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Multiplex methods provide effective integration of multi-omic data in genome-scale models

Claudio Angione, Max Conway, Pietro Lió
2016 BMC Bioinformatics  
We apply this multi-omic fusion to an updated genome-scale reconstruction of Escherichia coli that includes underground metabolism and new gene-protein-reaction associations.  ...  Genomic, transcriptomic, and metabolic variations shape the complex adaptation landscape of bacteria to varying environmental conditions.  ...  Acknowledgements We would like to thank Naruemon Pratanwanich for initial discussion regarding this manuscript. Declarations The publication charges of this article were funded by FP7-Health-  ... 
doi:10.1186/s12859-016-0912-1 pmid:26961692 pmcid:PMC4896256 fatcat:vj5tn337qrgz7c55nz456o3sjq

Identifying essential genes in bacterial metabolic networks with machine learning methods

Kitiporn Plaimas, Roland Eils, Rainer König
2010 BMC Systems Biology  
In general, such a method is beneficial for inferring drug targets when experimental data about genome-wide knockout screens is not available for the investigated organism.  ...  However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.  ...  Acknowledgements This work was funded within the BMBF-FORSYS consortium Viroquant [#0313923]; the Nationales Genom-Forschungs-Netz (NGFN+) for the neuroblastoma project ENGINE, and the Commission on Higher  ... 
doi:10.1186/1752-0509-4-56 pmid:20438628 pmcid:PMC2874528 fatcat:uevlv6ablnbhtgqzogt4si377q

Weighting schemes in metabolic graphs for identifying biochemical routes

S. Ghosh, P. Baloni, S. Vishveshwara, N. Chandra
2013 Journal of Systems and Synthetic Biology  
Reconstruction of genome-scale metabolic graphs from genomics and other molecular or biochemical data is now feasible.  ...  The approach illustrated here is generic in nature and can be used in the analysis for metabolic network from any species and perhaps more importantly for comparing condition-specific networks.  ...  Kinetic parameters are not available for all reactions in this network; however transcriptome and metabolome data are available, which are incorporated into it.  ... 
doi:10.1007/s11693-013-9128-0 pmid:24592291 pmcid:PMC3933632 fatcat:a4oqjtksxjaorgbagcyiscjqri

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

D. McCloskey, B. O. Palsson, A. M. Feist
2014 Molecular Systems Biology  
The genome-scale model (GEM) of metabolism in the bacterium Escherichia coli K-12 has been in development for over a decade and is now in wide use.  ...  Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of  ...  We would like to thank Marc Abrams, Joshua Lerman, and Edward O'Brien for valuable input when composing the manuscript.  ... 
doi:10.1038/msb.2013.18 pmid:23632383 pmcid:PMC3658273 fatcat:rwxktywqebhgdptsdsetg4owle

Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

Hanseol Kim, Sinyeon Kim, Sung Ho Yoon
2018 PLoS ONE  
Here, we present the comprehensive metabolic network model of E. coli BL21(DE3), named iHK1487, based on the latest genome reannotation and phenome analysis.  ...  Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins.  ...  Use of transcriptome data for metabolic simulation Integrating transcriptome data into constraint-based models of metabolic network can improve flux prediction [60] [61] [62] .  ... 
doi:10.1371/journal.pone.0204375 pmid:30240424 pmcid:PMC6150544 fatcat:n3qiu2jpcvb4baqpcief5fzrb4

Genome-scale modeling for metabolic engineering

Evangelos Simeonidis, Nathan D. Price
2015 Journal of Industrial Microbiology & Biotechnology  
In large part owing to the advent of genomics and systems biology, we nowadays have a number of new tools that generate a wealth of data for analysis, contributing to our understanding of metabolism and  ...  developments in the field of metabolic and regulatory integration.  ...  We also thank Julie Bletz and Ben Heavner for critical readings of the manuscript, and James Eddy for assistance with the illustrations.  ... 
doi:10.1007/s10295-014-1576-3 pmid:25578304 pmcid:PMC4455951 fatcat:jrn652uygvaojb6tibg2iu5hqa

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

Cheng Zhang, Qiang Hua
2016 Frontiers in Physiology  
Genome-scale metabolic models (GEMs) have become a popular tool for systems biology, and they have been used in many fields such as industrial biotechnology and systems medicine.  ...  In addition, we describe the general principle of the applications and analyses built on GEMs.  ...  integrating transcriptomic or proteomic data into GEMs.  ... 
doi:10.3389/fphys.2015.00413 pmid:26779040 pmcid:PMC4703781 fatcat:j7ggvr7ntrgj7lqmn5kiwzq354

