Filters








17 Hits in 3.5 sec

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

Kevin P. Keegan, William L. Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer, Scott Markel
<span title="2012-06-07">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;
We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence  ...  For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference  ...  Acknowledgments The authors thank Dionysios A. Antonopoulos, Gail W. Pieper, and Jennifer F. Salazar for comments on the manuscript, as well as Elizabeth M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002541">doi:10.1371/journal.pcbi.1002541</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22685393">pmid:22685393</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3369934/">pmcid:PMC3369934</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b4fvqzj2bna6zljh37fwarr2yq">fatcat:b4fvqzj2bna6zljh37fwarr2yq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015135458/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002541&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/40/91/4091990052f8949afca87f67b473ff0aa1db4178.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002541"> <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/PMC3369934" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DRISEE overestimates errors in metagenomic sequencing data

A. Murat Eren, Hilary G. Morrison, Susan M. Huse, Mitchell L. Sogin
<span title="2013-05-22">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The extremely high error rates reported by Keegan et al. in 'A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE' (PLoS Comput Biol 2012;8:e1002541) for many next-generation  ...  We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.  ...  Key points DRISEE is proposed as a method for detecting errors in metagenomic sequencing data by binning reads that contain the same prefix and investigating their divergence.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbt010">doi:10.1093/bib/bbt010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23698723">pmid:23698723</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4171678/">pmcid:PMC4171678</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ufns5j5cpzdq3irb3sztpzfavm">fatcat:ufns5j5cpzdq3irb3sztpzfavm</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4171678/PMC4171678-bbt010.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] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/0f/e60f984b87703ee6b9982aea9878a8c959103d92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbt010"> <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/PMC4171678" 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 on Neonatal Microbiomes: What Neonatologists Need to Know

Michael P. Sherman, John Minnerly, William Curtiss, Shaukat Rangwala, Scott T. Kelley
<span title="">2014</span> <i title="S. Karger AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pbzuwadiqbbdvmnl7piwvdc25m" style="color: black;">Neonatology</a> </i> &nbsp;
Publications using metagenomics appear infrequently in the neonatal literature because clinicians are unaccustomed to the analytical techniques, data interpretation, and illustration of the results.  ...  After a brief introduction of neonatal citations forthcoming from metagenomic studies, the following topics are covered: (1) the history of metagenomics, (2) a description of current and emerging instruments  ...  The workflow for data analysis has three stages [23] . First, raw data in a storage format are filtered depending on the sequencing platform and the nature of the research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1159/000354944">doi:10.1159/000354944</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24193200">pmid:24193200</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3903415/">pmcid:PMC3903415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vn66vdqbmvhz7e6rjfygujobpi">fatcat:vn66vdqbmvhz7e6rjfygujobpi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218174514/http://pdfs.semanticscholar.org/0ee0/d3e962d0a1bbacd47fc96e539529527036fa.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/0e/e0/0ee0d3e962d0a1bbacd47fc96e539529527036fa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1159/000354944"> <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/PMC3903415" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols

Rebecca A. Reiss, Peter Guerra, Oleg Makhnin
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
A 3.6 log 2 fold increase in biomass as measured by DNA yield per mL water was measured, but there was a 9% decrease in the number of genera detected post-remediation.  ...  Pair-end libraries were prepared for high-throughput DNA sequencing and 90 basepairs from both ends of randomly fragmented 400 basepair DNA fragments were sequenced.  ...  The level of sequencing errors (the DRISEE score) in the dataset that passed both instrumental and MG-RAST QC metrics falls well within one standard deviation of the 6.4 mean for all the MG-RAST data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-016-0209-z">doi:10.1186/s40793-016-0209-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27980706">pmid:27980706</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5131427/">pmcid:PMC5131427</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ogax54os5napzpec32sdocs3km">fatcat:ogax54os5napzpec32sdocs3km</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015073506/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/82c/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczQwNzkzLTAxNi0wMjA5LXoucGRm.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/4a/d5/4ad5c71e64d269e4f5f232bd0e99a26b1948fe26.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40793-016-0209-z"> <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/PMC5131427" 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 Gastric Microbiome of Four Malaysian Gastroduodenal Disease Patients

