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description Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | INCEPTIONANR| INCEPTIONBertrand Neron; Remi Denise; Charles Coluzzi; Marie Touchon; Eduardo P. C. Rocha; Sophie S. Abby;Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models' constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.
Peer Community Journ... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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=10.1101/2022.09.02.506364&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 17 citations 17 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Peer Community Journ... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:UKRI | A Real-time Digital Platf..., ANR | PSLUKRI| A Real-time Digital Platform for Industry 4.0 Manufacturer Insurance ,ANR| PSLMatthieu Muffato; Alexandra Louis; Nga Thi Thuy Nguyen; Joseph Lucas; Camille Berthelot; Hugues Roest Crollius;AbstractAncestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic andin silicoreconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.
Nature Ecology & Evo... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYFull-Text: https://hal.science/hal-03943655/documentMémoires en Sciences de l'Information et de la CommunicationPreprint . 2022add 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=10.1101/2022.02.17.480882&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Nature Ecology & Evo... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYFull-Text: https://hal.science/hal-03943655/documentMémoires en Sciences de l'Information et de la CommunicationPreprint . 2022add 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 Other literature type , Article 2022 Spain, Sweden, Spain, Spain, Italy, United Kingdom, NetherlandsPublisher:Hindawi Limited Funded by:EC | NEUROMICS, EC | EJP RD, CIHR +7 projectsEC| NEUROMICS ,EC| EJP RD ,CIHR ,EC| RD-CONNECT ,NIH| Increasing the Yield and Utility of Pediatric Genomic Medicine with Exomiser ,EC| ELIXIR-EXCELERATE ,EC| Solve-RD ,UKRI| New genomic approaches to explore the neurogenetic disease burden of consanguineous marriages in Turkey ,EC| B1MG ,EC| BBMRI-LPCLaurie, Steven; Piscia, Davide; Matalonga, Leslie; Corvó, Alberto; Fernández-Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles; Luengo, Cristina; Martínez, Inés; Papakonstantinou, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Thompson, Rachel; Tonda, Raul; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Rémi; Alonso, Angel; Attimonelli, Marcella; Béroud, Christophe; Bros-Facer, Virginie; Buske, Orion J; Cañada-Pallarés, Andrés; Fernández, José M; Hansson, Mats G; Horvath, Rita; Jacobsen, Julius O B; Kaliyaperumal, Rajaram; Lair-Préterre, Séverine; Licata, Luana; Lopes, Pedro; López-Martín, Estrella; Mascalzoni, Deborah; Monaco, Lucia; Pérez-Jurado, Luis A; Posada De la Paz, Manuel; Rambla, Jordi; Rath, Ana; Riess, Olaf; Robinson, Peter N; Salgado, David; Smedley, Damian; Spalding, Dylan; 't Hoen, Peter A C; Töpf, Ana; Zaharieva, Irina; Graessner, Holm; Gut, Ivo G; Lochmüller, Hanns; Beltran, Sergi; Corvo, Alberto; Garcia, Carles; Fernandez‐Callejo, Marcos; Hernandez, Carles; Ntalis, Anastasios Papakonstantinou; Protassio, Joan; Martinez, Ines; Pico, Daniel; Bayes, Monica; Camps, Jordi; Trotta, Jean‐Remi; Bros‐Facer, Virginie; Buske, Orion; Cañada, Andrés; Fernandez, Josè Maria; Hansson, Mats; Jacobsen, Julius; Lair, Severine; López‐Martin, Estrella; Jurado, Luis Pérez; Posada, Manuel; Robinson, Peter; Spalding, Dylan J.; 't Hoen, Peter‐Bram; Gut, Ivo; Lochmúller, Hanns;handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
RD‐Connect (RD‐Connect, an integrated platform connecting registries, biobanks, and clinical bioinformatics) received funding from the Seventh Framework(FP7) Programme of the European Union under grant agreement No305444. Data were analyzed using the RD‐Connect GPAP, which received funding from EU projects Solve‐RD, EJP‐RD (grant numbersH2020 779257, H2020 825575), Instituto de Salud Carlos III (Grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB), ELIXIR‐EXCELERATE (Grant number EU H2020#676559) and ELIXIR Implementation Studies (Remote real‐time visualization of human rare disease genomics data (RD‐Connect) stored at the EGA ELIXIR. 