RNA: Computational Methods for Structure, Kinetics, and Rational Design: Volume One

Comprising two volumes, RNA: Computational Methods for Structure, Kinetics, and Rational Design is a comprehensive treatment of computational methods concerning the secondary structure, folding kinetics and rational design of RNA. Volume One concerns energy and structure and is divided into five chapters. Chapter 1 describes the molecular structure of ribonucleotides, basic classes of RNA and databases of RNA sequences and structure. Chapter 2 presents the basic concepts of thermodynamics, since thermodynamics-based algorithms constitute an essential tool in rational design of functional RNA molecules. Chapter 3 describes how empirical secondary structure energy parameters are obtained from ultraviolet absorbance experiments via Van 't Hoff plots and least-squares data fitting. Chapter 4 describes methods from combinatorics, automata and formal language theory, and complex analysis. Chapter 5 provides an overview of some of the most important thermodynamics-based algorithms related to secondary structure. Exercises and solutions are provided at the end of every chapter and source code is available at the book's website (sometimes including computer programs using Python and extensions Numpy and Scipy). This book provides the nuts, bolts and tools to take the next steps in computational RNA synthetic biology. It is perfect for advanced undergraduate, graduate and post-graduate readers having analytical interests and skills from areas such as physical chemistry, physics, mathematics, computer science, and statistics. Instructor slides, computer programs and solutions to all exercises from Volumes 1 and 2 can be found at the following website: https://github.com/pgclote/RNA-Computational-methods-for-structure-kinetics-and-rational-design-Solutions-slides-etc.-.

Peter Clote is Professor of Biology at Boston College, USA, with courtesy appointment in Computer Science. He is an international expert in computational biology, with focus on RNA. Earning B.Sc. and PhD degrees in mathematics from MIT and Duke University, as well as a Doctorat d'Etat from Université Paris 7, Clote has held faculty positions in mathematics, computer science, and biology departments at universities in France (Paris 7), the United States (BC), and Germany (LMU). As Gentzen Chair of Computer Science at the University of Munich (LMU), he played a leading role in the establishment of the bioinformatics graduate program there. He has held visiting positions at MIT, the Max Planck Institute in Berlin, CWI in Amsterdam, Ecole Polytechnique and Université Paris-Sud (as Digiteo Chair of Excellence in Computer Science), and other universities. Clote started and co-organized the MIT Bioinformatics Seminar over a period of ten years, he has served as Associate Editor of the Journal of Mathematical Biology, on the editorial board of four other journals, and has co-written two books, co-edited four books, and published around 100 research articles in computational biology, mathematics, and theoretical computer science. His research was and continues to be supported by NSF divisions of mathematical sciences, biology, and computer science, as well as by Digiteo (France) and DFG (Germany). He has received a Fulbright and a Guggenheim fellowship, as well as receiving an Alexander von Humboldt Foundation research grant.

Chapter 1 RNA biology. Chapter 2 Thermodynamics. Chapter 3 RNA energy parameters. Chapter 4 Combinatorics. Chapter 5 Algorithms