Reading List on Structural Modelling

Model building

1. Types of problems encountered in building metabolic models:

• Poolman, M. G., Bonde, B. K., Gevorgyan, A., Patel, H. H. and Fell, D. A. (2006) Challenges to be faced in the reconstruction of metabolic networks from public databases. IEE Proceedings Systems Biology 153, 379–384

2. A review of the issues involved in generating genome scale models of metabolism. The reference list refers to some of the original examples from the Palsson group:

• Fell, D. A., Poolman, M. G. and Gevorgyan, A. (2010) Building and analysing genome-scale metabolic models. Biochem. Soc. Trans. 38, 1197–1201

Mathematics of Stoichiometric Analysis

An accessible account:

• Cornish-Bowden, A. and Hofmeyr, J. (2002) The role of stoichiometric analysis in studies of metabolism: an example. J. Theor. Biol. 216, 179–191

Elementary Modes Analysis

1. The original publication introducing elementary modes analysis:

• Schuster, S., Dandekar, T. and Fell, D. A. (1999) Detection of Elementary Flux Modes in Biochemical Networks: a Promising Tool for Pathway Analysis and Metabolic Engineering. Trends. Biotechnol. 17, 53–60.

2. A more advanced description of elementary modes

• Schuster, S., Fell, D. A. and Dandekar, T. (2000) A General Definition of Metabolic Pathways Useful for Systematic Organization and Analysis of Complex Metabolic Networks. Nat. Biotechnol. 18, 326–332.

3. EMA reviewed:

• Trinh, C., Wlaschin, A. and Srienc, F. (2009) Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Environ Microbiol. 81, 813–826

4. Calvin cycle example for Practical 4:

• Mark G. Poolman, David A. Fell and Christine A. Raines (2003) Elementary modes analysis of photosynthate metabolism

in the chloroplast stroma. Eur. J. Biochem. 270, 430-439

Linear Programming/ Flux Balance Analysis

1. An example of genome scale modelling for analysis of eukaryotic metabolism:

• Poolman, M. G., Kundu, S., Shaw, R. and Fell, D. A. (2013) Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism. Plant Physiol. 162, 1060–1072

2. Using a genome–scale model to find drug targets:

• Hartman, H. B., Fell, D. A., Rossell, S., Jensen, P. R., Thorndahl, M. J. W. L., Jelsbak, L., Olsen, J. E., Raghunathan, A., Daefler, S. and Poolman, M. G. (2014) Identification of potential drug targets in Salmonella enterica sv. typhimurium using metabolic modelling and experimental validation. Microbiology 160, 1252–1266

Designs for Metabolic Engineering

1. Assessment of biotechnological potential:

• Pentjuss, A., Odzina, I., Kostromins, A., Fell, D. A., Stalidzans, E. and Kalnenieks, U. (2013) Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism. J. Biotechnology 165, 1–10

2. Another example of the use of metabolic modelling to consider options for metabolic engineering:

• Kalnenieks, U., Pentjuss, A., Rutkis, R., Stalidzans, E. and Fell, D. A. (February 2014) Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies. Front. Microbiol. 5

3. Designing a knock–out strategy to force ethanol production in E. coli:

• Trinh, C., Unrean, P. and Srienc, F. (2008) Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol. 74, 3634–3643

4. Potential products from rice straw hydrolysate:

• Ahmad, A., Hartman, H. B., Krishnakumar, S., Fell, D. A., Poolman, M. G. and Srivastava, S. (JUN 2017) A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate. Journal of Biotechnology 251, 30–37

5. Increasing alkane production in E. coli (Practical 5):

• Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams ⁠Yazdani (2018). Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production, Metabolic Engineering, 45, 134-141 DOI