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Enterotypes of the human gut microbiome

Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel (+31 others)
<span title="2011-06-08">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature10187">doi:10.1038/nature10187</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/47d23dy3mrezdhfst6vtyxaqie">fatcat:47d23dy3mrezdhfst6vtyxaqie</a> </span>
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Erratum: Addendum: Enterotypes of the human gut microbiome

Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel (+31 others)
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature13075">doi:10.1038/nature13075</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6oerjp3onzfidbyov5i4rl65we">fatcat:6oerjp3onzfidbyov5i4rl65we</a> </span>
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Microbiology: The inside story

Asher Mullard
<span title="2008-05-29">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Enter the as-yet-unlaunched International Human Microbiome Consortium.  ...  One of questions being addressed by the consortium is over intellectual property.  ... 
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Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

Agata Wesolowska-Andersen, Martin Bahl, Vera Carvalho, Karsten Kristiansen, Thomas Sicheritz-Pontén, Ramneek Gupta, Tine Licht
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wf7hw6dszneotfrzxhzcmknpdy" style="color: black;">Microbiome</a> </i> &nbsp;
The sequencing reads were also mapped to the assembled bacterial sequence catalogs generated by the HMP and the MetaHIT consortium, as well as to the gene catalog created for the purpose of this study,  ...  Comparison of gene catalog composition The reference gene catalogs created by both the HMP and MetaHIT consortiums had significantly more reads mapped to them when extracted with the HMP method ( Figure  ...  Authors' information KK, TSP and RG are part of the MetHIT consortium.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2049-2618-2-19">doi:10.1186/2049-2618-2-19</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24949196">pmid:24949196</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4063427/">pmcid:PMC4063427</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nmqxldbaxfgmxmcnrgcap6z7jm">fatcat:nmqxldbaxfgmxmcnrgcap6z7jm</a> </span>
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The human gut microbiome: are we our enterotypes?

Roland J. Siezen, Michiel Kleerebezem
<span title="2011-08-17">2011</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hqhbgym6bfdm5jsesxfb3g5wza" style="color: black;">Microbial Biotechnology</a> </i> &nbsp;
Acknowledgements The research that led to the discovery of the enterotypes was in part funded by the European Community's Seventh Framework Programme (FP7/2007(FP7/ -2013 in the project MetaHIT; grant  ...  (http://www.hmpdacc.org/project_ catalog.html) and 100 gut genomes by the MetaHIT Consortium (http://www.sanger.ac.uk/resources/downloads/ bacteria/metahit/).  ...  from many body sites (but mainly the GIT) by the Human Microbiome Jumpstart Reference Strains Consortium (Nelson et al., 2010) cells of uncultured gut bacteria by single-cell genome sequencing (de  ... 
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210802080623/https://repository.ubn.ru.nl/bitstream/handle/2066/96436/1/96436.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/0b/e3/0be3211f8f1974bda14ee87645e93bc8d6775311.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1751-7915.2011.00290.x"> <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/PMC3819005" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Methodology and Ontology in Microbiome Research

John Huss
<span title="2014-07-29">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rmjg5t2egra7tcezac7ftv27qu" style="color: black;">Biological Theory</a> </i> &nbsp;
As Erlich and The MetaHIT Consortium (2011, p. 308) note: MetaHIT seeks to be integrated in the world we live in.  ...  As announced on the MetaHIT consortium main page, http:// metahit.eu.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13752-014-0187-6">doi:10.1007/s13752-014-0187-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25484632">pmid:25484632</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4250566/">pmcid:PMC4250566</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ke7akdxod5cmhit2amnasrxxf4">fatcat:ke7akdxod5cmhit2amnasrxxf4</a> </span>
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A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

Mariel M. Finucane, Thomas J. Sharpton, Timothy J. Laurent, Katherine S. Pollard, Markus M. Heimesaat
<span title="2014-01-08">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;
In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically  ...  differences in phylum-level taxonomic composition between lean and obese individuals in several cohorts, we find no association between BMI and taxonomic composition of stool microbiomes in the larger HMP and MetaHIT  ...  The MetaHIT data was composed of shotgun metagenomes, which we downloaded from The European Bioinformatics Institute (www.ebi.ac.uk).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0084689">doi:10.1371/journal.pone.0084689</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24416266">pmid:24416266</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3885756/">pmcid:PMC3885756</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rjmr6kfjafcttlet7qgmrp5hrq">fatcat:rjmr6kfjafcttlet7qgmrp5hrq</a> </span>
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A framework for human microbiome research

