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description Publicationkeyboard_double_arrow_right Article 2020 France, Cyprus, Italy EnglishPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | chemREPEATEC| IDPfun ,EC| chemREPEATMier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.; Mier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.;Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd 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 hybrid 67 citations 67 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd 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 , 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 , 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.
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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 2017 France EnglishPublisher:Public Library of Science (PLoS) Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M.; Thiele, Sven; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne;pmc: PMC5302834
pmid: 28129330
Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system. Author Summary In the era of fast and massive genome sequencing, one challenge is to transform sequence information into biological knowledge. Reconstructing metabolic networks that include all biochemical reactions of a cell is a way to infer reactions from genomic data. Unfortunately, those data are usually incomplete, poorly annotated, and missing reactions create gaps in the metabolic networks. Here we introduce Meneco, a tool dedicated to the parsimonious gap-filling of metabolic networks. Unlike other tools, Meneco allows using sparse data (missing stoichiometries) and draft metabolic networks to suggest reactions to fill gaps in the networks. Subsequently, we apply it to two biological case studies and show that the flexibility of Meneco enables it to be adapted to a variety of research questions and types of available data. We show that Meneco performs better than reference tools with respect to large-scale heterogeneous reference database and with respect to the recovery of important reactions in highly degraded networks. Specifically, it allowed the analysis of two interacting metabolic networks and the reconstruction of the first metabolic network of Euglena mutabilis.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5302834Data sources: PubMed CentralHal-DiderotArticle . 2017License: CC BYFull-Text: https://hal.inria.fr/hal-01449100/documentData sources: Hal-Diderotadd 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 30 citations 30 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5302834Data sources: PubMed CentralHal-DiderotArticle . 2017License: CC BYFull-Text: https://hal.inria.fr/hal-01449100/documentData sources: Hal-Diderotadd 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=11858/00-001M-0000-002C-87B0-F&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2019 Cyprus, Portugal, France, Serbia, France, Denmark, Italy, Spain, Belgium EnglishPublisher:HAL CCSD Funded by:MESTD | Application of the EIIP/I..., EC | IDPfunMESTD| Application of the EIIP/ISM bioinformatics platform in discovery of novel therapeutic targets and potential therapeutic molecules ,EC| IDPfunAuthors: Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; +124 AuthorsHatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia; Davey, Norman E.; Davidović, Radoslav; Dunker, A. Keith; Elofsson, Arne; Gobeill, Julien; Foutel, Nicolás S. González; Sudha, Govindarajan; Guharoy, Mainak; Horvath, Tamas; Iglesias, Valentin; Kajava, Andrey V.; Kovacs, Orsolya P.; Lamb, John; Lambrughi, Matteo; Lazar, Tamas; Leclercq, Jeremy Y.; Leonardi, Emanuela; Macedo-Ribeiro, Sandra; Macossay-Castillo, Mauricio; Maiani, Emiliano; Manso, José A.; Marino-Buslje, Cristina; Martínez-Pérez, Elizabeth; Mészáros, Bálint; Mičetić, Ivan; Minervini, Giovanni; Murvai, Nikoletta; Necci, Marco; Ouzounis, Christos A.; Pajkos, Mátyás; Paladin, Lisanna; Pancsa, Rita; Papaleo, Elena; Parisi, Gustavo; Pasche, Emilie; Barbosa Pereira, Pedro J.; Promponas, Vasilis J.; Pujols, Jordi; Quaglia, Federica; Ruch, Patrick; Salvatore, Marco; Schad, Eva; Szabo, Beata; Szaniszló, Tamás; Tamana, Stella; Tantos, Agnes; Veljkovic, Nevena; Ventura, Salvador; Vranken, Wim; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C. E.; Piovesan, Damiano; Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia; Davey, Norman E.; Davidović, Radoslav; Dunker, A. Keith; Elofsson, Arne; Gobeill, Julien; Foutel, Nicolás S. González; Sudha, Govindarajan; Guharoy, Mainak; Horvath, Tamas; Iglesias, Valentin; Kajava, Andrey V.; Kovacs, Orsolya P.; Lamb, John; Lambrughi, Matteo; Lazar, Tamas; Leclercq, Jeremy Y.; Leonardi, Emanuela; Macedo-Ribeiro, Sandra; Macossay-Castillo, Mauricio; Maiani, Emiliano; Manso, José A.; Marino-Buslje, Cristina; Martínez-Pérez, Elizabeth; Mészáros, Bálint; Mičetić, Ivan; Minervini, Giovanni; Murvai, Nikoletta; Necci, Marco; Ouzounis, Christos A.; Pajkos, Mátyás; Paladin, Lisanna; Pancsa, Rita; Papaleo, Elena; Parisi, Gustavo; Pasche, Emilie; Barbosa Pereira, Pedro J.; Promponas, Vasilis J.; Pujols, Jordi; Quaglia, Federica; Ruch, Patrick; Salvatore, Marco; Schad, Eva; Szabo, Beata; Szaniszló, Tamás; Tamana, Stella; Tantos, Agnes; Veljkovic, Nevena; Ventura, Salvador; Vranken, Wim; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C. E.; Piovesan, Damiano;The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome. Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared.
Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; Archivio istituzionale della ricerca - Università di PadovaOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145575Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2020Data sources: Vrije Universiteit Brussel Research PortalRepositório Aberto da Universidade do PortoArticle . 2020Data sources: Repositório Aberto da Universidade do PortoOpenAIRE; Copenhagen University Research Information SystemArticle . 2020 . 2019Recolector de Ciencia Abierta, RECOLECTA; Dipòsit Digital de Documents de la UABArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 154 citations 154 popularity Top 1% influence Top 10% impulse Top 0.1% Powered by BIP!visibility 71visibility views 71 download downloads 172 Powered bymore_vert Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; Archivio istituzionale della ricerca - Università di PadovaOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145575Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2020Data sources: Vrije Universiteit Brussel Research PortalRepositório Aberto da Universidade do PortoArticle . 2020Data sources: Repositório Aberto da Universidade do PortoOpenAIRE; Copenhagen University Research Information SystemArticle . 2020 . 2019Recolector de Ciencia Abierta, RECOLECTA; Dipòsit Digital de Documents de la UABArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2015 France, France, France, France, Netherlands, Spain EnglishPublisher:HAL CCSD Funded by:FCT | Specific isotopic labelli..., EC | EGI-INSPIRE, EC | WENMR +4 projectsFCT| Specific isotopic labelling of membrane proteins as a new tool to monitor structural and conformation changes ,EC| EGI-INSPIRE ,EC| WENMR ,EC| BIOMEDBRIDGES ,AKA| ELIXIR - Data for Life European Life Science Infrastructure for Biological Information ,FCT| SFRH/BPD/78075/2011 ,WTAuthors: Duarte, Afonso M S; Psomopoulos, Fotis E; Blanchet, Christophe; Bonvin, Alexandre M J J; +9 AuthorsDuarte, Afonso M S; Psomopoulos, Fotis E; Blanchet, Christophe; Bonvin, Alexandre M J J; Corpas, Manuel; Franc, Alain; Jimenez, Rafael C; de Lucas, Jesus M; Nyrönen, Tommi; Sipos, Gergely; Suhr, Stephanie B; Sub NMR Spectroscopy; NMR Spectroscopy;With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community. AD was supported by Fundação para a Ciência e a Tecnologia, Portugal (SFRH/BPD/78075/2011 and EXPL/BBBBEP/1356/2013). FP has been supported by the National Grid Infrastructure