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OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production
[article]
2021
bioRxiv
pre-print
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Computational tools have been widely adopted for strain optimisation in metabolic engineering, contributing to numerous success stories of producing industrially relevant biochemicals. ...
In the second step, it computes optimal design strategies with limited manipulations (combining regulation and knockout) leading to high biochemical production. ...
Acknowledgement This work has been supported by the Engineering and Physical Sciences Research Council (EPSRC) for funding project "Synthetic Portabolomics: Leading the way at the crossroads of the Digital ...
doi:10.1101/2021.12.10.472123
fatcat:jbyzuw7atrfm7li4pjjp2vrelm
Computational Identification of Metabolic Pathways of Plasmodium falciparum using the k-Shortest Path Algorithm
2019
International Journal of Genomics
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The resulting modified iPfa GEM was a model using the k-shortest path algorithm to identify possible alternative metabolic pathways in glycolysis and pentose phosphate pathways of Plasmodium falciparum ...
In conclusion, the application of the intelligent search technique to the metabolic network of P. falciparum predicts potential biologically relevant alternative pathways using graph theory-based approach ...
Jelili Oyelade for the contribution from his PhD thesis. ...
doi:10.1155/2019/1750291
pmid:31662957
pmcid:PMC6791207
fatcat:tzblwk2ljfaffhidfbjcixlboe
NIHBA: A Network Interdiction Approach for Metabolic Engineering Design
2020
Bioinformatics
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To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems. ...
However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single ...
This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) for funding project 'Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies ...
doi:10.1093/bioinformatics/btaa163
pmid:32167529
pmcid:PMC7267835
fatcat:uokyr5vb5rgjvaekp25ilptc24
Metabolic Flux Analysis in Plants: From Intelligent Design to Rational Engineering
2008
Annual Review of Plant Biology
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The application of predictive tools to high quality flux maps in particular promises to be important in the rational metabolic engineering of plants. 625 ...
In microbial systems, powerful methods have been developed for the reconstruction of metabolic networks from genomic and transcriptomic data, pathway analysis, and predictive modeling. ...
This approach has been used to obtain information on the fluxes of glycolysis/gluconeogenesis and the oxidative pentose phosphate pathway in heterotrophic plant cells, and specifically to shed light on ...
doi:10.1146/annurev.arplant.58.032806.103822
pmid:18257707
fatcat:knkws3oha5enjlycwdkh6kirx4
Robustness: linking strain design to viable bioprocesses
2022
Trends in Biotechnology
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Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions. ...
Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals. ...
We thank the late Professor Stefan Hohmann for fruitful discussions about robustness.
Declaration of interests The authors declare no conflicts of interest. ...
doi:10.1016/j.tibtech.2022.01.004
pmid:35120750
fatcat:bysetjqpkzdk5mw7ab6y2z6uhy
Petri Net Based Model Validation in Systems Biology
[chapter]
2004
Lecture Notes in Computer Science
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Data Validation Models are widely used for biotechnological questions, e.g. for the optimization of pathways in order to maximize the yield of special products. ...
The examples used in this paper cover signal transduction pathways as well as metabolic pathways. ...
We would like to thank Bjoern Junker, Klaus Voss, and Jürgen Will for many fruitful discussions. ...
doi:10.1007/978-3-540-27793-4_13
fatcat:cekiclrstzdffbbfid7b7he3ze
NIHBA: A Network Interdiction Approach with Hybrid Benders Algorithm for Strain Design
[article]
2019
bioRxiv
pre-print
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To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems. ...
However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single ...
Likewise, many reactions can be excluded from consideration with a priori knowledge that, for example, they are vital for cell growth or their knockout is not likely to improve target production. ...
doi:10.1101/752923
fatcat:kbgst3c3cfd4jlt4bxpgeqpj54
An Overview on Target-Based Drug Design against Kinetoplastid Protozoan Infections: Human African Trypanosomiasis, Chagas Disease and Leishmaniases
2021
Molecules
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Target-based design expands the horizon of drug design and development and offers novel chemical entities and potential drug candidates to the therapeutic arsenal against the aforementioned neglected diseases ...
Infections: Drug Design, Synthesis and Pharmacology". ...
Acknowledgments: The authors would like to thank the graphic designer, Mirto Altani, for generating the Graphical Abstract and Figure 1 . ...
doi:10.3390/molecules26154629
pmid:34361781
pmcid:PMC8348971
fatcat:g54vkhk3bjflrkpie4mwufm46m
The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
2020
Life
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Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, ...
Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production ...
Controlling the expression of pentose phosphate pathway (PPP) genes is essential for the production of bioethanol. ...
doi:10.3390/life10110299
pmid:33233378
fatcat:bmdzyt5l4fgcde2zdmn75vnsde
Heurstic search for metabolic engineering: de novo synthesis of vanillin
2005
Computers and Chemical Engineering
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We present the application of heuristic search to in silico metabolic pathway engineering. ...
This paper represents a novel integration of artificial intelligence and biochemistry for computational metabolic engineering. ...
Acknowledgments The authors acknowledge Weiming Zhang for the visualization software. This work is sponsored by the National Science Foundation (BES-9911447), the Department of En- ...
doi:10.1016/j.compchemeng.2004.08.038
fatcat:ef4imsd2dffz7is2gze7fzcrkq
STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow
2018
BMC Bioinformatics
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STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. ...
This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. ...
Competing interests The authors declare that they have no competing interests. ...
doi:10.1186/s12859-018-2174-6
pmid:30066630
pmcid:PMC6069750
fatcat:zif5evrgm5cwlcwgpi7kbvvekq
Leveraging knowledge engineering and machine learning for microbial bio-manufacturing
2018
Biotechnology Advances
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Data driven frameworks can offer new constraints for mechanistic models to describe cellular regulations, to design pathways, to search gene targets, and to estimate fermentation titer/rate/yield under ...
Metabolic models play important role in design-build-test-learn cycles for strain improvement, and machine learning (ML) may provide a viable complementary approach for driving strain design and deciphering ...
This work was also part of the Joint BioEnergy Institute (http://www.jbei.org) and part of the Agile BioFoundry (http://agilebiofoundry.org) supported by the U.S. ...
doi:10.1016/j.biotechadv.2018.04.008
pmid:29729378
fatcat:wvoe5qasjbcr5efrshwjibdbvu
Advanced strategies for production of natural products in yeast
2020
iScience
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We then discuss advanced strategies in metabolic engineering at three different dimensions, including point, line, and plane (corresponding to the individual enzymes and cofactors, metabolic pathways, ...
In particular, we comprehensively discuss how to engineer cofactor biosynthesis for enhancing the biosynthesis efficiency, other than the enzyme activity. ...
ACKNOWLEDGMENTS
AUTHOR CONTRIBUTIONS R.C. and S.Y. wrote and revised the manuscript. L.Z. revised and provided feedback on the manuscript. Y.J.Z. conceived this study and wrote the manuscript. ...
doi:10.1016/j.isci.2020.100879
pmid:32087574
pmcid:PMC7033514
fatcat:aq7vevol6fhinh6rji325pq4vy
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
2020
Nature Communications
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We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning ...
tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. ...
The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). ...
doi:10.1038/s41467-020-17910-1
pmid:32978375
fatcat:xkk2647vp5bgddr5uguhehgsg4
A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions
2021
Metabolites
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cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways ...
Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively ...
Acknowledgments: The University of Johannesburg is thanked for providing a scholarship to K.C.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/metabo11120820
pmid:34940578
pmcid:PMC8709197
fatcat:liohk7epdzdy5fhroxm4haho5m
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