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description Publicationkeyboard_double_arrow_right Article , Other literature type 2010 FrancePublisher:Wiley Fabrice Legeai; Shuji Shigenobu; Jean-Pierre Gauthier; John K. Colbourne; Claude Rispe; Olivier Collin; Stephen Richards; Alex C.C. Wilson; Terence Murphy; Denis Tagu;AbstractAphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.
Insect Molecular Bio... arrow_drop_down Insect Molecular BiologyArticle . 2010 . Peer-reviewedLicense: Wiley Online Library User AgreementData 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=10.1111/j.1365-2583.2009.00930.x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 104 citations 104 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Insect Molecular Bio... arrow_drop_down Insect Molecular BiologyArticle . 2010 . Peer-reviewedLicense: Wiley Online Library User AgreementData 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=10.1111/j.1365-2583.2009.00930.x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 FrancePublisher:Oxford University Press (OUP) Funded by:WT, EC | NEUROXSYSWT ,EC| NEUROXSYSAuthors: Louis A; Muffato M; Roest Crollius H;Louis A; Muffato M; Roest Crollius H;Genomicus (http://www.dyogen.ens.fr/genomicus/) is a database and an online tool that allows easy comparative genomic visualization in >150 eukaryote genomes. It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. We extended the Genomicus database originally dedicated to vertebrate to four new clades, including plants, non-vertebrate metazoa, protists and fungi. This visualization tool allows evolutionary phylogenomics analysis and exploration. Here, we describe the graphical modules of Genomicus and show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and study the evolution of a locus through homology relationships.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3531091Data 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/gks1156&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 155 citations 155 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3531091Data 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/gks1156&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article , Other literature type 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | GENMEDANR| GENMEDThibord, Florian; Perret, Claire; Roux, Maguelonne; Suchon, Pierre; Germain, Marine; Deleuze, Jean-François; Morange, Pierre-Emmanuel; Trégouët, David-Alexandre;AbstractNext-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs’ detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy.OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers.OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
bioRxiv arrow_drop_down bioRxivPreprint . 2018add 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=10.1101/479097&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 4 citations 4 popularity Average influence Average impulse Average Powered by BIP!visibility 33visibility views 33 download downloads 79 Powered bymore_vert bioRxiv arrow_drop_down bioRxivPreprint . 2018add 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=10.1101/479097&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Conference object 2016 FrancePublisher:Oxford University Press (OUP) Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre;pmc: PMC4897896 , PMC5094008
Background Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0131-8) contains supplementary material, which is available to authorized users.
Agritrop arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC5094008Data sources: PubMed CentralEurope PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4897896Data sources: PubMed CentralAgritropArticle . 2016Full-Text: http://agritrop.cirad.fr/580745/1/Sempere-2016-Gigwa-Genotype%20investigator%20for%20g.pdfData sources: AgritropINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la Communication; HAL-IRDArticle . 2016License: CC BYFull-Text: https://hal.science/hal-01411506/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=10.1186/s13742-016-0131-8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 21 citations 21 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert Agritrop arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC5094008Data sources: PubMed CentralEurope PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4897896Data sources: PubMed CentralAgritropArticle . 2016Full-Text: http://agritrop.cirad.fr/580745/1/Sempere-2016-Gigwa-Genotype%20investigator%20for%20g.pdfData sources: AgritropINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la Communication; HAL-IRDArticle . 2016License: CC BYFull-Text: https://hal.science/hal-01411506/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=10.1186/s13742-016-0131-8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2008 FrancePublisher:Oxford University Press (OUP) Filangi, Olivier; Beausse, Yoann; Assi, Anthony; Legrand, Ludovic; Larré, Jean-Marc; Martin, Véronique; Collin, Olivier; Caron, Christophe; Leroy, Hugues; Allouche, David;Abstract Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks. Availability: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license. Contact: biomaj@genouest.org
