63 books like A First Course in Systems Biology

By Eberhard Voit,

Here are 63 books that A First Course in Systems Biology fans have personally recommended if you like A First Course in Systems Biology. Shepherd is a community of 11,000+ authors and super readers sharing their favorite books with the world.

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

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

From my list on modelling biological systems and networks.

Why am I passionate about this?

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!

Karthik's book list on modelling biological systems and networks

Karthik Raman Why did Karthik 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 Networks: An Introduction

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

From my list on modelling biological systems and networks.

Why am I passionate about this?

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!

Karthik's book list on modelling biological systems and networks

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

From my list on modelling biological systems and networks.

Why am I passionate about this?

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!

Karthik's book list on modelling biological systems and networks

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

From my list on modelling biological systems and networks.

Why am I passionate about this?

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!

Karthik's book list on modelling biological systems and networks

Karthik Raman Why did Karthik 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.


Book cover of An Introduction to Systems Biology: Design Principles of Biological Circuits

Charlie Hodgman Author Of BIOS Instant Notes in Bioinformatics

From my list on the intersection of Bioinformatics and Systems Biology.

Why am I passionate about this?

Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.

Charlie's book list on the intersection of Bioinformatics and Systems Biology

Charlie Hodgman Why did Charlie love this book?

Of the various books available on this subject, I very much prefer this one because it makes it far easier to do systems biology.

First, it shows you how to view biological regulatory processes as a set of interacting components and their effect on each other. This alone can give clues to the behaviour of the system under different circumstances. However, it then goes on to show how these processes can be defined mathematically, which then enables us to get a quantitative view of what is going on.

When the predicted and observed numbers don’t match, we know that there is a gap in our knowledge and, hence, the place to discover new biology. Using this approach, I have.

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?

Praise for the first edition:

... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. - Nature

[This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final…


Book cover of Information Theory, Inference and Learning Algorithms

Simon J.D. Prince Author Of Understanding Deep Learning

From my list on machine learning and deep neural networks.

Why am I passionate about this?

I started my career in neuroscience. I wanted to understand brains. That is still proving difficult, and somewhere along the way, I realized my real motivation was to build things, and I wound up working in AI. I love the elegance of mathematical models of the world. Even the simplest machine learning model has complex implications, and exploring them is a joy.

Simon's book list on machine learning and deep neural networks

Simon J.D. Prince Why did Simon love this book?

The best parts of this book really represent a gold standard in pedagogical clarity.

Although it’s now twenty years old, there is still much to learn from this rather unconventional book that covers the boundary between machine learning, information theory, and Bayesian methods. There are also odd tangents and curiosities, some of which work better than others but are never dull.

Just writing this review makes me want to go back to it and squeeze more out of it.

By David JC MacKay,

Why should I read it?

2 authors picked Information Theory, Inference and Learning Algorithms as one of their favorite books, and they share why you should read it.

What is this book about?

Information theory and inference, taught together in this exciting textbook, lie at the heart of many important areas of modern technology - communication, signal processing, data mining, machine learning, pattern recognition, computational neuroscience, bioinformatics and cryptography. The book introduces theory in tandem with applications. Information theory is taught alongside practical communication systems such as arithmetic coding for data compression and sparse-graph codes for error-correction. Inference techniques, including message-passing algorithms, Monte Carlo methods and variational approximations, are developed alongside applications to clustering, convolutional codes, independent component analysis, and neural networks. Uniquely, the book covers state-of-the-art error-correcting codes, including low-density-parity-check codes, turbo…


Book cover of The Music of Life: Biology Beyond Genes

Charlie Hodgman Author Of BIOS Instant Notes in Bioinformatics

From my list on the intersection of Bioinformatics and Systems Biology.

Why am I passionate about this?

Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.

Charlie's book list on the intersection of Bioinformatics and Systems Biology

Charlie Hodgman Why did Charlie love this book?

This book vindicates my long-held view that biological objects do not act in isolation but interact with other things to make a living whole. It confirms my opinion that genes are not the master controllers of living things.

Furthermore, it showed me that systems occur at different physical scales (molecules, cells, organs, organisms, populations), that the systems at these scales influence each other, and that no scale is dominant. To understand biological/medical phenomena, including human consciousness, one must look at the (multi-scale) systems, not their individual components, in isolation. 

Finally, I found it a lot of fun to read because it uses hypothetical stories to illustrate points. For example, silicon-based aliens visit Earth but fail to understand why certain things and people behave the way that they do.

By Denis Noble,

Why should I read it?

