Here are 68 books that A First Course in Systems Biology fans have personally recommended if you like
A First Course in Systems Biology.
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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!
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.
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.
It is April 1st, 2038. Day 60 of China's blockade of the rebel island of Taiwan.
The US government has agreed to provide Taiwan with a weapons system so advanced that it can disrupt the balance of power in the region. But what pilot would be crazy enough to run…
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!
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.
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…
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!
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.
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…
A Duke with rigid opinions, a Lady whose beliefs conflict with his, a long disputed parcel of land, a conniving neighbour, a desperate collaboration, a failure of trust, a love found despite it all.
Alexander Cavendish, Duke of Ravensworth, returned from war to find that his father and brother had…
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!
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.
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.
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.
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.
... 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…
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.
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.
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…
The Duke's Christmas Redemption
by
Arietta Richmond,
A Duke who has rejected love, a Lady who dreams of a love match, an arranged marriage, a house full of secrets, a most unneighborly neighbor, a plot to destroy reputations, an unexpected love that redeems it all.
Lady Charlotte Wyndham, given in an arranged marriage to a man she…
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.
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.
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…
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.
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.
I have long been fascinated by how very complicated things can arise from comparatively simple ones, because it seems counterintuitive that this is even possible. This led me to lead a life in science, researching how a whole human body can come from a simple egg, and trying to apply what we learn to make new body parts for those who need them. Though much of my professional reading consists of detailed research papers, I have always relied on books to make me think and to show me the big picture. I write books myself, to share with others some of the amazing things that science lets us discover.
This is the best scientific novel I have ever read. The story is fiction (not 'science fiction' in the sense of fantasy, but a story that could easily take place in the real world right now), but its portrayal of how science is done, by a bunch of completely believable characters, is really true-to-life. It's a great way for young people considering a research career to taste what they are really like, and a great way for everyone to ask why we do science the way we do, while enjoying a well-paced multi-layer story, that is written with real wit. [Declaration for transparency: I know the author as a scientific collaborator, but this is nothing to do with my recommendation of her fiction].
Sexism, Secrets and Science: Cat Zero by Jennifer Rohn
Scientist Artie Marshall is perpetually underfunded, relegated to a damp basement, and besieged on all sides by sexist colleagues. Added to that, she is immersed in a messy divorce. But she’s never been happier, studying an obscure cat virus that nobody else in the world seems to have heard of – or cares about.
Everything changes when local cats start dropping dead and Artie’s arcane little research problem becomes worryingly relevant. Matters get worse when people start getting infected too.
Working with her right-hand man Mark, her vet friends and her…
This book follows the journey of a writer in search of wisdom as he narrates encounters with 12 distinguished American men over 80, including Paul Volcker, the former head of the Federal Reserve, and Denton Cooley, the world’s most famous heart surgeon.
In these and other intimate conversations, the book…
I am a psychiatrist, researcher, and bioethicist who has conducted studies on infectious diseases, genetics, the mind and the brain at the National Institutes of Health, in the rain forest of Papua New Guinea, at Columbia University, and elsewhere, seeking and discovering knowledge and scientific truths about nature, people, and the world. I have published 10 books, over 200 scientific articles, and essays in The New York Times, The Washington Post, The Wall Street Journal, and elsewhere, conveying the excitement and extraordinary power of scientific discoveries, but also the moral, cultural, and psychological dilemmas that can arise, and the ways we can best address these.
Thomas captured the beauty and mystery of nature and science—how billions of cells in our body work intricately together to form tissues and organs that make us breathe, move, see, think, and fight infections, and how the world itself is analogous to one big cell.
I was amazed to understand the extraordinary complexities of Nature—how ants plan, communicate, and build farms, how our noses smell, how our eyes see and communicate to our brains, and how we hear and appreciate music.
Elegant, suggestive, and clarifying, Lewis Thomas's profoundly humane vision explores the world around us and examines the complex interdependence of all things. Extending beyond the usual limitations of biological science and into a vast and wondrous world of hidden relationships, this provocative book explores in personal, poetic essays to topics such as computers, germs, language, music, death, insects, and medicine. Lewis Thomas writes, "Once you have become permanently startled, as I am, by the realization that we are a social species, you tend to keep an eye out for the pieces of evidence that this is, by and large, good…