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2008Full-Text: http://europepmc.org/articles/PMC3293366Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2008Full-Text: https://hal.inria.fr/inria-00327502/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/bioinformatics/btn325&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 10 citations 10 popularity Average influence Top 10% impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2008Full-Text: http://europepmc.org/articles/PMC3293366Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2008Full-Text: https://hal.inria.fr/inria-00327502/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/bioinformatics/btn325&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Funded by:FCT | EMC2, NIH | Specificity and Selectivi..., FCT | EMC2 +4 projectsFCT| EMC2 ,NIH| Specificity and Selectivity in Protein-Ion Binding ,FCT| EMC2 ,NIH| Specificity and Selectivity in Protein-Ion Binding ,EC| EMC2 ,FCT| EMC2 ,NIH| DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELDAdjoua, Olivier; Lagardère, Louis; Jolly, Luc-Henri; Durocher, Arnaud; Very, Thibaut; Dupays, Isabelle; Wang, Zhi; Inizan, Théo Jaffrelot; Célerse, Frédéric; Ren, Pengyu; Ponder, Jay W.; Piquemal, Jean-Philip;International audience; We present the extension of the Tinker-HP package (Lagardere, et al. Chem. Sci. 2018, 9, 956−972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new highperformance module allows for an efficient use of single-and multiple-GPU architectures ranging from research laboratories to modern supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OPENACC and CUDA, we discuss the various capabilities of the package. Among them, the multiprecision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model. Testing various NVIDIA platforms including 2080Ti, 3090, V100, and A100 cards, we provide illustrative benchmarks of the code for single-and multicards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multinode massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics (see https://github.com/ TinkerTools/tinker-hp).
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8047816Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2011.01207&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 15 citations 15 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/PMC8047816Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2011.01207&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2007 FrancePublisher:Oxford University Press (OUP) Publicly fundedFunded by:EC | ASSEMBLE, WTEC| ASSEMBLE ,WTM A, Larkin; G, Blackshields; N P, Brown; R, Chenna; P A, McGettigan; H, McWilliam; F, Valentin; I M, Wallace; A, Wilm; R, Lopez; J D, Thompson; T J, Gibson; D G, Higgins;pmid: 17846036
Abstract Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact: clustalw@ucd.ie
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/bioinformatics/btm404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 25K citations 25,346 popularity Top 0.01% influence Top 0.01% impulse Top 0.01% Powered by BIP!more_vert 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/bioinformatics/btm404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017 United Kingdom, France, Belgium, DenmarkPublisher:Oxford University Press (OUP) Funded by:UKRI | DanioPeaks: A Central Res..., UKRI | Computational Regulatory ..., NSERC +2 projectsUKRI| DanioPeaks: A Central Resource for Standardised Annotation and Re-annotation of Whole-Genome Data for the Model Vertebrate Zebrafish ,UKRI| Computational Regulatory Genomics ,NSERC ,CIHR ,WT| The core promoter: an unexplored regulatory level of transcription during vertebrate development.Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A. Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada Rajabhau Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoit Ballester; Wyeth W. Wasserman; François Parcy; Anthony Mathelier;pmc: PMC5753243 , PMC5753202
handle: 1854/LU-8558108
International audience; JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package .
Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753243Data sources: PubMed CentralEurope PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753202Data sources: PubMed CentralSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic BibliographySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryCopenhagen University Research Information SystemArticle . 2018Data sources: Copenhagen University Research Information SystemMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic Bibliographyadd 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/gkx1126&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1K citations 1,384 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!visibility 26visibility views 26 download downloads 174 Powered bymore_vert Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753243Data sources: PubMed CentralEurope PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753202Data sources: PubMed CentralSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic BibliographySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryCopenhagen University Research Information SystemArticle . 2018Data sources: Copenhagen University Research Information SystemMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic Bibliographyadd 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/gkx1126&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 FrancePublisher:Proceedings of the National Academy of Sciences Funded by:EC | BacCellEpiEC| BacCellEpiJuan J. Quereda; Olivier Dussurget; Marie-Anne Nahori; Amine Ghozlane; Stevenn Volant; Marie-Agnès Dillies; Béatrice Regnault; Sean Kennedy; Stanislas Mondot; Barbara Villoing; Pascale Cossart; Javier Pizarro-Cerdá;SignificanceListeria monocytogenesis a bacterial pathogen responsible for listeriosis, a foodborne disease characterized by septicemia and abortion in pregnant women. The most severe listeriosis outbreaks are associated with a subset of bacterial epidemic clones, although the underlying virulence mechanisms of these clones remain elusive. Here, we demonstrate, to our knowledge for the first time, that these epidemic strains secrete a bacteriocin specifically in the gut and alter host intestinal microbiota, allowingL. monocytogenescolonization of the intestine and, consequently, invasion of deeper organs. Therefore, our work shows that epidemic listeriosis implicates not only interactions betweenL. monocytogenesand host cells, but also interactions betweenL. monocytogenesand the host intestinal microbiota that are critical for the establishment of infection.
Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 154 citations 154 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Belgium, France, Belgium EnglishPublisher:Oxford University Press (OUP) Authors: Brysbaert, Guillaume; Lorgouilloux, Kevin; Vranken, Wim F; Lensink, Marc F;Brysbaert, Guillaume; Lorgouilloux, Kevin; Vranken, Wim F; Lensink, Marc F;Motivation Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments. Results We combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated. info:eu-repo/semantics/published SCOPUS: ar.j
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5860209Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2018Data sources: Vrije Universiteit Brussel Research PortalHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2018add 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=PMC5860209&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu19 citations 19 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5860209Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2018Data sources: Vrije Universiteit Brussel Research PortalHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2018add 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=PMC5860209&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Article , Other literature type 2010 FrancePublisher:Wiley Fabrice Legeai; Shuji Shigenobu; Jean-Pierre Gauthier; John K. Colbourne; Claude Rispe; Olivier Collin; Stephen Richards; Alex C.C. Wilson; Terence Murphy; Denis Tagu;AbstractAphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.
Insect Molecular Bio... arrow_drop_down Insect Molecular BiologyArticle . 2010 . Peer-reviewedLicense: Wiley Online Library User AgreementData 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 bronze 104 citations 104 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Insect Molecular Bio... arrow_drop_down Insect Molecular BiologyArticle . 2010 . Peer-reviewedLicense: Wiley Online Library User AgreementData 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=10.1111/j.1365-2583.2009.00930.x&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 FrancePublisher:Oxford University Press (OUP) Funded by:WT, EC | NEUROXSYSWT ,EC| NEUROXSYSAuthors: Louis A; Muffato M; Roest Crollius H;Louis A; Muffato M; Roest Crollius H;Genomicus (http://www.dyogen.ens.fr/genomicus/) is a database and an online tool that allows easy comparative genomic visualization in >150 eukaryote genomes. It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. We extended the Genomicus database originally dedicated to vertebrate to four new clades, including plants, non-vertebrate metazoa, protists and fungi. This visualization tool allows evolutionary phylogenomics analysis and exploration. Here, we describe the graphical modules of Genomicus and show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and study the evolution of a locus through homology relationships.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3531091Data 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/gks1156&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 155 citations 155 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3531091Data 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/gks1156&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article , Other literature type 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | GENMEDANR| GENMEDThibord, Florian; Perret, Claire; Roux, Maguelonne; Suchon, Pierre; Germain, Marine; Deleuze, Jean-François; Morange, Pierre-Emmanuel; Trégouët, David-Alexandre;AbstractNext-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs’ detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy.OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers.OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
bioRxiv arrow_drop_down bioRxivPreprint . 2018add 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=10.1101/479097&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 4 citations 4 popularity Average influence Average impulse Average Powered by BIP!visibility 33visibility views 33 download downloads 79 Powered bymore_vert bioRxiv arrow_drop_down bioRxivPreprint . 2018add 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=10.1101/479097&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Conference object 2016 FrancePublisher:Oxford University Press (OUP) Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre;pmc: PMC4897896 , PMC5094008
Background Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0131-8) contains supplementary material, which is available to authorized users.
Agritrop arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC5094008Data sources: PubMed CentralEurope PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4897896Data sources: PubMed CentralAgritropArticle . 2016Full-Text: http://agritrop.cirad.fr/580745/1/Sempere-2016-Gigwa-Genotype%20investigator%20for%20g.pdfData sources: AgritropINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la Communication; HAL-IRDArticle . 2016License: CC BYFull-Text: https://hal.science/hal-01411506/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=10.1186/s13742-016-0131-8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 21 citations 21 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert Agritrop arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC5094008Data sources: PubMed CentralEurope PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4897896Data sources: PubMed CentralAgritropArticle . 2016Full-Text: http://agritrop.cirad.fr/580745/1/Sempere-2016-Gigwa-Genotype%20investigator%20for%20g.pdfData sources: AgritropINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la Communication; HAL-IRDArticle . 2016License: CC BYFull-Text: https://hal.science/hal-01411506/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=10.1186/s13742-016-0131-8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2008 FrancePublisher:Oxford University Press (OUP) Filangi, Olivier; Beausse, Yoann; Assi, Anthony; Legrand, Ludovic; Larré, Jean-Marc; Martin, Véronique; Collin, Olivier; Caron, Christophe; Leroy, Hugues; Allouche, David;Abstract Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks. Availability: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license. Contact: biomaj@genouest.org
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2008Full-Text: http://europepmc.org/articles/PMC3293366Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2008Full-Text: https://hal.inria.fr/inria-00327502/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/bioinformatics/btn325&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 10 citations 10 popularity Average influence Top 10% impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2008Full-Text: http://europepmc.org/articles/PMC3293366Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2008Full-Text: https://hal.inria.fr/inria-00327502/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/bioinformatics/btn325&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Funded by:FCT | EMC2, NIH | Specificity and Selectivi..., FCT | EMC2 +4 projectsFCT| EMC2 ,NIH| Specificity and Selectivity in Protein-Ion Binding ,FCT| EMC2 ,NIH| Specificity and Selectivity in Protein-Ion Binding ,EC| EMC2 ,FCT| EMC2 ,NIH| DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELDAdjoua, Olivier; Lagardère, Louis; Jolly, Luc-Henri; Durocher, Arnaud; Very, Thibaut; Dupays, Isabelle; Wang, Zhi; Inizan, Théo Jaffrelot; Célerse, Frédéric; Ren, Pengyu; Ponder, Jay W.; Piquemal, Jean-Philip;International audience; We present the extension of the Tinker-HP package (Lagardere, et al. Chem. Sci. 2018, 9, 956−972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new highperformance module allows for an efficient use of single-and multiple-GPU architectures ranging from research laboratories to modern supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OPENACC and CUDA, we discuss the various capabilities of the package. Among them, the multiprecision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model. Testing various NVIDIA platforms including 2080Ti, 3090, V100, and A100 cards, we provide illustrative benchmarks of the code for single-and multicards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multinode massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics (see https://github.com/ TinkerTools/tinker-hp).
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8047816Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2011.01207&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 15 citations 15 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/PMC8047816Data sources: PubMed Centralhttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2011.01207&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2007 FrancePublisher:Oxford University Press (OUP) Publicly fundedFunded by:EC | ASSEMBLE, WTEC| ASSEMBLE ,WTM A, Larkin; G, Blackshields; N P, Brown; R, Chenna; P A, McGettigan; H, McWilliam; F, Valentin; I M, Wallace; A, Wilm; R, Lopez; J D, Thompson; T J, Gibson; D G, Higgins;pmid: 17846036
Abstract Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact: clustalw@ucd.ie
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/bioinformatics/btm404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 25K citations 25,346 popularity Top 0.01% influence Top 0.01% impulse Top 0.01% Powered by BIP!more_vert 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/bioinformatics/btm404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017 United Kingdom, France, Belgium, DenmarkPublisher:Oxford University Press (OUP) Funded by:UKRI | DanioPeaks: A Central Res..., UKRI | Computational Regulatory ..., NSERC +2 projectsUKRI| DanioPeaks: A Central Resource for Standardised Annotation and Re-annotation of Whole-Genome Data for the Model Vertebrate Zebrafish ,UKRI| Computational Regulatory Genomics ,NSERC ,CIHR ,WT| The core promoter: an unexplored regulatory level of transcription during vertebrate development.Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A. Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada Rajabhau Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoit Ballester; Wyeth W. Wasserman; François Parcy; Anthony Mathelier;pmc: PMC5753243 , PMC5753202
handle: 1854/LU-8558108
International audience; JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package .
Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753243Data sources: PubMed CentralEurope PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753202Data sources: PubMed CentralSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic BibliographySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryCopenhagen University Research Information SystemArticle . 2018Data sources: Copenhagen University Research Information SystemMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic Bibliographyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1K citations 1,384 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!visibility 26visibility views 26 download downloads 174 Powered bymore_vert Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753243Data sources: PubMed CentralEurope PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5753202Data sources: PubMed CentralSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic BibliographySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryCopenhagen University Research Information SystemArticle . 2018Data sources: Copenhagen University Research Information SystemMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYMémoires en Sciences de l'Information et de la Communication; HAL AMU; HAL-CEAArticle . 2018License: CC BYGhent University Academic BibliographyArticle . 2018Data sources: Ghent University Academic Bibliographyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2016 FrancePublisher:Proceedings of the National Academy of Sciences Funded by:EC | BacCellEpiEC| BacCellEpiJuan J. Quereda; Olivier Dussurget; Marie-Anne Nahori; Amine Ghozlane; Stevenn Volant; Marie-Agnès Dillies; Béatrice Regnault; Sean Kennedy; Stanislas Mondot; Barbara Villoing; Pascale Cossart; Javier Pizarro-Cerdá;SignificanceListeria monocytogenesis a bacterial pathogen responsible for listeriosis, a foodborne disease characterized by septicemia and abortion in pregnant women. The most severe listeriosis outbreaks are associated with a subset of bacterial epidemic clones, although the underlying virulence mechanisms of these clones remain elusive. Here, we demonstrate, to our knowledge for the first time, that these epidemic strains secrete a bacteriocin specifically in the gut and alter host intestinal microbiota, allowingL. monocytogenescolonization of the intestine and, consequently, invasion of deeper organs. Therefore, our work shows that epidemic listeriosis implicates not only interactions betweenL. monocytogenesand host cells, but also interactions betweenL. monocytogenesand the host intestinal microbiota that are critical for the establishment of infection.
Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 154 citations 154 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Proceedings of the N... arrow_drop_down Proceedings of the National Academy of SciencesOther literature type . Article . 2016 . Peer-reviewedHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1073/pnas.1523899113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Belgium, France, Belgium EnglishPublisher:Oxford University Press (OUP) Authors: Brysbaert, Guillaume; Lorgouilloux, Kevin; Vranken, Wim F; Lensink, Marc F;Brysbaert, Guillaume; Lorgouilloux, Kevin; Vranken, Wim F; Lensink, Marc F;Motivation Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments. Results We combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated. info:eu-repo/semantics/published SCOPUS: ar.j
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5860209Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2018Data sources: Vrije Universiteit Brussel Research PortalHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2018add 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=PMC5860209&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu19 citations 19 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC5860209Data sources: PubMed CentralVrije Universiteit Brussel Research PortalOther literature type . 2018Data sources: Vrije Universiteit Brussel Research PortalHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2018add 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=PMC5860209&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu