References

Alon, Uri. 2007. “Network Motifs: Theory and Experimental Approaches.” Nature Reviews Genetics 8 (6): 450–61. https://doi.org/10.1038/nrg2102.
Alon, Uri. 2019. An Introduction to Systems Biology: Design Principles of Biological Circuits. 2nd ed. Chapman; Hall/CRC. https://doi.org/10.1201/9780429283321.
Alon, Uri, Michael G. Surette, Naama Barkai, and Stanislas Leibler. 1999. “Robustness in Bacterial Chemotaxis.” Nature 397 (6715): 168–71. https://doi.org/10.1038/16483.
Antebi, Yaron E., James M. Linton, Heidi Klumpe, et al. 2017. “Combinatorial Signal Perception in the BMP Pathway.” Cell 170 (6): 1184–1196.e24. https://doi.org/10.1016/j.cell.2017.08.015.
Barkai, Naama, and Stanislas Leibler. 1997. “Robustness in Simple Biochemical Networks.” Nature 387 (6636): 913–17. https://doi.org/10.1038/43199.
Batchelor, Eric, and Mark Goulian. 2003. “Robustness and the Cycle of Phosphorylation and Dephosphorylation in a Two-Component Regulatory System.” Proc. Natl. Acad. Sci. U. S. A. 100 (2): 691–96.
Bintu, Lacramioara, Nicolas E. Buchler, Hernan G. Garcia, et al. 2005. “Transcriptional Regulation by the Numbers: Models.” Current Opinion in Genetics & Development 15 (2): 116–24. https://doi.org/10.1016/j.gde.2005.02.007.
Bleris, Leonidas, Zhen Xie, David Glass, Asa Adadey, Eduardo D. Sontag, and Yaakov Benenson. 2011. “Synthetic Incoherent Feedforward Circuits Show Adaptation to the Amount of Their Genetic Template.” Molecular Systems Biology 7: 519. https://doi.org/10.1038/msb.2011.49.
Bray, Sarah J. 2006. “Notch Signalling: A Simple Pathway Becomes Complex.” Nature Reviews Molecular Cell Biology 7 (9): 678–89. https://doi.org/10.1038/nrm2009.
Clevers, Hans, Susanne Rafelski, Michael Elowitz, et al. 2017. “What Is Your Conceptual Definition of ‘Cell Type’ in the Context of a Mature Organism?” Cell Systems 4 (3): 255–59. https://doi.org/10.1016/j.cels.2017.03.006.
Escalante-Chong, Renan, Yonatan Savir, Sean M. Carroll, et al. 2015. “Galactose Metabolic Genes in Yeast Respond to a Ratio of Galactose and Glucose.” Proceedings of the National Academy of Sciences of the United States of America 112 (5): 1636–41. https://doi.org/10.1073/pnas.1418058112.
Ferrell, James E. Jr. 1999. “Xenopus Oocyte Maturation: New Lessons from a Good Egg.” BioEssays 21 (10): 833–42. https://doi.org/10.1002/(SICI)1521-1878(199910)21:10<833::AID-BIES5>3.0.CO;2-P.
Gerland, Urligh, and Terrence Hwa. 2009. “Evolutionary Selection Between Alternative Modes of Gene Regulation.” Proceedings of the National Academy of Sciences USA 106 (22): 8841–46. https://doi.org/10.1073/pnas.0808500106.
Goentoro, Lea, and Marc W. Kirschner. 2009. “Evidence That Fold-Change, and Not Absolute Level, of β-Catenin Dictates Wnt Signaling.” Molecular Cell 36 (5): 872–84. https://doi.org/10.1016/j.molcel.2009.11.017.
Goentoro, Lea, Oren Shoval, Marc W. Kirschner, and Uri Alon. 2009. “The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation.” Molecular Cell 36 (5): 894–99. https://doi.org/10.1016/j.molcel.2009.11.018.
Gunawardena, Jeremy. 2014. “Models in Biology: Accurate Descriptions of Our Pathetic Thinking.” BMC Biology 12 (1): 29. https://doi.org/10.1186/1741-7007-12-29.
Hanahan, Douglas, and Robert A. Weinberg. 2000. “The Hallmarks of Cancer.” Cell 100 (1): 57–70. https://doi.org/10.1016/S0092-8674(00)81683-9.
Hasty, Jeff, Milos Dolnik, Vivi Rottschäfer, and James J. Collins. 2002. “Synthetic Gene Network for Entraining and Amplifying Cellular Oscillations.” Physical Review Letters 88 (14): 148101. https://doi.org/10.1103/PhysRevLett.88.148101.
Hopfield, John J. 1974. “Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity.” Proceedings of the National Academy of Sciences of the United States of America 71 (10): 4135–39. https://doi.org/10.1073/pnas.71.10.4135.
Horowitz, Paul, and Winfield Hill. 2015. The Art of Electronics. 3rd ed. Cambridge University Press. https://artofelectronics.net/.
Huang, Sui. 2021. “Should Biophysics Study Nonphysical Quantities of Biological Systems? Take Max Delbrück for Inspiration.” Biophysics Reviews 2 (4): 040401. https://doi.org/10.1063/5.0079700.
Jacob, François, and Jaqcues Monod. 1961. “On the Regulation of Gene Activity.” Cold Spring Harbor Symposia on Quantitative Biology 26 (0): 193–211. https://doi.org/10.1101/sqb.1961.026.01.024.
Judson, Horace Freeland. 1996. The Eighth Day of Creation: The Makers of the Revolution in Biology. Cold Spring Harbor Laboratory Press. https://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=294.
Kafri, Ran, Arren Bar-Even, and Yitzhak Pilpel. 2005. “Transcription Control Reprogramming in Genetic Backup Circuits.” Nature Genetics 37 (3): 295–99. https://doi.org/10.1038/ng1523.
Kalir, Shiraz, Shmoolik Mangan, and Uri Alon. 2005. “A Coherent Feed-Forward Loop with a SUM Input Function Prolongs Flagella Expression in Escherichia Coli.” Molecular Systems Biology 1: 2005.0006. https://doi.org/10.1038/msb4100010.
Klumpe, Heidi E., Matthew A. Langley, James M. Linton, Christina J. Su, Yaron E. Antebi, and Michael B. Elowitz. 2022. “The Context-Dependent, Combinatorial Logic of BMP Signaling.” Cell Systems 13 (5): 388–407.e10. https://doi.org/10.1016/j.cels.2022.03.002.
Lewis, Julian. 2003. “Autoinhibition with Transcriptional Delay: A Simple Mechanism for the Zebrafish Somitogenesis Oscillator.” Current Biology 13 (16): 1398–408. https://doi.org/10.1016/S0960-9822(03)00534-7.
Li, Mingshan, and Gerald L. Hazelbauer. 2004. “Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex.” Journal of Bacteriology 186 (12): 3687–94. https://doi.org/10.1128/JB.186.12.3687-3694.2004.
Mangan, Shmoolik, Shalev Itzkovitz, Alon Zaslaver, and Uri Alon. 2006. “The Incoherent Feed-Forward Loop Accelerates the Response-Time of the Gal System of Escherichia Coli.” Journal of Molecular Biology 356 (5): 1073–81. https://doi.org/10.1016/j.jmb.2005.12.003.
Mangan, Shmoolik, Alon Zaslaver, and Uri Alon. 2003. “The Coherent Feedforward Loop Serves as a Sign-Sensitive Delay Element in Transcription Networks.” Journal of Molecular Biology 334 (2): 197–204. https://doi.org/10.1016/j.jmb.2003.09.049.
Milo, Ron, Shalev Itzkovitz, Nadav Kashtan, et al. 2004. “Superfamilies of Evolved and Designed Networks.” Science 303 (5663): 1538–42. https://doi.org/10.1126/science.1089167.
Milo, Ron, Shai Shen-Orr, Shalev Itzkovitz, Nadav Kashtan, Dmitri Chklovskii, and Uri Alon. 2002. “Network Motifs: Simple Building Blocks of Complex Networks.” Science 298 (5594): 824–27. https://doi.org/10.1126/science.298.5594.824.
Morsut, Leonardo, Kole T. Roybal, Xin Xiong, et al. 2016. “Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors.” Cell 164 (4): 780–91. https://doi.org/10.1016/j.cell.2016.01.012.
Müller-Hill, Benno. 1996. The lac Operon: A Short History of a Genetic Paradigm. De Gruyter. https://doi.org/10.1515/9783110879476.
Newman, Mark E. J., Steven H. Strogatz, and Duncan J. Watts. 2001. “Random Graphs with Arbitrary Degree Distributions and Their Applications.” Physical Review E 64 (2): 026118. https://doi.org/10.1103/PhysRevE.64.026118.
Nickel, Joachim, and Thomas D. Mueller. 2019. “Specification of BMP Signaling.” Cells 8 (12): 1579. https://doi.org/10.3390/cells8121579.
