The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Autor: Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis

Publikováno v: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-25 (2021)

Abstract Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built a

Externí odkaz: https://doaj.org/article/e251023e0a2946ffa85283b56b52a2b3

MEMOTE for standardized genome-scale metabolic model testing

Autor: Kiran Raosaheb Patil, Jens Nielsen, Vassily Hatzimanikatis, Hyun Uk Kim, Nathan D. Price, Edda Klipp, Parizad Babaei, Lars K. Nielsen, Moritz Emanuel Beber, Sang Yup Lee, Radhakrishnan Mahadevan, Meiyappan Lakshmanan, Lars M. Blank, Jon Olav Vik, Steffen Klamt, Nikolaus Sonnenschein, Saeed Shoaie, Bernhard O. Palsson, Georgios Fengos, Christian Diener, Christopher S. Henry, Andreas Dräger, Janaka N. Edirisinghe, Daniel Machado, Beatriz García-Jiménez, Osbaldo Resendis-Antonio, Hongwu Ma, Peter J. Schaap, Dong-Yup Lee, Wout van Helvoirt, José P. Faria, Judith A. H. Wodke, Adam M. Feist, Siddharth Chauhan, Isabel Rocha, Henning Hermjakob, Qianqian Yuan, Brett G. Olivier, Rahuman S. Malik Sheriff, Markus J. Herrgård, Frank Bergmann, Adil Mardinoglu, Anne Richelle, Filipe Liu, Joana C. Xavier, Maksim Zakhartsev, Paulo Vilaça, Cheng Zhang, Ronan M. T. Fleming, Birgitta E. Ebert, Gregory L. Medlock, Ali Kaafarani, Nathan E. Lewis, Mark G. Poolman, Intawat Nookaew, Jonathan M. Monk, Jason A. Papin, Benjamin Sanchez, Christian Lieven, Matthias König, Juan Nogales, Paulo Maia, Sunjae Lee, Jasper J. Koehorst, Meriç Ataman, Jennifer A. Bartell, Bas Teusink, Kevin Correia, Zachary A. King

Publikováno v: Nature Biotechnology
Lieven, C, Beber, M E, Olivier, B G, Bergmann, F T, Ataman, M, Babaei, P, Bartell, J A, Blank, L M, Chauhan, S, Correia, K, Diener, C, Dräger, A, Ebert, B E, Edirisinghe, J N, Faria, J P, Feist, A M, Fengos, G, Fleming, R M T, García-Jiménez, B, Hatzimanikatis, V, van Helvoirt, W, Henry, C S, Hermjakob, H, Herrgard, M J, Kaafarani, A, Kim, H U, King, Z, Klamt, S, Klipp, E, Koehorst, J J, König, M, Lakshmanan, M, Lee, D-Y, Lee, S Y, Lee, S, Lewis, N E, Liu, F, Ma, H, Machado, D, Mahadevan, R, Maia, P, Mardinoglu, A, Medlock, G L, Monk, J M, Nielsen, J, Nielsen, L K, Nogales, J, Nookaew, I, Palsson, B O, Papin, J A, Patil, K R, Poolman, M, Price, N D, Resendis-Antonio, O, Richelle, A, Rocha, I, Sánchez, B J, Schaap, P J, Malik Sheriff, R S, Shoaie, S, Sonnenschein, N, Teusink, B, Vilaca, P, Vik, J O, Wodke, J A H, Xavier, J C, Yuan, Q, Zakhartsev, M & Zhang, C 2020, ' MEMOTE for standardized genome-scale metabolic model testing ', Nature Biotechnology, vol. 38, no. 3, pp. 272-276 . https://doi.org/10.1038/s41587-020-0446-y
Nature Biotechnology, 38(3), 272-276. Nature Publishing Group
Nature Biotechnology, 38(3), 272-276
Nature Biotechnology 38 (2020) 3
Nature biotechnology 38, 272-276 (2020). doi:10.1038/s41587-020-0446-y
Lieven, C, Beber, M E, Olivier, B G, Bergmann, F T, Ataman, M, Babaei, P, Bartell, J A, Blank, L M, Chauhan, S, Correia, K, Diener, C, Dräger, A, Ebert, B E, Edirisinghe, J N, Faria, J P, Feist, A M, Fengos, G, Fleming, R M T, García-Jiménez, B, Hatzimanikatis, V, van Helvoirt, W, Henry, C S, Hermjakob, H, Herrgård, M J, Kaafarani, A, Kim, H U, King, Z, Klamt, S, Klipp, E, Koehorst, J J, König, M, Lakshmanan, M, Lee, D Y, Lee, S Y, Lee, S, Lewis, N E, Liu, F, Ma, H, Machado, D, Mahadevan, R, Maia, P, Mardinoglu, A, Medlock, G L, Monk, J M, Nielsen, J, Nielsen, L K, Nogales, J, Nookaew, I, Palsson, B O, Papin, J A, Patil, K R, Poolman, M, Price, N D, Resendis-Antonio, O, Richelle, A, Rocha, I, Sánchez, B J, Schaap, P J, Malik Sheriff, R S, Shoaie, S, Sonnenschein, N, Teusink, B, Vilaça, P, Vik, J O, Wodke, J A H, Xavier, J C, Yuan, Q, Zakhartsev, M & Zhang, C 2020, ' MEMOTE for standardized genome-scale metabolic model testing ', Nature Biotechnology, vol. 38, no. 3, pp. 272-276 . https://doi.org/10.1038/s41587-020-0446-y
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Supplementary information is available for this paper at https://doi.org/10.1038/s41587-020-0446-y
Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5d61d5a36be06a47bc97af59e732f38d
http://europepmc.org/articles/PMC7082222

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Autor: Isabel Rocha, Jon Olav Vik, Jonathan Monk, Kiran Raosaheb Patil, Christopher S. Henry, Jason A. Papin, Rahuman S. Malik Sheriff, Gregory L. Medlock, Jasper J. Koehorst, Meriç Ataman, Juan Nogales, Ali Kaafarani, Radhakrishnan Mahadevan, Adil Mardinoglu, Anne Richelle, Janaka N. Edirisinghe, Qianqian Yuan, Paulo Maia, Bas Teusink, José P. Faria, Brett G. Olivier, Intawat Nookaew, Lars M. Blank, Cheng Zhang, Meiyappan Lakshmanan, Hongwu Ma, Ronan M. T. Fleming, Beatriz García-Jiménez, Andreas Dräger, Nathan D. Price, Filipe Liu, Joana C. Xavier, Daniel Machado, Jennifer A. Bartell, Sunjae Lee, Osbaldo Resendis-Antonio, Hyun Uk Kim, Edda Klipp, Henning Hermjakob, Kevin Correia, Parizad Babaei, Peter J. Schaap, Christian Diener, Benjamin Sanchez, Markus J. Herrgård, Frank Bergmann, Jens Nielsen, Siddharth Chauhan, Zachary A. King, Wout van Helvoirt, Steffen Klamt, Nathan E. Lewis, Mark G. Poolman, Nikolaus Sonnenschein, Dong-Yup Lee, Christian Lieven, Maksim Zakhartsev, Paulo Vilaça, Matthias König, Birgitta E. Ebert, Georgios Fengos, Bernhard O. Palsson, Adam M. Feist, Judith A. H. Wodke, Saeed Shoaie, Vassily Hatzimanikatis, Lars K. Nielsen, Moritz Emanuel Beber, Sang Yup Lee

Publikováno v: Nature Biotechnology 38 (2020) 4
Nature biotechnology, vol 38, iss 4
Nature Biotechnology, 38(4)
Nature Biotechnology, 38, 504. NATURE PUBLISHING GROUP
Nature biotechnology 38, 504-504 (2020). doi:10.1038/s41587-020-0477-4

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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info:eu-repo/semantics/publishedVersion

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bee9d532b56132ff2a658c2f469b1bb
https://research.wur.nl/en/publications/publisher-correction-memote-for-standardized-genome-scale-metabol

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Autor: Hongwu Ma, Judith A. H. Wodke, Ronan M. T. Fleming, Steffen Klamt, Vassily Hatzimanikatis, Janaka N. Edirisinghe, Christian Lieven, Nathan D. Price, Edda Klipp, Meiyappan Lakshmanan, Matthias König, Jennifer A. Bartell, Daniel Machado, B. E. Ebert, Lars K. Nielsen, Georgios Fengos, Juan Nogales, Moritz Emanuel Beber, Sang Yup Lee, Andreas Dräger, Hyun Uk Kim, Dong-Yup Lee, Rahuman S. Malik Sheriff, Beatriz García-Jiménez, Osbaldo Resendis-Antonio, Parizad Babaei, Sunjae Lee, Adam M. Feist, Adil Mardinoglu, Benjamin Sanchez, Peter J. Schaap, José P. Faria, Anne Richelle, Jonathan M. Monk, Paulo Maia, Markus J. Herrgård, Jason A. Papin, Frank Bergmann, Siddharth Chauhan, Saeed Shoaie, Wout van Helvoirt, Jon Olav Vik, Jasper J. Koehorst, Jens Nielsen, Meriç Ataman, Filipe Liu, Christopher S. Henry, Joana C. Xavier, Gregory L. Medlock, Maksim Zakhartsev, Paulo Vilaça, Ali Kaafarani, Nikolaus Sonnenschein, Intawat Nookaew, Bernhard O. Palsson, Nathan E. Lewis, Mark G. Poolman, Cheng Zhang, Radhakrishnan Mahadevan, Bas Teusink, Isabel Rocha, Christian Diener, Kevin Correia, Zachary A. King, Lars M. Blank, Kiran Raosaheb Patil, Henning Hermjakob, Qianqian Yuan, Brett G. Olivier

Publikováno v: bioRxiv

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of mo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0e8bd74c6bd0c3c153194a6dfd59e812
https://doi.org/10.1101/350991

Predictive models for cellular signaling networks

Autor: Dagmar, Iber, Georgios, Fengos

Publikováno v: Methods in molecular biology (Clifton, N.J.). 880

This chapter provides an introduction to the formulation and analysis of differential-equation-based models for biological regulatory networks. In the first part, we discuss basic reaction types and the use of mass action kinetics and of simplifying

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::326d54ae7f8225ce378f81c7b61132f6
https://pubmed.ncbi.nlm.nih.gov/23361978