- home
- Advanced Search
- ELIXIR GR
- Publications
- Other literature type
- European Commission
- HAL-Pasteur
- ELIXIR GR
- Publications
- Other literature type
- European Commission
- HAL-Pasteur
Loading
description Publicationkeyboard_double_arrow_right Article , Preprint 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | IGNITE, EC | SynarchiCEC| IGNITE ,EC| SynarchiCCyril Matthey-Doret; Lyam Baudry; Axel Breuer; Rémi Montagne; Nadège Guiglielmoni; Vittore F. Scolari; Etienne Jean; Arnaud Campeas; Philippe Henri Chanut; Edgar Oriol; Adrien Meot; Laurent Politis; Antoine Vigouroux; Pierrick Moreau; Romain Koszul; Axel Cournac;Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols. Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 60 citations 60 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Conference object , Article 2017 France Funded by:EC | OpenMinTeDEC| OpenMinTeDAuthors: Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;pmid: 30910089
pmc: PMC6460834
Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & MethodsWe propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, we analyzed terms that designate Microbial and Habitat entities in text. Microorganism names were predicted using the NCBI taxonomy. Habitat entities were detected using the syntactic structure of the terms and the OntoBiotope ontology. This ontology has been specifically enriched for the recognition of food terms in text. In a second time, we predicted links between microorganisms and their habitats (labeled “Lives_in” relationships) using pattern and machine-learning based methods. The results of text-mining predictions are indexed and presented in a semantic search engine. Result The AlvisIR search engine for microbe literature gives online access to 1.2 million PubMed abstracts in 2015, among which 13% are specific to food. This tool makes it possible to use text-mining results to search for information on bacterial biodiversity. It covers all types of microbial habitats to help understand the origin of microbial presence in food. Significance This work presents the first semantic search engine dedicated to better understand microbial food biodiversity from text.
Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6460834&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 10 citations 10 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6460834&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Netherlands, Netherlands, Italy, United Kingdom, United Kingdom, Netherlands, Netherlands, France, United Kingdom, Spain EnglishPublisher:HAL CCSD Funded by:EC | PhenoMeNalEC| PhenoMeNalvan Rijswijk, M; van Rijswijk, M; Beirnaert, C; Beirnaert, C; Caron, C; Cascante, M; Dominguez, V; Dunn, WB; Ebbels, TMD; Giacomoni, F; Gonzalez-Beltran, A; Hankemeier, T; Haug, K; Haug, K; Izquierdo-Garcia, JL; Jimenez, RC; Jimenez, RC; Jourdan, F; Kale, N; Klapa, MI; Kohlbacher, O; Koort, K; Kultima, K; Le Corguillé, G; Moreno, P; Moschonas, NK; Moschonas, NK; Neumann, S; O'Donovan, C; Reczko, M; Rocca-Serra, P; Rosato, A; Rosato, A; Rosato, A; Salek, RM; Salek, RM; Sansone, S-A; Satagopam, V; Schober, D; Shimmo, R; Spicer, RA; Spicer, RA; Spjuth, O; Spjuth, O; Spjuth, O; Thévenot, EA; Thévenot, EA; Viant, MR; Weber, RJM; Willighagen, EL; Willighagen, EL; Zanetti, G; Steinbeck, C; Steinbeck, C;Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases. The meeting was funded by PhenoMeNal, European Commission's Horizon2020 programme, grant agreement number 654241 Sí
HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.12342.1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 34visibility views 34 download downloads 65 Powered bymore_vert HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.12342.1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Article 2016 France, Switzerland, Brazil, Denmark, United Kingdom, GermanyPublisher:Springer Science and Business Media LLC Funded by:EC | PHARMASEAEC| PHARMASEAMingxun Wang; Jeremy Carver; Vanessa V. Phelan; Laura M. Sanchez; Neha Garg; Yao Peng; Don D. Nguyen; Jeramie D. Watrous; Clifford A. Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V. Melnik; Michael J. Meehan; Wei-Ting Liu; Max Crüsemann; Paul D. Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D. Kersten; Laura A. Pace; Robert A. Quinn; Katherine R. Duncan; Cheng-Chih Hsu; Dimitrios J. Floros; Ronnie G. Gavilan; Karin Kleigrewe; Trent R. Northen; Rachel J. Dutton; Delphine Parrot; Erin E. Carlson; Bertrand Aigle; Charlotte Frydenlund Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel A. Pevzner; Anna Edlund; Jeffrey S. McLean; Jörn Piel; Brian T. Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A. Keyzers; Amy C. Sims; Andrew R. Johnson; Ashley M. Sidebottom; Brian E. Sedio; Andreas Klitgaard; Charles B. Larson; Cristopher A. Boya P.; Daniel Torres-Mendoza; David Gonzalez; Denise Brentan Silva; Lucas Miranda Marques; Daniel P. Demarque; Egle Pociute; Ellis C. O’Neill; Enora Briand; Eric J. N. Helfrich; Eve A. Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J. Kharbush; Yi Zeng; Julia A. Vorholt; Kenji L. Kurita; Pep Charusanti; Kerry L. McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F. Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B. Vining; Ralph S. Baric; Ricardo Pianta Rodrigues da Silva; Samantha J. Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat R. Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G. Williams; Jingqui Dai; Ram P. Neupane; Joshua R. Gurr; Andrés M. C. Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M. Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Félix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E. Kyle; Thomas O. Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M. Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R. Jensen; Bernhard O. Palsson; Kit Pogliano; Roger G. Linington; Marcelino Gutiérrez; Norberto Peporine Lopes; William H. Gerwick; Bradley S. Moore; Pieter C. Dorrestein; Nuno Bandeira;International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 3K citations 2,812 popularity Top 0.01% influence Top 0.1% impulse Top 0.01% Powered by BIP!visibility 19visibility views 19 download downloads 417 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 FrancePublisher:Proceedings of the National Academy of Sciences Funded by:EC | BacCellEpiEC| BacCellEpiJuan J. Quereda; Olivier Dussurget; Marie-Anne Nahori; Amine Ghozlane; Stevenn Volant; Marie-Agnès Dillies; Béatrice Regnault; Sean Kennedy; Stanislas Mondot; Barbara Villoing; Pascale Cossart; Javier Pizarro-Cerdá;SignificanceListeria monocytogenesis a bacterial pathogen responsible for listeriosis, a foodborne disease characterized by septicemia and abortion in pregnant women. The most severe listeriosis outbreaks are associated with a subset of bacterial epidemic clones, although the underlying virulence mechanisms of these clones remain elusive. Here, we demonstrate, to our knowledge for the first time, that these epidemic strains secrete a bacteriocin specifically in the gut and alter host intestinal microbiota, allowingL. monocytogenescolonization of the intestine and, consequently, invasion of deeper organs. Therefore, our work shows that epidemic listeriosis implicates not only interactions betweenL. monocytogenesand host cells, but also interactions betweenL. monocytogenesand the host intestinal microbiota that are critical for the establishment of infection.
Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 154 citations 154 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
Loading
description Publicationkeyboard_double_arrow_right Article , Preprint 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | IGNITE, EC | SynarchiCEC| IGNITE ,EC| SynarchiCCyril Matthey-Doret; Lyam Baudry; Axel Breuer; Rémi Montagne; Nadège Guiglielmoni; Vittore F. Scolari; Etienne Jean; Arnaud Campeas; Philippe Henri Chanut; Edgar Oriol; Adrien Meot; Laurent Politis; Antoine Vigouroux; Pierrick Moreau; Romain Koszul; Axel Cournac;Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols. Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 60 citations 60 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Conference object , Article 2017 France Funded by:EC | OpenMinTeDEC| OpenMinTeDAuthors: Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;pmid: 30910089
pmc: PMC6460834
Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & MethodsWe propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, we analyzed terms that designate Microbial and Habitat entities in text. Microorganism names were predicted using the NCBI taxonomy. Habitat entities were detected using the syntactic structure of the terms and the OntoBiotope ontology. This ontology has been specifically enriched for the recognition of food terms in text. In a second time, we predicted links between microorganisms and their habitats (labeled “Lives_in” relationships) using pattern and machine-learning based methods. The results of text-mining predictions are indexed and presented in a semantic search engine. Result The AlvisIR search engine for microbe literature gives online access to 1.2 million PubMed abstracts in 2015, among which 13% are specific to food. This tool makes it possible to use text-mining results to search for information on bacterial biodiversity. It covers all types of microbial habitats to help understand the origin of microbial presence in food. Significance This work presents the first semantic search engine dedicated to better understand microbial food biodiversity from text.
Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6460834&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 10 citations 10 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6460834&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Netherlands, Netherlands, Italy, United Kingdom, United Kingdom, Netherlands, Netherlands, France, United Kingdom, Spain EnglishPublisher:HAL CCSD Funded by:EC | PhenoMeNalEC| PhenoMeNalvan Rijswijk, M; van Rijswijk, M; Beirnaert, C; Beirnaert, C; Caron, C; Cascante, M; Dominguez, V; Dunn, WB; Ebbels, TMD; Giacomoni, F; Gonzalez-Beltran, A; Hankemeier, T; Haug, K; Haug, K; Izquierdo-Garcia, JL; Jimenez, RC; Jimenez, RC; Jourdan, F; Kale, N; Klapa, MI; Kohlbacher, O; Koort, K; Kultima, K; Le Corguillé, G; Moreno, P; Moschonas, NK; Moschonas, NK; Neumann, S; O'Donovan, C; Reczko, M; Rocca-Serra, P; Rosato, A; Rosato, A; Rosato, A; Salek, RM; Salek, RM; Sansone, S-A; Satagopam, V; Schober, D; Shimmo, R; Spicer, RA; Spicer, RA; Spjuth, O; Spjuth, O; Spjuth, O; Thévenot, EA; Thévenot, EA; Viant, MR; Weber, RJM; Willighagen, EL; Willighagen, EL; Zanetti, G; Steinbeck, C; Steinbeck, C;Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases. The meeting was funded by PhenoMeNal, European Commission's Horizon2020 programme, grant agreement number 654241 Sí
HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.12342.1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 34visibility views 34 download downloads 65 Powered bymore_vert HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.12688/f1000research.12342.1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Article 2016 France, Switzerland, Brazil, Denmark, United Kingdom, GermanyPublisher:Springer Science and Business Media LLC Funded by:EC | PHARMASEAEC| PHARMASEAMingxun Wang; Jeremy Carver; Vanessa V. Phelan; Laura M. Sanchez; Neha Garg; Yao Peng; Don D. Nguyen; Jeramie D. Watrous; Clifford A. Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V. Melnik; Michael J. Meehan; Wei-Ting Liu; Max Crüsemann; Paul D. Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D. Kersten; Laura A. Pace; Robert A. Quinn; Katherine R. Duncan; Cheng-Chih Hsu; Dimitrios J. Floros; Ronnie G. Gavilan; Karin Kleigrewe; Trent R. Northen; Rachel J. Dutton; Delphine Parrot; Erin E. Carlson; Bertrand Aigle; Charlotte Frydenlund Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel A. Pevzner; Anna Edlund; Jeffrey S. McLean; Jörn Piel; Brian T. Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A. Keyzers; Amy C. Sims; Andrew R. Johnson; Ashley M. Sidebottom; Brian E. Sedio; Andreas Klitgaard; Charles B. Larson; Cristopher A. Boya P.; Daniel Torres-Mendoza; David Gonzalez; Denise Brentan Silva; Lucas Miranda Marques; Daniel P. Demarque; Egle Pociute; Ellis C. O’Neill; Enora Briand; Eric J. N. Helfrich; Eve A. Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J. Kharbush; Yi Zeng; Julia A. Vorholt; Kenji L. Kurita; Pep Charusanti; Kerry L. McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F. Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B. Vining; Ralph S. Baric; Ricardo Pianta Rodrigues da Silva; Samantha J. Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat R. Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G. Williams; Jingqui Dai; Ram P. Neupane; Joshua R. Gurr; Andrés M. C. Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M. Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Félix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E. Kyle; Thomas O. Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M. Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R. Jensen; Bernhard O. Palsson; Kit Pogliano; Roger G. Linington; Marcelino Gutiérrez; Norberto Peporine Lopes; William H. Gerwick; Bradley S. Moore; Pieter C. Dorrestein; Nuno Bandeira;International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 3K citations 2,812 popularity Top 0.01% influence Top 0.1% impulse Top 0.01% Powered by BIP!visibility 19visibility views 19 download downloads 417 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 FrancePublisher:Proceedings of the National Academy of Sciences Funded by:EC | BacCellEpiEC| BacCellEpiJuan J. Quereda; Olivier Dussurget; Marie-Anne Nahori; Amine Ghozlane; Stevenn Volant; Marie-Agnès Dillies; Béatrice Regnault; Sean Kennedy; Stanislas Mondot; Barbara Villoing; Pascale Cossart; Javier Pizarro-Cerdá;SignificanceListeria monocytogenesis a bacterial pathogen responsible for listeriosis, a foodborne disease characterized by septicemia and abortion in pregnant women. The most severe listeriosis outbreaks are associated with a subset of bacterial epidemic clones, although the underlying virulence mechanisms of these clones remain elusive. Here, we demonstrate, to our knowledge for the first time, that these epidemic strains secrete a bacteriocin specifically in the gut and alter host intestinal microbiota, allowingL. monocytogenescolonization of the intestine and, consequently, invasion of deeper organs. Therefore, our work shows that epidemic listeriosis implicates not only interactions betweenL. monocytogenesand host cells, but also interactions betweenL. monocytogenesand the host intestinal microbiota that are critical for the establishment of infection.
Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 154 citations 154 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu