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description 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.
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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.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 FrancePublisher:Oxford University Press (OUP) Funded by:UKRI | SynBioNT: A Synthetic Bio..., EC | MICROME, UKRI | Towards a Universal Biolo...UKRI| SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions ,EC| MICROME ,UKRI| Towards a Universal Biological-Cell Operating System (AUdACiOuS)Glaab, E.; Baudot, A.; Krasnogor, N.; Schneider, R.; Valencia, A.;Abstract Motivation: Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale functional genomics data. For this purpose, a frequently used approach is to apply an over-representation-based enrichment analysis. However, this approach has four drawbacks: (i) it can only score functional associations of overlapping gene/proteins sets; (ii) it disregards genes with missing annotations; (iii) it does not take into account the network structure of physical interactions between the gene/protein sets of interest and (iv) tissue-specific gene/protein set associations cannot be recognized. Results: To address these limitations, we introduce an integrative analysis approach and web-application called EnrichNet. It combines a novel graph-based statistic with an interactive sub-network visualization to accomplish two complementary goals: improving the prioritization of putative functional gene/protein set associations by exploiting information from molecular interaction networks and tissue-specific gene expression data and enabling a direct biological interpretation of the results. By using the approach to analyse sets of genes with known involvement in human diseases, new pathway associations are identified, reflecting a dense sub-network of interactions between their corresponding proteins. Availability: EnrichNet is freely available at http://www.enrichnet.org. Contact: Natalio.Krasnogor@nottingham.ac.uk, reinhard.schneider@uni.lu or avalencia@cnio.es Supplementary Information: Supplementary data are available at Bioinformatics Online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3436816Data sources: PubMed Centraladd 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.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 259 citations 259 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3436816Data sources: PubMed Centraladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2004 Spain, France, Germany, Germany, GermanyPublisher:Oxford University Press (OUP) Güldener, U.; Münsterkötter, M.; Kastenmüller, G.; Strack, N.; van Helden, J.; Lemer, C.; Richelles, J.; Wodak, S. J.; García-Martínez, J.; Pérez-Ortín, J. E.; Michael, H.; Kaps, A.; Talla, E.; Dujon, B.; André, Bernard; Souciet, J. L.; de Montigny, J.; Bon, Elisabeth; Gaillardin, C.; Mewes, H. W.;The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.; International audience; The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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=10.1093/nar/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 309 citations 309 popularity Top 10% influence Top 1% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/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=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd 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=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd 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=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FrancePublisher:Springer Science and Business Media LLC Jorge Bernal; Aymeric Histace; Marc Masana; Quentin Angermann; Cristina Sánchez-Montes; Cristina Rodríguez de Miguel; Maroua Hammami; Ana García-Rodríguez; Henry Córdova; Olivier Romain; Gloria Fernández-Esparrach; Xavier Dray; F. Javier Sánchez;pmid: 30255462
Methodology evaluation for decision support systems for health is a time-consuming task. To assess performance of polyp detection methods in colonoscopy videos, clinicians have to deal with the annotation of thousands of images. Current existing tools could be improved in terms of flexibility and ease of use. We introduce GTCreator, a flexible annotation tool for providing image and text annotations to image-based datasets. It keeps the main basic functionalities of other similar tools while extending other capabilities such as allowing multiple annotators to work simultaneously on the same task or enhanced dataset browsing and easy annotation transfer aiming to speed up annotation processes in large datasets. The comparison with other similar tools shows that GTCreator allows to obtain fast and precise annotation of image datasets, being the only one which offers full annotation editing and browsing capabilites. Our proposed annotation tool has been proven to be efficient for large image dataset annotation, as well as showing potential of use in other stages of method evaluation such as experimental setup or results analysis.
HAL CY Cergy Paris U... arrow_drop_down International Journal of Computer Assisted Radiology and SurgeryArticle . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefInternational Journal of Computer Assisted Radiology and SurgeryArticle . 2018Data sources: Europe PubMed Centraladd 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=10.1007/s11548-018-1864-x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 25 citations 25 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert HAL CY Cergy Paris U... arrow_drop_down International Journal of Computer Assisted Radiology and SurgeryArticle . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefInternational Journal of Computer Assisted Radiology and SurgeryArticle . 2018Data sources: Europe PubMed Centraladd 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=10.1007/s11548-018-1864-x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2013 United Kingdom, Spain, France, United StatesPublisher:Springer Science and Business Media LLC Funded by:NIH | Epistatic and Cross Tissu..., NIH | Using the Transcriptome f..., NIH | CNS Mechanisms in Cocaine... +4 projectsNIH| Epistatic and Cross Tissue Analysis for Human Gene Expression Traits ,NIH| Using the Transcriptome for SNP and Gene Annotation ,NIH| CNS Mechanisms in Cocaine-Related Sudden Death ,NIH| Statistical analysis of gene expression quantitative trait loci (eQTL) ,NIH| Methods for high-resolution analysis of genetic effects on gene expression ,NIH| FACILITATING GTEx, DISEASE, AND GxE ANALYSES VIA FAST EXPRESSION (e)QTL MAPPING ,WTJohn T. Lonsdale; Jeffrey Thomas; Mike Salvatore; Rebecca Phillips; Edmund Lo; Saboor Shad; Richard Hasz; Gary Walters; Fernando U. Garcia; Nancy Young; Barbara A. Foster; Mike Moser; Ellen Karasik; Bryan Gillard; Kimberley Ramsey; Susan L. Sullivan; Jason Bridge; Harold Magazine; John Syron; Johnelle Fleming; Laura A. Siminoff; Heather M. Traino; Maghboeba Mosavel; Laura Barker; Scott D. Jewell; Daniel C. Rohrer; Dan Maxim; Dana Filkins; Philip Harbach; Eddie Cortadillo; Bree Berghuis; Lisa Turner; Eric Hudson; Kristin Feenstra; Leslie H. Sobin; James A. Robb; Phillip Branton; Greg E. Korzeniewski; Charles Shive; David Tabor; Liqun Qi; Kevin Groch; Sreenath Nampally; Steve Buia; Angela Zimmerman; Anna M. Smith; Robin Burges; Karna Robinson; Kim Valentino; Deborah Bradbury; Mark Cosentino; Norma Diaz-Mayoral; Mary Kennedy; Theresa Engel; Penelope Williams; Kenyon Erickson; Kristin G. Ardlie; Wendy Winckler; Gad Getz; David S. DeLuca; MacArthur Daniel MacArthur; Manolis Kellis; Alexander Thomson; Taylor Young; Ellen Gelfand; Molly Donovan; Yan Meng; George B. Grant; Deborah C. Mash; Yvonne Marcus; Margaret J. Basile; Jun Liu; Jun Zhu; Zhidong Tu; Nancy J. Cox; Dan L. Nicolae; Eric R. Gamazon; Hae Kyung Im; Anuar Konkashbaev; Jonathan K. Pritchard; Matthew Stevens; Timothée Flutre; Xiaoquan Wen; Emmanouil T. Dermitzakis; Tuuli Lappalainen; Roderic Guigó; Jean Monlong; Michael Sammeth; Daphne Koller; Alexis Battle; Sara Mostafavi; Mark I. McCarthy; Manual Rivas; Julian Maller; Ivan Rusyn; Andrew B. Nobel; Fred A. Wright; Andrey A. Shabalin; Mike Feolo; Nataliya Sharopova; Anne Sturcke; Justin Paschal; James M. Anderson; Elizabeth L. Wilder; Leslie Derr; Eric D. Green; Jeffery P. Struewing; Gary F. Temple; Simona Volpi; Joy T. Boyer; Elizabeth J. Thomson; Mark S. Guyer; Cathy Ng; Assya Abdallah; Deborah Colantuoni; Thomas R. Insel; Susan E. Koester; Roger Little; Patrick Bender; Thomas Lehner; Yin Yao; Carolyn C. Compton; Jimmie B. Vaught; Sherilyn Sawyer; Nicole C. Lockhart; Joanne P. Demchok; Helen F. Moore;Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues. National Institutes of Health (U.S.) (US NIH to the Broad Institute of Harvard and MIT, R01 DA006227-17) National Institute of Neurological Disorders and Stroke (U.S.) National Institute of Mental Health (U.S.) National Institute of Drug Abuse
Europe PubMed Centra... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveMémoires en Sciences de l'Information et de la CommunicationArticle . 2013License: CC BY NC SAFull-Text: https://hal.science/hal-01374823/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=10.1038/ng.2653&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 7K citations 6,577 popularity Top 0.01% influence Top 0.01% impulse Top 0.01% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveMémoires en Sciences de l'Information et de la CommunicationArticle . 2013License: CC BY NC SAFull-Text: https://hal.science/hal-01374823/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=10.1038/ng.2653&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018Publisher:Cold Spring Harbor Laboratory Funded by:ANR | France Génomique, EC | BLUEPRINT, ANR | INRT +2 projectsANR| France Génomique ,EC| BLUEPRINT ,ANR| INRT ,ANR| UNISTRA ,EC| CHROMTOPOLOGYYousra Ben Zouari; Anne Molitor; Natalia Sikorska; Vera Pancaldi; Tom Sexton;Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks. Electronic supplementary material The online version of this article (10.1186/s13059-019-1706-3) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6532271Data sources: PubMed CentralbioRxivPreprint . 2018Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019Full-Text: https://hal.science/hal-04083921/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=10.1101/445023&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 27 citations 27 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 20visibility views 20 download downloads 68 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6532271Data sources: PubMed CentralbioRxivPreprint . 2018Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019Full-Text: https://hal.science/hal-04083921/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=10.1101/445023&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Pio-Lopez, Léo; Valdeolivas, Alberto; Tichit, Laurent; Remy, Élisabeth; Baudot, Anaïs;Network embedding approaches are gaining momentum to analyse a large variety of networks. Indeed, these approaches have demonstrated their efficiency for tasks such as community detection, node classification, and link prediction. However, very few network embedding methods have been specifically designed to handle multiplex networks, i.e. networks composed of different layers sharing the same set of nodes but having different types of edges. Moreover, to our knowledge, existing approaches cannot embed multiple nodes from multiplex-heterogeneous networks, i.e. networks composed of several layers containing both different types of nodes and edges. In this study, we propose MultiVERSE, an extension of the VERSE method with Random Walks with Restart on Multiplex (RWR-M) and Multiplex-Heterogeneous (RWR-MH) networks. MultiVERSE is a fast and scalable method to learn node embeddings from multiplex and multiplex-heterogeneous networks. We evaluate MultiVERSE on several biological and social networks and demonstrate its efficiency. MultiVERSE indeed outperforms most of the other methods in the tasks of link prediction and network reconstruction for multiplex network embedding, and is also efficient in the task of link prediction for multiplex-heterogeneous network embedding. Finally, we apply MultiVERSE to study rare disease-gene associations using link prediction and clustering. MultiVERSE is freely available on github at https://github.com/Lpiol/MultiVERSE. Comment: 29 pages, 6 figures
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8062697Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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=10.48550/arxiv.2008.10085&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 3 citations 3 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8062697Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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=10.48550/arxiv.2008.10085&type=result"></script>'); --> </script>
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description 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 Article 2012 FrancePublisher:Oxford University Press (OUP) Funded by:UKRI | SynBioNT: A Synthetic Bio..., EC | MICROME, UKRI | Towards a Universal Biolo...UKRI| SynBioNT: A Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions ,EC| MICROME ,UKRI| Towards a Universal Biological-Cell Operating System (AUdACiOuS)Glaab, E.; Baudot, A.; Krasnogor, N.; Schneider, R.; Valencia, A.;Abstract Motivation: Assessing functional associations between an experimentally derived gene or protein set of interest and a database of known gene/protein sets is a common task in the analysis of large-scale functional genomics data. For this purpose, a frequently used approach is to apply an over-representation-based enrichment analysis. However, this approach has four drawbacks: (i) it can only score functional associations of overlapping gene/proteins sets; (ii) it disregards genes with missing annotations; (iii) it does not take into account the network structure of physical interactions between the gene/protein sets of interest and (iv) tissue-specific gene/protein set associations cannot be recognized. Results: To address these limitations, we introduce an integrative analysis approach and web-application called EnrichNet. It combines a novel graph-based statistic with an interactive sub-network visualization to accomplish two complementary goals: improving the prioritization of putative functional gene/protein set associations by exploiting information from molecular interaction networks and tissue-specific gene expression data and enabling a direct biological interpretation of the results. By using the approach to analyse sets of genes with known involvement in human diseases, new pathway associations are identified, reflecting a dense sub-network of interactions between their corresponding proteins. Availability: EnrichNet is freely available at http://www.enrichnet.org. Contact: Natalio.Krasnogor@nottingham.ac.uk, reinhard.schneider@uni.lu or avalencia@cnio.es Supplementary Information: Supplementary data are available at Bioinformatics Online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3436816Data sources: PubMed Centraladd 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=10.1093/bioinformatics/bts389&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 259 citations 259 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3436816Data sources: PubMed Centraladd 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=10.1093/bioinformatics/bts389&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2004 Spain, France, Germany, Germany, GermanyPublisher:Oxford University Press (OUP) Güldener, U.; Münsterkötter, M.; Kastenmüller, G.; Strack, N.; van Helden, J.; Lemer, C.; Richelles, J.; Wodak, S. J.; García-Martínez, J.; Pérez-Ortín, J. E.; Michael, H.; Kaps, A.; Talla, E.; Dujon, B.; André, Bernard; Souciet, J. L.; de Montigny, J.; Bon, Elisabeth; Gaillardin, C.; Mewes, H. W.;The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.; International audience; The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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=10.1093/nar/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 309 citations 309 popularity Top 10% influence Top 1% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/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=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/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=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd 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=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd 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=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FrancePublisher:Springer Science and Business Media LLC Jorge Bernal; Aymeric Histace; Marc Masana; Quentin Angermann; Cristina Sánchez-Montes; Cristina Rodríguez de Miguel; Maroua Hammami; Ana García-Rodríguez; Henry Córdova; Olivier Romain; Gloria Fernández-Esparrach; Xavier Dray; F. Javier Sánchez;pmid: 30255462
Methodology evaluation for decision support systems for health is a time-consuming task. To assess performance of polyp detection methods in colonoscopy videos, clinicians have to deal with the annotation of thousands of images. Current existing tools could be improved in terms of flexibility and ease of use. We introduce GTCreator, a flexible annotation tool for providing image and text annotations to image-based datasets. It keeps the main basic functionalities of other similar tools while extending other capabilities such as allowing multiple annotators to work simultaneously on the same task or enhanced dataset browsing and easy annotation transfer aiming to speed up annotation processes in large datasets. The comparison with other similar tools shows that GTCreator allows to obtain fast and precise annotation of image datasets, being the only one which offers full annotation editing and browsing capabilites. Our proposed annotation tool has been proven to be efficient for large image dataset annotation, as well as showing potential of use in other stages of method evaluation such as experimental setup or results analysis.
HAL CY Cergy Paris U... arrow_drop_down International Journal of Computer Assisted Radiology and SurgeryArticle . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefInternational Journal of Computer Assisted Radiology and SurgeryArticle . 2018Data sources: Europe PubMed Centraladd 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=10.1007/s11548-018-1864-x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 25 citations 25 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert HAL CY Cergy Paris U... arrow_drop_down International Journal of Computer Assisted Radiology and SurgeryArticle . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefInternational Journal of Computer Assisted Radiology and SurgeryArticle . 2018Data sources: Europe PubMed Centraladd 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=10.1007/s11548-018-1864-x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2013 United Kingdom, Spain, France, United StatesPublisher:Springer Science and Business Media LLC Funded by:NIH | Epistatic and Cross Tissu..., NIH | Using the Transcriptome f..., NIH | CNS Mechanisms in Cocaine... +4 projectsNIH| Epistatic and Cross Tissue Analysis for Human Gene Expression Traits ,NIH| Using the Transcriptome for SNP and Gene Annotation ,NIH| CNS Mechanisms in Cocaine-Related Sudden Death ,NIH| Statistical analysis of gene expression quantitative trait loci (eQTL) ,NIH| Methods for high-resolution analysis of genetic effects on gene expression ,NIH| FACILITATING GTEx, DISEASE, AND GxE ANALYSES VIA FAST EXPRESSION (e)QTL MAPPING ,WTJohn T. Lonsdale; Jeffrey Thomas; Mike Salvatore; Rebecca Phillips; Edmund Lo; Saboor Shad; Richard Hasz; Gary Walters; Fernando U. Garcia; Nancy Young; Barbara A. Foster; Mike Moser; Ellen Karasik; Bryan Gillard; Kimberley Ramsey; Susan L. Sullivan; Jason Bridge; Harold Magazine; John Syron; Johnelle Fleming; Laura A. Siminoff; Heather M. Traino; Maghboeba Mosavel; Laura Barker; Scott D. Jewell; Daniel C. Rohrer; Dan Maxim; Dana Filkins; Philip Harbach; Eddie Cortadillo; Bree Berghuis; Lisa Turner; Eric Hudson; Kristin Feenstra; Leslie H. Sobin; James A. Robb; Phillip Branton; Greg E. Korzeniewski; Charles Shive; David Tabor; Liqun Qi; Kevin Groch; Sreenath Nampally; Steve Buia; Angela Zimmerman; Anna M. Smith; Robin Burges; Karna Robinson; Kim Valentino; Deborah Bradbury; Mark Cosentino; Norma Diaz-Mayoral; Mary Kennedy; Theresa Engel; Penelope Williams; Kenyon Erickson; Kristin G. Ardlie; Wendy Winckler; Gad Getz; David S. DeLuca; MacArthur Daniel MacArthur; Manolis Kellis; Alexander Thomson; Taylor Young; Ellen Gelfand; Molly Donovan; Yan Meng; George B. Grant; Deborah C. Mash; Yvonne Marcus; Margaret J. Basile; Jun Liu; Jun Zhu; Zhidong Tu; Nancy J. Cox; Dan L. Nicolae; Eric R. Gamazon; Hae Kyung Im; Anuar Konkashbaev; Jonathan K. Pritchard; Matthew Stevens; Timothée Flutre; Xiaoquan Wen; Emmanouil T. Dermitzakis; Tuuli Lappalainen; Roderic Guigó; Jean Monlong; Michael Sammeth; Daphne Koller; Alexis Battle; Sara Mostafavi; Mark I. McCarthy; Manual Rivas; Julian Maller; Ivan Rusyn; Andrew B. Nobel; Fred A. Wright; Andrey A. Shabalin; Mike Feolo; Nataliya Sharopova; Anne Sturcke; Justin Paschal; James M. Anderson; Elizabeth L. Wilder; Leslie Derr; Eric D. Green; Jeffery P. Struewing; Gary F. Temple; Simona Volpi; Joy T. Boyer; Elizabeth J. Thomson; Mark S. Guyer; Cathy Ng; Assya Abdallah; Deborah Colantuoni; Thomas R. Insel; Susan E. Koester; Roger Little; Patrick Bender; Thomas Lehner; Yin Yao; Carolyn C. Compton; Jimmie B. Vaught; Sherilyn Sawyer; Nicole C. Lockhart; Joanne P. Demchok; Helen F. Moore;Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues. National Institutes of Health (U.S.) (US NIH to the Broad Institute of Harvard and MIT, R01 DA006227-17) National Institute of Neurological Disorders and Stroke (U.S.) National Institute of Mental Health (U.S.) National Institute of Drug Abuse
Europe PubMed Centra... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveMémoires en Sciences de l'Information et de la CommunicationArticle . 2013License: CC BY NC SAFull-Text: https://hal.science/hal-01374823/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=10.1038/ng.2653&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 7K citations 6,577 popularity Top 0.01% influence Top 0.01% impulse Top 0.01% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveMémoires en Sciences de l'Information et de la CommunicationArticle . 2013License: CC BY NC SAFull-Text: https://hal.science/hal-01374823/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=10.1038/ng.2653&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018Publisher:Cold Spring Harbor Laboratory Funded by:ANR | France Génomique, EC | BLUEPRINT, ANR | INRT +2 projectsANR| France Génomique ,EC| BLUEPRINT ,ANR| INRT ,ANR| UNISTRA ,EC| CHROMTOPOLOGYYousra Ben Zouari; Anne Molitor; Natalia Sikorska; Vera Pancaldi; Tom Sexton;Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks. Electronic supplementary material The online version of this article (10.1186/s13059-019-1706-3) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6532271Data sources: PubMed CentralbioRxivPreprint . 2018Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019Full-Text: https://hal.science/hal-04083921/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=10.1101/445023&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 27 citations 27 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 20visibility views 20 download downloads 68 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6532271Data sources: PubMed CentralbioRxivPreprint . 2018Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019Full-Text: https://hal.science/hal-04083921/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=10.1101/445023&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Pio-Lopez, Léo; Valdeolivas, Alberto; Tichit, Laurent; Remy, Élisabeth; Baudot, Anaïs;Network embedding approaches are gaining momentum to analyse a large variety of networks. Indeed, these approaches have demonstrated their efficiency for tasks such as community detection, node classification, and link prediction. However, very few network embedding methods have been specifically designed to handle multiplex networks, i.e. networks composed of different layers sharing the same set of nodes but having different types of edges. Moreover, to our knowledge, existing approaches cannot embed multiple nodes from multiplex-heterogeneous networks, i.e. networks composed of several layers containing both different types of nodes and edges. In this study, we propose MultiVERSE, an extension of the VERSE method with Random Walks with Restart on Multiplex (RWR-M) and Multiplex-Heterogeneous (RWR-MH) networks. MultiVERSE is a fast and scalable method to learn node embeddings from multiplex and multiplex-heterogeneous networks. We evaluate MultiVERSE on several biological and social networks and demonstrate its efficiency. MultiVERSE indeed outperforms most of the other methods in the tasks of link prediction and network reconstruction for multiplex network embedding, and is also efficient in the task of link prediction for multiplex-heterogeneous network embedding. Finally, we apply MultiVERSE to study rare disease-gene associations using link prediction and clustering. MultiVERSE is freely available on github at https://github.com/Lpiol/MultiVERSE. Comment: 29 pages, 6 figures
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8062697Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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=10.48550/arxiv.2008.10085&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 3 citations 3 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8062697Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd 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=10.48550/arxiv.2008.10085&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu