Anne Goelzer
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Contact - CV - Publications - Softwares - PhD



Contact
Institut National de la Recherche Agronomique
Unit; MaIAGE - Applied Mathematics and Computer Science, from Genomes to the Environment Mail : anne.goelzer 'at' inra.fr
Domaine de Vilvert, Bâtiment 210 Tel : +33(0)1.34.65.28.79
78350 Jouy en Josas Fax : +33(0)1.34.65.29.01



CV
Background:
Professional Background:
Skills:


Publications
Peer reviewed articles:
  1. A. Goelzer, V. Fromion. RBA for eukaryotic cells: foundations and theoretical developments. BioRxiv, (2019).

  2. A. Bulovic, S. Fischer, M. Dinh, 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).

  3. V.J. Henry, A. Goelzer, A. Ferré, S. Fischer, M. Dinh, V. Loux, C. Froidevaux, V. Fromion. The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. Journal of Biomedical Semantics, 8:53 (2017).

  4. A. Goelzer, V. Fromion. Resource allocation in living organisms. Biochemical Society Transactions, BST20160436(2017).

  5. 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).

  6. A. Kalantari, T. Chen, B. Ji, I. Stancik, V. Ravikumar, D. Franjevic, C. Saulou-Berion, A. Goelzer, I. Mijakovic. Conversion of glycerol to 3-hydroxypropanoic acid by genetically engineered Bacillus subtilis. Frontiers in Microbiology, 8:638 (2017).

  7. O. Borkowski, A. Goelzer, M. Schaffer, U. Mäder, S. Aymerich, M. Jules, V. Fromion. Translation elicits a growth-rate dependent and genome-wide, differential production of proteins in Bacillus subtilis. Molecular Systems Biology, 12(5):870 (2016).

  8. J. Faria, R. Overbeek, R. Taylor, N. Conrad, V. Vonstein, A. Goelzer, V. Fromion, M. Rocha, I. Rocha, and C. Henry. Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data. Frontiers in Microbiology, 7 (2016).

  9. 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).

  10. J. Muntel, V. Fromion, A. Goelzer, A. Maass, U. Mader, K. Buttner, M. Hecker, D. Becher. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by multiplexed LC/MS (LC/MSE). Molecular and Cellular Proteomics, 13(4):1008-1019 (2014).

  11. L. Aichaoui, M. Jules, L. Le Chat, S. Aymerish, V. Fromion, A. Goelzer. BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array. Bioinformatics, 28(20): 2705-2706 (2012).

  12. M. Celton, I. Sanchez, A. Goelzer, V. Fromion, C. Camarasa, S. Dequin. A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genomics, 13(1):317 (2012).

  13. M. Celton, A. Goelzer, C. Camarasa, V. Fromion, S. Dequin. A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metabolic Engineering, 14(4):366-379 (2012).

  14. Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessières P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science, 335(6072):1099-1103 (2012).

  15. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science, 335(6072):1103-1106 (2012).

  16. A. Goelzer, V. Fromion, G. Scorletti. Cell design in bacteria as a convex optimization problem. Automatica, 47(6):1210-1218 (2011).

  17. A. Goelzer, V. Fromion. Bacterial growth rate reflects a bottleneck in resource allocation. BBA General Subjects, 1810(10):978-88 (2011).

  18. A. Goelzer, B. Charnomordic, S. Colombié, V. Fromion, J.M. Sablayrolles. Simulation and optimization software for alcoholic fermentation in winemaking conditions. Food Control, 20(7), pp 635-642 (2009).

  19. A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete, P. Noirot, P. Bessières, S. Aymerich, V. Fromion. Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Systems Biology, 2:20 (2008).

  20. A. Goelzer, Émergence de structures modulaires dans les régulations des systèmes biologiques: théorie et applications à Bacillus subtilis. PhD Thesis, Ecole Centrale de Lyon (2010).

Peer reviewed conference papers:
  1. G. Jeanne, A. Goelzer, S. Tebbani, V. Fromion, D. Dumur. Towards a realistic and integrated strain design in batch bioreactor. In Proceedings of the 57th IEEE Conference on Decision and Control, pages 2698-2703, Miami, USA, 2018.

