We thank all the authors and everyone else who worked on our book! Special thanks go to Maarten Droste and Michela Pauletti for proofreading many chapters of the book. If you would like to join us, please get in touch anytime.
1. The cell as a factory This chapter was planned and outlined by O. Golan, with the help of W. Liebermeister and E. Noor
2. What makes up a cell This chapter was planned and outlined by P. Grigaitis and D. Széliová, with the help of W. Liebermeister and E. Noor. Feedback was provided by S. van den Bogaard.
3. The dynamics of metabolic systems We thank Francesco Moro, Markus Arthur Köbis, and Maarten Droste for comments on an earlier version of this chapter. We acknowledge funding from the UK's Biotechnology and Biological Sciences Research Council (BBSRC) grant ID BB/T010150/1 and from the Gordon and Betty Moore Foundation grant ID GBMF9200.
4. Metabolic flux distributions This chapter was planned, outlined and written by D. de Groot, D. Tourigny and F. Scott, with input by D. Ruckerbauer on Minimal Cut Sets. Part of the introduction was written by W. Liebermeister. Exercises were added by F. Scott and A. Kremling. Feedback was provided by Diana Széliová, Samira van den Bogaard, Maarten Droste, W. Liebermeister, E. Noor, and H. Sauro.
5. Optimal metabolic fluxes in constraint-based models This chapter was planned and written by Daan de Groot, David Tourigny and Felipe Scott. Exercises were added by Felipe Scott. Feedback was provided by Diana Széliová, Samira van den Bogaard, Maarten Droste, Wolfram Liebermeister, Elad Noor, and Herbert Sauro.
6. Metabolic pathways and their enzyme efficiency This chapter was drafted and written by W. Liebermeister and E. Noor and has been reviewed by Avi Flamholz, Daan de Groot, Maarten Droste, and Ohad Golan.
7. Metabolism in states of maximal enzyme efficiency This chapter was planned and written by the authors and initially discussed with J. Zanghellini. The chapter was reviewed by D.S. Tourigny and H. Dourado and discussed with S. Müller.
8. Models of growing cells Ohad Golan conceived and designed the chapter. Ohad Golan, Hidde de Jong, and Andrea Weiße wrote sections 1.1-1.3. All authors provided critical feedback and helped shape the chapter. Hidde de Jong acknowledges support from the Agence National de la Recherche (MAXIMIC, ANR-17-CE40-0024-01).
9. Large resource allocation models of cells This chapter was planned and outlined by the authors after discussions with O. Bodeit, M. Lercher, and R. Steuer, and has been reviewed by S. Waldherr and F. Moro.
10. Optimal cell behavior in time This chapter was planned and outlined by Hidde de Jong and Steffen Waldherr (chapter editors). The sections were written Diego Oyarzún (dynamic optimization of enzyme expression in metabolic pathways), Hidde de Jong and Agustín Yabo (dynamic optimization of coarse-grained models of cellular growth), and Dafni Giannari and Steffen Waldherr (dynamic flux balance analysis). Agustín Yabo performed the numerical optimization studies for the examples discussed in the chapter. Andreas Kremling, Wolfram Liebermeister, and Felipe Scott provided comments on the chapter draft. Hidde de Jong acknowledges support from the Agence National de la Recherche (MAXIMIC, ANR-17-CE40-0024-01).
11. Control of cell division This chapter was planned and outlined by MCL, with the help of the other authors. All the authors wrote the introduction and discussion sections (11.1 and 11.7). MC drafted section 11.5, MCL drafted sections 11.2 and 11.6, JG drafted section 11.3, GM drafted section 11.4. We thank Andrea De Martino for proof correction and feedback on our manuscript.
12. Metabolic diversity in cell populations This chapter was planned and outlined by the authors, who are indebted with Daan de Groot for many useful comments and suggestions, as well as with Daniele De Martino, Wolfram Liebermeister, Elad Noor and David Tourigny for discussions.
13. Cells facing uncertainty The chapter was written by D. Lacoste, O. Rivoire, and D. Tourigny. We thank Daan de Groot for reviewing this chapter.
14. Economy of organ shapes and function C. Karamaoun, B. Mauroy and F. Noël wrote the major content of the chapter, and contributed equally to this work. Interlude boxes were written by C. Goupil and E. Herbert. This chapter has been kindly reviewed by P. Ross.
We are grateful for public funding that allows us to write this book, coming from