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description Publicationkeyboard_double_arrow_right Other literature type , Article 2023 BelgiumPublisher:Public Library of Science (PLoS) Funded by:EC | RNActEC| RNActAuthors: Roca-Martínez, Joel; Dhondge, Hrishikesh; Sattler, Michael; Vranken, Wim F.;Roca-Martínez, Joel; Dhondge, Hrishikesh; Sattler, Michael; Vranken, Wim F.;pmid: 36689472
pmc: PMC9894542
RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.
PLoS Computational B... arrow_drop_down Vrije Universiteit Brussel Research PortalOther literature type . 2023Data sources: Vrije Universiteit Brussel Research Portaladd 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.1010859&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 4 citations 4 popularity Top 10% influence Average impulse Average Powered by BIP!visibility 17visibility views 17 download downloads 22 Powered bymore_vert PLoS Computational B... arrow_drop_down Vrije Universiteit Brussel Research PortalOther literature type . 2023Data sources: Vrije Universiteit Brussel Research Portaladd 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.1010859&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2023 SwitzerlandPublisher:MDPI AG Funded by:EC | CY-BIOBANKEC| CY-BIOBANKAuthors: Vasileios L. Zogopoulos; Apostolos Malatras; Konstantinos Kyriakidis; Chrysanthi Charalampous; +10 AuthorsVasileios L. Zogopoulos; Apostolos Malatras; Konstantinos Kyriakidis; Chrysanthi Charalampous; Evanthia A. Makrygianni; Stéphanie Duguez; Marianna A. Koutsi; Marialena Pouliou; Christos Vasileiou; William J. Duddy; Marios Agelopoulos; George P. Chrousos; Vassiliki A. Iconomidou; Ioannis Michalopoulos;handle: 20.500.11850/599339
Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint. ISSN:2073-4409 Cells, 12 (3)
Cells arrow_drop_down CellsOther literature type . Article . 2023 . Peer-reviewedLicense: CC BYFull-Text: https://www.mdpi.com/2073-4409/12/3/388/pdfadd 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 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Cells arrow_drop_down CellsOther literature type . Article . 2023 . Peer-reviewedLicense: CC BYFull-Text: https://www.mdpi.com/2073-4409/12/3/388/pdfadd 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 2022 ItalyPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | REFRACTEC| IDPfun ,EC| REFRACTAuthors: Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; +3 AuthorsDamiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; Giovanni Minervini; Damiano Piovesan; Silvio C E Tosatto;AbstractResidue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https://ring.biocomputingup.it/.
Archivio istituziona... arrow_drop_down add 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 Routesgold 61 citations 61 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Archivio istituziona... arrow_drop_down add 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/gkac365&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Article 2022 Spain, Sweden, Spain, Spain, Italy, United Kingdom, NetherlandsPublisher:Hindawi Limited Funded by:EC | NEUROMICS, EC | EJP RD, CIHR +7 projectsEC| NEUROMICS ,EC| EJP RD ,CIHR ,EC| RD-CONNECT ,NIH| Increasing the Yield and Utility of Pediatric Genomic Medicine with Exomiser ,EC| ELIXIR-EXCELERATE ,EC| Solve-RD ,UKRI| New genomic approaches to explore the neurogenetic disease burden of consanguineous marriages in Turkey ,EC| B1MG ,EC| BBMRI-LPCLaurie, Steven; Piscia, Davide; Matalonga, Leslie; Corvó, Alberto; Fernández-Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles; Luengo, Cristina; Martínez, Inés; Papakonstantinou, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Thompson, Rachel; Tonda, Raul; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Rémi; Alonso, Angel; Attimonelli, Marcella; Béroud, Christophe; Bros-Facer, Virginie; Buske, Orion J; Cañada-Pallarés, Andrés; Fernández, José M; Hansson, Mats G; Horvath, Rita; Jacobsen, Julius O B; Kaliyaperumal, Rajaram; Lair-Préterre, Séverine; Licata, Luana; Lopes, Pedro; López-Martín, Estrella; Mascalzoni, Deborah; Monaco, Lucia; Pérez-Jurado, Luis A; Posada De la Paz, Manuel; Rambla, Jordi; Rath, Ana; Riess, Olaf; Robinson, Peter N; Salgado, David; Smedley, Damian; Spalding, Dylan; 't Hoen, Peter A C; Töpf, Ana; Zaharieva, Irina; Graessner, Holm; Gut, Ivo G; Lochmüller, Hanns; Beltran, Sergi; Corvo, Alberto; Garcia, Carles; Fernandez‐Callejo, Marcos; Hernandez, Carles; Ntalis, Anastasios Papakonstantinou; Protassio, Joan; Martinez, Ines; Pico, Daniel; Bayes, Monica; Camps, Jordi; Trotta, Jean‐Remi; Bros‐Facer, Virginie; Buske, Orion; Cañada, Andrés; Fernandez, Josè Maria; Hansson, Mats; Jacobsen, Julius; Lair, Severine; López‐Martin, Estrella; Jurado, Luis Pérez; Posada, Manuel; Robinson, Peter; Spalding, Dylan J.; 't Hoen, Peter‐Bram; Gut, Ivo; Lochmúller, Hanns;handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
