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proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

<span title="2020-01-08">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database.  ...  Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the Bork group, in particular Yan-Ping Yuan for technical support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1002">doi:10.1093/nar/gkz1002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31647096">pmid:31647096</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145564/">pmcid:PMC7145564</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hqvc3agp5rarlcwm62ekvrkzta">fatcat:hqvc3agp5rarlcwm62ekvrkzta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200305173838/http://edoc.mdc-berlin.de/18492/1/18492oa.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/e5/7d/e57d9af6a216e9c46a3b08e98b0ad04c67cdfd2f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145564" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
<span title="2020-02-11">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ii4mp46mlndibnz4acpdnnmvou" style="color: black;">The ISME Journal</a> </i> &nbsp;
Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size.  ...  strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned.  ...  To establish this collection, we filtered the proGenomes database of annotated prokaryotic genomes [32] to select consistently defined species (see "Methods", also [31] ) for which at least ten high-quality  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41396-020-0600-z">doi:10.1038/s41396-020-0600-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32047279">pmid:32047279</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7174425/">pmcid:PMC7174425</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vkxd73n52jdnzkq3fdve6mntay">fatcat:vkxd73n52jdnzkq3fdve6mntay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200511145458/https://www.nature.com/articles/s41396-020-0600-z.pdf?error=cookies_not_supported&amp;code=85ec7817-94ea-4a1c-b959-861d0666020f" 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/5e/89/5e896a6426b44bda2a3db532e3f7eb54cd87abe0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41396-020-0600-z"> <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/PMC7174425" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

Clémence Frioux, Dipali Singh, Tamas Korcsmaros, Falk Hildebrand
<span title="2020-06-25">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
However, functional annotations and estimating metabolic processes from single species - or communities - is still challenging.  ...  This has led to breakthrough developments in bioinformatic disciplines such as assembly, gene clustering, metagenomic binning of species genomes and the discovery of an incredible, so far undiscovered,  ...  Acknowledgements We acknowledge Rachel Gilroy and Raven Reynolds for their constructive comments and their help in proof-reading the manuscript.  ... 
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