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Learning to Classify Organic and Conventional Wheat – A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform

Nikolas Kessler, Anja Bonte, Stefan P. Albaum, Paul Mäder, Monika Messmer, Alexander Goesmann, Karsten Niehaus, Georg Langenkämper, Tim W. Nattkemper
<span title="2015-03-24">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tkuhrcyiufdxtkdmjqvay6f2ua" style="color: black;">Frontiers in Bioengineering and Biotechnology</a> </i> &nbsp;
More than 300 GC-MS measurements were recorded and subsequently processed and analyzed in the MeltDB 2.0 metabolomics analysis platform, being briefly outlined in this paper.  ...  We present results of our machine learning approach to the problem of classifying GC-MS data originating from wheat grains of different farming systems.  ...  Funding: The authors acknowledge the financial support provided by the German Federal Ministry of Food and Agriculture under the Federal Scheme for Organic Farming and other forms of sustainable agriculture  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00035">doi:10.3389/fbioe.2015.00035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25853128">pmid:25853128</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4371749/">pmcid:PMC4371749</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2zoeadoqbbesff7m5mn35t4som">fatcat:2zoeadoqbbesff7m5mn35t4som</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007162612/http://publisher-connector.core.ac.uk/resourcesync/data/Frontiers/pdf/c86/aHR0cDovL2pvdXJuYWwuZnJvbnRpZXJzaW4ub3JnL2FydGljbGUvMTAuMzM4OS9mYmlvZS4yMDE1LjAwMDM1L3BkZg%3D%3D.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/1b/26/1b26d38955d4293e1f143e154590c70959045580.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371749" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

J. Xia, N. Psychogios, N. Young, D. S. Wishart
<span title="2009-05-08">2009</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;
The data processing challenges in metabolomics are quite unique and often require specialized (or expensive) data analysis software and a detailed knowledge of cheminformatics, bioinformatics and statistics  ...  MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses.  ...  INTRODUCTION Metabolomics is a field of 'omics' science that aims to study global metabolic changes in biological systems (1) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp356">doi:10.1093/nar/gkp356</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19429898">pmid:19429898</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2703878/">pmcid:PMC2703878</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y2s3onankbdgbagkj2mqhfjnoi">fatcat:y2s3onankbdgbagkj2mqhfjnoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227180544/http://pdfs.semanticscholar.org/9454/9a171a61039ed1f9b5954ce42181c574ccc3.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/94/54/94549a171a61039ed1f9b5954ce42181c574ccc3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp356"> <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/PMC2703878" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Plants Metabolome Study: Emerging Tools and Techniques

Manish Kumar Patel, Sonika Pandey, Manoj Kumar, Md Intesaful Haque, Sikander Pal, Narendra Singh Yadav
<span title="2021-11-08">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3wvjgpafonfk5f6pu57vw72ave" style="color: black;">Plants</a> </i> &nbsp;
Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.  ...  Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants.  ...  Data Availability Statement: All data included in the main text. Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/plants10112409">doi:10.3390/plants10112409</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34834772">pmid:34834772</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8621461/">pmcid:PMC8621461</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kd4y3zlz3fg6zlwcqbyjwpjc5m">fatcat:kd4y3zlz3fg6zlwcqbyjwpjc5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211120182130/https://mdpi-res.com/d_attachment/plants/plants-10-02409/article_deploy/plants-10-02409-v2.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/d9/91/d99151f11b53e50ed0cccc41c5d8c063b77ea66b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/plants10112409"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8621461" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metabolomics: A Way Forward for Crop Improvement

Ali Razzaq, Bushra Sadia, Ali Raza, Muhammad Khalid Hameed, Fozia Saleem
<span title="2019-12-14">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ie7tehbfsfhs5pdyyt2rrdmnpm" style="color: black;">Metabolites</a> </i> &nbsp;
This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement.  ...  Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo9120303">doi:10.3390/metabo9120303</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31847393">pmid:31847393</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6md7ljmpvjakjf7oa7mcdeauoa">fatcat:6md7ljmpvjakjf7oa7mcdeauoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191217090452/https://res.mdpi.com/d_attachment/metabolites/metabolites-09-00303/article_deploy/metabolites-09-00303.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/f8/e1/f8e134caf45801b2677aa31928100089c5d88194.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo9120303"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Online Metabolomics Databases and Pipelines [chapter]

