Resource Balance Analysis

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Overview   -   Theory   -   Literature

Literature about RBA

Review articles

  1. A. Goelzer, V. Fromion. Resource allocation in living organisms . Biochemical Society Transactions, BST20160436 (2017).
  2. A. Goelzer, V. Fromion. Bacterial growth rate reflects a bottleneck in resource allocation. BBA General Subjects, 1810(10):978-88 (2011).

RBA organism models

  1. Bacillus subtilis: A. Goelzer, J. Muntel, V. Chubukov, M. Jules, E. Prestel, R. Nolker, M. Mariadassou, S. Aymerich, M. Hecker, P. Noirot, D. Becher, V. Fromion. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, 32: 232-243 (2015).
  2. Escherichia coli: A. Bulović, S. Fischer, F. Golib, W. Liebermeister, C. Poirier, L. Tournier, E. Klipp, V. Fromion, A. Goelzer. Automated generation of bacterial resource allocation models. Metabolic Engineering, 55 12-22 (2019) [pdf].
  3. Cupriavidus necator: M. Jahn, N. Crang, M. Janasch, A. Hober, B. Forsström, K. Kimler, A. Mattausch, Q. Chen, J. Asplund-Samuelsson, E.P. Hudson. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife, 10, e69019 (2021).
  4. Vibrio natriegens: L. Coppens, T. Tschirhart, D.H. Leary, S.M. Colston, J.R. Compton. W.J. Hervey, K.L. Dana, G.J. Vora, S. Bordel., R. Ledesma-Amaro, Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation, Molecular Systems Biology e10523 (2023).

RBA theory, model construction and validation

  1. O. Bodeit, I. Ben Samir, J.R. Karr, A. Goelzer, W. Liebermeister. RBAtools: a programming interface for Resource Balance Analysis models. Bioinformatics Advances, vbad056 doi: 10.1093/bioadv/vbad056.
  2. A. Bulović, S. Fischer, F. Golib, W. Liebermeister, C. Poirier, L. Tournier, E. Klipp, V. Fromion, A. Goelzer. Automated generation of bacterial resource allocation models. Metabolic Engineering, 55 12-22 (2019) [pdf].
  3. A. Goelzer, J. Muntel, V. Chubukov, M. Jules, E. Prestel, R. Nolker, M. Mariadassou, S. Aymerich, M. Hecker, P. Noirot, D. Becher, V. Fromion. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, 32: 232-243 (2015).
  4. A. Goelzer, V. Fromion, G. Scorletti. Cell design in bacteria as a convex optimization problem. Automatica, 47(6):1210-1218 (2011).
  5. A. Goelzer, V. Fromion, G. Scorletti. Cell design in bacteria as a convex optimization problem. IEEE 48th Conference on Decision and Control (CDC), 4517-4522, (2009).

RBA for biotechnology

  1. M. Dinh, V. Fromion. A RBA model for the chemostat modeling. IEEE 58th Conference on Decision and Control (CDC). 7536-7541. (2019) [pdf]
  2. G. Jeanne, A. Goelzer, S. Tebbani, D. Dumur, V. Fromion. Towards a realistic and integrated strain design in batch bioreactor. IEEE 57th Conference on Decision and Control (CDC). 7536-7541. (2018) [pdf]
  3. G. Jeanne, A. Goelzer, S. Tebbani, D. Dumur, V. Fromion. Dynamical resource allocation models for bioreactor optimization. IFAC-PapersOnLine. 51(19): 20-23. (2018). [pdf]

RBA extensions/advances

  1. A. Goelzer, V. Fromion. RBA for eukaryotic cells: foundations and theoretical developments. bioRxiv. 750182. (2019).
  2. L. Tournier, A. Goelzer, V. Fromion. Optimal resource allocation enables mathematical exploration of microbial metabolic configurations. Journal of Mathematical Biology, 75(6-7): 1349-1380 (2017).
  3. M. Dinh, V. Fromion. RBA like problem with thermo-kinetics is non convex. arXiv:1706.01312.(2017)