RD‐Connect (RD‐Connect, an integrated platform connecting registries, biobanks, and clinical bioinformatics) received funding from the Seventh Framework(FP7) Programme of the European Union under grant agreement No305444. Data were analyzed using the RD‐Connect GPAP, which received funding from EU projects Solve‐RD, EJP‐RD (grant numbersH2020 779257, H2020 825575), Instituto de Salud Carlos III (Grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB), ELIXIR‐EXCELERATE (Grant number EU H2020#676559) and ELIXIR Implementation Studies (Remote real‐time visualization of human rare disease genomics data (RD‐Connect) stored at the EGA ELIXIR. 2017‐2018; ELIXIR IT‐2017‐INTEGRATION, Rare Disease Infrastructure ELIXIR, 2019‐2020 and the Beacon ELIXIR, 2019‐2021). The RD‐Connect GPAP has leveraged developments funded through project VEIS (001‐P‐001647 co‐financed by the European Regional Development Fund of the European Union in the framework of the Operational Program FEDER of Catalonia 2014‐2020 with the support of the Secretariad' Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya) and URD‐Cat (PERIS SLT002/16/00174, Departament de Salut, Generalitat de Catalunya). The research leading to these results has received funding from Consequitur (Newton Fund UK/Turkey, MR/N027302/1), BBMRI‐LPC (EU FP7 #313010), NeurOmics (EU FP7 #305121), the Economic Development Department of the Navarra Government (Grant number 001114112017), the European Reference Networkfor Rare Neurological Diseases (Project ID number 739510) and NIH,National Institute of Child Health and Human Development (1R01HD103805‐01). We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Program/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and Co‐financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014‐2020 Smart Growth Operating Program. HL receives support from the Canadian Institutes of Health Research (Foundation Grant FDN‐167281), the Canadian Institutes of Health Research and Muscular Dystrophy Canada (Network Catalyst Grant for NMD4C), the Canada Foundation for Innovation (CFI‐JELF 38412), and the Canada Research Chairs program (Canada Research Chair in Neuromuscular Genomics and Health, 950‐232279) Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes. Sí
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add 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 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 42visibility views 42 download downloads 71 Powered bymore_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add 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 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 2021 Czech RepublicPublisher:Oxford University Press (OUP) Funded by:EC | OBERON, EC | HBM4EUEC| OBERON ,EC| HBM4EUFlorence Jornod; Thomas Jaylet; Ludek Blaha; Denis Sarigiannis; Luc Tamisier; Karine Audouze;Abstract Motivation Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php Supplementary information Supplementary data are available at Bioinformatics online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd 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 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd 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/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 SpainPublisher:Oxford University Press (OUP) Funded by:EC | MicrobioSEC| MicrobioSCarlos Pérez Cantalapiedra; Ana Hernández-Plaza; Ivica Letunic; Peer Bork; Jaime Huerta-Cepas;Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de. This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B). Centro de Biotecnología y Genómica de Plantas (CBGP) Peer reviewed 5 Pág.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8662613Data sources: PubMed CentralMolecular Biology and EvolutionOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2022 . Peer-reviewedRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2023add 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/molbev/msab293&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 1K citations 1,011 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!visibility 46visibility views 46 download downloads 216 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8662613Data sources: PubMed CentralMolecular Biology and EvolutionOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2022 . Peer-reviewedRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2023add 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/molbev/msab293&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 ItalyPublisher:Oxford University Press (OUP) Funded by:EC | iPC, EC | IMforFUTUREEC| iPC ,EC| IMforFUTUREAuthors: Pietro Di Lena; Claudia Sala; Christine Nardini;Pietro Di Lena; Claudia Sala; Christine Nardini;Abstract Methylage is an epigenetic marker of biological age that exploits the correlation between the methylation state of specific CG dinucleotides (CpGs) and chronological age (in years), gestational age (in weeks), cellular age (in cell cycles or as telomere length, in kilobases). Using DNA methylation data, methylage is measurable via the so called epigenetic clocks. Importantly, alterations of the correlation between methylage and age (age acceleration or deceleration) have been stably associated with pathological states and occur long before clinical signs of diseases become overt, making epigenetic clocks a potentially disruptive tool in preventive, diagnostic and also in forensic applications. Nevertheless, methylage dependency from CpGs selection, mathematical modelling, tissue specificity and age range, still makes the potential of this biomarker limited. In order to enhance model comparisons, interchange, availability, robustness and standardization, we organized a selected set of clocks within a hub webservice, EstimAge (Estimate of methylation Age, http://estimage.iac.rm.cnr.it), which intuitively and informatively enables quick identification, computation and comparison of available clocks, with the support of standard statistics. Graphical Abstract Graphical AbstractEstimAge enables the computation of methylage via the largest selection of epigenetic clocks, offering multiple tabular and graphical outputs to be readily used for scientific reporting or further processing, including refined/alternative rounds of EstimAge selection.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262735Data sources: PubMed CentralNucleic Acids Research; ZENODOOther literature type . Article . 2021 . 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.
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/gkab426&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 7 citations 7 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 119visibility views 119 download downloads 63 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262735Data sources: PubMed CentralNucleic Acids Research; ZENODOOther literature type . Article . 2021 . 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.
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/gkab426&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 NetherlandsPublisher:Oxford University Press (OUP) Funded by:EC | DECIPHEREC| DECIPHERVictòria Pascal Andreu; Jorge Roel-Touris; Dylan Dodd; Michael A. Fischbach; Marnix H. Medema;Abstract Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect the host. The production of these molecules, mostly derived from their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite the importance of microbiome-derived primary metabolites, no tool existed to predict the gene clusters responsible for their production. For this reason, we recently introduced gutSMASH. gutSMASH can predict 41 different known pathways, including MGCs involved in bioenergetics, but also putative ones that are candidates for novel pathway discovery. To make the tool more user-friendly and accessible, we here present the gutSMASH web server, hosted at https://gutsmash.bioinformatics.nl/. The user can either input the GenBank assembly accession or upload a genome file in FASTA or GenBank format. Optionally, the user can enable additional analyses to obtain further insights into the predicted MGCs. An interactive HTML output (viewable online or downloadable for offline use) provides a user-friendly way to browse functional gene annotations and sequence comparisons with reference gene clusters as well as gene clusters predicted in other genomes. Thus, this web server provides the community with a streamlined and user-friendly interface to analyze the metabolic potential of gut microbiomes. Graphical Abstract Graphical AbstractOverview of the gutSMASH pipeline for identification of primary metabolic gene clusters.
NARCIS; Research@WUR arrow_drop_down NARCIS; Research@WUROther literature type . Article . 2021License: CC BYFull-Text: https://edepot.wur.nl/551291Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262752Data 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/nar/gkab353&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!more_vert NARCIS; Research@WUR arrow_drop_down NARCIS; Research@WUROther literature type . Article . 2021License: CC BYFull-Text: https://edepot.wur.nl/551291Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262752Data 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/nar/gkab353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 SpainPublisher:Oxford University Press (OUP) Funded by:EC | INSTRUCT-ULTRA, EC | EOSC-Life, EC | CORBELEC| INSTRUCT-ULTRA ,EC| EOSC-Life ,EC| CORBELAuthors: Jose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; +8 AuthorsJose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; Marta Martinez Gonzalez; Carlos Wert-Carvajal; Alberto M Parra-Perez; Joan Segura Mora; Sam Horrell; Andrea Thorn; Carlos Oscar S. Sorzano; José María Carazo;The web platform 3DBionotes-WS integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic Electron Microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context we have developed 3DBionotes-COVID-19 as an answer to: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy. We acknowledge financial support from: CSIC (PIE/COVID-19 number 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects (SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00 / AEI / 10.13039/501100011033), the Instituto de Salud Carlos III: PT17/0009/0010 (ISCIII-SGEFI / ERDF-) and the European Union and Horizon 2020 through grant: CORBEL (INFRADEV-01-2014- 1, Proposal 654248) and EOSC Life (INFRAEOSC-04-2018, Proposal: 824087). This work was supported by Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. Contributions from the Coronavirus Structural Task Force were supported by the German Federal Ministry of Education and Research [grant no. 05K19WWA] and Deutsche Forschungsgemeinschaft [project TH2135/2-1]. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. https://3dbionotes.cnb.csic.es/ws/covid19 Peer reviewed
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8241415Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; BioinformaticsOther literature type . Article . 2021 . Peer-reviewedLicense: CC BY NCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . Peer-reviewedActa Crystallographica Section A Foundations and AdvancesArticle . 2021 . Peer-reviewedLicense: IUCr Copyright and Licensing PolicyData sources: Crossrefadd 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/btab397&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!visibility 19visibility views 19 download downloads 83 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8241415Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; BioinformaticsOther literature type . Article . 2021 . Peer-reviewedLicense: CC BY NCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . Peer-reviewedActa Crystallographica Section A Foundations and AdvancesArticle . 2021 . Peer-reviewedLicense: IUCr Copyright and Licensing PolicyData sources: Crossrefadd 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/btab397&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Other literature type , Article 2023 BelgiumPublisher:Public Library of Science (PLoS) Funded by:EC | RNActEC| RNActAuthors: Roca-Martínez, Joel; Dhondge, Hrishikesh; Sattler, Michael; Vranken, Wim F.;Roca-Martínez, Joel; Dhondge, Hrishikesh; Sattler, Michael; Vranken, Wim F.;pmid: 36689472
pmc: PMC9894542
RNA recognition motifs (RRM) are the most prevalent class of RNA binding domains in eucaryotes. Their RNA binding preferences have been investigated for almost two decades, and even though some RRM domains are now very well described, their RNA recognition code has remained elusive. An increasing number of experimental structures of RRM-RNA complexes has become available in recent years. Here, we perform an in-depth computational analysis to derive an RNA recognition code for canonical RRMs. We present and validate a computational scoring method to estimate the binding between an RRM and a single stranded RNA, based on structural data from a carefully curated multiple sequence alignment, which can predict RRM binding RNA sequence motifs based on the RRM protein sequence. Given the importance and prevalence of RRMs in humans and other species, this tool could help design RNA binding motifs with uses in medical or synthetic biology applications, leading towards the de novo design of RRMs with specific RNA recognition.
PLoS Computational B... arrow_drop_down Vrije Universiteit Brussel Research PortalOther literature type . 2023Data sources: Vrije Universiteit Brussel Research Portaladd 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.1010859&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 4 citations 4 popularity Top 10% influence Average impulse Average Powered by BIP!visibility 17visibility views 17 download downloads 22 Powered bymore_vert PLoS Computational B... arrow_drop_down Vrije Universiteit Brussel Research PortalOther literature type . 2023Data sources: Vrije Universiteit Brussel Research Portaladd 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.1010859&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2023 SwitzerlandPublisher:MDPI AG Funded by:EC | CY-BIOBANKEC| CY-BIOBANKAuthors: Vasileios L. Zogopoulos; Apostolos Malatras; Konstantinos Kyriakidis; Chrysanthi Charalampous; +10 AuthorsVasileios L. Zogopoulos; Apostolos Malatras; Konstantinos Kyriakidis; Chrysanthi Charalampous; Evanthia A. Makrygianni; Stéphanie Duguez; Marianna A. Koutsi; Marialena Pouliou; Christos Vasileiou; William J. Duddy; Marios Agelopoulos; George P. Chrousos; Vassiliki A. Iconomidou; Ioannis Michalopoulos;handle: 20.500.11850/599339
Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint. ISSN:2073-4409 Cells, 12 (3)
Cells arrow_drop_down CellsOther literature type . Article . 2023 . Peer-reviewedLicense: CC BYFull-Text: https://www.mdpi.com/2073-4409/12/3/388/pdfadd 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=10.3390/cells12030388&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Cells arrow_drop_down CellsOther literature type . Article . 2023 . Peer-reviewedLicense: CC BYFull-Text: https://www.mdpi.com/2073-4409/12/3/388/pdfadd 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=10.3390/cells12030388&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2022 ItalyPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | REFRACTEC| IDPfun ,EC| REFRACTAuthors: Damiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; +3 AuthorsDamiano Clementel; Alessio Del Conte; Alexander Miguel Monzon; Giorgia F Camagni; Giovanni Minervini; Damiano Piovesan; Silvio C E Tosatto;AbstractResidue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks to the advances in network theory, RINs have been proved effective as an alternative to coordinate data in the analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present the new RING 3.0 version extending the previous functionality in several ways. The underlying software library has been re-engineered to improve speed by an order of magnitude. RING now also supports the mmCIF format and provides typed interactions for the entire PDB chemical component dictionary, including nucleic acids. Moreover, RING now employs probabilistic graphs, where multiple conformations (e.g. NMR or molecular dynamics ensembles) are mapped as weighted edges, opening up new ways to analyze structural data. The web interface has been expanded to include a simultaneous view of the RIN alongside a structure viewer, with both synchronized and clickable. Contact evolution across models (or time) is displayed as a heatmap and can help in the discovery of correlating interaction patterns. The web server, together with an extensive help and tutorial, is available from URL: https://ring.biocomputingup.it/.
Archivio istituziona... arrow_drop_down add 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/gkac365&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 61 citations 61 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Archivio istituziona... arrow_drop_down add 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/gkac365&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Article 2022 Spain, Sweden, Spain, Spain, Italy, United Kingdom, NetherlandsPublisher:Hindawi Limited Funded by:EC | NEUROMICS, EC | EJP RD, CIHR +7 projectsEC| NEUROMICS ,EC| EJP RD ,CIHR ,EC| RD-CONNECT ,NIH| Increasing the Yield and Utility of Pediatric Genomic Medicine with Exomiser ,EC| ELIXIR-EXCELERATE ,EC| Solve-RD ,UKRI| New genomic approaches to explore the neurogenetic disease burden of consanguineous marriages in Turkey ,EC| B1MG ,EC| BBMRI-LPCLaurie, Steven; Piscia, Davide; Matalonga, Leslie; Corvó, Alberto; Fernández-Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles; Luengo, Cristina; Martínez, Inés; Papakonstantinou, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Thompson, Rachel; Tonda, Raul; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Rémi; Alonso, Angel; Attimonelli, Marcella; Béroud, Christophe; Bros-Facer, Virginie; Buske, Orion J; Cañada-Pallarés, Andrés; Fernández, José M; Hansson, Mats G; Horvath, Rita; Jacobsen, Julius O B; Kaliyaperumal, Rajaram; Lair-Préterre, Séverine; Licata, Luana; Lopes, Pedro; López-Martín, Estrella; Mascalzoni, Deborah; Monaco, Lucia; Pérez-Jurado, Luis A; Posada De la Paz, Manuel; Rambla, Jordi; Rath, Ana; Riess, Olaf; Robinson, Peter N; Salgado, David; Smedley, Damian; Spalding, Dylan; 't Hoen, Peter A C; Töpf, Ana; Zaharieva, Irina; Graessner, Holm; Gut, Ivo G; Lochmüller, Hanns; Beltran, Sergi; Corvo, Alberto; Garcia, Carles; Fernandez‐Callejo, Marcos; Hernandez, Carles; Ntalis, Anastasios Papakonstantinou; Protassio, Joan; Martinez, Ines; Pico, Daniel; Bayes, Monica; Camps, Jordi; Trotta, Jean‐Remi; Bros‐Facer, Virginie; Buske, Orion; Cañada, Andrés; Fernandez, Josè Maria; Hansson, Mats; Jacobsen, Julius; Lair, Severine; López‐Martin, Estrella; Jurado, Luis Pérez; Posada, Manuel; Robinson, Peter; Spalding, Dylan J.; 't Hoen, Peter‐Bram; Gut, Ivo; Lochmúller, Hanns;handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
RD‐Connect (RD‐Connect, an integrated platform connecting registries, biobanks, and clinical bioinformatics) received funding from the Seventh Framework(FP7) Programme of the European Union under grant agreement No305444. Data were analyzed using the RD‐Connect GPAP, which received funding from EU projects Solve‐RD, EJP‐RD (grant numbersH2020 779257, H2020 825575), Instituto de Salud Carlos III (Grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB), ELIXIR‐EXCELERATE (Grant number EU H2020#676559) and ELIXIR Implementation Studies (Remote real‐time visualization of human rare disease genomics data (RD‐Connect) stored at the EGA ELIXIR. 2017‐2018; ELIXIR IT‐2017‐INTEGRATION, Rare Disease Infrastructure ELIXIR, 2019‐2020 and the Beacon ELIXIR, 2019‐2021). The RD‐Connect GPAP has leveraged developments funded through project VEIS (001‐P‐001647 co‐financed by the European Regional Development Fund of the European Union in the framework of the Operational Program FEDER of Catalonia 2014‐2020 with the support of the Secretariad' Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya) and URD‐Cat (PERIS SLT002/16/00174, Departament de Salut, Generalitat de Catalunya). The research leading to these results has received funding from Consequitur (Newton Fund UK/Turkey, MR/N027302/1), BBMRI‐LPC (EU FP7 #313010), NeurOmics (EU FP7 #305121), the Economic Development Department of the Navarra Government (Grant number 001114112017), the European Reference Networkfor Rare Neurological Diseases (Project ID number 739510) and NIH,National Institute of Child Health and Human Development (1R01HD103805‐01). We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Program/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and Co‐financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014‐2020 Smart Growth Operating Program. HL receives support from the Canadian Institutes of Health Research (Foundation Grant FDN‐167281), the Canadian Institutes of Health Research and Muscular Dystrophy Canada (Network Catalyst Grant for NMD4C), the Canada Foundation for Innovation (CFI‐JELF 38412), and the Canada Research Chairs program (Canada Research Chair in Neuromuscular Genomics and Health, 950‐232279) Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes. Sí
