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Challenges in experimental data integration within genome-scale metabolic models [article]

Pierre-Yves Bourguignon, Areejit Samal, François Képès, Jürgen Jost, Olivier C. Martin
2010 arXiv   pre-print
A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11 2009, organized by the CNRS-MPG joint program  ...  in Systems Biology.  ...  Challenges in experimental data integration within genome-scale metabolic models The meeting "Challenges in experimental data integration within genomescale metabolic models" was held at the Institut Henri  ... 
arXiv:1004.4387v1 fatcat:ehgonun67vbcvpkrsicq4wtgma

Challenges in experimental data integration within genome-scale metabolic models

Pierre-Yves Bourguignon, Areejit Samal, François Képès, Jürgen Jost, Olivier C Martin
2010 Algorithms for Molecular Biology  
A report of the meeting "Challenges in experimental data integration within genomescale metabolic models", Institut Henri Poincaré, Paris  ...  Challenges in experimental data integration within genome-scale metabolic models The meeting "Challenges in experimental data integration within genomescale metabolic models" was held at the Institut Henri  ...  Wolfram Liebermeister (Humboldt University, Berlin, Germany) presented various methods leveraging such mathematical theories to integrate experimental data within metabolic models.  ... 
doi:10.1186/1748-7188-5-20 pmid:20412574 pmcid:PMC2865480 fatcat:gwzqbxi6k5gwjgyzn24su4ga64

Data Management and Modeling in Plant Biology

Maria Krantz, David Zimmer, Stephan O. Adler, Anastasia Kitashova, Edda Klipp, Timo Mühlhaus, Thomas Nägele
2021 Frontiers in Plant Science  
Experimental findings need to be combined by computational models to gain a mechanistic understanding of plant metabolism.  ...  Summarizing experimental output results in complex data arrays, which need computational statistics and numerical methods for building quantitative models.  ...  ON A LARGE SCALE: HOW DOES GENOME-SCALE METABOLIC NETWORK RECONSTRUCTION SUPPORT DATA INTEGRATION IN PLANT BIOLOGY?  ... 
doi:10.3389/fpls.2021.717958 pmid:34539712 pmcid:PMC8446634 fatcat:t7kxxyeklfg3rc7t47ekfqc2sy

Expanding the uses of genome‐scale models with protein structures

Nathan Mih, Bernhard O Palsson
2019 Molecular Systems Biology  
In this commentary, we highlight the challenges of integrating these two fields, with a focus on genome-scale metabolic modeling, and the novel findings that are made possible from such a merger.  ...  In contrast, systems biology and genome-scale modeling have organically grown out of the wealth of data now being generated by diverse omics measurements.  ...  In this commentary, we highlight the challenges of integrating these two fields, with a focus on genome-scale metabolic modeling, and the novel findings that are made possible from such a merger.  ... 
doi:10.15252/msb.20188601 pmid:31777175 pmcid:PMC6880182 fatcat:um26g7wm3bfojjcox5eie4f66y

Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology [article]

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
2020 arXiv   pre-print
We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems, and  ...  we discuss several challenges for the realization of our vision.  ...  We sincerely thank Dr Kathleen Sedgley for her support with the workshop organization, and Dr Thomas Gorochowski for participating in discussions.  ... 
arXiv:2006.02720v1 fatcat:zyv26a5mhvfxnfm2wsmcyjn5km

Advances in metabolic flux analysis toward genome-scale profiling of higher organisms

Georg Basler, Alisdair R. Fernie, Zoran Nikoloski
2018 Bioscience Reports  
We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps.  ...  In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental  ...  Funding This work was supported by the Federal Ministry of Education and Research of Germany within the projects RECONSTRUCT (031B0200 A-E) and FULLTHROTTLE (031B0205 B), the University of Potsdam, and  ... 
doi:10.1042/bsr20170224 fatcat:ekblt65h4zhqdcmlbtzfc6e27e

Data-driven integration of genome-scale regulatory and metabolic network models

Saheed Imam, Sascha Schäuble, Aaron N. Brooks, Nitin S. Baliga, Nathan D. Price
2015 Frontiers in Microbiology  
Citation: Imam S, Schäuble S, Brooks AN, Baliga NS and Price ND (2015) Data-driven integration of genome-scale regulatory and metabolic network models. Front. Microbiol. 6:409.  ...  is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion.  ...  Acknowledgments This work was funded in part by DOE-ABY (DEEE0006315) (NSB, NDP), DOE ARPA-E program (DE-AR0000426) (NDP),  ... 
doi:10.3389/fmicb.2015.00409 pmid:25999934 pmcid:PMC4419725 fatcat:vp3skde33rgs3asbda7vhgrqly

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Daniel Craig Zielinski, Arjun Patel, Bernhard O. Palsson
2020 Microorganisms  
We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence  ...  Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow.  ...  Thus, the 'kinetome', a genome-scale collection of the kinetic properties of metabolic enzymes, may soon be within reach [86] .  ... 
doi:10.3390/microorganisms8122050 pmid:33371386 pmcid:PMC7767376 fatcat:wpqrmia4wnagjjgirkj4ceb2cy

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Mark Hanemaaijer, Wilfred F. M. Röling, Brett G. Olivier, Ruchir A. Khandelwal, Bas Teusink, Frank J. Bruggeman
2015 Frontiers in Microbiology  
This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators.  ...  Therefore, the inference of the community structure from experimental data is a major current challenge.  ...  For the key species in the community, genome-scale metabolic reconstructions could be created using genomic, literature, and experimental data.  ... 
doi:10.3389/fmicb.2015.00213 pmid:25852671 pmcid:PMC4365725 fatcat:3mm3xev3l5hbfjxvmgvzytsgne

Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
2020 Frontiers in Bioengineering and Biotechnology  
We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems.  ...  We also discuss several challenges for the realization of our vision.  ...  Developing a WCM is a challenging task, which requires the collection of extensive experimental data, integration of sub-cellular models and in silico/in vivo model validation.  ... 
doi:10.3389/fbioe.2020.00942 pmid:32850764 pmcid:PMC7426639 fatcat:w4k5h3aaqbaifl55khnsxkgima

Systems biology approaches integrated with artificial intelligence for optimized food-focused metabolic engineering

Mohamed Helmy, Derek Smith, Kumar Selvarajoo
2020 Metabolic Engineering Communications  
Here, we review the latest attempts of combining systems biology and AI in metabolic engineering research, and highlight how this alliance can help overcome the current challenges facing industrial biotechnology  ...  To achieve this goal, a large system of experimental techniques, compound libraries, computational methods and data resources, including the multi-omics data, are used.  ...  The simulations from a standard genome-scale metabolic models were used to add additional features. Consequently, ensemble modelling was used to improve dealing with data challenges.  ... 
doi:10.1016/j.mec.2020.e00149 pmid:33072513 pmcid:PMC7546651 fatcat:6zvbeckdmbhllm7dnnsrefnxla

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson
2004 Current Opinion in Biotechnology  
These models can further be combined with genome-scale metabolic models to build integrated models of cellular function including both metabolism and its regulation.  ...  Recent developments in experimental techniques have allowed the generation of vast amounts of data related to regulatory networks.  ...  Boolean network models can also be readily integrated with, for example, whole-genome scale metabolic models to formulate integrated models of cellular function [59] .  ... 
doi:10.1016/j.copbio.2003.11.002 pmid:15102470 fatcat:zzadypbtcbchzdtwz7xyzbgaq4

Computational approaches to metabolic engineering utilizing systems biology and synthetic biology

Stephen S. Fong
2014 Computational and Structural Biotechnology Journal  
Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes.  ...  Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering.  ...  The problem of identifying in vivo flux states within the context of genome-scale metabolic models has been approached using a combination of high-throughput experimental data and computational algorithms  ... 
doi:10.1016/j.csbj.2014.08.005 pmid:25379141 pmcid:PMC4212286 fatcat:72tewj4mvvemnldwlksvps6kwm

In silico models of cancer

Lucas B. Edelman, James A. Eddy, Nathan D. Price
2009 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
The development of these in silico models is facilitated by rapidly advancing experimental and analytical tools that generate information-rich, high-throughput biological data.  ...  Statistical models of cancer at the genomic, transcriptomic, and pathway levels have proven effective in developing diagnostic and prognostic molecular signatures, as well as in identifying perturbed pathways  ...  Integration of many molecular pathways for quantitative genome-scale modeling remains an ongoing challenge, with statistical inference of cellular networks currently possible only in a very limited context  ... 
doi:10.1002/wsbm.75 pmid:20836040 pmcid:PMC3157287 fatcat:p4imvwq6rbh5bnfelckytawwyy

Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Saratram Gopalakrishnan, Costas Maranas
2015 Metabolites  
Recent efforts have successfully accomplished genome-scale 13C-MFA in E. coli [30] , highlighting the loss of information associated with the assumptions contained within core MFA models, the role of alternate  ...  This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while  ...  in the context of genome-scale models.  ... 
doi:10.3390/metabo5030521 pmid:26393660 pmcid:PMC4588810 fatcat:fogpc34hqbbuhl4gy7sbw5gjom
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