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NEW BIOINFORMATICS RESOURCES FOR METABOLOMICS

JOHN L. MARKLEY, MARK E. ANDERSON, QIU CUI, HAMID R. EGHBALNIA, IAN A. LEWIS, ADRIAN D. HEGEMAN, JING LI, CHRISTOPHER F. SCHULTE, MICHAEL R. SUSSMAN, WILLIAM M. WESTLER, ELDON L. ULRICH, ZSOLT ZOLNAI
<span title="">2006</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2007 </i> &nbsp;
We recently developed two databases and a laboratory information system as resources for the metabolomics community.  ...  In addition to these databases, we have developed a new module for the Sesame laboratory information management system (http://www.sesame.wisc.edu) that captures all of the experimental protocols, background  ...  Madison Metabolomics Consortium Database (MMCD) Overview The purpose of the MMCD is to be a resource for MS and NMR based metabolomics by providing tools for metabolite identification and characterization  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812772435_0016">doi:10.1142/9789812772435_0016</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dywllrjv3jbszfnys5petgnxtq">fatcat:dywllrjv3jbszfnys5petgnxtq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160307052926/http://psb.stanford.edu/psb-online/proceedings/psb07/markley.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/d3/31/d3315b46f5709fac9a3e94652a6f54713083fd61.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812772435_0016"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

MetaboLights: towards a new COSMOS of metabolomics data management

Christoph Steinbeck, Pablo Conesa, Kenneth Haug, Tejasvi Mahendraker, Mark Williams, Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Reza M. Salek, Julian L. Griffin
<span title="2012-09-25">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o4ujczzsbjczzlknbsx2dlunuu" style="color: black;">Metabolomics</a> </i> &nbsp;
This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third  ...  Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights).  ...  Metabolomics datasets in the early stages of the MetaboLights launch.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11306-012-0462-0">doi:10.1007/s11306-012-0462-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23060735">pmid:23060735</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3465651/">pmcid:PMC3465651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wpbzp5mllrgd5clytm2wjolbca">fatcat:wpbzp5mllrgd5clytm2wjolbca</a> </span>
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Technological developments and opportunities with Workflow4Metabolomics

Giacomoni Franck
<span title="2020-01-21">2020</span> <i title="Zenodo"> Zenodo </i> &nbsp;
W4M also proposes new community resources promoting open science in metabolomics.  ...  Metabolomics data analysis is a complex, multistep process, which is constantly evolving with the development of new analytical technologies, mathematical methods, bioinformatics tools and databases.  ...  . • New database resources for metabolite and contaminant annotation [4, 5, 6] and the BARSA new algorithm for NMR-2D spectral annotation. W4M is fully involved in the Open science movement.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3618162">doi:10.5281/zenodo.3618162</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p5npavc5o5am7nl3ziu6xb76au">fatcat:p5npavc5o5am7nl3ziu6xb76au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211100318/https://zenodo.org/record/3618163/files/200107_Poster_rfmf_metabomeeting_W4M%28FG%29_V02.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/ba/bb/babb49ad6185ecefe30bee7254ea06aef2480963.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3618162"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

F. Giacomoni, G. Le Corguille, M. Monsoor, M. Landi, P. Pericard, M. Petera, C. Duperier, M. Tremblay-Franco, J.-F. Martin, D. Jacob, S. Goulitquer, E. A. Thevenot (+1 others)
<span title="2014-12-19">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation  ...  W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB).  ...  ., 2012) is provided as a reference for new module and workflow evaluation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu813">doi:10.1093/bioinformatics/btu813</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25527831">pmid:25527831</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4410648/">pmcid:PMC4410648</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fjpldwbksfgclbcdg65hnxvzdm">fatcat:fjpldwbksfgclbcdg65hnxvzdm</a> </span>
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Training needs in metabolomics

Ralf J. M. Weber, Catherine L. Winder, Lee D. Larcombe, Warwick B. Dunn, Mark R. Viant
<span title="2015-05-29">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o4ujczzsbjczzlknbsx2dlunuu" style="color: black;">Metabolomics</a> </i> &nbsp;
It is notable that the number of metabolomics datasets in these public repositories is growing at a very encouraging rate (http:// metabolomexchange.org) given they are relatively new resources, yet only  ...  There is a strong preference for advanced training versus introductory courses in bioinformatics related topics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11306-015-0815-6">doi:10.1007/s11306-015-0815-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26109924">pmid:26109924</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4475540/">pmcid:PMC4475540</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mmoprb4hpndzthy25jhpppjdeu">fatcat:mmoprb4hpndzthy25jhpppjdeu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171014062434/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/6f8/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjEwMDcvczExMzA2LTAxNS0wODE1LTYucGRm.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/02/db/02db80b8e1b644bdae263b6bbe9620c31d8aeb9f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11306-015-0815-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475540" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The future of metabolomics in ELIXIR

Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia (+27 others)
<span title="2017-09-06">2017</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
Acknowledgements We are grateful to the proteomics community for sharing their experiences from their meeting "The future of proteomics in ELIXIR" on March 1-2 2017 in Tübingen, allowing us to build on  ...  Conversely, new modules can be developed to integrate and harmonize annotations from complementary resources.  ...  of phenotype diversity and for the identification of new biomarkers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12342.1">doi:10.12688/f1000research.12342.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29043062">pmid:29043062</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5627583/">pmcid:PMC5627583</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x2ddsosu7re4pnkc64vyl42rri">fatcat:x2ddsosu7re4pnkc64vyl42rri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722114322/https://f1000researchdata.s3.amazonaws.com/manuscripts/13363/408f187d-ef27-4b7a-bbea-35cbe23314b6_12342_-_Namrata_Kale.pdf?doi=10.12688/f1000research.12342.1" 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/2b/02/2b02669cb6560cbf46a3371153efd1a4c421be85.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12342.1"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627583" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The future of metabolomics in ELIXIR

Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia (+28 others)
<span title="2017-10-30">2017</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
Acknowledgements We are grateful to the proteomics community for sharing their experiences from their meeting "The future of proteomics in ELIXIR" on March 1-2 2017 in Tübingen, allowing us to build on  ...  of phenotype diversity and for the identification of new biomarkers.  ...  Conversely, new modules can be developed to integrate and harmonize annotations from complementary resources.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12342.2">doi:10.12688/f1000research.12342.2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29043062">pmid:29043062</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5627583/">pmcid:PMC5627583</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eatb35wrknghvefwetltlvoh2u">fatcat:eatb35wrknghvefwetltlvoh2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223182719/http://pdfs.semanticscholar.org/4b51/75b85622941385c24751f3c09f74d9961469.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/4b/51/4b5175b85622941385c24751f3c09f74d9961469.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12342.2"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627583" 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 and Bioinformatics: An Essential Toolbox for Systems Analyses of Plant Functions Beyond 2010

K. Shinozaki, H. Sakakibara
<span title="2009-07-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qyzgzqbtjbd3xewtgies5bhl2e" style="color: black;">Plant and Cell Physiology</a> </i> &nbsp;
In tandem with the advance of genomics, other omics technologies such as metabolomics and proteomics have developed extensively, built upon new mass spectrometry methods.  ...  For these integrated analyses, databases of metabolomic, proteomic and transcriptomic information comprise an essential toolbox.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcp085">doi:10.1093/pcp/pcp085</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19596708">pmid:19596708</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2709552/">pmcid:PMC2709552</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gray7sxqlzgihcfki77t4v3znq">fatcat:gray7sxqlzgihcfki77t4v3znq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191106161634/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2709552&amp;blobtype=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/c4/16/c4164dfc0ed47de1e0acc4a523001ffde3801f58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pcp085"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709552" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

<span title="2019-01-04">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a7p5unsuyff7bnvxtpt272ocfq" style="color: black;">Plant Direct</a> </i> &nbsp;
(b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics).  ...  and publicly-shared resources.  ...  One priority is the need for new or improved standards in proteomics and metabolomics. These might be achieved by consensus among the major producers/publishers in these fields.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pld3.109">doi:10.1002/pld3.109</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31245752">pmid:31245752</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6508773/">pmcid:PMC6508773</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7vrvjbolnzaaxjs6kghbkvtgje">fatcat:7vrvjbolnzaaxjs6kghbkvtgje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501013807/https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1209&amp;context=gdcb_las_pubs" 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/ab/90/ab90962217b1deb032ee4c6654aee119f0a020be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pld3.109"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508773" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The European Bioinformatics Institute in 2016: Data growth and integration

Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler
<span title="2015-12-15">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;
Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework  ...  In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.uk) are continually expanding: total disk capacity increases significantly every year to keep  ...  FUNDING Funding for open access charge: EMBL (www.embl.org). Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1352">doi:10.1093/nar/gkv1352</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26673705">pmid:26673705</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702932/">pmcid:PMC4702932</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2oonfh72mrbpfi2ywith6updti">fatcat:2oonfh72mrbpfi2ywith6updti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227171902/http://pdfs.semanticscholar.org/841d/bff787e715ffb5b4c6b5a9841e0a2da0f1a0.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/84/1d/841dbff787e715ffb5b4c6b5a9841e0a2da0f1a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1352"> <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/PMC4702932" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Research Opportunities for Metabolomics at NIH

