A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Challenges in experimental data integration within genome-scale metabolic models
[article]
2010
arXiv
pre-print
Preserved Fulltext
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
2010
Algorithms for Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
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
2021
Frontiers in Plant Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2019
Molecular Systems Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Bioscience Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2015
Frontiers in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
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
2020
Microorganisms
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2015
Frontiers in Microbiology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2020
Frontiers in Bioengineering and Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2020
Metabolic Engineering Communications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2004
Current Opinion in Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
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
2014
Computational and Structural Biotechnology Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2009
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2015
Metabolites
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 59,477 results