The best books on modelling biological systems and networks

Karthik Raman Author Of An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks
By Karthik Raman

Who am I?

Ever since I studied control theory as an undergrad chemical engineer, mathematical models of complex phenomena have fascinated me. Mathematical models have the uncanny ability to uncover key aspects of biological systems, whose complexity poses a great challenge for understanding. As a researcher in systems biology for over 15 years, I have enjoyed reading several books that explore the exciting interface between computation and biology, trying to capture the burgeoning literature on this rapidly advancing field. I hope you enjoy these books and will join these authors on an exciting journey into the cartography of molecular networks underlying every living cell, using a variety of mathematical models!


I wrote...

An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks

By Karthik Raman,

Book cover of An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks

What is my book about?

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. The book adopts a hands-on approach to modelling, covering a broad spectrum of paradigms, from static networks to dynamic models and constraint-based models. Every chapter includes thoughtful exercises to test and enable understanding of concepts.

The book has a rich companion website featuring lecture videos, codes, supplementary exercises, further reading, and appendices. Much like the field itself, the book is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians, and others.

The books I picked & why

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An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical and Computational Biology)

By Uri Alon,

Book cover of An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical and Computational Biology)

Why this book?

One of the earliest books on this subject, Uri Alon presents an engaging account of biological networks. Focussing on transcriptional networks, and their motifs, the book illustrates the nexus between network structures and functions. The second edition of the book launched a few years ago and has some updated content and new material on interesting functionalities such as fold change detection. Uri Alon is a very accomplished scientist, mentor, and a leader in the field of biological networks/systems biology.


A First Course in Systems Biology

By Eberhard Voit,

Book cover of A First Course in Systems Biology

Why this book?

One of the best broad-based textbooks covering a wide gamut of topics, and in-depth coverage of dynamic models. I like this book for a particularly engaging introduction to the practice of mathematical modelling, excellent catchy illustrations, and nice exercise problems/reading material at the end of each chapter. The book chooses to organise the methods by the type of network (gene systems, protein systems, metabolic systems, and so on). Voit is a very accomplished researcher in the area of dynamic systems modelling and is particularly known for his contributions to Biochemical Systems Theory.


Networks: An Introduction

By Mark Newman,

Book cover of Networks: An Introduction

Why this book?

Perhaps the most authoritative text on Networks, especially for the mathematically inclined. Spanning over 700 pages, this book covers the basics of different types of real-world networks, followed by a detailed run-down of network theory fundamentals, a variety of network models, and finally, their applications. Newman is a highly regarded computer scientist and has contributed several seminal papers to the field of networks.  


Systems Biology: Constraint-Based Reconstruction and Analysis

By Bernhard Ø. Palsson,

Book cover of Systems Biology: Constraint-Based Reconstruction and Analysis

Why this book?

An outstanding and authoritative reference on metabolic networks. Discusses all the mathematical foundations of constraint-based methods, followed by detailed discussions of various constraint-based modelling methods. Despite the age, this remains a thorough and excellent account of constraint-based modelling. A revised second edition of this book presents a more detailed overview of metabolic networks in different organisms and is up-to-date with several advances in the field. Palsson is one of the leaders in the field of systems biology and metabolic networks, and his lab is home to many of the most important constraint-based modelling methods, such as flux balance analysis.


Systems Biology: A Textbook

By Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald

Book cover of Systems Biology: A Textbook

Why this book?

A very useful reference on systems biology, a sort of handbook, that provides a lot of breadth on systems biology topics. A unique aspect of this book is a set of chapters, introducing basic biology, mathematical techniques, experimental techniques, and a somewhat elaborate collection of databases/tools. Also includes material on stochastic modelling of biochemical reaction systems.


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