Filters








234 Hits in 4.2 sec

Development of joint application strategies for two microbial gene finders

A. C. McHardy, A. Goesmann, A. Puhler, F. Meyer
<span title="2004-02-26">2004</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;
Results: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance.  ...  Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem.  ...  References reduction of the necessary manual validation effort of the gene finding results for the human annotators, especially for GC rich genomes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth137">doi:10.1093/bioinformatics/bth137</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14988122">pmid:14988122</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vlt5ku3kgrbqbcwpjcra6nx4fu">fatcat:vlt5ku3kgrbqbcwpjcra6nx4fu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20040922053016/http://bioinformatics.oupjournals.org:80/cgi/screenpdf/20/10/1622.pdf?ijkey=714yw1MBNx2zM&amp;keytype=ref" 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/09/8e/098e6c6f8572c594bdf8cd6388d6627cce95c91f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth137"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Genome Sequence Databases: Sequencing and Assembly [chapter]

A.L. Lapidus
<span title="">2009</span> <i title="Elsevier"> Encyclopedia of Microbiology </i> &nbsp;
Repeat Finder) algorithms for their detection.  ...  gene finders (it was shown (Besemer, 1999) that GeneMark family sofware (Besemer, 2005) can be applied for gene finding in segments with length starting from 400 bp; FGENESB (Solovyev, 1997) , GLIMMER  ...  F Assembly Views of Desulforudis audaxviator. nd two rounds of primer walk combined with 454 ata (for details see legend for Fig.3) . A. B. C.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-012373944-5.00028-6">doi:10.1016/b978-012373944-5.00028-6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/64othzpkpfbfhnh7ivqbqr4npe">fatcat:64othzpkpfbfhnh7ivqbqr4npe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324164052/https://digital.library.unt.edu/ark:/67531/metadc934645/m2/1/high_res_d/963025.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/4f/71/4f71f776f6fa2f122c6e527ad84a31dcf8c8dc0d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/b978-012373944-5.00028-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Informatics for Infectious Disease Research and Control [chapter]

Vitali Sintchenko
<span title="2009-10-03">2009</span> <i title="Springer New York"> Infectious Disease Informatics </i> &nbsp;
Problems with the accuracy of current gene finders reflect not only the performance of their algorithms but also the quality of the primary resources and the abundance of non-coding DNA regions in microbial  ...  Not surprisingly, the comparative assembly strategy works best when the two species are more than 90% identical.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4419-1327-2_1">doi:10.1007/978-1-4419-1327-2_1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/usfwlegnrfcjtedpvrzu2vmaue">fatcat:usfwlegnrfcjtedpvrzu2vmaue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200421200758/https://link.springer.com/content/pdf/10.1007%2F978-1-4419-1327-2_1.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/a8/1e/a81e7bbcd497e074152b82776930e77cee57612c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4419-1327-2_1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era

Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi
<span title="2013-09-30">2013</span> <i title="Korea Genome Organization"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/acfgmfmleze4rfuugy66fpl4ky" style="color: black;">Genomics &amp; Informatics</a> </i> &nbsp;
Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances  ...  As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary.  ...  Classical gene finders that have been developed for a single genome are unsuitable for metagenomic analysis, because metagenome data are made up of a mixture of sequences from different organisms and often  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2013.11.3.102">doi:10.5808/gi.2013.11.3.102</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24124405">pmid:24124405</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3794082/">pmcid:PMC3794082</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lotsy2zoxzgl3mn2pd2a3zkobi">fatcat:lotsy2zoxzgl3mn2pd2a3zkobi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171202070034/https://genominfo.org/upload/pdf/gni-11-102.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/70/56/705679bfe3674be9cd7d0ed14de2ff5bb3093cc9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5808/gi.2013.11.3.102"> <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/PMC3794082" 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 challenges of new sequencing technology