NGI_GRNET, HellasGRID, as part of the EGI. IFB acknowledges funding from the “National Infrastructures in Biology and Health” call of the French “Investments for the Future” initiative. The WeNMR project has been funded by a European FP7 e-Infrastructure grant, contract no. 261572. AF was supported by a grant from Labex CEBA (Centre d’études de la Biodiversité Amazonienne) from ANR. MC is supported by UK’s BBSRC core funding. CSC was supported by Academy of Finland grant No. 273655 for ELIXIR Finland. The EGI-InSPIRE project (Integrated Sustainable Pan-European Infrastructure for Researchers in Europe) is co-funded by the European Commission (contract number: RI-261323). The BioMedBridges project is funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number 284209. This is an open-access article.-- et al. Peer Reviewed
NARCIS; Utrecht Univ... arrow_drop_down NARCIS; Utrecht University RepositoryArticle . 2015Frontiers in Genetics; FrontiersOther literature type . Article . 2015 . Peer-reviewedEurope PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4477178Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2015 . 2016 . Peer-reviewedadd 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 8 citations 8 popularity Average influence Average impulse Top 10% Powered by BIP!visibility 16visibility views 16 download downloads 20 Powered bymore_vert NARCIS; Utrecht Univ... arrow_drop_down NARCIS; Utrecht University RepositoryArticle . 2015Frontiers in Genetics; FrontiersOther literature type . Article . 2015 . Peer-reviewedEurope PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4477178Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2015 . 2016 . Peer-reviewedadd 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 2018 France EnglishPublisher:Oxford University Press (OUP) Funded by:EC | PhenoMeNal, WT | Institutional Strategic S...EC| PhenoMeNal ,WT| Institutional Strategic Support Fund Phase2 FY2014/16Cottret, Ludovic; Frainay, Clément; Chazalviel, Maxime; Cabanettes, Floréal; Gloaguen, Yoann; Camenen, Etienne; Merlet, Benjamin; Heux, Stéphanie; Portais, Jean-Charles; Poupin, Nathalie; Vinson, Florence; Jourdan, Fabien;pmc: PMC6030842
pmid: 29718355
Abstract Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/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 49 citations 49 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/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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description Publicationkeyboard_double_arrow_right Article 2020 France, Cyprus, Italy EnglishPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | chemREPEATEC| IDPfun ,EC| chemREPEATMier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.; Mier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.;Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd 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 hybrid 67 citations 67 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd 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 , 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 , 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.
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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.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017 France EnglishPublisher:Public Library of Science (PLoS) Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M.; Thiele, Sven; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne;pmc: PMC5302834
pmid: 28129330
Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system. Author Summary In the era of fast and massive genome sequencing, one challenge is to transform sequence information into biological knowledge. Reconstructing metabolic networks that include all biochemical reactions of a cell is a way to infer reactions from genomic data. Unfortunately, those data are usually incomplete, poorly annotated, and missing reactions create gaps in the metabolic networks. Here we introduce Meneco, a tool dedicated to the parsimonious gap-filling of metabolic networks. Unlike other tools, Meneco allows using sparse data (missing stoichiometries) and draft metabolic networks to suggest reactions to fill gaps in the networks. Subsequently, we apply it to two biological case studies and show that the flexibility of Meneco enables it to be adapted to a variety of research questions and types of available data. We show that Meneco performs better than reference tools with respect to large-scale heterogeneous reference database and with respect to the recovery of important reactions in highly degraded networks. Specifically, it allowed the analysis of two interacting metabolic networks and the reconstruction of the first metabolic network of Euglena mutabilis.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5302834Data sources: PubMed CentralHal-DiderotArticle . 2017License: CC BYFull-Text: https://hal.inria.fr/hal-01449100/documentData sources: Hal-Diderotadd 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 30 citations 30 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5302834Data sources: PubMed CentralHal-DiderotArticle . 2017License: CC BYFull-Text: https://hal.inria.fr/hal-01449100/documentData sources: Hal-Diderotadd 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 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2019 Cyprus, Portugal, France, Serbia, France, Denmark, Italy, Spain, Belgium EnglishPublisher:HAL CCSD Funded by:MESTD | Application of the EIIP/I..., EC | IDPfunMESTD| Application of the EIIP/ISM bioinformatics platform in discovery of novel therapeutic targets and potential therapeutic molecules ,EC| IDPfunAuthors: Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; +124 AuthorsHatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia; Davey, Norman E.; Davidović, Radoslav; Dunker, A. Keith; Elofsson, Arne; Gobeill, Julien; Foutel, Nicolás S. González; Sudha, Govindarajan; Guharoy, Mainak; Horvath, Tamas; Iglesias, Valentin; Kajava, Andrey V.; Kovacs, Orsolya P.; Lamb, John; Lambrughi, Matteo; Lazar, Tamas; Leclercq, Jeremy Y.; Leonardi, Emanuela; Macedo-Ribeiro, Sandra; Macossay-Castillo, Mauricio; Maiani, Emiliano; Manso, José A.; Marino-Buslje, Cristina; Martínez-Pérez, Elizabeth; Mészáros, Bálint; Mičetić, Ivan; Minervini, Giovanni; Murvai, Nikoletta; Necci, Marco; Ouzounis, Christos A.; Pajkos, Mátyás; Paladin, Lisanna; Pancsa, Rita; Papaleo, Elena; Parisi, Gustavo; Pasche, Emilie; Barbosa Pereira, Pedro J.; Promponas, Vasilis J.; Pujols, Jordi; Quaglia, Federica; Ruch, Patrick; Salvatore, Marco; Schad, Eva; Szabo, Beata; Szaniszló, Tamás; Tamana, Stella; Tantos, Agnes; Veljkovic, Nevena; Ventura, Salvador; Vranken, Wim; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C. E.; Piovesan, Damiano; Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia; Davey, Norman E.; Davidović, Radoslav; Dunker, A. Keith; Elofsson, Arne; Gobeill, Julien; Foutel, Nicolás S. González; Sudha, Govindarajan; Guharoy, Mainak; Horvath, Tamas; Iglesias, Valentin; Kajava, Andrey V.; Kovacs, Orsolya P.; Lamb, John; Lambrughi, Matteo; Lazar, Tamas; Leclercq, Jeremy Y.; Leonardi, Emanuela; Macedo-Ribeiro, Sandra; Macossay-Castillo, Mauricio; Maiani, Emiliano; Manso, José A.; Marino-Buslje, Cristina; Martínez-Pérez, Elizabeth; Mészáros, Bálint; Mičetić, Ivan; Minervini, Giovanni; Murvai, Nikoletta; Necci, Marco; Ouzounis, Christos A.; Pajkos, Mátyás; Paladin, Lisanna; Pancsa, Rita; Papaleo, Elena; Parisi, Gustavo; Pasche, Emilie; Barbosa Pereira, Pedro J.; Promponas, Vasilis J.; Pujols, Jordi; Quaglia, Federica; Ruch, Patrick; Salvatore, Marco; Schad, Eva; Szabo, Beata; Szaniszló, Tamás; Tamana, Stella; Tantos, Agnes; Veljkovic, Nevena; Ventura, Salvador; Vranken, Wim; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C. E.; Piovesan, Damiano;The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome. Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared.
Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; Archivio istituzionale della ricerca - Università di PadovaOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145575Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2020Data sources: Vrije Universiteit Brussel Research PortalRepositório Aberto da Universidade do PortoArticle . 2020Data sources: Repositório Aberto da Universidade do PortoOpenAIRE; Copenhagen University Research Information SystemArticle . 2020 . 2019Recolector de Ciencia Abierta, RECOLECTA; Dipòsit Digital de Documents de la UABArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 154 citations 154 popularity Top 1% influence Top 10% impulse Top 0.1% Powered by BIP!visibility 71visibility views 71 download downloads 172 Powered bymore_vert Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; Archivio istituzionale della ricerca - Università di PadovaOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145575Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2020Data sources: Vrije Universiteit Brussel Research PortalRepositório Aberto da Universidade do PortoArticle . 2020Data sources: Repositório Aberto da Universidade do PortoOpenAIRE; Copenhagen University Research Information SystemArticle . 2020 . 2019Recolector de Ciencia Abierta, RECOLECTA; Dipòsit Digital de Documents de la UABArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2015 France, France, France, France, Netherlands, Spain EnglishPublisher:HAL CCSD Funded by:FCT | Specific isotopic labelli..., EC | EGI-INSPIRE, EC | WENMR +4 projectsFCT| Specific isotopic labelling of membrane proteins as a new tool to monitor structural and conformation changes ,EC| EGI-INSPIRE ,EC| WENMR ,EC| BIOMEDBRIDGES ,AKA| ELIXIR - Data for Life European Life Science Infrastructure for Biological Information ,FCT| SFRH/BPD/78075/2011 ,WTAuthors: Duarte, Afonso M S; Psomopoulos, Fotis E; Blanchet, Christophe; Bonvin, Alexandre M J J; +9 AuthorsDuarte, Afonso M S; Psomopoulos, Fotis E; Blanchet, Christophe; Bonvin, Alexandre M J J; Corpas, Manuel; Franc, Alain; Jimenez, Rafael C; de Lucas, Jesus M; Nyrönen, Tommi; Sipos, Gergely; Suhr, Stephanie B; Sub NMR Spectroscopy; NMR Spectroscopy;With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community. AD was supported by Fundação para a Ciência e a Tecnologia, Portugal (SFRH/BPD/78075/2011 and EXPL/BBBBEP/1356/2013). FP has been supported by the National Grid Infrastructure NGI_GRNET, HellasGRID, as part of the EGI. IFB acknowledges funding from the “National Infrastructures in Biology and Health” call of the French “Investments for the Future” initiative. The WeNMR project has been funded by a European FP7 e-Infrastructure grant, contract no. 261572. AF was supported by a grant from Labex CEBA (Centre d’études de la Biodiversité Amazonienne) from ANR. MC is supported by UK’s BBSRC core funding. CSC was supported by Academy of Finland grant No. 273655 for ELIXIR Finland. The EGI-InSPIRE project (Integrated Sustainable Pan-European Infrastructure for Researchers in Europe) is co-funded by the European Commission (contract number: RI-261323). The BioMedBridges project is funded by the European Commission within Research Infrastructures of the FP7 Capacities Specific Programme, grant agreement number 284209. This is an open-access article.-- et al. Peer Reviewed
NARCIS; Utrecht Univ... arrow_drop_down NARCIS; Utrecht University RepositoryArticle . 2015Frontiers in Genetics; FrontiersOther literature type . Article . 2015 . Peer-reviewedEurope PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4477178Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2015 . 2016 . Peer-reviewedadd 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 8 citations 8 popularity Average influence Average impulse Top 10% Powered by BIP!visibility 16visibility views 16 download downloads 20 Powered bymore_vert NARCIS; Utrecht Univ... arrow_drop_down NARCIS; Utrecht University RepositoryArticle . 2015Frontiers in Genetics; FrontiersOther literature type . Article . 2015 . Peer-reviewedEurope PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4477178Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2015 . 2016 . Peer-reviewedadd 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 2018 France EnglishPublisher:Oxford University Press (OUP) Funded by:EC | PhenoMeNal, WT | Institutional Strategic S...EC| PhenoMeNal ,WT| Institutional Strategic Support Fund Phase2 FY2014/16Cottret, Ludovic; Frainay, Clément; Chazalviel, Maxime; Cabanettes, Floréal; Gloaguen, Yoann; Camenen, Etienne; Merlet, Benjamin; Heux, Stéphanie; Portais, Jean-Charles; Poupin, Nathalie; Vinson, Florence; Jourdan, Fabien;pmc: PMC6030842
pmid: 29718355
Abstract Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/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 49 citations 49 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/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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