<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
We would also like to thank our collaborators throughout the International Human Microbiome Consortium, particularly the investigators of the MetaHIT project, for advancing human microbiome research.  ...  Acknowledgements The consortium would like to thank our external scientific advisory board: R. Blumberg, J. Davies, R. Holt, P. Ossorio, F. Ouellette, G. Schoolnik and A. Williamson.  ...  Approximately 79% of the HMPderived novel gene clusters were orthologous to one or more clusters in MetaHIT, while an additional 16% were unique to this study versus 5% for MetaHIT-derived data 5 ( Supplementary  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11209">doi:10.1038/nature11209</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22699610">pmid:22699610</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3377744/">pmcid:PMC3377744</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3wxs7jcehzf4hmm53e5jsx2rfi">fatcat:3wxs7jcehzf4hmm53e5jsx2rfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200506155853/https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1365&amp;context=foodsciefacpub" 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/cd/6d/cd6df2525542ade5c41ca05593b7c826d3d2f875.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11209"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377744" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bacterial Bile Metabolising Gene Abundance in Crohn's, Ulcerative Colitis and Type 2 Diabetes Metagenomes

Alain Labbé, Jorge G. Ganopolsky, Christopher J. Martoni, Satya Prakash, Mitchell L. Jones, Simon Patrick Hogan
<span title="2014-12-17">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;
We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh), 7 alpha-dehydroxylase gene  ...  One of the largest sets, from the MetaHIT consortium, still included only 4 CD patients.  ...  The amino acid fragment length was selected as the maximum length that could be obtained from the 75 bp sequencing length of the illumina reads for the MetaHIT consortium data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0115175">doi:10.1371/journal.pone.0115175</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25517115">pmid:25517115</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4269443/">pmcid:PMC4269443</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/urjl5ws55bbqdgfnvamsfvu5jq">fatcat:urjl5ws55bbqdgfnvamsfvu5jq</a> </span>
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CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

A. Stern, E. Mick, I. Tirosh, O. Sagy, R. Sorek
<span title="2012-06-25">2012</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
In a recent study by the MetaHIT Consortium (Metagenomics of Human Intestinal Tract) (Qin et al. 2010) , DNA from fecal samples of 124 Europeans was sequenced to generate deep coverage of the human gut  ...  CRISPR-derived phage-host assignment (Fig. 3) , now opens the window for future, detailed timecourse studies on the dynamic effect of phages on individual bacterial species and on the gut microbial consortium  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.138297.112">doi:10.1101/gr.138297.112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22732228">pmid:22732228</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3460193/">pmcid:PMC3460193</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ewzlvl2ihrb67da32fjhnn62k4">fatcat:ewzlvl2ihrb67da32fjhnn62k4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220092551/http://pdfs.semanticscholar.org/21bd/dd69dd390a6912f8a736fe06308e3373376a.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/21/bd/21bddd69dd390a6912f8a736fe06308e3373376a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.138297.112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460193" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metagenomics Health Claim: Are you Rich Enough in your Gut Micro biota?

Muthuswamy Balasubramanyam
<span title="">2014</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zjhalrsadngw3ar2o5gvk5wjgq" style="color: black;">Biology and Medicine</a> </i> &nbsp;
MetaHIT consortium focused on a cohort of 292 Danish adults, comprising 123 non-obese and 169 obese subjects.  ...  The French consortium Microbes study [2] comprised of a cohort of 49 French obese or overweight persons, also confirms the results of the MetaHIT study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/0974-8369.1000220">doi:10.4172/0974-8369.1000220</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2rvpyw65cvdfbhn25nxy4jbdvi">fatcat:2rvpyw65cvdfbhn25nxy4jbdvi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161223035834/http://biolmedonline.com/Articles/Vol6_4_2014/BM_Vol6_4_metagenomics-health-claim-Are-you-Rich-Enough-in-your-Gut-Micro-biota-0974-8369.1000220.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/84/2a/842a6da524b9a9ab4cc280fec7ea427318b8264f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/0974-8369.1000220"> <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>

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Francesco Asnicar, George Weingart, Timothy L. Tickle, Curtis Huttenhower, Nicola Segata
<span title="2015-06-18">2015</span> <i title="PeerJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyfkjqp7sva5bbnwatk5zazi7q" style="color: black;">PeerJ</a> </i> &nbsp;
The two files (hmp metahit functional.txt and hmp metahit functional.lefse.txt) represent the result of HUMAnN on the HMP and MetaHIT datasets and the result of LEfSe executed on the former file.  ...  However, GraPhlAn is not limited to microbiome data and has additionally been applied to animal and plant taxonomies (Tree of Sex Consortium, 2014) and to large prokaryotic phylogenies built using reference  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.1029">doi:10.7717/peerj.1029</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26157614">pmid:26157614</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4476132/">pmcid:PMC4476132</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zcgu4mbnozhfrbozu25iokwul4">fatcat:zcgu4mbnozhfrbozu25iokwul4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161018062715/https://peerj.com/articles/1029.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/e5/29/e52997ad54523f4851a589ef1cb2573bfb50ca55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.1029"> <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/PMC4476132" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

