|
Size: 4621
Comment:
|
Size: 4726
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 5: | Line 5: |
| == International Study Group for Systems Biology, 2018 == . The 18th ISGSB meeting will be in Tromsø/Norway, 24-28 September 2018. The meeting will be preceded by the Young ISGSB meeting, providing an introductory workshop for PhD students. The meeting web site is at https://site.uit.no/isgsb2018/ |
== Metabolic Pathway Analysis 2019 == . This will be held in Riga, Latvia, 12-16 August. Details are at https://events.lu.lv/MPA2019 |
| Line 9: | Line 9: |
| . David Fell's 1997 book is now available as a [[Publications/UCM|downloadable pdf]] on this website. | . David Fell's 1997 book is now available via !ResearchGate. |
| Line 12: | Line 12: |
| === Latest papers: === * Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams Yazdani. ''Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production'', Metabolic Engineering (in press, 2018). [[https://doi.org/10.1016/j.ymben.2018.01.002|DOI]] Available [[https://authors.elsevier.com/c/1WYUR_OxxoPbi~|here]] without subscription until 3 April 2018. * Ahmad Ahmad, Hassan B. Hartman , S. Krishnakumar, David A. Fell , Mark G. Poolman , Shireesh Srivastava. ''A Genome Scale Model of ''Geobacillus thermoglucosidasius'' (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate''. J. Biotech. '''251,''' 30-37 (2017) [[http://dx.doi.org/10.1016/j.jbiotec.2017.03.031|DOI]]<<BR>><<BR>>This work was part of the [[http://www.ricefuel.net/index.html|Ricefuel]] project funded by the BBSRC and the DBT (India). <<BR>> |
== Latest papers: == 1. Rupert O. J. Norman, Thomas Millat, Sarah Schatschneider, Anne M. Henstra, Ronja Breitkopf, Bart Pander, Florence J. Annan, Pawel Piatek, Hassan B. Hartman, Mark G. Poolman, David A.Fell, Klaus Winzer, Nigel P. Minton and Charlie Hodgman. ''A genome-scale model of ''Clostridium autoethanogenum'' reveals optimal bioprocess conditions for .high-value chemical production from<<BR>>carbon monoxide. ''Engineering Biology, (2019). [[http://ietdl.org/t/gbNTm|Open Access]] 1. Huma, Benazir; Kundu, Sudip; Poolman, Mark; Kruger, Nicholas; Fell, David. ''Stoichiometric analysis of the energetics and metabolic impact of photorespiration in C3 plants. ''The Plant Journal, '''96, '''1228-1241 (2018) [[https://doi.org/10.1111/tpj.14105|DOI]] == Previous papers: == * Pfau, Christian, Masakapalli, Poolman, Sweetlove & Ebenhoe. ''The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. ''Nature Scientific Reports, (2018) https://www.nature.com/articles/s41598-018-30884-x [[https://doi.org/10.1038/s41598-018-30884-x|DOI]] * Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams Yazdani. ''Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production'', Metabolic Engineering, 45, 134-141 (2018). [[https://doi.org/10.1016/j.ymben.2018.01.002|DOI]] * Ahmad Ahmad, Hassan B. Hartman , S. Krishnakumar, David A. Fell , Mark G. Poolman , Shireesh Srivastava. ''A Genome Scale Model of ''Geobacillus thermoglucosidasius'' (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate''. J. Biotech. '''251,''' 30-37 (2017) [[http://dx.doi.org/10.1016/j.jbiotec.2017.03.031|DOI]] (This work was part of the [[http://www.ricefuel.net/index.html|Ricefuel]] project funded by the BBSRC and the DBT, India). <<BR>> |
| Line 17: | Line 23: |
| === Previous papers: === Near-dead heat between: |
= Background = . Our '''group''' began nearly forty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results. |
| Line 20: | Line 26: |
| 1. Dipali Singh, Ross Carlson, David Fell and Mark Poolman. Modelling Metabolism of the Diatom ''Phaeodactylum tricornutum''. Biochem. Soc. Trans. 43, 1182- (2015) [[http://www.biochemsoctrans.org/content/43/6/1182|PDF]] doi:10.1042/BST20150152 | . Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team. |
| Line 22: | Line 28: |
| 1. Huili Yuan, C. Y. Maurice Cheung, Mark G. Poolman, Peter A.J. Hilbers and Natal A.W. van Riel. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism. The Plant Journal, accepted m/s DOI: 10.1111/tpj.13075 [[http://onlinelibrary.wiley.com/doi/10.1111/tpj.13075/abstract|abstract]] = Background = Our '''group''' began nearly thirty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results. Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team. Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals. |
. Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals. |
News
Metabolic Pathway Analysis 2019
This will be held in Riga, Latvia, 12-16 August. Details are at https://events.lu.lv/MPA2019
Understanding the Control of Metabolism
David Fell's 1997 book is now available via ResearchGate.
Latest papers:
Rupert O. J. Norman, Thomas Millat, Sarah Schatschneider, Anne M. Henstra, Ronja Breitkopf, Bart Pander, Florence J. Annan, Pawel Piatek, Hassan B. Hartman, Mark G. Poolman, David A.Fell, Klaus Winzer, Nigel P. Minton and Charlie Hodgman. A genome-scale model of Clostridium autoethanogenum reveals optimal bioprocess conditions for .high-value chemical production from
carbon monoxide. Engineering Biology, (2019). Open AccessHuma, Benazir; Kundu, Sudip; Poolman, Mark; Kruger, Nicholas; Fell, David. Stoichiometric analysis of the energetics and metabolic impact of photorespiration in C3 plants. The Plant Journal, 96, 1228-1241 (2018) DOI
Previous papers:
Pfau, Christian, Masakapalli, Poolman, Sweetlove & Ebenhoe. The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Nature Scientific Reports, (2018) https://www.nature.com/articles/s41598-018-30884-x DOI
Zia Fatma, Hassan Hartman, Mark G. Poolman, David A. Fell, Shireesh Srivastava , Tabinda Shakeela and Syed Shams Yazdani. Model-assisted metabolic engineering of Escherichia coli for long chain alkane and alcohol production, Metabolic Engineering, 45, 134-141 (2018). DOI
Ahmad Ahmad, Hassan B. Hartman , S. Krishnakumar, David A. Fell , Mark G. Poolman , Shireesh Srivastava. A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate. J. Biotech. 251, 30-37 (2017) DOI (This work was part of the Ricefuel project funded by the BBSRC and the DBT, India).
Pentjuss A., Stalidzans E., Liepins J., Kokina A., Martynova J., Zikmanis P., Mozga I., Scherbaka R., Hartman H., Poolman M. G., Fell D. A., Vigants A. Model based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. J. Industrial Microbiology and Biotechnology, 44, 1177-1190 (2017). DOI
Background
Our group began nearly forty years ago with initial interests in computer simulation of metabolism and the theoretical analysis of metabolic control and regulation. Whilst these still remain areas of interest, we have since developed interests in modelling signal transduction, in various different approaches to network analysis of metabolism, and in reconstructing metabolic networks from genomic data. In the course of this research, we have addressed problems in microbial, plant and mammalian metabolism, often in conjunction with collaborators who have contributed experimental results.
- Our current work centres on modelling the networks of reactions in cells, with particular emphasis on metabolism. It forms part of the emerging field of Systems Biology, in that we are concerned with understanding how biological function arises from the interactions between many components, and with building predictive models. We have to develop and apply suitable theoretical tools, including metabolic control analysis, computer simulation and other forms of algebraic and numerical analysis. In addition, we are investigating how to decipher the metabolic information contained in genome sequences. We are involved in projects on microbial, plant and animal metabolism, each in collaboration with an experimental team.
- Potential applications of our work include the design of changes in cellular metabolism to improve the output of product such as antibiotics, detecting vulnerable sites in cellular networks that could be targets for drugs to control disease-causing organisms, and improved understanding of how organisms manage to adjust their metabolism in response to environmental changes and other signals.
Related Sites
We also host the following web sites related to our research: