961- editor
Saito, Masahico, 1959- editor
ISBN 9783642401930 (electronic bk.)
3642401937 (electronic bk.)
3642401929
9783642401923