Mukesh Verma
<span title="">2012</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/725mfs2xfzfptd2w2m3qgwelba" style="color: black;">Journal of Proteomics &amp; Bioinformatics</a> </i> &nbsp;
The number of publications in the year 2010 was 4000 for proteomics, 3000 for genomics, and only 600 for metabolomics related topics.  ...  The funding for metabolomics related research at NIH from 2008-2011was $25,656,838.  ...  for new research project grant.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jpb.10000e11">doi:10.4172/jpb.10000e11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5q74vjh5mjafjh7fnpieqpu4je">fatcat:5q74vjh5mjafjh7fnpieqpu4je</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724044726/https://www.omicsonline.org/research-opportunities-for-metabolomics-at-nih-jpb.10000e11.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jpb.10000e11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Chapter 3: Small Molecules and Disease

David S. Wishart, Fran Lewitter, Maricel Kann
<span title="2012-12-27">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.  ...  This article is part of the "Translational Bioinformatics" collection for PLOS Computational Biology.  ...  This has led to the emergence of a new field of bioinformatics -called chemical bioinformatics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002805">doi:10.1371/journal.pcbi.1002805</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23300405">pmid:23300405</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3531289/">pmcid:PMC3531289</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kfa4lvpiu5cs3nwvkeysrbnpcu">fatcat:kfa4lvpiu5cs3nwvkeysrbnpcu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015140118/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002805&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/03/27/0327c21c440285e6151b365f821fe4a6eeae905a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002805"> <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/PMC3531289" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, Maria Luisa Chiusano
<span title="2019-10-11">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ec2qn47apbbfjgxx4e2oivikr4" style="color: black;">Marine Drugs</a> </i> &nbsp;
for biotechnology applications from marine resources.  ...  In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities  ...  In this review, we focus on the main resources of bioinformatics and methodologies, discussing their role in supporting and accelerating the discovery of new marine-derived products, describing major applications  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/md17100576">doi:10.3390/md17100576</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31614509">pmid:31614509</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6835618/">pmcid:PMC6835618</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jch7dwrhgrhipihvf42zr6bljm">fatcat:jch7dwrhgrhipihvf42zr6bljm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200216105956/https://res.mdpi.com/d_attachment/marinedrugs/marinedrugs-17-00576/article_deploy/marinedrugs-17-00576.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/6d/50/6d50a5e2f33a44bcc651b36467ac73729c51fe7a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/md17100576"> <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/PMC6835618" 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 roadmap for the XCMS family of software solutions in metabolomics

Nathaniel G Mahieu, Jessica Lloyd Genenbacher, Gary J Patti
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o5uh5dlljbbfjm7vgxk2jibrwu" style="color: black;">Current Opinion in Chemical Biology</a> </i> &nbsp;
The latter types of applications have necessitated the development of new software programs, which have introduced additional functionalities that facilitate data analysis.  ...  The objective of this review is to provide an overview of the freely available bioinformatic solutions that are either based upon or are compatible with the algorithms in XCMS, which we broadly refer to  ...  Acknowledgements GJP received financial support for this work from the National Institutes of Health Grants R01 ES022181 and L30 AG0 038036, as well as the Alfred P.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cbpa.2015.11.009">doi:10.1016/j.cbpa.2015.11.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26673825">pmid:26673825</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4831061/">pmcid:PMC4831061</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gppt6zz3xvbslgp2och4gzkr4q">fatcat:gppt6zz3xvbslgp2och4gzkr4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191101221906/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4831061&amp;blobtype=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/7b/5e/7b5eb98e24ec372ea0eaaf7126fb77cce0ec3c8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cbpa.2015.11.009"> <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/PMC4831061" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Toxicogenomics through the eyes of informatics: conference overview and recommendations

Kenneth Olden, Neysa Call, Bruno Sobral, Robin Oakes
<span title="">2004</span> <i title="Environmental Health Perspectives"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3w6amv3ecja7fa3ext35ndpiky" style="color: black;">Environmental Health Perspectives</a> </i> &nbsp;
biology, and information technology infrastructure for data and tool management.  ...  Researchers around the world met to discuss how the application of bioinformatics tools, methodologies, and technologies will enhance our understanding of how cells and organisms respond to toxins.  ...  For investigators to catalyze forward movement in these new directions, however, baseline (or normal) data for systems, including normal ranges of variation, must be generated and centrally stored in publicly  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1289/ehp.112-1241996">doi:10.1289/ehp.112-1241996</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15159210">pmid:15159210</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1241996/">pmcid:PMC1241996</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4wk32hsjvvhqpnkkx2akljqwqy">fatcat:4wk32hsjvvhqpnkkx2akljqwqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200428080453/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1241996&amp;blobtype=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/a0/44/a044465d4b1f110ade7caa1c6c43a5889486d516.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1289/ehp.112-1241996"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241996" 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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