Khosravi Yalda, Gan Han Ming, Chia Patrick Jing Yi, Croft Larry J, Ng Chow Goon, Goh Khean Lee, Vellasamy Kumutha Malar, Mariappan Vanitha, Ong Kien Chai, Wong Kum Thong, Loke Mun Fai, Vadivelu Jamuna
<span title="2017-04-27">2017</span> <i title="sPage.direcT"> Archives of Gene and Genome Research </i> &nbsp;
Meta Genome Rapid Annotation using Subsystem Technology (MG-RAST, v3.1) server was used for data analysis.  ...  In addition, investigation of non-human eukaryota identified a novel Toxoplasma species in surprisingly high abundance in the gastric microbiome.  ...  Availability of data and material The unfiltered sequenced reads were deposited as project "Shotgun metagenomics of the human stomach" (ID 5712) with MG-RAST.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.36959/998/781">doi:10.36959/998/781</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ba4qq5r6wvdj5ig2rbynjzf3qu">fatcat:ba4qq5r6wvdj5ig2rbynjzf3qu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200507085857/https://scholars.direct/Articles/gene-and-genome-research/aggr-1-001.pdf?jid=gene-and-genome-research" 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/f3/35/f33524a47e13ae9ad383f4a5a2d7296bd9cc4f23.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.36959/998/781"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations

Rodrigo García-López, Jorge Francisco Vázquez-Castellanos, Andrés Moya
<span title="2015-09-17">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;
Since it was reported that DRISEE tends to overestimate errors in metagenomic data due to the presence of conserved artificial sequences, such as adapters (Eren et al., 2014) , we removed such sequences  ...  On the other hand, reference-free methods are powerful methods for filtering bacterial sequences in viral metagenomes.  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00141">doi:10.3389/fbioe.2015.00141</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26442255">pmid:26442255</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4585024/">pmcid:PMC4585024</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uwmjosvavfhexnimztajadtyca">fatcat:uwmjosvavfhexnimztajadtyca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007154559/http://publisher-connector.core.ac.uk/resourcesync/data/Frontiers/pdf/c4f/aHR0cDovL2pvdXJuYWwuZnJvbnRpZXJzaW4ub3JnL2FydGljbGUvMTAuMzM4OS9mYmlvZS4yMDE1LjAwMTQxL3BkZg%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/f9/87/f987eac2a14361a03ad05096abbdd2ec05c160a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2015.00141"> <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/PMC4585024" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

LEMMI: A continuous benchmarking platform for metagenomics classifiers

Mathieu Seppey, Mose Manni, Evgeny M Zdobnov
<span title="2020-07-02">2020</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;
The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification.  ...  We see this platform eventually as a community-driven effort where method developers can showcase novel approaches and get unbiased benchmarks for publications, while users can make informed choices and  ...  Acknowledgments We thank all members of the Zdobnov group for discussions and feedback and Maxime Arbez for his help.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.260398.119">doi:10.1101/gr.260398.119</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32616517">pmid:32616517</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7462069/">pmcid:PMC7462069</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yayqy443enelzjmrndog7rhp2y">fatcat:yayqy443enelzjmrndog7rhp2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106112124/https://genome.cshlp.org/content/30/8/1208.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/88/71/88717cc11f43929f1dd7c168ca4cdfaeb7ff6dc9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.260398.119"> <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/PMC7462069" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms

J. Michael Day, Brian B. Oakley, Bruce S. Seal, Laszlo Zsak
<span title="2015-01-30">2015</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;
There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status  ...  This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has PLOS ONE |  ...  Acknowledgments We acknowledge Fenglan Li and Laura Ferguson for excellent technical assistance, the IT staff at the Agricultural Research Service, Athens, Georgia locations for outstanding support, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0117210">doi:10.1371/journal.pone.0117210</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25635690">pmid:25635690</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4311960/">pmcid:PMC4311960</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sz4zl45lpvhyhjngz3s36eawhi">fatcat:sz4zl45lpvhyhjngz3s36eawhi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191114200234/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4311960&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/21/fd/21fd38266c7336a6ace6ca87ee9ac07a580cfdeb.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.0117210"> <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/PMC4311960" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps

Yohei Yamazaki, Pedro Milet Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Fabiano L. Thompson, Yuichi Sakai, Toko Sawabe, Tomoo Sawabe
<span title="2016-02-24">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;
The increasing demand for A. japonicus livestock has led to further research seeking optimal conditions for seeding and farming.  ...  Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual.  ...  Hattori (The University of Tokyo) for 16S sequencing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep21631">doi:10.1038/srep21631</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26905381">pmid:26905381</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4764845/">pmcid:PMC4764845</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e36mx7kcj5bolfwvd5xv3cvxda">fatcat:e36mx7kcj5bolfwvd5xv3cvxda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307060759/http://pdfs.semanticscholar.org/f494/90f73ca518c103a9e6a8dc72d20e37794ec4.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/f4/94/f49490f73ca518c103a9e6a8dc72d20e37794ec4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep21631"> <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/PMC4764845" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome

C. De Tender, B. Mesuere, F. Van der Jeugt, A. Haegeman, T. Ruttink, B. Vandecasteele, P. Dawyndt, J. Debode, E. E. Kuramae
<span title="2019-07-09">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate.  ...  First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured.  ...  Acknowledgements This research was funded by the ILVO Genomics platform.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-019-46106-x">doi:10.1038/s41598-019-46106-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31289280">pmid:31289280</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6617458/">pmcid:PMC6617458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bwr7xpffsfhnzpuoq63tbehs4a">fatcat:bwr7xpffsfhnzpuoq63tbehs4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200315162312/https://www.nature.com/articles/s41598-019-46106-x.pdf?error=cookies_not_supported&amp;code=3c1cef48-2f42-45b6-a20f-2c923fb633d5" 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/1c/d8/1cd81c1138991b86b5e21ddc5cc1ce023a00c697.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-019-46106-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/PMC6617458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation [article]

Mathieu Seppey, Mose Manni, Evgeny M Zdobnov
<span title="2018-12-28">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This is obscuring an informed choice of a method for biologists as well as the impact of certain innovations for method developers.  ...  Only a subset of these has appeared in independent benchmarking assessments, which are also quickly becoming obsolete.  ...  Acknowledgement We would like to thanks all members of the Zdobnov group, in particular Christopher Rands for his useful comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/507731">doi:10.1101/507731</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y3ql4enfrbaatfensxz4gidvey">fatcat:y3ql4enfrbaatfensxz4gidvey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430130825/https://www.biorxiv.org/content/biorxiv/early/2018/12/28/507731.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/27/fa/27fa52a81c8e446f543bd95630ad2d8b6b8de5d8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/507731"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Deep Sequencing Analysis Reveals Temporal Microbiota Changes Associated with Development of Bovine Digital Dermatitis

Adam C. Krull, Jan K. Shearer, Patrick J. Gorden, Vickie L. Cooper, Gregory J. Phillips, Paul J. Plummer, S. R. Blanke
<span title="2014-05-27">2014</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2tq6zpkjr5dhfiie5yo4un2uiq" style="color: black;">Infection and Immunity</a> </i> &nbsp;
Over 175 million sequences were evaluated by utilizing both shotgun and 16S metagenomic techniques. Based on the shotgun sequencing results, there was no evidence of a fungal or DNA viral etiology.  ...  This study details the deep sequencing-based metagenomic evaluation of 48 staged DD biopsy specimens collected during a 3-year longitudinal study of disease progression.  ...  ACKNOWLEDGMENTS We thank Cory Haglund, Michael Slattery, Tim Kruse, Lance Dahlquist, Mackenzie Dickson, and the ISU Dairy Farm staff for their assistance in sample collection and animal management.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/iai.02077-14">doi:10.1128/iai.02077-14</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24866801">pmid:24866801</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4136199/">pmcid:PMC4136199</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hdy7qfpgrzb3ziwbkxljwuxdyu">fatcat:hdy7qfpgrzb3ziwbkxljwuxdyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430102805/https://iai.asm.org/content/iai/82/8/3359.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/28/e6288d975a49aee723111c8c755252f88fc06453.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/iai.02077-14"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136199" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds

MA Saxton, NS Naqvi, F Rahman, CP Thompson, RM Chambers, JM Kaste, KE Williamson
<span title="2016-06-07">2016</span> <i title="Inter-Research Science Center"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/khso35z75bgi7fuaveq2bpfzoa" style="color: black;">Aquatic Microbial Ecology</a> </i> &nbsp;
Metagenomic sequencing of pond viral communities suggested that viral taxa were influenced by external inputs, with viromes composed of bacteriophage that infect environmental bacteria, as well as viruses  ...  Stormwater retention ponds are ubiquitous in urban and suburban landscapes of the United States.  ...  We thank Timothy Russell at the Keck Environmental Field Laboratory, College of William & Mary, for water chemical analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3354/ame01786">doi:10.3354/ame01786</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2qvdhjkytngvfn4mwuyfdgfa6i">fatcat:2qvdhjkytngvfn4mwuyfdgfa6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181114124423/https://www.wm.edu/as/geology/documents/facultypubs/kaste/saxton_ame_2016.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/14/94/1494e5121d42dc5489a02ea7e6e19fc059097586.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3354/ame01786"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

Roland Wirth, Gyula Kádár, Balázs Kakuk, Gergely Maróti, Zoltán Bagi, Árpád Szilágyi, Gábor Rákhely, József Horváth, Kornél L. Kovács
<span title="2018-09-24">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements.  ...  A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified.  ...  Next Generation Sequencing and Data Handling In sample preparation for total metagenome and metatranscriptome sequencing, the recommendations of the Ion Torrent PGM TM sequencing platform were followed  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.02285">doi:10.3389/fmicb.2018.02285</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30319585">pmid:30319585</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6165872/">pmcid:PMC6165872</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/skv27unfy5ahfczidhfkesjnsa">fatcat:skv27unfy5ahfczidhfkesjnsa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427191342/http://publicatio.bibl.u-szeged.hu/14387/1/20180924Publishedfmicb.2018.02285.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/c9/7e/c97ec38ff44500899aeefd956c6d77a85006d0ea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.02285"> <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/PMC6165872" 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 MGX framework for microbial community analysis

Sebastian Jaenicke
<span title="2020-01-23">2020</span>
Acknowledgements Alexander Goesmann and Jens Stoye are acknowledged for the opportunity and supervision of this PhD thesis.  ...  I'm also grateful to Peter Belmann and Patrick Blumenkamp for the contribution of software components which they developed during their B.Sc. and M.Sc. theses under my supervision.  ...  Kubernetes as a platform for data analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4119/unibi/2940338">doi:10.4119/unibi/2940338</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ef3zg6nqlrhdzm4ysj533576ee">fatcat:ef3zg6nqlrhdzm4ysj533576ee</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209115417/https://pub.uni-bielefeld.de/download/2940338/2940339/DissertationJaenicke.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/9b/bd/9bbd2cae5a760bab2a185a3a51bdd4e92fcd7b9c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4119/unibi/2940338"> <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>
&laquo; Previous Showing results 1 &mdash; 15 out of 17 results