2017‐2018; ELIXIR IT‐2017‐INTEGRATION, Rare Disease Infrastructure ELIXIR, 2019‐2020 and the Beacon ELIXIR, 2019‐2021). The RD‐Connect GPAP has leveraged developments funded through project VEIS (001‐P‐001647 co‐financed by the European Regional Development Fund of the European Union in the framework of the Operational Program FEDER of Catalonia 2014‐2020 with the support of the Secretariad' Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya) and URD‐Cat (PERIS SLT002/16/00174, Departament de Salut, Generalitat de Catalunya). The research leading to these results has received funding from Consequitur (Newton Fund UK/Turkey, MR/N027302/1), BBMRI‐LPC (EU FP7 #313010), NeurOmics (EU FP7 #305121), the Economic Development Department of the Navarra Government (Grant number 001114112017), the European Reference Networkfor Rare Neurological Diseases (Project ID number 739510) and NIH,National Institute of Child Health and Human Development (1R01HD103805‐01). We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Program/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and Co‐financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014‐2020 Smart Growth Operating Program. HL receives support from the Canadian Institutes of Health Research (Foundation Grant FDN‐167281), the Canadian Institutes of Health Research and Muscular Dystrophy Canada (Network Catalyst Grant for NMD4C), the Canada Foundation for Innovation (CFI‐JELF 38412), and the Canada Research Chairs program (Canada Research Chair in Neuromuscular Genomics and Health, 950‐232279) Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes. Sí
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 42visibility views 42 download downloads 71 Powered bymore_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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 2021 France, Belgium, DenmarkPublisher:Oxford University Press (OUP) Funded by:CIHR, NIH | The UCSC Genome Browser, NSERCCIHR ,NIH| The UCSC Genome Browser ,NSERCAuthors: Jaime A. Castro-Mondragon; Rafael Riudavets-Puig; Ieva Rauluseviciute; Roza Berhanu Lemma; +19 AuthorsJaime A. Castro-Mondragon; Rafael Riudavets-Puig; Ieva Rauluseviciute; Roza Berhanu Lemma; Laura Turchi; Romain Blanc-Mathieu; Jérémy Lucas; Paul Boddie; Aziz Khan; Nicolás Manosalva Pérez; Oriol Fornes; Tiffany Y. Leung; Alejandro Aguirre; Fayrouz Hammal; Daniel Schmelter; Damir Baranasic; Benoit Ballester; Albin Sandelin; Boris Lenhard; Klaas Vandepoele; Wyeth W. Wasserman; François Parcy; Anthony Mathelier;Abstract JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728201Data sources: PubMed CentralCopenhagen University Research Information SystemArticle . 2022Data sources: Copenhagen University Research Information SystemGhent University Academic BibliographyArticle . 2022Data sources: Ghent University Academic BibliographyHAL Descartes; HAL-Inserm; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463821/documentGhent University Academic BibliographyArticle . 2022Data 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.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 685 citations 685 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728201Data sources: PubMed CentralCopenhagen University Research Information SystemArticle . 2022Data sources: Copenhagen University Research Information SystemGhent University Academic BibliographyArticle . 2022Data sources: Ghent University Academic BibliographyHAL Descartes; HAL-Inserm; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463821/documentGhent University Academic BibliographyArticle . 2022Data 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 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 FrancePublisher:Oxford University Press (OUP) Funded by:ANR | PSLANR| PSLNga Nguyen; Pierre Vincens; Jean-François Dufayard; Hugues Roest Crollius; Alexandra Louis;Abstract Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728260Data sources: PubMed CentralHAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03438462/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 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/PMC8728260Data sources: PubMed CentralHAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03438462/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1091&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021Authors: HAMMAL Fayrouz; Benoit Ballester; Pierre de Langen;HAMMAL Fayrouz; Benoit Ballester; Pierre de Langen;doi: 10.1093/nar/gkab996
Abstract ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches 4.8M peaks, 423 TRs across 694 datasets. Also, this ReMap release is enriched by two new regulatory catalogs for Mus musculus and Drosophila melanogaster. First, the Mouse regulatory catalog consists of 123M peaks across 648 TRs as a result of the integration and validation of 5503 ChIP-seq datasets. Second, the Drosophila melanogaster catalog contains 16.6M peaks across 550 TRs from the integration of 1205 datasets. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers. Finally, ReMap 2022 comes with a new Cis Regulatory Module identification method, improved quality controls, faster search results, and better user experience with an interactive tour and video tutorials on browsing and filtering ReMap catalogs.
Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; OpenAPC Global InitiativeArticle . Conference object . 2021 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab996&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu132 citations 132 popularity Top 1% influence Top 10% impulse Top 0.1% Powered by BIP!more_vert Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; OpenAPC Global InitiativeArticle . Conference object . 2021 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab996&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 Czech RepublicPublisher:Oxford University Press (OUP) Funded by:EC | OBERON, EC | HBM4EUEC| OBERON ,EC| HBM4EUFlorence Jornod; Thomas Jaylet; Ludek Blaha; Denis Sarigiannis; Luc Tamisier; Karine Audouze;Abstract Motivation Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php Supplementary information Supplementary data are available at Bioinformatics online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | INFERNETEC| INFERNETAuthors: Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;AbstractBackgroundBoltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting for residue conservation, and pairwise terms to model epistatic coevolution between residues. From the model parameters, it is possible to extract an accurate prediction of the three-dimensional contact map of the target domain. More recently, the accuracy of these models has been also assessed in terms of their ability in predicting mutational effects and generatingin silicofunctional sequences.ResultsOur adaptive implementation of Boltzmann machine learning, , can be generally applied to both protein and RNA families and accomplishes several learning set-ups, depending on the complexity of the input data and on the user requirements. The code is fully available athttps://github.com/anna-pa-m/adabmDCA. As an example, we have performed the learning of three Boltzmann machines modeling the Kunitz and Beta-lactamase2 protein domains and TPP-riboswitch RNA domain.ConclusionsThe models learned by are comparable to those obtained by state-of-the-art techniques for this task, in terms of the quality of the inferred contact map as well as of the synthetically generated sequences. In addition, the code implements both equilibrium and out-of-equilibrium learning, which allows for an accurate and lossless training when the equilibrium one is prohibitive in terms of computational time, and allows for pruning irrelevant parameters using an information-based criterion.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/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/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 10 citations 10 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/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/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/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 FrancePublisher:Oxford University Press (OUP) Authors: Maria Bernard; Olivier Rué; Mahendra Mariadassou; Géraldine Pascal;Maria Bernard; Olivier Rué; Mahendra Mariadassou; Géraldine Pascal;doi: 10.1093/bib/bbab318
pmid: 34410336
AbstractFungi are present in all environments. They fulfil important ecological functions and play a crucial role in the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi are ITSs. These markers are the best documented in public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads in a significant fraction of the fungi. When these reads are filtered out, traditional metabarcoding pipelines lose part of the information and consequently produce biased pictures of the composition and structure of the environment under study. We developed a solution that enables processing of the entire set of reads including both overlapping and non-overlapping, thus providing a more accurate picture of fungal communities. Our comparative tests using simulated and real data demonstrated the effectiveness of our solution, which can be used by both experts and non-specialists on a command line or through the Galaxy-based web interface.
Briefings in Bioinfo... arrow_drop_down Briefings in BioinformaticsArticle . 2021 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bib/bbab318&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 14 citations 14 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Briefings in Bioinfo... arrow_drop_down Briefings in BioinformaticsArticle . 2021 . Peer-reviewedLicense: OUP Standard Publication ReuseData 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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description Publicationkeyboard_double_arrow_right Article , Preprint 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | INCEPTIONANR| INCEPTIONBertrand Neron; Remi Denise; Charles Coluzzi; Marie Touchon; Eduardo P. C. Rocha; Sophie S. Abby;Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models' constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.
Peer Community Journ... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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=10.1101/2022.09.02.506364&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 17 citations 17 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Peer Community Journ... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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=10.1101/2022.09.02.506364&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2022 FrancePublisher:Cold Spring Harbor Laboratory Funded by:UKRI | A Real-time Digital Platf..., ANR | PSLUKRI| A Real-time Digital Platform for Industry 4.0 Manufacturer Insurance ,ANR| PSLMatthieu Muffato; Alexandra Louis; Nga Thi Thuy Nguyen; Joseph Lucas; Camille Berthelot; Hugues Roest Crollius;AbstractAncestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic andin silicoreconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.
Nature Ecology & Evo... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYFull-Text: https://hal.science/hal-03943655/documentMémoires en Sciences de l'Information et de la CommunicationPreprint . 2022add 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 Routeshybrid 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Nature Ecology & Evo... arrow_drop_down HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2023License: CC BYFull-Text: https://hal.science/hal-03943655/documentMémoires en Sciences de l'Information et de la CommunicationPreprint . 2022add 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=10.1101/2022.02.17.480882&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Article 2022 Spain, Sweden, Spain, Spain, Italy, United Kingdom, NetherlandsPublisher:Hindawi Limited Funded by:EC | NEUROMICS, EC | EJP RD, CIHR +7 projectsEC| NEUROMICS ,EC| EJP RD ,CIHR ,EC| RD-CONNECT ,NIH| Increasing the Yield and Utility of Pediatric Genomic Medicine with Exomiser ,EC| ELIXIR-EXCELERATE ,EC| Solve-RD ,UKRI| New genomic approaches to explore the neurogenetic disease burden of consanguineous marriages in Turkey ,EC| B1MG ,EC| BBMRI-LPCLaurie, Steven; Piscia, Davide; Matalonga, Leslie; Corvó, Alberto; Fernández-Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles; Luengo, Cristina; Martínez, Inés; Papakonstantinou, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Thompson, Rachel; Tonda, Raul; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Rémi; Alonso, Angel; Attimonelli, Marcella; Béroud, Christophe; Bros-Facer, Virginie; Buske, Orion J; Cañada-Pallarés, Andrés; Fernández, José M; Hansson, Mats G; Horvath, Rita; Jacobsen, Julius O B; Kaliyaperumal, Rajaram; Lair-Préterre, Séverine; Licata, Luana; Lopes, Pedro; López-Martín, Estrella; Mascalzoni, Deborah; Monaco, Lucia; Pérez-Jurado, Luis A; Posada De la Paz, Manuel; Rambla, Jordi; Rath, Ana; Riess, Olaf; Robinson, Peter N; Salgado, David; Smedley, Damian; Spalding, Dylan; 't Hoen, Peter A C; Töpf, Ana; Zaharieva, Irina; Graessner, Holm; Gut, Ivo G; Lochmüller, Hanns; Beltran, Sergi; Corvo, Alberto; Garcia, Carles; Fernandez‐Callejo, Marcos; Hernandez, Carles; Ntalis, Anastasios Papakonstantinou; Protassio, Joan; Martinez, Ines; Pico, Daniel; Bayes, Monica; Camps, Jordi; Trotta, Jean‐Remi; Bros‐Facer, Virginie; Buske, Orion; Cañada, Andrés; Fernandez, Josè Maria; Hansson, Mats; Jacobsen, Julius; Lair, Severine; López‐Martin, Estrella; Jurado, Luis Pérez; Posada, Manuel; Robinson, Peter; Spalding, Dylan J.; 't Hoen, Peter‐Bram; Gut, Ivo; Lochmúller, Hanns;handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
handle: 20.500.12105/15877 , 20.500.12105/15566 , 1887/3564237 , 2454/43348
pmid: 35178824
pmc: PMC9324157