2 authors picked The Music of Life as one of their favorite books, and they share why you should read it.

What is this book about?

What is Life? Decades of research have resulted in the full mapping of the human genome - three billion pairs of code whose functions are only now being understood. The gene's eye view of life, advocated by evolutionary biology, sees living bodies as mere vehicles for the replication of the genetic codes.

But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question - one that becomes deeply significant in terms of the living, breathing organism. The genome is…


Book cover of Understanding the Control of Metabolism

Charlie Hodgman Author Of BIOS Instant Notes in Bioinformatics

From my list on the intersection of Bioinformatics and Systems Biology.

Why am I passionate about this?

Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.

Charlie's book list on the intersection of Bioinformatics and Systems Biology

Charlie Hodgman Why did Charlie love this book?

This book turns on its head what I was taught about what controls metabolite flow through a pathway. It covers highly remarkable discoveries concerning which steps control changes in metabolite levels: those at the end rather than the start of pathways. This is amazing because it explains why decades of effort by bioengineers to overproduce particular metabolites was unsuccessful.

In response to a request from such a project, I explained how to block the inhibitory regulation by the early pathway step but added that, according to metabolic control theory, this would leave the end-product levels unchanged. I was correct on both counts! When my group later provided results from using a systems biology approach, they achieved their production target levels.

By David Fell,

Why should I read it?

1 author picked Understanding the Control of Metabolism as one of their favorite books, and they share why you should read it.

What is this book about?

Book by Fell, David


Book cover of Sex and Death: An Introduction to Philosophy of Biology

Samir Okasha Author Of Philosophy of Biology: A Very Short Introduction

From my list on the philosophy of evolution.

Why am I passionate about this?

I am Professor of Philosophy of Science at the University of Bristol. I am interested in most areas of contemporary philosophy, in particular the interplay between philosophy and the natural and social sciences. Much of my recent work has focused on evolutionary biology, a science that is replete with implications for traditional philosophical debates about human nature, knowledge, and our place in the world.

Samir's book list on the philosophy of evolution

Samir Okasha Why did Samir love this book?

This book is an engaging treatment of philosophical issues in biology, with a strong though not exclusive focus on evolution. Written by two leading practitioners, the book continues to be an excellent entry point into the subject despite being more than 20 years old. For any reader of my own book who wants more detail, Sterelny and Griffiths’ text is ideal. Chock full of real-life examples, the book offers an excellent model of how philosophy can engage with biology. Topics discussed include function and adaptation, reductionism, levels of selection, the “selfish gene” theory, and more. 

By Kim Sterelny, Paul E. Griffiths,

Why should I read it?

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

What is this book about?

Is the history of life a series of accidents or a drama scripted by selfish genes? Is there an "essential" human nature, determined at birth or in a distant evolutionary past? What should we conserve-species, ecosystems, or something else?

Informed answers to questions like these, critical to our understanding of ourselves and the world around us, require both a knowledge of biology and a philosophical framework within which to make sense of its findings. In this accessible introduction to philosophy of biology, Kim Sterelny and Paul E. Griffiths present both the science and the philosophical context necessary for a critical…


Book cover of Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life

Samir Okasha Author Of Philosophy of Biology: A Very Short Introduction

From my list on the philosophy of evolution.

Why am I passionate about this?

I am Professor of Philosophy of Science at the University of Bristol. I am interested in most areas of contemporary philosophy, in particular the interplay between philosophy and the natural and social sciences. Much of my recent work has focused on evolutionary biology, a science that is replete with implications for traditional philosophical debates about human nature, knowledge, and our place in the world.

Samir's book list on the philosophy of evolution

Samir Okasha Why did Samir love this book?

The traditional neo-Darwinian view of evolution understands inheritance in genetic terms, as the transmission of DNA from parents to offspring. Jablonka and Lamb argue convincingly that in addition to genetic inheritance, there exist three other inheritance systems in nature – epigenetic, symbolic, and behavioural – all of which play an important role in evolution. The book is not a work of philosophy in the strict sense, but rather a fascinating and conceptually-rich synthesis of a diverse body of empirical findings which, the authors argue, can only be accommodated by going beyond a purely geno-centric view of evolution.

By Eva Jablonka, Marion J. Lamb, Anna Zeligowski

Why should I read it?

2 authors picked Evolution in Four Dimensions as one of their favorite books, and they share why you should read it.

What is this book about?

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic (or non-DNA cellular transmission of traits), behavioral, and symbolic (transmission through language and other forms of symbolic communication). These systems, they argue, can all provide variations on which…


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