OP021 Steroid-free remission in adalimumab-treated paediatric patients with moderately to severely active Crohn's disease in the IMAgINE 1 trial

A. Griffiths, W. Crandall, R. Colletti, F. Ruemmele, W.A. Faubion, J. Hyams, A. Lazar, Y. Li, S. Eichner, R.B. Thakkar
<span title="">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kfgj6hzhofdrldh5it763tjdf4" style="color: black;">Journal of Crohn&#39;s &amp; Colitis</a> </i> &nbsp;
Guarner 1 , on behalf of MetaHIT Consortium 1,2 . 1 Hospital Universitari Vall d'Hebron, Unitat Atenció Crohn-Colitis, Barcelona, Spain, 2 MetaHIT Network, Partner Centres, Paris, France s) [1] Hyams  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1873-9946(14)60022-2">doi:10.1016/s1873-9946(14)60022-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rwlm2abvsrcerbia4akkqcjjzy">fatcat:rwlm2abvsrcerbia4akkqcjjzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729114428/https://watermark.silverchair.com/8-Supplement_1-S12.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAdEwggHNBgkqhkiG9w0BBwagggG-MIIBugIBADCCAbMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMlzQmKeB-c3vdRG6oAgEQgIIBhKtQSajbOQbyvLuZnkKj2cmxd94DEipTnd139RtwwSgd4NbQf-0Lbw56tfPI7ek6HNhm9tzM8VuPKKqT2mttjaqsme9XwiB4H6XoUPjEkA8PfNLH-78BEj0VLPy8ddWxJLZaZHG4XRVgOSa5D_fKzIXTput0ns5ODdeHOKz_iLvIb2uJ_VVO3esDrYWGSJ5aja2-rivEUSQLEv3sVZRUA3FiGZ2HaFgWGJBJl54HAsNUxqSSFFSeb2FLUUq5ai5j3j0kN7_KI42LcSrGbu18noxYsEFS1m1uQ10n6YsT7JZ9-r6JHw1fQ3pbYNWHkTiy4uzRe2XC3rrTiN5hQQXMoB7BjRu0psTYoS1HChcrJ8-_6X_vuWSnPwCHMN1eo7El01hkTFxKBCzl6_a-DQecAA7AnIx2x-aZUKDkaW-knwO222JoILmpIqc7uG3tGX-AqvjFSZKMENXpg2Tb9vVppfrNocx4TeUv91r9JruFyVavjAWY0hncww59GJ2S8Bp1z_qT-lQ" 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/50/7c/507cedf06c5154b1d075a46ccf6c7de81e9ac378.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1873-9946(14)60022-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A decade and genome of change

Clare Garvey
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
simply the sum of our genes. e contribution to our development and immunity from bacterial communities that reside in the human body is relatively unknown. e Human Microbiome Project (HMP) [7] and the MetaHit  ...  As with all large consortium efforts, vast quantities of sequencing data are generated and, eventually, one has to address the issue of what to do with all of the data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2010-11-5-120">doi:10.1186/gb-2010-11-5-120</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20441617">pmid:20441617</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2898078/">pmcid:PMC2898078</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3smzd6w4wrdjlistzqt7m4paiy">fatcat:3smzd6w4wrdjlistzqt7m4paiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170916112509/https://link.springer.com/content/pdf/10.1186%2Fgb-2010-11-5-120.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/8b/5c/8b5c3b2f304d67143b54f52eeba96e91eb6a2965.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2010-11-5-120"> <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/PMC2898078" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MetaTrans: an open-source pipeline for metatranscriptomics

Xavier Martinez, Marta Pozuelo, Victoria Pascal, David Campos, Ivo Gut, Marta Gut, Fernando Azpiroz, Francisco Guarner, Chaysavanh Manichanh
<span title="2016-05-23">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Over the last decade, the human microbiome has been the focus of important international consortia such as the Human Microbiome Project, a NIH initiative, and MetaHIT, a European consortium.  ...  Kraken) and mRNA mapped with SOAP2 against MetaHIT-2014 (mRNA.MetaHIT).  ...  To prevent overestimates of accuracy based solely on well-known genomes, we removed from the MetaHIT database those reads that had more than 90% identity with the MetaHIT genes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep26447">doi:10.1038/srep26447</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27211518">pmid:27211518</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4876386/">pmcid:PMC4876386</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bdqoscfvgjatdharwhwshe7idq">fatcat:bdqoscfvgjatdharwhwshe7idq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721061649/https://repositori.upf.edu/bitstream/handle/10230/28008/Gut_sr_meta.pdf;jsessionid=BBC2A1E663BBF343B9B319DCD1EB36E9?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/49/62/496228052d6427608c8d02f213619d72c0654161.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep26447"> <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/PMC4876386" 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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