RD‐Connect (RD‐Connect, an integrated platform connecting registries, biobanks, and clinical bioinformatics) received funding from the Seventh Framework(FP7) Programme of the European Union under grant agreement No305444. Data were analyzed using the RD‐Connect GPAP, which received funding from EU projects Solve‐RD, EJP‐RD (grant numbersH2020 779257, H2020 825575), Instituto de Salud Carlos III (Grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB), ELIXIR‐EXCELERATE (Grant number EU H2020#676559) and ELIXIR Implementation Studies (Remote real‐time visualization of human rare disease genomics data (RD‐Connect) stored at the EGA ELIXIR. 2017‐2018; ELIXIR IT‐2017‐INTEGRATION, Rare Disease Infrastructure ELIXIR, 2019‐2020 and the Beacon ELIXIR, 2019‐2021). The RD‐Connect GPAP has leveraged developments funded through project VEIS (001‐P‐001647 co‐financed by the European Regional Development Fund of the European Union in the framework of the Operational Program FEDER of Catalonia 2014‐2020 with the support of the Secretariad' Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya) and URD‐Cat (PERIS SLT002/16/00174, Departament de Salut, Generalitat de Catalunya). The research leading to these results has received funding from Consequitur (Newton Fund UK/Turkey, MR/N027302/1), BBMRI‐LPC (EU FP7 #313010), NeurOmics (EU FP7 #305121), the Economic Development Department of the Navarra Government (Grant number 001114112017), the European Reference Networkfor Rare Neurological Diseases (Project ID number 739510) and NIH,National Institute of Child Health and Human Development (1R01HD103805‐01). We acknowledge the support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, and the CERCA Program/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and Co‐financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014‐2020 Smart Growth Operating Program. HL receives support from the Canadian Institutes of Health Research (Foundation Grant FDN‐167281), the Canadian Institutes of Health Research and Muscular Dystrophy Canada (Network Catalyst Grant for NMD4C), the Canada Foundation for Innovation (CFI‐JELF 38412), and the Canada Research Chairs program (Canada Research Chair in Neuromuscular Genomics and Health, 950‐232279) Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes. Sí
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 42visibility views 42 download downloads 71 Powered bymore_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Data sources: Recolector de Ciencia Abierta, RECOLECTAHuman Mutation; Archivio della Ricerca - Università di Roma Tor vergata; NARCISOther literature type . Article . 2022 . Peer-reviewedLicense: Wiley Online Library User AgreementAcademica-e; Recolector de Ciencia Abierta, RECOLECTAArticle . 2022Full-Text: https://doi.org/10.1002/humu.24353Archivio della Ricerca - Università di Roma Tor vergataArticle . 2022Data sources: Archivio della Ricerca - Università di Roma Tor vergataLUMC Scholarly Publications; Leiden University Scholarly Publications RepositoryOther literature type . 2022add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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=10.1002/humu.24353&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 France, Belgium, DenmarkPublisher:Oxford University Press (OUP) Funded by:CIHR, NIH | The UCSC Genome Browser, NSERCCIHR ,NIH| The UCSC Genome Browser ,NSERCAuthors: Jaime A. Castro-Mondragon; Rafael Riudavets-Puig; Ieva Rauluseviciute; Roza Berhanu Lemma; +19 AuthorsJaime A. Castro-Mondragon; Rafael Riudavets-Puig; Ieva Rauluseviciute; Roza Berhanu Lemma; Laura Turchi; Romain Blanc-Mathieu; Jérémy Lucas; Paul Boddie; Aziz Khan; Nicolás Manosalva Pérez; Oriol Fornes; Tiffany Y. Leung; Alejandro Aguirre; Fayrouz Hammal; Daniel Schmelter; Damir Baranasic; Benoit Ballester; Albin Sandelin; Boris Lenhard; Klaas Vandepoele; Wyeth W. Wasserman; François Parcy; Anthony Mathelier;Abstract JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728201Data sources: PubMed CentralCopenhagen University Research Information SystemArticle . 2022Data sources: Copenhagen University Research Information SystemGhent University Academic BibliographyArticle . 2022Data sources: Ghent University Academic BibliographyHAL Descartes; HAL-Inserm; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463821/documentGhent University Academic BibliographyArticle . 2022Data 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/gkab1113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 685 citations 685 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Norwegian Open Resea... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728201Data sources: PubMed CentralCopenhagen University Research Information SystemArticle . 2022Data sources: Copenhagen University Research Information SystemGhent University Academic BibliographyArticle . 2022Data sources: Ghent University Academic BibliographyHAL Descartes; HAL-Inserm; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463821/documentGhent University Academic BibliographyArticle . 2022Data 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/gkab1113&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 Serbia, Belgium, France, France, Italy, Denmark, Italy, FrancePublisher:Oxford University Press (OUP) Funded by:MESTD | Ministry of Education, Sc..., EC | SMILE, NIH | Gene Ontology Consortium +3 projectsMESTD| Ministry of Education, Science and Technological Development, Republic of Serbia, Grant no. 451-03-68/2020-14/200017 (University of Belgrade, Institute of Nuclear Sciences 'Vinca', Belgrade-Vinca) ,EC| SMILE ,NIH| Gene Ontology Consortium ,EC| IDPfun ,EC| MIMIC ,EC| PhasAGEFederica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; Erzsébet Fichó; Maria Cristina Aspromonte; Claudio Bassot; Anastasia Chasapi; Norman E. Davey; Radoslav Davidovic; László Dobson; Arne Elofsson; Gábor Erdős; Pascale Gaudet; Michelle G. Giglio; Juliana Glavina; Javier Iserte; Valentin Iglesias; Zsofia E. Kalman; Matteo Lambrughi; Emanuela Leonardi; Sonia Longhi; Sandra Macedo-Ribeiro; Emiliano Maiani; Julia Marchetti; Cristina Marino-Buslje; Attila Mészáros; Alexander Miguel Monzon; Giovanni Minervini; Suvarna Nadendla; Juliet F Nilsson; Marian Novotný; Christos A. Ouzounis; Nicolas Palopoli; Elena Papaleo; Pedro Pereira; Gabriele Pozzati; Vasilis J. Promponas; Jordi Pujols; Alma Carolina Sanchez Rocha; Martín N. Salas; Luciana Rodriguez Sawicki; Eva Schad; Aditi Shenoy; Tamás Szaniszló; Konstantinos D. Tsirigos; Nevena Veljkovic; Gustavo Parisi; Salvador Ventura; Zsuzsanna Dosztányi; Peter Tompa; Silvio C. E. Tosatto; Damiano Piovesan;The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 100 citations 100 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 71visibility views 71 download downloads 76 Powered bymore_vert Archivio Istituziona... arrow_drop_down Archivio Istituzionale (AperTO); Nucleic Acids Research; Archivio istituzionale della ricerca - Università di Padova; Vrije Universiteit Brussel Research PortalOther literature type . Article . 2022 . 2021 . Peer-reviewedLicense: CC BYEurope PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728214Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2022Data sources: Online Research Database In TechnologyHAL Descartes; HAL AMU; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03463975/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1082&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 FrancePublisher:Oxford University Press (OUP) Funded by:ANR | PSLANR| PSLNga Nguyen; Pierre Vincens; Jean-François Dufayard; Hugues Roest Crollius; Alexandra Louis;Abstract Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8728260Data sources: PubMed CentralHAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03438462/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1091&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 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/PMC8728260Data sources: PubMed CentralHAL-Inserm; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2022License: CC BY NCFull-Text: https://hal.science/hal-03438462/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab1091&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021Authors: HAMMAL Fayrouz; Benoit Ballester; Pierre de Langen;HAMMAL Fayrouz; Benoit Ballester; Pierre de Langen;doi: 10.1093/nar/gkab996
Abstract ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches 4.8M peaks, 423 TRs across 694 datasets. Also, this ReMap release is enriched by two new regulatory catalogs for Mus musculus and Drosophila melanogaster. First, the Mouse regulatory catalog consists of 123M peaks across 648 TRs as a result of the integration and validation of 5503 ChIP-seq datasets. Second, the Drosophila melanogaster catalog contains 16.6M peaks across 550 TRs from the integration of 1205 datasets. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers. Finally, ReMap 2022 comes with a new Cis Regulatory Module identification method, improved quality controls, faster search results, and better user experience with an interactive tour and video tutorials on browsing and filtering ReMap catalogs.
Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; OpenAPC Global InitiativeArticle . Conference object . 2021 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab996&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu132 citations 132 popularity Top 1% influence Top 10% impulse Top 0.1% Powered by BIP!more_vert Nucleic Acids Resear... arrow_drop_down Nucleic Acids Research; OpenAPC Global InitiativeArticle . Conference object . 2021 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkab996&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 Czech RepublicPublisher:Oxford University Press (OUP) Funded by:EC | OBERON, EC | HBM4EUEC| OBERON ,EC| HBM4EUFlorence Jornod; Thomas Jaylet; Ludek Blaha; Denis Sarigiannis; Luc Tamisier; Karine Audouze;Abstract Motivation Adverse outcome pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently, a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php Supplementary information Supplementary data are available at Bioinformatics online.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8796376Data sources: PubMed CentralUniverzitní repozitář Masarykovy univerzityArticle . 2022Data sources: Univerzitní repozitář Masarykovy univerzityadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btab750&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | INFERNETEC| INFERNETAuthors: Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;Muntoni, Anna Paola; Pagnani, Andrea; Weigt, Martin; Zamponi, Francesco;AbstractBackgroundBoltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting for residue conservation, and pairwise terms to model epistatic coevolution between residues. From the model parameters, it is possible to extract an accurate prediction of the three-dimensional contact map of the target domain. More recently, the accuracy of these models has been also assessed in terms of their ability in predicting mutational effects and generatingin silicofunctional sequences.ResultsOur adaptive implementation of Boltzmann machine learning, , can be generally applied to both protein and RNA families and accomplishes several learning set-ups, depending on the complexity of the input data and on the user requirements. The code is fully available athttps://github.com/anna-pa-m/adabmDCA. As an example, we have performed the learning of three Boltzmann machines modeling the Kunitz and Beta-lactamase2 protein domains and TPP-riboswitch RNA domain.ConclusionsThe models learned by are comparable to those obtained by state-of-the-art techniques for this task, in terms of the quality of the inferred contact map as well as of the synthetically generated sequences. In addition, the code implements both equilibrium and out-of-equilibrium learning, which allows for an accurate and lossless training when the equilibrium one is prohibitive in terms of computational time, and allows for pruning irrelevant parameters using an information-based criterion.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/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/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 10 citations 10 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/PMC8555268Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2021License: CC BYFull-Text: https://hal.science/hal-03410137/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/s12859-021-04441-9&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 FrancePublisher:Oxford University Press (OUP) Authors: Maria Bernard; Olivier Rué; Mahendra Mariadassou; Géraldine Pascal;Maria Bernard; Olivier Rué; Mahendra Mariadassou; Géraldine Pascal;doi: 10.1093/bib/bbab318
pmid: 34410336
AbstractFungi are present in all environments. They fulfil important ecological functions and play a crucial role in the food industry. Their accurate characterization is thus indispensable, particularly through metabarcoding. The most frequently used markers to monitor fungi are ITSs. These markers are the best documented in public databases but have one main weakness: polymerase chain reaction amplification may produce non-overlapping reads in a significant fraction of the fungi. When these reads are filtered out, traditional metabarcoding pipelines lose part of the information and consequently produce biased pictures of the composition and structure of the environment under study. We developed a solution that enables processing of the entire set of reads including both overlapping and non-overlapping, thus providing a more accurate picture of fungal communities. Our comparative tests using simulated and real data demonstrated the effectiveness of our solution, which can be used by both experts and non-specialists on a command line or through the Galaxy-based web interface.
Briefings in Bioinfo... arrow_drop_down Briefings in BioinformaticsArticle . 2021 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bib/bbab318&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 14 citations 14 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Briefings in Bioinfo... arrow_drop_down Briefings in BioinformaticsArticle . 2021 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bib/bbab318&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu