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MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

<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;
Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions.  ...  Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic  ...  ACKNOWLEDGEMENTS The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz926">doi:10.1093/nar/gkz926</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31647104">pmid:31647104</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145621/">pmcid:PMC7145621</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dwdxeaytnvar7iq3kudicrcz2q">fatcat:dwdxeaytnvar7iq3kudicrcz2q</a> </span>
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MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

<span title="2019-07-19">2017</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;
Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic  ...  The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative  ...  Acknowledgements The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx113">doi:10.1093/bib/bbx113</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28968784">pmid:28968784</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6931091/">pmcid:PMC6931091</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3kbei6onubhe3cobdiuk72xt4a">fatcat:3kbei6onubhe3cobdiuk72xt4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718124401/https://hal.archives-ouvertes.fr/hal-02626039/file/MicroScope-an_integrated_resource_for_community_ex.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/01/82/0182e08c9c3e7b86db77de4e48fd7badb714280f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx113"> <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/PMC6931091" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli (+1 others)
<span title="2016-11-29">2016</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;
Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management  ...  The annotation of genomes from NGS platforms needs to be automated and fully integrated.  ...  ACKNOWLEDGEMENTS The authors would like to thank all MicroScope users for their feedback, which helped greatly in optimizing and improving many functionalities of the system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw1101">doi:10.1093/nar/gkw1101</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27899624">pmid:27899624</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5210572/">pmcid:PMC5210572</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tpk2vklznzeuroyna7s62kanm4">fatcat:tpk2vklznzeuroyna7s62kanm4</a> </span>
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Complete genome sequencing and comparative genome characterization of the lignocellulosic biomass degrading bacterium Pseudomonas stutzeri MP4687 from cattle rumen

Maulik Patel, Hiral M. Patel, Nasim Vohra, Sanjay Dave
<span title="2020-09-10">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wv7n5tsoivddjgbfmvnoy5f32a" style="color: black;">Biotechnology Reports</a> </i> &nbsp;
The pangenome analysis further revealed that MP4687 has a very high number of unique genes (>2100) compared to other P. stutzeri genomes, which might have an important role in rumen functioning.  ...  The genome encodes for 4,790 protein coding genes including 164 CAZymes and 345 carbohydrate processing genes.  ...  Acknowledgment The authors wish to thank Dr. Michael Ladisch and Eduardo Ximenes for their internal review of this article.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.btre.2020.e00530">doi:10.1016/j.btre.2020.e00530</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32983925">pmid:32983925</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7498857/">pmcid:PMC7498857</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/syznfqacrrfy3ni6zzgc2vbkwy">fatcat:syznfqacrrfy3ni6zzgc2vbkwy</a> </span>
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Plateforme numérique pour l'antibiorésistance, ABRomics [article]

Claudine Médigue, Philippe Glaser, Consortium ABRomics
<span title="2021-08-21">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
The integration and analysis of omics data with associated metadata requires the development of databases accessible to the community, the automatic use of standard pipelines for genomic and metagenomic  ...  data analysis, and the development of new bioinformatics and mathematical methods to meet the demands of the various communities.  ...  Interactions with WP2 will be required in order to address metagenomic data processing with standardized pipelines of ABROmics and pangenome annotation for antimicrobial resistance genes, virulence factors  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5230261">doi:10.5281/zenodo.5230261</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lhtpmfwdjnddhi6cdilfpccc7q">fatcat:lhtpmfwdjnddhi6cdilfpccc7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210831195547/https://zenodo.org/record/5230261/files/ABRomics-PF-%20April%202021.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/a5/aa/a5aaeb8978d7ed0818ba3dbb042f26e18f622cca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5230261"> <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>

PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features

Narendrakumar M. Chaudhari, Anupam Gautam, Vinod Kumar Gupta, Gagneet Kaur, Chitra Dutta, Sandip Paul
<span title="2018-10-08">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;
As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized  ...  The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes.  ...  Sucheta Tripathy for technical support and server provisions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.02322">doi:10.3389/fmicb.2018.02322</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30349509">pmid:30349509</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6187978/">pmcid:PMC6187978</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hsj2dq43ijctbhpxror2rjeb6m">fatcat:hsj2dq43ijctbhpxror2rjeb6m</a> </span>
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The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

Alejandra Escobar-Zepeda, Arturo Vera-Ponce de León, Alejandro Sanchez-Flores
<span title="2015-12-17">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
The study of microorganisms that pervade each and every part of this planet has encountered many challenges through time such as the discovery of unknown organisms and the understanding of how they interact  ...  New computational methods are constantly developed to collect, process, and extract useful biological information from a variety of samples and complex datasets, but metagenomics needs the integration  ...  ACKNOWLEDGMENTS AE and AV are Ph.D. students from Programa de Doctorado en Ciencias Bioquímicas and Programa de Doctorado en Ciencias Biomédicas Universidad Nacional Autónoma de México (UNAM) with scholarship  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2015.00348">doi:10.3389/fgene.2015.00348</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26734060">pmid:26734060</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4681832/">pmcid:PMC4681832</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2f7f7fybdnhtnddsyawd4qjsbm">fatcat:2f7f7fybdnhtnddsyawd4qjsbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830030846/https://fjfsdata01prod.blob.core.windows.net/articles/files/155161/pubmed-zip/.versions/1/.package-entries/fgene-06-00348/fgene-06-00348.pdf?sv=2015-12-11&amp;sr=b&amp;sig=mO9NI3y3BNiczAEY%2ByexGYgFaBUZ7aSCoNv%2FXTdtQTI%3D&amp;se=2017-08-30T03%3A08%3A59Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-06-00348.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/cc/a5/cca5e74bf5303d9504e78bc58d61d9fe653d160d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2015.00348"> <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/PMC4681832" 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 Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

Damien Mornico, Lucie Miché, Gilles Béna, Nico Nouwen, André Verméglio, David Vallenet, Alexander A.T. Smith, Eric Giraud, Claudine Médigue, Lionel Moulin
<span title="2011-12-21">2011</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/githwx23ynaxdoftesby3jya3y" style="color: black;">Genes</a> </i> &nbsp;
Comparative genomics allowed us to infer the core, OPEN ACCESS Genes 2012, 3 36 pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands  ...  Second, some photosynthetic bradyrhizobia lack the canonical nodulation genes (genome-based analyses on ORS278 and BTAi1) and use an unknown nod gene-independent pathway to form nodules on some Aeschynomene  ...  Acknowledgments This study was funded by Agence Nationale de la Recherche (ANR, France), through a Young Researcher grant (ANR-BOA-JC05_52208) and Blanc projects (ANR-NEWNOD-2006-BLAN-0095  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes3010035">doi:10.3390/genes3010035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24704842">pmid:24704842</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3899966/">pmcid:PMC3899966</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/stztth6c2bccdormmua4jawco4">fatcat:stztth6c2bccdormmua4jawco4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170815115624/http://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers12-11/010056379.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/df/9bdf895d8255bdbf53935d056e37126cc3d0e70b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes3010035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899966" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Microbial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium

Amjad Ali
<span title="">2013</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nw2nohnuurhgjcfkjdrmz6tsnq" style="color: black;">Journal of Bacteriology &amp; Parasitology</a> </i> &nbsp;
Consequently, comparative genomic analysis remains powerful tools for identifying the orthologous genes in species, presence and absence of specific genes, evolutionary signals, and candidate regions associated  ...  In this article, we present an overview of microbial comparative genomics pre-requisites: sequencing technologies, alignment tools, annotation pipelines, databases and resources, visualization and comparative  ...  Acknowledgments CNPq and FAPEMIG; TWAS-CNPq for PhD Fellowship.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2155-9597.1000167">doi:10.4172/2155-9597.1000167</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sisv37hygzf2fcg6w2vissouea">fatcat:sisv37hygzf2fcg6w2vissouea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429091614/https://www.longdom.org/open-access/microbial-comparative-genomics-an-overview-of-tools-and-insights-into-the-genus-corynebacterium-2155-9597.1000167.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/a9/f7/a9f7cc309133c17d65491c1b0fe3970d0be4e827.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/2155-9597.1000167"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs

Graciela M. Dias, Adeline Bidault, Patrick Le Chevalier, Gwenaëlle Choquet, Clio Der Sarkissian, Ludovic Orlando, Claudine Medigue, Valerie Barbe, Sophie Mangenot, Cristiane C. Thompson, Fabiano L. Thompson, Annick Jacq (+2 others)
<span title="2018-02-19">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;
HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not.  ...  The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.  ...  Genome Annotation, Comparative Genomics, and Core Genome Phylogeny Expert annotation of the reference strain CECT4600 T was done using the MaGe tools of the MicroScope platform (Vallenet et al., 2017)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.00227">doi:10.3389/fmicb.2018.00227</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29515533">pmid:29515533</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5825899/">pmcid:PMC5825899</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xpb42fdqvbhbrcxdpf5gy7ryii">fatcat:xpb42fdqvbhbrcxdpf5gy7ryii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313092446/https://hal.archives-ouvertes.fr/hal-02177600/file/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/2a/d6/2ad6c638f0f386a1eb5c044b89ee57ba18f7480e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2018.00227"> <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/PMC5825899" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise (+3 others)
<span title="2020-03-19">2020</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;
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species.  ...  The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative  ...  Acknowledgments We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1007732">doi:10.1371/journal.pcbi.1007732</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32191703">pmid:32191703</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7108747/">pmcid:PMC7108747</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ff6ccvwavzcutaxtxcvntfb74e">fatcat:ff6ccvwavzcutaxtxcvntfb74e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429125711/https://hal.archives-ouvertes.fr/hal-03089210/document" 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/82/41/82411807745239a4ecb67ff9223173be90c973ac.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.1007732"> <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/PMC7108747" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery [article]

Marina Muñoz, Enzo Guerrero-Araya, Catalina Cortés-Tapia, Ángela Plaza-Garrido, Trevor D. Lawley, Daniel Paredes-Sabja
<span title="2020-04-16">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Pangenome analysis on the established dataset revealed that although S. intestinalis seems to have a highly conserved genome (with 50.1% of its coding potential being part of the coregenome), some recombination  ...  which matches with the metabolic profile previously reported for healthy microbiota.  ...  BLAST algorithm, included inside the server. 391 Annotation and pangenome analysis 392 An automated annotation pipeline was applied to the complete set of evaluated 393 genomes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.14.041921">doi:10.1101/2020.04.14.041921</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/77ctb73fhndczljg7p7ucbdxeq">fatcat:77ctb73fhndczljg7p7ucbdxeq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710173227/https://www.biorxiv.org/content/10.1101/2020.04.14.041921v1.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/b6/16/b616ac4c5e7ace9962d74be82b67ec8b3ffc9af2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.14.041921"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph [article]

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Remi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Medigue, Alexandra Calteau, Stephane Cruveiller, Catherine Matias, Christophe Ambroise (+2 others)
<span title="2019-11-09">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species.  ...  The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative  ...  Acknowledgements We acknowledge Alexandre Renaux and Jonathan Mercier for their preliminary insights on pangenome graphs. We thank Mélanie Buy for drawing the PPanGGOLiN logo.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/836239">doi:10.1101/836239</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/utqwlatqkncbleusf2edbx54ei">fatcat:utqwlatqkncbleusf2edbx54ei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200305090235/https://www.biorxiv.org/content/biorxiv/early/2019/11/09/836239.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/80/10/8010436326f9ce3113310e5799c5d30542107a76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/836239"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The 27th annual Nucleic Acids Research database issue and molecular biology database collection

Daniel J Rigden, Xosé M Fernández
<span title="2019-12-22">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;
PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser.  ...  hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva, especially, and the rest of the Oxford University Press team led by Joanna Ventikos for their help in compiling this issue.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1161">doi:10.1093/nar/gkz1161</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31906604">pmid:31906604</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6943072/">pmcid:PMC6943072</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2dx37pg3krcs5hamrlmgyb4h5e">fatcat:2dx37pg3krcs5hamrlmgyb4h5e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200107010336/https://watermark.silverchair.com/gkz1161.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAlgwggJUBgkqhkiG9w0BBwagggJFMIICQQIBADCCAjoGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM0KmptdQRuuiCGKHyAgEQgIICC3UTHphWmhnUMgVObN_qRYzv80XIn4_GZbbvDk6vf7dVNfy29dbPqgXOb87mEdqB-xCvDHDSEyW77uc599-oA0mE2h-AUk5B064yfmQ8raF3jHzSHcDn0Dzsex3ySqY2ftMBcJJe42IiCGU_DwEVIgNa4jwq-wsEqNbGDdD4zlXTbArm7T1gHc_276oU9_Bze5tWG_ILeAknWaN9i-Ni-9aOhCiIniyxG5XX63fWWIzMrNhvw1uRbbTMhU6kUjKV4VLelFbFteQl5pvQFAcUO8ZmAFAGMuVFApMBGRAlX7NN0-578zSy0F5ifd3zmO6A8itZZoK2Y2aOeOA-ZW-L9FS7VBVQLqvzcZ1J6-u6nLQ3v379kwGe0uBfDhhITJ5tzefA9MIW17H8h1CwrIa8Xpo7FEasFma44PUgFG05nLkFMQ9HH91HLYMttpivR309cLCv4WN629Bo2XXedjnINdGplPslnvmACRfiLFMNwrDwN-jkDCVd38yYiz4LFhJdPWAszm_4Lr_u3sFlMGshtdiXkzJRXbOXBkSDdpPNpKg9uwXzPCQCthkW6v2-1FkGOe-V1XC8zeaeUXP7QNrGE_7bAj9iUGbLVJjBVdxX8mFXFy_4TrAZatgEJSJ0R4aOkWtOSvMidIp3srsHVspoTdkJeBDh5l-5po9n4wYLqtsw2SKlRBYgt7FWezk" 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/a4/e8/a4e8f23557e81f1434e55f6008b3ba71330e3ed0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1161"> <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/PMC6943072" 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;
This funding will lay down the basis of IFB infrastructure for our 2021-2025 roadmap, and strengthen several priority activities, e.g., FAIR data, integration of imaging, multi-omics and phenomics data  ...  challenges. 2019 paved the way to consolidate IFB sustainability, with a very positive evaluation of our 2018-2021 roadmap, a validation of the IFB renewal through funding by the Ministry of Science and  ...  >> 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>
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