- home
- Advanced Search
Filters
Clear All- ELIXIR GR
- French National Research Agency (AN...
- INCEPTION
- EU
- ELIXIR GR
- French National Research Agency (AN...
- INCEPTION
- EU
Loading
integration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:bio.tools Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAuthors: Bardiaux, Benjamin;Bardiaux, Benjamin;ARIAweb is a a server for that implements the ARIA software (Ambiguous Restraints for Iterative Assignment) for automated NMR structure calculation with enhanced analysis and visualization.
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=__bioTools__::aafa7ed7cc46d6b04fc6e2b20baab657&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::aafa7ed7cc46d6b04fc6e2b20baab657&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 FrancePublisher:Oxford University Press (OUP) Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAllain, Fabrice; Mareuil, Fabien; Ménager, Hervé; Nilges, Michael; Bardiaux, Benjamin;Abstract Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: 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/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: 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/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 PythonPublisher:bio.tools Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Zhukova, Anna; Gascuel, Olivier;Zhukova, Anna; Gascuel, Olivier;Fast inference and visualization of ancestral scenarios. PastML infers ancestral characters on a rooted phylogenetic tree with annotated tips, using maximum likelihood or parsimony. The result is then visualised as a zoomable html map.
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=__bioTools__::bbc51bdc32caec9238ac013c697f92dc&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::bbc51bdc32caec9238ac013c697f92dc&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;AbstractThe reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: 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=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 144 citations 144 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/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: 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=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2016 PythonPublisher:bio.tools Funded by:EC | EVOMOBILOME, ANR | INCEPTIONEC| EVOMOBILOME ,ANR| INCEPTIONAuthors: Néron, Bertrand; Néron, Bertrand; Abby, Sophie;Néron, Bertrand; Néron, Bertrand; Abby, Sophie;Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.
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=__bioTools__::da6973e20bd063ed274dc45c808f8499&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::da6973e20bd063ed274dc45c808f8499&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
Loading
integration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:bio.tools Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAuthors: Bardiaux, Benjamin;Bardiaux, Benjamin;ARIAweb is a a server for that implements the ARIA software (Ambiguous Restraints for Iterative Assignment) for automated NMR structure calculation with enhanced analysis and visualization.
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=__bioTools__::aafa7ed7cc46d6b04fc6e2b20baab657&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::aafa7ed7cc46d6b04fc6e2b20baab657&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 FrancePublisher:Oxford University Press (OUP) Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAllain, Fabrice; Mareuil, Fabien; Ménager, Hervé; Nilges, Michael; Bardiaux, Benjamin;Abstract Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: 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/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: 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/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 PythonPublisher:bio.tools Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Zhukova, Anna; Gascuel, Olivier;Zhukova, Anna; Gascuel, Olivier;Fast inference and visualization of ancestral scenarios. PastML infers ancestral characters on a rooted phylogenetic tree with annotated tips, using maximum likelihood or parsimony. The result is then visualised as a zoomable html map.
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=__bioTools__::bbc51bdc32caec9238ac013c697f92dc&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::bbc51bdc32caec9238ac013c697f92dc&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;AbstractThe reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: 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=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 144 citations 144 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/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: 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=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2016 PythonPublisher:bio.tools Funded by:EC | EVOMOBILOME, ANR | INCEPTIONEC| EVOMOBILOME ,ANR| INCEPTIONAuthors: Néron, Bertrand; Néron, Bertrand; Abby, Sophie;Néron, Bertrand; Néron, Bertrand; Abby, Sophie;Program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems to reflect these conserved features, and to allow their efficient detection.
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=__bioTools__::da6973e20bd063ed274dc45c808f8499&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 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=__bioTools__::da6973e20bd063ed274dc45c808f8499&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu