An Introduction to Systems Biology: Design Principles of Biological Circuits
Abstract
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 aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. … Alon’s book should become a standard part of the training of graduate students. – Physics Today Written for students and researchers, the second edition of this best-selling textbook continues to offer a clear presentation of design principles that govern the structure and behavior of biological systems. It highlights simple, recurring circuit elements that make up the regulation of cells and tissues. Rigorously classroom-tested, this edition includes new chapters on exciting advances made in the last decade. Features: Includes seven new chapters The new edition has 189 exercises, the previous edition had 66 Offers new examples relevant to human physiology and disease The book website including course videos can be found here: https://www.weizmann.ac.il/mcb/UriAlon/introduction-systems-biology-design-principles-biological-circuits.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Because transcription factors typically form dimers, the nonlinearity associated with dimerization implies cooperative, threshold-like responses.
“because TF typically forms dimers, the nonlinearity associated with dimerization automatically implies cooperative, threshold-like responses [272,273]”
From Fundamental constraints to the logic of living systems (2024) · cites this paper as [272]
Cited by
Sorted by citations
Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M. H., Abudu, Y. P., Acevedo-Arozena, A., et al. (2021) · Autophagy · doi:10.1080/15548627.2020.1797280 · Cited by 2,622 · see citing works
Molecular Signals of Epigenetic States
Bonasio, R., Tu, S., & Reinberg, D. (2010) · Science · doi:10.1126/science.1191078 · Cited by 912 · see citing works
Forcing cells to change lineages
Graf, T., & Enver, T. (2009) · Nature · doi:10.1038/nature08533 · Cited by 899 · see citing works
Modular cell biology: retroactivity and insulation
Del Vecchio, D., Ninfa, A. J., & Sontag, E. D. (2008) · Molecular Systems Biology · doi:10.1038/msb4100204 · Cited by 519 · see citing works
The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
Goentoro, L., Shoval, O., Kirschner, M. W., & Alon, U. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.018 · Cited by 424 · see citing works
Self-citationArchitectures of neuronal circuits
Luo, L. (2021) · Science · doi:10.1126/science.abg7285 · Cited by 390 · see citing works
Evidence that Fold-Change, and Not Absolute Level, of β-Catenin Dictates Wnt Signaling
Goentoro, L., & Kirschner, M. W. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.017 · Cited by 300 · see citing works
Optimization in computational systems biology
Banga, J. R. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-47 · Cited by 278 · see citing works
Causal role for inheritance of H3K27me3 in maintaining the OFF state of a <i>Drosophila</i> HOX gene
Coleman, R. T., & Struhl, G. (2017) · Science · doi:10.1126/science.aai8236 · Cited by 221 · see citing works
Pimanda, J. E., Ottersbach, K., Knezevic, K., Kinston, S., Chan, W. Y. I., Wilson, N. K., Landry, J.-R., Wood, A. D., Kolb-Kokocinski, A., Green, A. R., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707045104 · Cited by 228 · see citing works
A new model for the HPA axis explains dysregulation of stress hormones on the timescale of weeks
Karin, O., Raz, M., Tendler, A., Bar, A., Korem Kohanim, Y., Milo, T., & Alon, U. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209510 · Cited by 200 · see citing works
Self-citationProtein Homeostasis and the Phenotypic Manifestation of Genetic Diversity: Principles and Mechanisms
Jarosz, D. F., Taipale, M., & Lindquist, S. (2010) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090412 · Cited by 179 · see citing works
Principles of Cell Circuits for Tissue Repair and Fibrosis
Adler, M., Mayo, A., Zhou, X., Franklin, R. A., Meizlish, M. L., Medzhitov, R., Kallenberger, S. M., & Alon, U. (2020) · iScience · doi:10.1016/j.isci.2020.100841 · Cited by 177 · see citing works
Self-citationAutomatic design of digital synthetic gene circuits
Marchisio, M. A., & Stelling, J. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001083 · Cited by 103 · see citing works
The investigation of bone fracture healing under intramembranous and endochondral ossification
Ghimire, S., Miramini, S., Edwards, G., Rotne, R., Xu, J., Ebeling, P., & Zhang, L. (2021) · Bone Reports · doi:10.1016/j.bonr.2020.100740 · Cited by 83 · see citing works
‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators
Hafner, M., Koeppl, H., Hasler, M., & Wagner, A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000534 · Cited by 63 · see citing works
Kell, D. B. (2007) · IUBMB Life · doi:10.1080/15216540701694252 · Cited by 52 · see citing works
The enigmatic HCN channels: A cellular neurophysiology perspective
Mishra, P., & Narayanan, R. (2025) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26643 · Cited by 40 · see citing works
Fundamental constraints to the logic of living systems
Solé, R., Kempes, C. P., Corominas-Murtra, B., De Domenico, M., Kolchinsky, A., Lachmann, M., Libby, E., Saavedra, S., Smith, E., & Wolpert, D. (2024) · Interface Focus · doi:10.1098/rsfs.2024.0010 · Cited by 34 · see citing works
Demori, I., Siriya, S., & Burlando, B. (2025) · Applied Sciences · doi:10.3390/app151910483 · Cited by 2 · see citing works
Theoretical Analysis of Resource-Induced Phase Transitions in Estimation Strategies
Tottori, T., & Kobayashi, T. J. (2026) · Physical Review Letters · doi:10.1103/5ynb-7k4v
- Authors
- Alon, U.
- Corresponding author
- Alon, Uri
- ORCID
- Alon, Uri
- Venue
- Chapman & Hall/CRC eBooks
- Publisher
- Chapman and Hall/CRC
- Published
- 2019-07-12
- OpenAlex
- W2528271650
- Cited by
- 955
- References
- 0
- Citations by year
- 2026: 64 · 2025: 73 · 2024: 62 · 2023: 47 · 2022: 47 · 2021: 56 · 2020: 45 · 2019: 18 · 2018: 21 · 2017: 20 · 2016: 38 · 2015: 37 · 2014: 41 · 2013: 52 · 2012: 42
- FWCI
- 35.58
- Type
- book
- Language
- en
- Open access
- closed
- Locations
- Chapman & Hall/CRC eBooks (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- systems biology, biological circuits, transcriptional regulation, transcriptional activation, gene regulatory networks, human physiology, disease
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
