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MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan Bridge, Anne Morgat, Marco Pagni
<span title="2015-11-02">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular  ...  The MetaNetX.org website (http://www. metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation  ...  ACKNOWLEDGEMENTS Computation and maintenance of the MetaNetX.org server are provided by the Vital-IT center for high-performance computing of the SIB Swiss Institute of Bioinformatics (http://www.vital-it.ch  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1117">doi:10.1093/nar/gkv1117</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26527720">pmid:26527720</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702813/">pmcid:PMC4702813</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ccrzjdpzbjaoneo6bzhodes4ii">fatcat:ccrzjdpzbjaoneo6bzhodes4ii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720173949/https://serval.unil.ch/resource/serval:BIB_58AEB83D57CC.P001/REF.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/06/a006676679b8e490d4adf26ee3063e371ea46b2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1117"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702813" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Systematic Assessment Of Current Genome-Scale Metabolic Reconstruction Tools [article]

Sebastian N. Mendoza, Brett G. Olivier, Douwe Molenaar, Bas Teusink
<span title="2019-02-22">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated.  ...  However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models  ...  MetaNetX/MNXref -Reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res. 2016;44: D523- D526. doi:10.1093/nar/gkv1117 55.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/558411">doi:10.1101/558411</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ilpyd2acmzcg7cvh2pstf2cs3q">fatcat:ilpyd2acmzcg7cvh2pstf2cs3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200322183311/https://www.biorxiv.org/content/biorxiv/early/2019/02/22/558411.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/3b/5e3b03ea1ca2b46416eb0a5ee81c0dbfb65ceca6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/558411"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Inferring biochemical reactions and metabolite structures to understand metabolic pathway drift

Arnaud Belcour, Jean Girard, Méziane Aite, Ludovic Delage, Camille Trottier, Charlotte Marteau, Cédric Leroux, Simon M. Dittami, Pierre Sauleau, Erwan Corre, Jacques Nicolas, Catherine Boyen (+4 others)
<span title="2020-01-17">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5u6jlpnlzndwrequnssxehzurq" style="color: black;">iScience</a> </i> &nbsp;
Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution.  ...  Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally.  ...  ., 2017 Saito and Idler, 1966; Tasende et al., 2000 ; Santos et al., 2015 Saito and Idler, 1966 ; Tasende et al., 2000 Tasende et al., 2000 Santos et al., 2015 Saito and Idler, 1966; Tasende et  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.isci.2020.100849">doi:10.1016/j.isci.2020.100849</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32058961">pmid:32058961</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6997860/">pmcid:PMC6997860</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nhml3bs34vcsjlmwnk6etgqsbi">fatcat:nhml3bs34vcsjlmwnk6etgqsbi</a> </span>
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HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes [article]

Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A Cuche, Andrea Auchincloss, Elisabeth COUDERT, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios (+2 others)
<span title="2019-04-24">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Motivation: Genome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal  ...  and tools for genome and proteome annotation.  ...  Marco Pagni of the SIB Swiss Institute of Bioinformatics for interesting discussions and critical reading of the manuscript.  ... 
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711024927/https://www.biorxiv.org/content/biorxiv/early/2019/04/24/615294.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/0e/fe0ec3d154e559b0930efc0e92c6aa34deb2bb66.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/615294"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production

Snorre Sulheim, Tjaša Kumelj, Dino van Dissel, Ali Salehzadeh-Yazdi, Chao Du, Gilles P. van Wezel, Kay Nieselt, Eivind Almaas, Alexander Wentzel, Eduard J. Kerkhoven
<span title="2020-09-03">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5u6jlpnlzndwrequnssxehzurq" style="color: black;">iScience</a> </i> &nbsp;
Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor.  ...  We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences  ...  ., and Pagni, M. (2016). MetaNetX/ MNXref -reconciliation of metabolites and biochemical reactions to bring together genomescale metabolic networks. Nucleic Acids Res. 44, D523-D526.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.isci.2020.101525">doi:10.1016/j.isci.2020.101525</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32942174">pmid:32942174</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7501462/">pmcid:PMC7501462</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wkiyquwnpjemzgaqmkofzwvjja">fatcat:wkiyquwnpjemzgaqmkofzwvjja</a> </span>
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Network design and analysis for multi-enzyme biocatalysis [article]

Lisa Katharina Schuh, Universität Des Saarlandes
<span title="2020-11-24">2020</span>
Additionally, a comprehensive workflow for the reconstruction of metabolic networks based on data of the Kyoto Encyclopedia of Genes and Genomes (KEGG) combined with thermodynamic data for the determination  ...  There is therefore a demand for in silico tools to guide the design of such synthesis routes using computational methods for the path-finding, as well as the reconstruction of suitable genome-scale metabolic  ...  ., & PAGNI, M. (2016): MetaNetX/MNXref-reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22028/d291-32592">doi:10.22028/d291-32592</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dvjqffluevhkldazjcjdqlr5v4">fatcat:dvjqffluevhkldazjcjdqlr5v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201128203053/https://publikationen.sulb.uni-saarland.de/bitstream/20.500.11880/30081/1/DissertationLisaKatharinaSchuh2020.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/f2/33f2397e3009f01255b285746df0b3fd0f66d17f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22028/d291-32592"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Abstract Book, 3rd International SystemsX.ch Conference on Systems Biology

SystemsX.Ch
<span title="2017-09-04">2017</span>
The publisher does not have any control over and does not assume any responsibility for the correctness, accuracy, reliability or completeness of the content of this book.  ...  Poster | 68 MetaNetX/MNXref release 3: Major improvements in the reconciliation of metabolites and biochemical reactions to ease metabolic network reconstruction.  ...  create, analyse and compare genome-scale metabolic networks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3929/ethz-b-000176201">doi:10.3929/ethz-b-000176201</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f6flr7w5n5g3dn4ihwcjevzley">fatcat:f6flr7w5n5g3dn4ihwcjevzley</a> </span>
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20. Nachwuchswissenschaftlerkonferenz [article]

Dirk Sackmann, Jessika Rix, Ivette Witkowski, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität
<span title="2020-10-15">2020</span>
of cellular metabolism with constraintbased models: the COBRA Toolbox v2.0", Nat Protoc 6(9), 1290-1307 (2011) 4 Moretti S et al., "MetaNetX/MNXref -reconciliation of metabolites and biochemical reactions  ...  to bring together genome-scale metabolic networks", Nucleic Acids Research (2016), 44(D1):D523-D526 5 Siurana M, "Modelling and multi-objective optimisation for simulation of cyanobacterial metabolism  ... 
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