Mihai Pop, Steven L. Salzberg
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Gene finding in smaller eukaryotes tends to be more accurate because of their smaller introns and greater gene density, and gene finders for bacteria, archaea and viruses are very accurate, predicting  ...  Ab initio gene finders, of which there are many, are not nearly so robust in the presence of errors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2007.12.006">doi:10.1016/j.tig.2007.12.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18262676">pmid:18262676</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2680276/">pmcid:PMC2680276</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/23n5uq5c75a43beag2ihomgfye">fatcat:23n5uq5c75a43beag2ihomgfye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120622214757/http://cbcb.umd.edu/%7Esalzberg/docs/Pop_Salzberg_TIG_2008_reprint.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/ef/8d/ef8de7a5a27a54115c1caf1878a9493e016c0c13.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2007.12.006"> <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/PMC2680276" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An experimental metagenome data management and analysis system

V. M. Markowitz, N. Ivanova, K. Palaniappan, E. Szeto, F. Korzeniewski, A. Lykidis, I. Anderson, K. Mavrommatis, V. Kunin, H. Garcia Martin, I. Dubchak, P. Hugenholtz (+1 others)
<span title="2006-07-15">2006</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;
Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive  ...  The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms.  ...  ACKNOWLEDGEMENTS We thank all our colleagues who have contributed to the development of IMG and IMG/M. Special thanks to Eddy Rubin and James Bristow for their encouragement throughout this project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl217">doi:10.1093/bioinformatics/btl217</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16873494">pmid:16873494</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4qqlrfgdgndxvfja75u7kbo6fi">fatcat:4qqlrfgdgndxvfja75u7kbo6fi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727160757/https://watermark.silverchair.com/btl217.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM0oeFSP91IYwFB6u4AgEQgIIBc6jz39XeFF2dfe6h6hdPvpwtGXe6phmA2yTZBW5KRfbykOGJhztc8qABTq4jPZKD9DFkCpfeei9c_m6-KTb_fdg6oyoPHvIOWipDTAuBw1FefFwW9Cyej8AD2CZtMkUZxOb0srbJFvyvffYdpZMer78Qs9psuDrvitRYBCv5rR2sR1A9oDtERLbMRvjtOLF5rydMuRTIuxGWZs3cofrvsu9yplHlqFYAmkvZsQ0JET-dlY-n3rqDproW7zt3EJyJVHtfCsZ9RC5vxYHLMQuMkZRPR5wJNjMFeYXkp2EjKBmQmaKKy5QOnW2wO65GMxduibDyMCDj6V-ZJmwdm9FKKy6LEtAEmf4BJUAOa7noO9lJzNdPrMeqSVcjiDLSpRNxK-FHFh6pkUoI1z49QzyalFDTlqWnx-02ONu-677n_aJBANECR0sNrs30h33QgdMePTFnCvXYjdROVOeVmrn-uPWT_StmRMCBtoVMc8Ei-L66Wc73" 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/fc/0f/fc0ffb7a841eb3ba10fa18542366f01b892fa5bf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btl217"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Illuminating the Virosphere Through Global Metagenomics

Lee Call, Stephen Nayfach, Nikos C. Kyrpides
<span title="2021-07-20">2021</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qixnghadmzf7vczl4drljfgq4a" style="color: black;">Annual Review of Biomedical Data Science</a> </i> &nbsp;
Development and implementation of new standards, along with careful study of the newly discovered viruses, have transformed and will continue to transform our understanding of microbial evolution, ecology  ...  In terms of outright numbers of novel viruses discovered, however, the last few years have been by far the most transformative for the field.  ...  The largest database of viral genomes is IMG/VR (Integrated Microbial Genomes/Virus) at the Department of Energy's Joint Genome Institute (41) , which houses over two million sequences derived from mostly  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-biodatasci-012221-095114">doi:10.1146/annurev-biodatasci-012221-095114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34465172">pmid:34465172</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g3mzsvugu5fbjdhufrypftrm5a">fatcat:g3mzsvugu5fbjdhufrypftrm5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220221184314/https://www.annualreviews.org/doi/pdf/10.1146/annurev-biodatasci-012221-095114" 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/d0/05/d0054c18294c73c391997f771e5fce5c397f4ae7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-biodatasci-012221-095114"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

Tilmann Weber, Hyun Uk Kim
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rh2yip2wojczfm2le3mfozfd2m" style="color: black;">Synthetic and Systems Biotechnology</a> </i> &nbsp;
Acknowledgments The work of the authors is supported by a grant of the Novo Nordisk Foundation, Denmark.  ...  There are two principal strategies in the implementation of bioinformatic tools. Rule-based approaches can be used to identify gene clusters encoding known biosynthetic routes with high precision.  ...  , such tools are also essential for the development of synthetic biology strategies, which aim at the efficient production of rationally designed molecules. 112 While there exist several generic synthetic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.synbio.2015.12.002">doi:10.1016/j.synbio.2015.12.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29062930">pmid:29062930</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5640684/">pmcid:PMC5640684</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6hbbrigasjakrorunrhwymkmwe">fatcat:6hbbrigasjakrorunrhwymkmwe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190324005506/https://core.ac.uk/download/pdf/43257325.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/0d/710d73dc981df8021ca40cff4a4795c91803bcd1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.synbio.2015.12.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640684" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Signal Processing for Metagenomics: Extracting Information from the Soup

Gail Rosen, Bahrad Sokhansanj, Robi Polikar, Mary Bruns, Jacob Russell, Elaine Garbarine, Steve Essinger, Non Yok
<span title="2009-11-01">2009</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mqegkl27nzckpogkyj47kjwblu" style="color: black;">Current Genomics</a> </i> &nbsp;
Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.  ...  without the need for cultivation.  ...  This can be done by developing a microarray that has probes for genes from multiple genomes, such as was done in [146] for the study of 4 microbial species cultured together.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920209789208255">doi:10.2174/138920209789208255</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20436876">pmid:20436876</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808676/">pmcid:PMC2808676</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lb67lmbuhzaxlpok6itzeift5y">fatcat:lb67lmbuhzaxlpok6itzeift5y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100621175600/http://www.ece.drexel.edu/gailr/class_papers/current_genomics_revision.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/a6/4b/a64b650c1366b43da9a165085f636f9b687d71e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920209789208255"> <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/PMC2808676" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Using Genomics to Track Global Antimicrobial Resistance

Rene S. Hendriksen, Valeria Bortolaia, Heather Tate, Gregory H. Tyson, Frank M. Aarestrup, Patrick F. McDermott
<span title="2019-09-04">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/athqjlcrona7rgynvfhqsnauza" style="color: black;">Frontiers in Public Health</a> </i> &nbsp;
The advancement in whole genome sequencing and the application of online tools for real-time detection of AMR determinants are essential to identify control and prevention strategies to combat the increasing  ...  At least 47 freely accessible bioinformatics resources for detection of AMR determinants in DNA or amino acid sequence data have been developed to date.  ...  At a recent meeting (October 2017) organized by the European Commission Joint Research Center, the challenges of designing a benchmarking strategy for assessing bioinformatics tools to detect AMR determinants  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpubh.2019.00242">doi:10.3389/fpubh.2019.00242</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31552211">pmid:31552211</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6737581/">pmcid:PMC6737581</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/opk2dnbgxbcancw4n6tgkuroc4">fatcat:opk2dnbgxbcancw4n6tgkuroc4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210132804/https://fjfsdata01prod.blob.core.windows.net/articles/files/478239/pubmed-zip/.versions/1/.package-entries/fpubh-07-00242/fpubh-07-00242.pdf?sv=2015-12-11&amp;sr=b&amp;sig=Br1%2ByNQI6wKPl2m%2BbCitwbVLvBXRLtJ3nrDyqYc%2Bth0%3D&amp;se=2020-02-10T13%3A28%3A28Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fpubh-07-00242.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/61/3e/613e784079d0b91b04e92ab58e257861fdfec051.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpubh.2019.00242"> <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/PMC6737581" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties

Wen Wei, Feng Gao, Meng-Ze Du, Hong-Li Hua, Ju Wang, Feng-Biao Guo
<span title="2016-03-18">2016</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;
Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences.  ...  Overall, the tool provides an alternative solution over other tools, which expands the field of island prediction and offers a supplement to increase the performance of the distinct predicting strategy  ...  Chun-Ting Zhang for inspiring discussion and invaluable assistance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbw019">doi:10.1093/bib/bbw019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26992782">pmid:26992782</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5429010/">pmcid:PMC5429010</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jbjcyjrrmnbmdf3n6x6df6taey">fatcat:jbjcyjrrmnbmdf3n6x6df6taey</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222124401/http://pdfs.semanticscholar.org/3ef8/0e22a43bed48234995a8ffc220c7eb0bbe88.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/3e/f8/3ef80e22a43bed48234995a8ffc220c7eb0bbe88.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbw019"> <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/PMC5429010" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
genes.  ...  Conclusions: We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and  ...  The HMP datasets We downloaded the whole metagenome assemblies (HASM) and gene annotations (HMGI) for the HMP datasets from the DACC website [42] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2013-14-4-r40">doi:10.1186/gb-2013-14-4-r40</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23628424">pmid:23628424</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4053933/">pmcid:PMC4053933</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l5qe2qkmmrbefhisergkrktdba">fatcat:l5qe2qkmmrbefhisergkrktdba</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4053933/PMC4053933-gb-2013-14-4-r40.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2013-14-4-r40"> <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/PMC4053933" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
<span title="2021-08-29">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
We pursued our usual activities and attempted to keep as well as possible our missions of support, training and innovative developments, despite the inherent difficulties of remote working.  ...  , applications of IA to life sciences, deployment of certified Health Data Storage (HDS) digital spaces. 2020 was definitely marked by the worldwide sanitary crisis with the COVID-19 pandemic.  ...  >> Detailed report of the survey  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5324333">doi:10.5281/zenodo.5324333</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/py5xp6q7ungkdevdqx25zxfwmq">fatcat:py5xp6q7ungkdevdqx25zxfwmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210907234401/https://zenodo.org/record/5324334/files/Rapport%20IFB%202019-2020.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/89/fe89e044b3439f5b69cc5323f11af36be8f885f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5324333"> <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>

Synbiological systems for complex natural products biosynthesis

Jianhua Li, Hailin Meng, Yong Wang
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rh2yip2wojczfm2le3mfozfd2m" style="color: black;">Synthetic and Systems Biotechnology</a> </i> &nbsp;
The rapid development of synthetic biology has conferred the strategies of NPs production.  ...  Enormous endeavors have been taken for mentioned issues.  ...  Thus, expelling heterologous compounds out of hosts by transporters is a potential strategy to enhance product titers in microbial cell factories.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.synbio.2016.08.002">doi:10.1016/j.synbio.2016.08.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29062947">pmid:29062947</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5625725/">pmcid:PMC5625725</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eapmrdzykbdnlcp2t4rby4hv3y">fatcat:eapmrdzykbdnlcp2t4rby4hv3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190327011019/https://core.ac.uk/download/pdf/82250778.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/82/bc/82bcdb6d6280691cd7c84bfea868592441bdc63d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.synbio.2016.08.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625725" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

Rosa Sagita, Wim J. Quax, Kristina Haslinger
<span title="2021-03-15">2021</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;
Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel  ...  As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (  ...  ACKNOWLEDGMENTS The authors were grateful to Sadaf Deravi and Kahraman Gercek, who compiled the list of publicly accessible genomes of endophytic fungi as part of their B.Sc. theses.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2021.649906">doi:10.3389/fbioe.2021.649906</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33791289">pmid:33791289</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8005728/">pmcid:PMC8005728</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/352waj7zxngt5do4v74eao6i3i">fatcat:352waj7zxngt5do4v74eao6i3i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210319210047/https://fjfsdata01prod.blob.core.windows.net/articles/files/649906/pubmed-zip/.versions/1/.package-entries/fbioe-09-649906/fbioe-09-649906.pdf?sv=2018-03-28&amp;sr=b&amp;sig=ohpOlVd%2BqUt5G%2BIztfqy1bKJeS5aB%2FYMMaWZwMdKk4M%3D&amp;se=2021-03-19T21%3A01%3A16Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fbioe-09-649906.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/ea/8b/ea8b5e206032f06aeddd15d06bff042c743a670b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fbioe.2021.649906"> <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/PMC8005728" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 234 results