Obradovic Wagner, Darja, Christina Sieber, Raghu Bhushan, Jan H. Börgermann, Daniel Graf, and Petra Knaus. 2010. “BMPs: From Bone to Body Morphogenetic Proteins.” Science Signaling 3 (107): mr1. https://doi.org/10.1126/scisignal.3107mr1.
Phillips, Rob. 2020. The Molecular Switch: Signaling and Allostery. Princeton University Press. https://doi.org/10.2307/j.ctvx5w8pf.
Ptashne, Mark. 2004. A Genetic Switch: Phage Lambda Revisited. 3rd ed. Cold Spring Harbor Laboratory Press.
Regev, Aviv, Sarah A. Teichmann, Eric S. Lander, et al. 2017. “Science Forum: The Human Cell Atlas.” eLife 6: e27041. https://doi.org/10.7554/eLife.27041.
Rosenfeld, Nir, Michael B. Elowitz, and Uri Alon. 2002. “Negative Autoregulation Speeds the Response Times of Transcription Networks.” Journal of Molecular Biology 323 (5): 785–93. https://doi.org/10.1016/S0022-2836(02)00994-4.
Savageau, M A. 1977. “Design of Molecular Control Mechanisms and the Demand for Gene Expression.” Proceedings of the National Academy of Sciences USA 74 (12): 5647–51. https://doi.org/10.1073/pnas.74.12.5647.
Segall-Shapiro, Thomas H, Eduardo D Sontag, and Christopher A Voigt. 2018. “Engineered Promoters Enable Constant Gene Expression at Any Copy Number in Bacteria.” Nature Biotechnology 36 (4): 352–58. https://doi.org/10.1038/nbt.4111.
Shen-Orr, Shai S., Ron Milo, Shmoolik Mangan, and Uri Alon. 2002. “Network Motifs in the Transcriptional Regulation Network of Escherichia Coli.” Nature Genetics 31 (1): 64–68. https://doi.org/10.1038/ng881.
Shinar, Guy, Erez Dekel, Tsvi Tlusty, and Uri Alon. 2006. “Rules for Biological Regulation Based on Error Minimization.” Proceedings of the National Academy of Sciences USA 103 (11): 3999–4004. https://doi.org/10.1073/pnas.0506610103.
Shinar, Guy, Ron Milo, María Rodríguez Martínez, and Uri Alon. 2007. “Input–Output Robustness in Simple Bacterial Signaling Systems.” Proceedings of the National Academy of Sciences USA 105 (50): 19931–35. https://doi.org/10.1073/pnas.0706792104.
Spencer, Shawn L., Suzanne Gaudet, John G. Albeck, John M. Burke, and Peter K. Sorger. 2009. “Non-Genetic Origins of Cell-to-Cell Variability in TRAIL-Induced Apoptosis.” Nature 459 (7245): 428–32. https://doi.org/10.1038/nature08012.
Sprinzak, David, Anupriya Lakhanpal, Laurent LeBon, Jordi Garcia-Ojalvo, and Michael B. Elowitz. 2011. “Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning.” PLoS Computational Biology 7 (6): e1002069. https://doi.org/10.1371/journal.pcbi.1002069.
Stricker, Jesse, Scott Cookson, Matthew R. Bennett, William H. Mather, Lev S. Tsimring, and Jeff Hasty. 2008. “A Fast, Robust and Tunable Synthetic Gene Oscillator.” Nature 456 (7221): 516–19. https://doi.org/10.1038/nature07389.
Su, Christina J., Arvind Murugan, James M. Linton, et al. 2022. “Ligand-Receptor Promiscuity Enables Cellular Addressing.” Cell Systems 13 (5): 408–425.e12. https://doi.org/10.1016/j.cels.2022.03.001.
Swinburne, Ian A., David G. Miguez, Dominic Landgraf, and Pamela A. Silver. 2008. “Intron Length Increases Oscillatory Periods of Gene Expression in Animal Cells.” Genes & Development 22 (17): 2342–46. https://doi.org/10.1101/gad.1696108.
Tinsley, Jonathan N, Maxim I Molodtsov, Robert Prevedel, et al. 2016. “Direct Detection of a Single Photon by Humans.” Nat. Commun. 7 (July): 12172. https://doi.org/10.1038/ncomms12172.
Tsai, Tony Yu-Chen, Yoon Sup Choi, Wenzhe Ma, Joseph R. Pomerening, Chao Tang, and James E. Ferrell. 2008. “Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops.” Science 321 (5885): 126–29. https://doi.org/10.1126/science.1156951.