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add 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 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 42visibility views 42 download downloads 71 Powered bymore_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add 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 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 2021 Czech RepublicPublisher:Oxford University Press (OUP) Funded by:EC | OBERON, EC | HBM4EUEC| OBERON ,EC| HBM4EUFlorence Jornod; Thomas Jaylet; Ludek Blaha; Denis Sarigiannis; Luc Tamisier; Karine Audouze;Abstract Motivation Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php Supplementary information Supplementary data are available at Bioinformatics online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd 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 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd 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/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 SpainPublisher:Oxford University Press (OUP) Funded by:EC | MicrobioSEC| MicrobioSCarlos Pérez Cantalapiedra; Ana Hernández-Plaza; Ivica Letunic; Peer Bork; Jaime Huerta-Cepas;Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de. This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B). Centro de Biotecnología y Genómica de Plantas (CBGP) Peer reviewed 5 Pág.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8662613Data sources: PubMed CentralMolecular Biology and EvolutionOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2022 . Peer-reviewedRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2023add 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/molbev/msab293&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 1K citations 1,011 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!visibility 46visibility views 46 download downloads 216 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8662613Data sources: PubMed CentralMolecular Biology and EvolutionOther literature type . Article . 2021 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2022 . Peer-reviewedRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . 2023add 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/molbev/msab293&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 ItalyPublisher:Oxford University Press (OUP) Funded by:EC | iPC, EC | IMforFUTUREEC| iPC ,EC| IMforFUTUREAuthors: Pietro Di Lena; Claudia Sala; Christine Nardini;Pietro Di Lena; Claudia Sala; Christine Nardini;Abstract Methylage is an epigenetic marker of biological age that exploits the correlation between the methylation state of specific CG dinucleotides (CpGs) and chronological age (in years), gestational age (in weeks), cellular age (in cell cycles or as telomere length, in kilobases). Using DNA methylation data, methylage is measurable via the so called epigenetic clocks. Importantly, alterations of the correlation between methylage and age (age acceleration or deceleration) have been stably associated with pathological states and occur long before clinical signs of diseases become overt, making epigenetic clocks a potentially disruptive tool in preventive, diagnostic and also in forensic applications. Nevertheless, methylage dependency from CpGs selection, mathematical modelling, tissue specificity and age range, still makes the potential of this biomarker limited. In order to enhance model comparisons, interchange, availability, robustness and standardization, we organized a selected set of clocks within a hub webservice, EstimAge (Estimate of methylation Age, http://estimage.iac.rm.cnr.it), which intuitively and informatively enables quick identification, computation and comparison of available clocks, with the support of standard statistics. Graphical Abstract Graphical AbstractEstimAge enables the computation of methylage via the largest selection of epigenetic clocks, offering multiple tabular and graphical outputs to be readily used for scientific reporting or further processing, including refined/alternative rounds of EstimAge selection.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262735Data sources: PubMed CentralNucleic Acids Research; ZENODOOther literature type . Article . 2021 . 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 gold 7 citations 7 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 119visibility views 119 download downloads 63 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262735Data sources: PubMed CentralNucleic Acids Research; ZENODOOther literature type . Article . 2021 . 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.
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/gkab426&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 NetherlandsPublisher:Oxford University Press (OUP) Funded by:EC | DECIPHEREC| DECIPHERVictòria Pascal Andreu; Jorge Roel-Touris; Dylan Dodd; Michael A. Fischbach; Marnix H. Medema;Abstract Anaerobic bacteria from the human microbiome produce a wide array of molecules at high concentrations that can directly or indirectly affect the host. The production of these molecules, mostly derived from their primary metabolism, is frequently encoded in metabolic gene clusters (MGCs). However, despite the importance of microbiome-derived primary metabolites, no tool existed to predict the gene clusters responsible for their production. For this reason, we recently introduced gutSMASH. gutSMASH can predict 41 different known pathways, including MGCs involved in bioenergetics, but also putative ones that are candidates for novel pathway discovery. To make the tool more user-friendly and accessible, we here present the gutSMASH web server, hosted at https://gutsmash.bioinformatics.nl/. The user can either input the GenBank assembly accession or upload a genome file in FASTA or GenBank format. Optionally, the user can enable additional analyses to obtain further insights into the predicted MGCs. An interactive HTML output (viewable online or downloadable for offline use) provides a user-friendly way to browse functional gene annotations and sequence comparisons with reference gene clusters as well as gene clusters predicted in other genomes. Thus, this web server provides the community with a streamlined and user-friendly interface to analyze the metabolic potential of gut microbiomes. Graphical Abstract Graphical AbstractOverview of the gutSMASH pipeline for identification of primary metabolic gene clusters.
NARCIS; Research@WUR arrow_drop_down NARCIS; Research@WUROther literature type . Article . 2021License: CC BYFull-Text: https://edepot.wur.nl/551291Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262752Data 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/nar/gkab353&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!more_vert NARCIS; Research@WUR arrow_drop_down NARCIS; Research@WUROther literature type . Article . 2021License: CC BYFull-Text: https://edepot.wur.nl/551291Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8262752Data 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/nar/gkab353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 SpainPublisher:Oxford University Press (OUP) Funded by:EC | INSTRUCT-ULTRA, EC | EOSC-Life, EC | CORBELEC| INSTRUCT-ULTRA ,EC| EOSC-Life ,EC| CORBELAuthors: Jose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; +8 AuthorsJose Ramon Macias; Rubén J. Sánchez-García; Pablo Conesa; Erney Ramírez-Aportela; Marta Martinez Gonzalez; Carlos Wert-Carvajal; Alberto M Parra-Perez; Joan Segura Mora; Sam Horrell; Andrea Thorn; Carlos Oscar S. Sorzano; José María Carazo;The web platform 3DBionotes-WS integrates multiple Web Services and an interactive Web Viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic Electron Microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context we have developed 3DBionotes-COVID-19 as an answer to: (1) The need to explore multi-omics data in a unified context with a special focus on structural information and (2) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryogenic Electron Microscopy. We acknowledge financial support from: CSIC (PIE/COVID-19 number 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects (SEV 2017-0712, FPU-2015/264, PID2019-104757RB-I00 / AEI / 10.13039/501100011033), the Instituto de Salud Carlos III: PT17/0009/0010 (ISCIII-SGEFI / ERDF-) and the European Union and Horizon 2020 through grant: CORBEL (INFRADEV-01-2014- 1, Proposal 654248) and EOSC Life (INFRAEOSC-04-2018, Proposal: 824087). This work was supported by Instruct-ULTRA (Grant 731005), an EU H2020 project to further develop the services of Instruct-ERIC. Contributions from the Coronavirus Structural Task Force were supported by the German Federal Ministry of Education and Research [grant no. 05K19WWA] and Deutsche Forschungsgemeinschaft [project TH2135/2-1]. The authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. https://3dbionotes.cnb.csic.es/ws/covid19 Peer reviewed
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8241415Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; BioinformaticsOther literature type . Article . 2021 . Peer-reviewedLicense: CC BY NCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . Peer-reviewedActa Crystallographica Section A Foundations and AdvancesArticle . 2021 . Peer-reviewedLicense: IUCr Copyright and Licensing PolicyData sources: Crossrefadd 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 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!visibility 19visibility views 19 download downloads 83 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8241415Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTA; BioinformaticsOther literature type . Article . 2021 . Peer-reviewedLicense: CC BY NCRecolector de Ciencia Abierta, RECOLECTA; DIGITAL.CSICArticle . 2021 . Peer-reviewedActa Crystallographica Section A Foundations and AdvancesArticle . 2021 . Peer-reviewedLicense: IUCr Copyright and Licensing PolicyData sources: Crossrefadd 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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