Textbooks for systems biologists
In assembling a list of textbooks that might be of use to systems biologists, we have attempted to accommodate a wide diversity of prior experience and different long-term goals. A mathematics text that would be elementary to an engineer might be advanced for a non-quantitative biologist. Conversely, few engineers have a solid foundation in genetics.
Consistent with our overall goal of producing an edited, rather than a comprehensive, compilation, we list books according to topic and, if appropriate, include one or more elementary (
), practitioner's (
) and advanced (
) text.
- Systems biology — general textbooks
- General biology, biochemistry and biophysics
- Laboratory practice
- Applied mathematics
Systems biology — general textbooks
- Edelstein-Keshet, L.
Mathematical Models in Biology
Cambridge University Press, 2005
This book features easily accessible and engaging biological examples and is a good choice for those new to modelling. The text covers difference equations, ordinary differential equations, partial differential equations, kinetic laws and basic dynamical systems.
- Alon, U.
An Introduction to Systems Biology
Chapman & Hall/CRC, 2006
Alon's new book is well suited to newcomers in systems biology, framing contemporary understanding of the mathematical and biological underpinnings of cell-signalling circuitry.
- Szallasi, Z., Stelling, J. & Periwal, V.
System Modeling in Cellular Biology
MIT Press, 2006
This book is an excellent collection of review articles that address issues faced by practicing systems biologists. Topics include modelling techniques, data collection, control theory, computational constraints and simulation, as well as software tools.
- Fall, C., Marland, E., Wagner, J. & Tyson, J.
Computational Cell Biology
Springer-Verlag, 2001
Although not as current, this text is an informative alternative to Szallasi et al. It also contains helpful appendices including a section that describes how to use XPPAUTO for model analysis.
- Segel, L. A.
Modeling Dynamic Phenomena in Molecular and Cellular Biology
Cambridge University Press, 1984
Segel's textbook uses in-depth, historical examples to illustrate key concepts in the formulation and analysis of biological systems. Most of the analysis techniques described are better suited for small or reduced models rather than complicated physicochemical models.
- Wilkinson, D. J.
Stochastic Modeling for Systems Biology
Chapman & Hall/CRC, 2006
This book covers a wide range of topics, from stochastic modelling and simulation to parameter estimation. The material in this book is self-contained, but it assumes basic knowledge in algebra and calculus.
General biology, biochemistry and biophysics
- Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P.
Molecular Biology of the Cell
Garland Science, 2002
Although a little out of date, this remains the textbook by which others are judged. The treatment of basic cell biology is very strong, but equations that are common to biochemistry and enzyme mechanisms are dealt with only superficially.
- Griffiths, A. J. F., Wessler, S. R., Lewontin, R. C., Gelbart, W. H., Suzuki, D. T. & Miller, J. H.
Introduction to Genetic Analysis
W. H. Freeman, 2004
This text provides a rigorous treatment of basic concepts in genetics. It is a good introductory textbook for modellers, presenting materials such as the structure of genes and genomes, principles of genetic inheritance, regulation of gene transcription and mutagenesis (both spontaneous and targeted). For systems biologists, its primary weakness is a lack of quantitative rigor.
- Voet, D. & Voet, J. G.
Biochemistry
Wiley, 2005
This well illustrated book presents classical biochemistry topics, such as enzyme mechanics and enzyme kinetics, metabolism and catabolism, in an accessible format. It is a useful textbook for systems biologists who lack formal training in biochemistry but who build mechanistic or metabolic models.
- Nelson, D. L. & Cox, M. M.
Lehninger: Principles of Biochemistry
W. H. Freeman, 2005
This book is an alternative to Voet & Voet as an introduction to biochemistry. It generally treats each subject with less detail, but includes more of the introductory basic principles.
- Nelson, P.
Biological Physics: Energy, Information, Life
W. H. Freeman, 2003
This text is an introduction to the application of physics to biological problems. It is written to serve both physicists and biologists, and assumes knowledge of basic calculus.
- Berg, H. C.
Random Walks in Biology
Princeton University Press, 1993
This book provides a short, lively and clear introduction to some diffusion-related problems that are relevant to biology, and their mathematical treatment. Topics include random motion of macromolecules and organelles, chromatography, sedimentation and bacterial motility.
Laboratory practice
- Barker, K.
At the Bench: A Laboratory Navigator, Updated Edition
Cold Spring Harbor Laboratory Press, 2005
This highly accessible introduction to practical laboratory procedures is ideal for students (or faculty) who are new to experimental biology. It includes all of the information on instruments, making solutions, performing procedures and so on that are left out of standard protocols.
- Ausubel, F., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith J. A. & Struhl, K.
Current Protocols in Molecular Biology
Wiley Quarterly Serials
- Coligan, J. E., Dunn, B. M., Ploegh, H. L., Speicher, D. W. & Wingfield, P. T.
Current Protocols in Protein Science
Wiley Quarterly Serials
These multi-volume books (also available on CD) are part of a series of comprehensive multi-author guides to laboratory procedure. Current Protocols are updated quarterly, giving them a contemporary feel that is absent from traditional volumes such as Molecular Cloning: A Laboratory Manual (Sambrook, J., Fritsh, E. F. & Maniatis, T., Cold Spring Harbor Laboratory Press, 1989). The commentary sections in each chapter are particularly helpful in their discussion of the conceptual basis, and potential pitfalls, of common procedures.
- Harlow, E. & Lane, D.
Using Antibodies
Cold Spring Harbor Laboratory Press, 1999
Although a little out of date, this text is a very practical guide to the generation and use of antibodies. It presents sufficient background information so that the reader can appreciate the pros and cons of different assays and select the most appropriate protocols.
- Goldman, R. D. & Spector, D. L.
Live Cell Imaging: A Laboratory Manual
Cold Spring Harbor Laboratory Press, 2005
This textbook will be very useful for scientists that use imaging to generate data for systems analysis. It presents a thorough discussion of methodologies and applications, including both their advantages and limitations.
- Sluder, G. & Wolf, D. E.
Digital Microscopy - Volume 72, Second Edition: A Second Edition of "Video Microscopy" (Methods in Cell Biology)
Academic Press, 2003
An alternative to Goldman and Spector, this book also covers a number of modes of microscopy, and treats the quantitative limits of data from digital light microscopes.
- Hecht, E.
Optics
Addison Wesley, 2001
This is a standard, comprehensive and accessible optics textbook that covers a broad range of topics including diffraction and Fourier optics. Hecht provides mathematical and physical fundamentals for imaging and microscopy techniques.
- Tufte, E. R.
The Visual Display of Quantitative information
Graphics Press, 2001
This book is the first of a series of three by Tufte (also including Envisioning Information and Visual Explanation) that explain best practices for the graphical representation of multivariate data. Through the use of many examples and counter-examples, Tufte beautifully illustrates the communicative power of information design.
Applied mathematics
General textbooks
- Greenberg, M.
Differential Equations and Linear Algebra
Prentice Hall, 2000
This elementary text on linear algebra and differential equations uses many application-oriented examples. It is a good starting point for those that are unfamiliar with mathematical jargon and approaches.
- Strang, G.
Introduction to Applied Mathematics
Wellesley, 1986
A standard in applied math, this book covers a broad range of topics such as linear algebra, differential equations, numerical methods, Fourier analysis and optimization. Strang is fast-paced and packed with information, and might be hard going for biologists who are new to applied mathematics.
- Kreyszig, E.
Advanced Engineering Mathematics
Wiley, 2005
This standard mathematics text for engineers focuses on practical, applied and engineering mathematics. An excellent reference for transforms (Laplace and Fourier), partial differential equations and complex analysis, it is well suited for readers who are comfortable with calculus and differential equations.
Dynamic systems
- Kaplan, D. & Glass, L.
Understanding Nonlinear Dynamics
Sprinfer-Verlag, 1995
Kaplan and Glass provide a clear and concise introduction to concepts of nonlinear dynamics in a book written for life scientists with basic mathematical training. The book introduces finite-difference and differential equations and concepts of stability, multistability, cellular automata, fractals and chaos.
- Strogatz, S.
Nonlinear, Dynamics and Chaos
Perseus Books, 1994
This book is an easy-to-read introduction to many basic concepts in dynamic systems, including steady-state and stability analysis, bifurcations and chaos. Systems biologists will probably find this book more conceptually, rather than practically, useful, as the examples focus on very small (two- or three-dimensional) dynamic systems.
- Guckenheimer, J. & Holmes, P.
Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields (Applied Mathematical Sciences Vol. 42)
Springer, 1983
This dense book is appropriate for readers who are already comfortable with basic dynamic systems and mathematics. It is a more complete reference for local bifurcation and chaos theory than the Strogatz text.
Statistics and probability
- Sheshkin, D. J.
Handbook of Parametric and Nonparametric Statistical Procedures
Chapman &Hall/CRC, 2004
Sheshkin is a solid reference for statistical analysis and provides practical advice on selecting a statistical test appropriate to a particular type of data and hypothesis. More than 130 statistical procedures are presented in a well organized compendium.
- Chen, M., Shao, Q. & Ibrahim, J. G.
Monte Carlo Methods in Bayesian Computation
Springer-Verlag, 2000
This book discusses Monte Carlo methods for computing posterior quantities using samples from the posterior distribution. It presents both theory and real applications. It assumes that the reader is familiar with statistical inference and Bayesian theory.
Regression and multivariate analysis
- Martens, H. & Martens, M.
Multivariate Analysis of Quality, An Introduction
Wiley, 2000
This text presents tools for analysis and model-building from multivariate data sets. Although intended for industrial food scientists and deriving its examples from industry, it is accessible to life scientists without formal training in linear algebra or statistics.
- Kleinbaum, D. G., Kupper, L. L., Muller, K. E. & Nizam, A.
Applied Regression Analysis and Multivariable Methods
Duxbury Press, 1997
This textbook presents many linear regression methods and related diagnostics. It requires minimal mathematical knowledge and is therefore easily accessible to life scientists without formal mathematical training.
- Seber, G. A. & Wild, C. J.
Nonlinear Regression
Wiley-Interscience, 2004
This book provides a broad and comprehensive discussion of nonlinear regression techniques. It is more mathematical than Kleinbaum et al., but the techniques it covers are essential for systems biologists as most problems are nonlinear.
Algorithms
- Cormen, T., Leiserson, C., Rivest, R. & Stein, C.
Introduction to Algorithms
MIT Press, 2001
Easy to read yet rich in concepts, Introduction to Algorithms is the standard algorithms text for computer-science students. It offers essential concepts in programming for systems biologists who need to write their own programs, including: functions, recursion, trees, sorting, data structures and graphs.
- Press, W. H., Flannery, B. P., Teukolsky, S. A. & Vetterling, W. T.
Numerical Recipes in C: the Art of Scientific Computing
Cambridge University Press, 1992
Numerical recipes in C and its sister books for other languages (C++, Pascal and Fortran) are packed with practical algorithms for scientific and mathematical computing. This is a classic reference for programmers, known for providing well designed and efficient algorithms.
About the list
This list has been compiled by Bree Aldridge, Suzanne Gaudet and Khuloud Jaqaman with additional input from other contributors to the Systems Biology: A User's Guide Focus.
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