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer Konig
2008 BMC Systems Biology  
We show that topologic, genomic and transcriptomic features describing the network are sufficient for defining the essentiality of a reaction.  ...  Results: This paper presents a machine learning strategy to study and validate essential enzymes of a metabolic network.  ...  This work was funded within the BMBF-FOR-SYS consortium Viroquant (# 0313923), the Deutscher Akademischer Auslandsdienst, the Helmholtz Alliance on Systems Biology of Cancer and the Commission on Higher  ... 
doi:10.1186/1752-0509-2-67 pmid:18652654 pmcid:PMC2526078 fatcat:qjnttyoz6jdhngd5535iezh5he

Flux balance analysis of biological systems: applications and challenges

K. Raman, N. Chandra
2009 Briefings in Bioinformatics  
In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used.  ...  Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric  ...  The availability of genome-scale transcriptomics data can be advantageous in the integrated reconstruction of metabolic and regulatory networks.  ... 
doi:10.1093/bib/bbp011 pmid:19287049 fatcat:542cezsctjdmznnpwyfwpkdj3a

Reconstruction of biochemical networks in microorganisms

Adam M. Feist, Markus J. Herrgård, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson
2008 Nature Reviews Microbiology  
The network reconstruction process is organism specific and is based on an annotated genome sequence, high-throughput network-wide data sets and bibliomic data on the detailed properties of individual  ...  We describe the procedures in which various experimental data types are integrated to reconstruct biochemical networks, the current status of network reconstructions and how network reconstructions can  ...  Acknowledgements The authors thank A. Osterman and N. Jamshidi for their insights.  ... 
doi:10.1038/nrmicro1949 pmid:19116616 pmcid:PMC3119670 fatcat:rzxjs54qizdl7gnzjeuisc6lw4

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

Nathan E. Lewis, Harish Nagarajan, Bernhard O. Palsson
2012 Nature Reviews Microbiology  
data has accelerated the evolution of constraint-based reconstruction and analysis (COBRA) methods from a set of basic tools for metabolic network analysis into a powerful analytical framework that is  ...  Constraint-based modelling defined The COBRA approach is based on a few fundamental concepts.  ...  Acknowledgements The authors thank M. Abrams, J. Monk, D. Taylor  ... 
doi:10.1038/nrmicro2737 pmid:22367118 pmcid:PMC3536058 fatcat:ybk5wpy67fbcpnbg5azcu4rrse

Machine and deep learning meet genome-scale metabolic modeling

Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione, Jens Nielsen
2019 PLoS Computational Biology  
The development and application of these methodological frameworks have occurred independently for the most part, whereas the potential of their integration for biological, biomedical, and biotechnological  ...  Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine learning.  ...  This strategy was first investigated to predict metabolic reaction essentiality in E. coli.  ... 
doi:10.1371/journal.pcbi.1007084 pmid:31295267 pmcid:PMC6622478 fatcat:othxoh2y6rfsbis7q5e2cacdrq

Network Analyses in Plant Pathogens

David Botero, Camilo Alvarado, Adriana Bernal, Giovanna Danies, Silvia Restrepo
2018 Frontiers in Microbiology  
The review comprises metabolic simulation, protein-protein interactions, regulatory control of gene expression, hostpathogen modeling, and genome evolution in bacteria.  ...  A scenario, where the application of systems biology constitutes a very powerful tool, is the study of interactions between hosts and pathogens using network approaches.  ...  We also want to thank the Administrative Department of Science and Technology in Colombia (Colciencias) for the award under contract number 0794-2013 for support to CA.  ... 
doi:10.3389/fmicb.2018.00035 pmid:29441045 pmcid:PMC5797656 fatcat:ebka5yqikzhm7fqqgqfvojl7ra

Metabolic network modeling of microbial communities

Matthew B. Biggs, Gregory L. Medlock, Glynis L. Kolling, Jason A. Papin
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
manual curation, and novel algorithms for integrating omics data and engineering communities.  ...  Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities.  ...  Exchange reactions are defined to allow metabolites to enter and leave the network. All reactions are compiled into a stoichiometric (S) matrix.  ... 
doi:10.1002/wsbm.1308 pmid:26109480 pmcid:PMC4575871 fatcat:xy2brs6dzvcupac6ywnipm5fgy

Understanding human metabolic physiology: a genome-to-systems approach

Monica L. Mo, Bernhard Ø. Palsson
2009 Trends in Biotechnology  
Acknowledgements We thank Neema Jamshidi and Ines Thiele for their valuable comments and suggestions during preparation of the manuscript.  ...  Once in its in silico form, the genome-scale model can be used to perform several biological studies, as demonstrated by the historical use of the Escherichia coli metabolic reconstructions [27, 45] .  ...  Collecting metabolic knowledge: a reaction network point-of-view The annotated human genome, along with literature (or 'bibliome') data, defines the known biological components present in the human body  ... 
doi:10.1016/j.tibtech.2008.09.007 pmid:19010556 fatcat:2dasytln5nagjn72cbuxvdlxxe
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