Adam J.
<span title="2012-02-10">2012</span> <i title="InTech"> Metabolomics </i> &nbsp;
No quantitative information is provided with metabolite detections and there is no way to compare the results of different experiments.  ...  Description: A study design database for GC/MS metabolomics experiments. Species: Plant species Reference data: Provides raw and processed GC/MS data for download together with metadata.  ...  Overrepresentation Analysis; DI/MS = Direct Infusion / Mass Spectrometry Feature / Tool Name: Metabolome Express XCMS Online Metabo Analyst MeltDB metDAT 2.0 Reference: (Carroll et al.,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/31021">doi:10.5772/31021</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7nkgmwx72nesleacrrulcrwf4a">fatcat:7nkgmwx72nesleacrrulcrwf4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815102306/http://cdn.intechopen.com/pdfs-wm/28003.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/9e/d7/9ed7087ccb866d33e1b61d7b9906a2c29ca72603.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/31021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data

Sergio Fructuoso, Ángel Sevilla, Cristina Bernal, Ana Lozano, José Iborra, Manuel Cánovas
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gl3hmlq4ebd3jcx3yuj2yfzivq" style="color: black;">BMC Research Notes</a> </i> &nbsp;
Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account  ...  Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out.  ...  In contrast, software tools require a version for every operating system with the exception of Java-based systems. Secondly, minimal installation is needed, as previously described.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0500-5-428">doi:10.1186/1756-0500-5-428</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22884039">pmid:22884039</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3494514/">pmcid:PMC3494514</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6hu3krfyuvhqhngixcgknoun5y">fatcat:6hu3krfyuvhqhngixcgknoun5y</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3494514/PMC3494514-1756-0500-5-428.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> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0500-5-428"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494514" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metabolomics: an emerging frontier of systems biology in marine macrophytes

Manoj Kumar, Unnikrishnan Kuzhiumparambil, Mathieu Pernice, Zhijian Jiang, Peter J. Ralph
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cctktt5zrbemtmbddrms4pg6eq" style="color: black;">Algal Research</a> </i> &nbsp;
The integration 179 of metabolomics with the allied 'omics disciplines of transcriptomic, 180 proteomic and fluxomics approaches are discussed in the context of 181 developing biological systems networks  ...  Finally, we provide a 37 comprehensive overview of an in silico plant metabolome database that can be utilized to advance our knowl-38 edge from a system biology approach to marine macrophytes. 39 128  ...  Application of metabolomics to the study of marine macrophyte system biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0 65 4.1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.algal.2016.02.033">doi:10.1016/j.algal.2016.02.033</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fgic4jcw35drjn3qwlioefkdti">fatcat:fgic4jcw35drjn3qwlioefkdti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428001217/https://opus.lib.uts.edu.au/bitstream/10453/58798/5/2-s2.0-84961999770%20am.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/68/32/68327b4cdb2adf8b268cdb46c8b2fe572f48c343.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.algal.2016.02.033"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles

Anne-Christin Hauschild, Tobias Frisch, Jörg Baumbach, Jan Baumbach
<span title="2015-06-10">2015</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ie7tehbfsfhs5pdyyt2rrdmnpm" style="color: black;">Metabolites</a> </i> &nbsp;
While the artificial data are utilized as a proof of concept, we will demonstrate how Carotta finds candidate markers in our real dataset associated with confounders rather than the primary disease (COPD  ...  The back-end is designed to be modular, allowing for easy extensions with plugins in the future, such as new clustering methods and statistics.  ...  Acknowledgments We are grateful for the anonymous COPD datasets of the IMS chromatograms related to the three groups as obtained by Michael Westhoff, Patrick Litterst and Barbara Obertrifter, all from  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo5020344">doi:10.3390/metabo5020344</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26065494">pmid:26065494</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4495376/">pmcid:PMC4495376</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4hl6exclwrfbroexbgcgwrqmeq">fatcat:4hl6exclwrfbroexbgcgwrqmeq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721222747/https://publikationen.reutlingen-university.de/frontdoor/deliver/index/docId/447/file/447.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/d3/02/d302a619d4402b2aba499ed1de6292347ba2101d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo5020344"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495376" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling

Miroslava Cuperlovic-Culf
<span title="2018-01-11">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ie7tehbfsfhs5pdyyt2rrdmnpm" style="color: black;">Metabolites</a> </i> &nbsp;
To a lesser extent, machine learning has also been utilized to take advantage of the increasing availability of genomics and metabolomics data for the optimization of metabolic network models and their  ...  for model optimization, parameter determination or system analysis using models, as well as the utilization of several different types of machine learning technologies.  ...  Acknowledgments: With the current explosion of the utilization of machine learning in biology, it was not possible to include all examples of applications in system biology, and unfortunately, many fascinating  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo8010004">doi:10.3390/metabo8010004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29324649">pmid:29324649</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5875994/">pmcid:PMC5875994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hdzmuzagcjbolhx6hpr4grvw24">fatcat:hdzmuzagcjbolhx6hpr4grvw24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727084939/https://res.mdpi.com/def50200c3b4186a9417d7beddcd90c185fe23ca58a7eb4a6072bb4ad8e26c4f9d08c141ae6176515f82a236044892c9190fe907020733da57e953dfd2b71d8786b35572589d9b92e0b015fd83ba6cd6ff98127f8ad50b1b8c773544002494395f8984eff2e5516307178c79a72c907b0936b2c74dad036415727f534c69bf12fbf5f9869b249a690a692c1e821c8bc9f388d152c76b9935d752f2eeb93bd8?filename=&amp;attachment=1" 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/4e/dd/4edd70173c73d7a0805124c25c1e7f1081633cc7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/metabo8010004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875994" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis

Nikolas Kessler, Frederik Walter, Marcus Persicke, Stefan P. Albaum, Jörn Kalinowski, Alexander Goesmann, Karsten Niehaus, Tim W. Nattkemper, Frederique Lisacek
<span title="2014-11-26">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
A common approach to correct for these effects is the addition of a U-13 C-labeled internal standard and the calculation of mass isotopomer ratios for each metabolite.  ...  An important step in compound identification is the deconvolution of mass signals.  ...  Acknowledgments The authors thank the BRF team for expert technical support. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0113909">doi:10.1371/journal.pone.0113909</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25426929">pmid:25426929</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4245236/">pmcid:PMC4245236</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u7fuqaqlovgnjb3uyj7lcfjicu">fatcat:u7fuqaqlovgnjb3uyj7lcfjicu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010120120/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0113909&amp;type=printable" 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/b1/fe/b1fed3026de61e834c7cd0ec822d736f7f7012fe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0113909"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245236" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An interactive online software platform for the analysis of small molecules using hyphenated mass spectrometry: MeltDB and ALLocator

Nikolas Kessler
<span title="2018-12-11">2018</span>
The MeltDB 2.0 software platform and its advancements are covered in chapter 7.  ...  The development of MeltDB 2.0 advanced the handling of 100s of analyses in a single experiment.  ...  MeltDB 2.0: Handling hundreds of chromatograms efficiently The MeltDB web platform can deal with large experiments containing hundreds of chromatograms, and it offers a vast toolbox of statistics that  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4119/unibi/2932648">doi:10.4119/unibi/2932648</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z54kr2wsxndf5m2wjqqiwgtwjy">fatcat:z54kr2wsxndf5m2wjqqiwgtwjy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200218034530/https://pub.uni-bielefeld.de/download/2932648/2932649/thesis_nkessler.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/71/18/7118b90f452b3a1f953bb59435ea0db07fb2e031.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4119/unibi/2932648"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Computational mass spectrometry for small molecules

Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
Finally, we list available software for different steps of the analysis pipeline. reproducibility of product ion spectra across eleven different mass spectrometers.  ...  The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data.  ...  (PRiMe) [67] , or MeltDB [68] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-5-12">doi:10.1186/1758-2946-5-12</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23453222">pmid:23453222</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3648359/">pmcid:PMC3648359</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r2l2i3tfi5hqfm7iidqxsza25e">fatcat:r2l2i3tfi5hqfm7iidqxsza25e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721002638/https://jcheminf.springeropen.com/track/pdf/10.1186/1758-2946-5-12?site=jcheminf.springeropen.com" 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/f8/5d/f85d12a6485579915a7ace5aabf83dca2daa3c64.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1758-2946-5-12"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648359" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational tools for metabolic engineering

Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p47wd2skxvdwbanewzmokbss3a" style="color: black;">Metabolic Engineering</a> </i> &nbsp;
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques.  ...  The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.  ...  The funders had no role in the decision to publish, or in the preparation of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2012.03.001">doi:10.1016/j.ymben.2012.03.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22629572">pmid:22629572</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3361690/">pmcid:PMC3361690</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xqnmydnnejcupp2ujup45krwnm">fatcat:xqnmydnnejcupp2ujup45krwnm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219211009/http://pdfs.semanticscholar.org/1aa6/e2a0a7518dcb9c018911de8494bd7acd7eba.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/1a/a6/1aa6e2a0a7518dcb9c018911de8494bd7acd7eba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2012.03.001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361690" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Omics Approaches for Understanding Heavy Metal Responses and Tolerance in Plants

Monica Jamla, Tushar Khare, Shrushti Joshi, Suraj Patil, Suprasanna Penna, Vinay Kumar
<span title="">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m3p3hvzakffdxnyoguxabfvqbm" style="color: black;">Current Plant Biology</a> </i> &nbsp;
(metabolomics) including metals (metallomics), which can ultimately be used for improving stress tolerance or generating resilience plant systems.  ...  State-of-the-art in Omics approaches including genomics, transcriptomics, metabolomics, miRNAomics and metallomics for plant HM research have been presented.  ...  Among the various approaches, metabolomics works in a wider range and is comparatively more advanced, popular and creates a larger database, giving extensive knowledge on the internal working and response  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpb.2021.100213">doi:10.1016/j.cpb.2021.100213</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xpxob5fycnh73p4f6norhp5xhe">fatcat:xpxob5fycnh73p4f6norhp5xhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210729030444/https://pdf.sciencedirectassets.com/305930/1-s2.0-S2214662821X00035/1-s2.0-S2214662821000189/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEHsaCXVzLWVhc3QtMSJIMEYCIQCGNR8iB%2F%2BnQx7QK12aRDwxR07qpP2UZfjPk8Zf2LSVhAIhAOwWcDuHJlkCicYe0NpGtGNsJLJFirQhGJU%2BkQvu%2B25gKoMECIP%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQBBoMMDU5MDAzNTQ2ODY1IgxRLrj8J8No5pOgvPUq1wM5dGsLOHH6pUKig7095YGxqKdmaVUEjlOIBwM8JG0BXoxl%2BtKAFJj1RJxR0mSqZxSinC%2B1KRR9Gcnz8wioryfI0qSUsfllH%2Fy%2BlOm4%2Fq88EHZwpNMxLjHUyDjjHtfYvHNECZeqzG8ixdYPUUgA6o4bOoFXdTqDTPMGzkpTPD8iF1WxaEpJ703MLYCrrJMtSyBxEpmFJapeD7BkheENN%2BZzh097ImO2sJNaFsw2GPreB2IJ7LXvtImjg81XE6AXSY9uuE0ANB4bDIKYJr5cnaVD5PuvmGMGaAqYzTTENspaItB7LLPKjYlvCDWcD6493B3Sj7xuBK9bXfbqgX5IkWSY8Ig6Von5ZbC8Ii087e3y5Oxrr4cT0I7KFevqiDONM3q6jX%2FRoRm2mjb0uQNmJ6BOxV5aJWVCZtnK7wUnnWWPFJ%2FpFWYxwgxgSv4J4YMg%2FRKHyPw3CDplY7OpiVMnR8JJuyDM2aLDZMNmbcDJGUp4Du7OVS%2BzCqrB0yxOkKjiQte%2Bv9edo5tAffRZUnKT0ZA9hbcP3ZFCQ5ZSUWcXNnn0ezVXHG0eOcNAITFFKpq1FqOJlCuepmnGUrkbox45iph%2FbQU9NCCAR2rz0gUv6YGOd7eRXreLSzMwvKGIiAY6pAHPRK%2Btc9%2FhIZs%2BCs4wtKgjI%2Bbc8cRWMUhU%2BAGwVtPwNQFQZL9P5RJYGqkDqGcy7g%2BLqtFUE8qSA4uOSO0oTazFEc8lwcmnuMofA10Y3xVUbErbpnmk%2FAcKD7rrHLW9eOO6qrVB60MScoheqauTcLL5qoacqlJopOg%2BFG1sV%2FfXyr3hFHevUcJ61X%2Br4orGgxCpNqW8XINnRcB4Er5U3Rg%2FeZKn4g%3D%3D&amp;X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Date=20210729T030438Z&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Expires=300&amp;X-Amz-Credential=ASIAQ3PHCVTY5GU5ZEPX%2F20210729%2Fus-east-1%2Fs3%2Faws4_request&amp;X-Amz-Signature=e2b2a1d58d4888945bb52c152b186a93ce2cda4389fc4ae1289f0315c62146ee&amp;hash=85dc1356dc0578386eceb6f44373757292d452ea3fe49005e1a009ecb1728f3c&amp;host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&amp;pii=S2214662821000189&amp;tid=spdf-3db2b338-5915-4453-886e-dd74826ed32b&amp;sid=c9a450389147b7463f08e4946106d5497b86gxrqa&amp;type=client" 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/97/82/9782647b647c2a51eaceacb338406599f8fbebec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpb.2021.100213"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data

Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger (+5 others)
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend.  ...  The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services.  ...  The development of the system was supported within the Grain Legumes Integrated Project (funded by the European Commission FP6 contract No.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-50">doi:10.1186/1471-2105-10-50</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19200358">pmid:19200358</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2645365/">pmcid:PMC2645365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vmficlw2vnfuvggnegr4zvyp5q">fatcat:vmficlw2vnfuvggnegr4zvyp5q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922003628/https://munin.uit.no/bitstream/handle/10037/3124/article.pdf?sequence=1" 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/02/85/028539afb9c5f115163fff3500e266fb29a7d8ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-50"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645365" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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