1st Edition

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

By Peter G. Clote Copyright 2025
    394 Pages 52 Color & 45 B/W Illustrations
    by Chapman & Hall

    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.

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


    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.

    "Prof. Peter Clote is a respected scholar with an unusually rich number of scientific interests: he started his career in mathematical logic, then moved into theoretical computer science and complexity theory. In the 1990’s he moved into the new research field of bioinformatics and developed a group at the University of Munich and then at Boston College. Since that time, he has produced with his students and some colleagues an impressive amount of work mainly relevant to RNA modeling.

    This book is the result of more than 25 years of research and teaching in Boston, Munich and Paris. What characterizes P. Clote’s work is the extreme care with which he explains the background, then the theoretical concepts coming from biology, chemistry, physics and mathematics that are necessary to model complex RNA molecules, their structure and their behaviour. Finally he describes the algorithms and computer programs that can solve what was considered to be a difficult challenge only a decade ago.

    The book is written in a very clear manner that makes it accessible to students as a textbook in a first reading, with additional optional material, borrowed from recent research, which will be useful to RNA design engineers and researchers. P. Clote is known as an excellent lecturer and the book inherits of his qualities and competence in the domain.

    Through the numerous exercises at the end of chapters, this book favors an active reading and opening to current research; the important bibliography will be useful as well. By all standards, this book should become a major reference for an active and comprehensive understanding of RNA, its structure, kinetics and rational design."

    --Prof. Jean-Marc Steyaert, Emeritus Professor of the Computer Science Department at Ecole Polytechnique, France

    "In "RNA: Computational Methods for Structure, Kinetics, and Rational Design," Professor Peter Clote offers a comprehensive and insightful exploration into the intricate world of RNA, combining the realms of biology, mathematics, and computational science with finesse. This book is the beautiful outcome of Clote's profound expertise in the field, presenting a treasure trove of knowledge that will undoubtedly captivate both novices and seasoned researchers alike.

    What sets this book apart is its seamless integration of theoretical principles with practical applications, making complex concepts accessible to readers from diverse backgrounds. Clote's lucid explanations, coupled with illustrative examples and meticulously curated exercises, empower readers to navigate the intricate landscape of RNA research with confidence. Throughout the book, Clote's passion for his subject matter shines through, infusing each page with enthusiasm and intellectual curiosity. Whether you are a student delving into the fundamentals of RNA or a seasoned researcher seeking to push the boundaries of knowledge, this book is an indispensable companion on your scientific journey.

    In summary, Professor Peter Clote's "RNA: Computational Methods for Structure, Kinetics, and Rational Design" is a tour de force that deserves a place on the bookshelf of every scientist, educator, and enthusiast interested in the fascinating world of RNA. With its unparalleled depth, clarity, and visionary insights, this book not only informs but also inspires, leaving an indelible mark on the landscape of computational biology."

    -- Dr. Henri Orland, Institute of Theoretical Physics, Paris-Saclay University, CNRS, CEA, France