The best books on modelling biological systems and networks

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.

Shepherd is reader supported. When you buy books, we may earn an affiliate commission.

The books I picked & why

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

Karthik Raman Why did I love 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.

By Uri Alon,

Why should I read it?

1 author picked An Introduction to Systems Biology as one of their favorite books, and they share why you should read it.

What is this book about?

Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles.

An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.


Book cover of A First Course in Systems Biology

Karthik Raman Why did I love 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.

By Eberhard Voit,

Why should I read it?

1 author picked A First Course in Systems Biology as one of their favorite books, and they share why you should read it.

What is this book about?

A First Course in Systems Biology is a textbook designed for advanced undergraduate and graduate students. Its main focus is the development of computational models and their applications to diverse biological systems.

Because the biological sciences have become so complex that no individual can acquire complete knowledge in any given area of specialization, the education of future systems biologists must instead develop a student's ability to retrieve, reformat, merge, and interpret complex biological information.

This book provides the reader with the background and mastery of methods to execute standard systems biology tasks, understand the modern literature, and launch into specialized…


Book cover of Networks: An Introduction

Karthik Raman Why did I love 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.  

By Mark Newman,

Why should I read it?

1 author picked Networks as one of their favorite books, and they share why you should read it.

What is this book about?

The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availability of inexpensive computers have made it possible to gather and analyze network data on a large scale, and the development of a variety of new theoretical tools has allowed us to extract new knowledge from many different kinds of networks. The study
of networks is broadly interdisciplinary and important developments have occurred in many fields, including mathematics, physics, computer and information sciences, biology, and the social…


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

Karthik Raman Why did I love 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.

By Bernhard Ø. Palsson,

Why should I read it?

1 author picked Systems Biology as one of their favorite books, and they share why you should read it.

What is this book about?

Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of…


Book cover of Systems Biology: A Textbook

Karthik Raman Why did I love 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.

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

Why should I read it?

1 author picked Systems Biology as one of their favorite books, and they share why you should read it.

What is this book about?

This advanced textbook is tailored to the needs of introductory course in Systems Biology. It has a compagnion website (WWW.WILEY-VCH.DE/HOME/SYSTEMSBIOLOGY) with solutions to questions in the book and several additional extensive working models. The book is related to the very successful previous title 'Systems Biology in Practice' and has incorporated the feedback and suggestions from many lecturers worldwide. The book addresses biologists as well as engineers and computer scientists. The interdisciplinary team of acclaimed authors worked closely together to ensure a comprehensive coverage with no overlaps in a homogenous and compelling style.


You might also like...

Diary of a Citizen Scientist: Chasing Tiger Beetles and Other New Ways of Engaging the World

By Sharman Apt Russell,

Book cover of Diary of a Citizen Scientist: Chasing Tiger Beetles and Other New Ways of Engaging the World

Sharman Apt Russell Author Of Diary of a Citizen Scientist: Chasing Tiger Beetles and Other New Ways of Engaging the World

New book alert!

Who am I?

Author Explorer Runner Mother

Sharman's 3 favorite reads in 2023

What is my book about?

Citizen Scientist begins with this extraordinary statement by the Keeper of Entomology at the London Museum of Natural History, “Study any obscure insect for a week and you will then know more than anyone else on the planet.”

As the author chases the obscure Western red-bellied tiger beetle across New Mexico, where she lives, she explores a dozen other citizen science programs with lyrical prose, humor, and a profound sense of connection to place. Diary of a Citizen Scientist celebrates a renewed optimism in the mysteries of the world and a renewed faith in how ordinary people can contribute to science and environmental activism.

Diary of a Citizen Scientist: Chasing Tiger Beetles and Other New Ways of Engaging the World

By Sharman Apt Russell,

What is this book about?

A critically acclaimed nature writer explores the citizen scientist movement through the lens of entomological field research in the American Southwest.

Award-winning nature writer Sharman Apt Russell felt pressed by the current environmental crisis to pick up her pen yet again. Encouraged by the phenomenon of citizen science, she decided to turn her attention to the Western red-bellied tiger beetle, an insect found widely around the world and near her home in the Gila River Valley of New Mexico.

In a lyrical, often humorous voice, Russell shares her journey across a wild, rural landscape tracking this little-known species, an insect…


Interested in biology, mathematical models, and economic history?

10,000+ authors have recommended their favorite books and what they love about them. Browse their picks for the best books about biology, mathematical models, and economic history.

Biology Explore 173 books about biology
Mathematical Models Explore 22 books about mathematical models
Economic History Explore 47 books about economic history