  2. G. Jeanne, S. Tebbani, D. Dumur, A. Goelzer, V. Fromion. Integration of protein dynamics in batch bioprocess optimization. In Proceedings of the 37th Benelux Meeting on Systems and Control, Soesterberg, Netherlands, 2018.

  3. G. Jeanne, A. Goelzer, S. Tebbani, V. Fromion, D. Dumur. Dynamical resource allocation models for bioreactor optimization. In Foundations of Systems Biology in Engineering (FOSBE). Chicago, USA, 2018.

  4. V. Henry, F. Sais, E. Marchadier, J. Dibie, A. Goelzer, V. Fromion. BiPOm: Biological interlocked Process Ontology for metabolism. How to infer molecule knowledge from biological process? International Conference on Biomedical Ontology, Newcastle, United Kingdom, 2017.

  5. G. Jeanne, S. Tebbani, A. Goelzer, V. Fromion, D. Dumur. Optimization of a micro-organisms culture in a fedbatch bioreactor using an intracellular model. Mediterranean Conference on Control and Automation, Valletta, Malta, 2017.

  6. G. Jeanne, S. Tebbani, A. Goelzer, V. Fromion, D. Dumur. Modelling and Optimization of Metabolic Pathways in Bacteria. International Conference on System Theory, Control and Computing. Sinaia, Roumanie, 2016.

  7. V. Henry, A. Ferré, C. Froidevaux, A. Goelzer, V. Fromion, S. Cohen-Boulakia, S. Dérozier, M. Dinh, G. Fiévet, S. Fischer, J.-F Gibrat, V. Loux, S. Peres. Représentation systémique multi-échelle des processus biologiques de la bactérie. Ingénierie des connaissances, Montpellier, 2016.

  8. N. Meslem, V. Fromion, A. Goelzer, L. Tournier. Stability Analysis for Bacterial Linear Metabolic Pathways with Monotone Control System Theory. ICINCO, Portugal (2010).

  9. A. Goelzer, V. Fromion, G. Scorletti. Cell design in bacteria as a convex optimization problem. 48th IEEE Conference on Decision and Control, China (2009).

Book chapters:
  1. A. Goelzer, V. Fromion. Towards the modular decomposition of the metabolic network. in System Theoretic Approach to Systems and Synthetic Biology , Ed. V. Kulkarni, G-B. Stan, and K. Raman, Springer Verlag, pp.121-152 (2014).

  2. S. Aymerich, A. Goelzer, V. Fromion. Transcriptional controls of the central carbon metabolism in Bacillus subtilis. in Global Regulatory Networks in Bacillus subtilis, Ed. Y. Fujita, pp.39-73 (2007).



Softwares


PhD
Abstract: This thesis consists in studying the organization of the control system of metabolic pathways of bacteria to identify systemic properties revealing its operation. At first, we show that control of metabolic pathways is highly structured and can be decomposed into modules strongly decoupled in steady-state. These modules are defined by their singular mathematical properties having important implications in biology. This decomposition, based inherently on the system outlook of automatic control, offers a formal theoretical analysis of general control of metabolic pathways, which has been effective in analyzing experimental data.
In a second step, we consider the possible reasons for the emergence of this modular control structure. We identify a set of structural constraints acting at the distribution of a common resource, the proteins between cellular processes. Satisfying these constraints for a given growth rate leads to formalize and to solve a non-differentiable convex optimization problem, that we call Resource Balance Analysis. This optimization problem is solved numerically at the scale of the bacteria through an equivalent linear programming problem. Several properties are derived from theoretical analysis of the obtained criterion. First, the growth rate is structurally limited by the distribution of a finite amount of proteins between the metabolic pathways and the ribosomes. Second, the emergence of modules in metabolic pathways arises from a policy of economy in proteins in the bacterium to increase the growth rate. Some well known transport strategies such as catabolite repression or the substitution between low/high affinity transporters are predicted by our method and could consequently be interpreted as ways to maximize growth while minimizing investment in proteins.

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