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description 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 , 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 France EnglishPublisher:Nature Publishing Group UK Funded by:EC | CaReSyAnEC| CaReSyAnBoizard, Franck; Buffin-Meyer, Bénédicte; Aligon, Julien; Teste, Olivier; Schanstra, Joost; Klein, Julie;pmc: PMC7952700
pmid: 33707596
International audience; Abstract The urinary proteome is a promising pool of biomarkers of kidney disease. However, the protein changes observed in urine only partially reflect the deregulated mechanisms within kidney tissue. In order to improve on the mechanistic insight based on the urinary protein changes, we developed a new prioritization strategy called PRYNT (PRioritization bY protein NeTwork) that employs a combination of two closeness-based algorithms, shortest-path and random walk, and a contextualized protein–protein interaction (PPI) network, mainly based on clique consolidation of STRING network. To assess the performance of our approach, we evaluated both precision and specificity of PRYNT in prioritizing kidney disease candidates. Using four urinary proteome datasets, PRYNT prioritization performed better than other prioritization methods and tools available in the literature. Moreover, PRYNT performed to a similar, but complementary, extent compared to the upstream regulator analysis from the commercial Ingenuity Pathway Analysis software. In conclusion, PRYNT appears to be a valuable freely accessible tool to predict key proteins indirectly from urinary proteome data. In the future, PRYNT approach could be applied to other biofluids, molecular traits and diseases. The source code is freely available on GitHub at: https://github.com/Boizard/PRYNT and has been integrated as an interactive web apps to improved accessibility ( https://github.com/Boizard/PRYNT/tree/master/AppPRYNT ).
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC7952700Data 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=PMC7952700&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC7952700Data 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=PMC7952700&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 France, BelgiumPublisher:Elsevier BV Funded by:FCT | MS3, EC | POPMETFCT| MS3 ,EC| POPMETSandrien Desmet; Yvan Saeys; Kevin Verstaen; Rebecca Dauwe; Hoon Kim; Claudiu Niculaes; Atsushi Fukushima; Geert Goeminne; Ruben Vanholme; John Ralph; Wout Boerjan; Kris Morreel;Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/). Graphical abstract
Computational and St... arrow_drop_down Computational and Structural Biotechnology JournalArticle . 2021Full-Text: http://europepmc.org/articles/PMC7890092Data sources: PubMed CentralComputational and Structural Biotechnology JournalArticle . 2020Data sources: Europe PubMed CentralGhent University Academic BibliographyArticle . 2021Data sources: Ghent University Academic BibliographyComputational and Structural Biotechnology JournalOther literature type . Article . 2021 . Peer-reviewedLicense: Elsevier TDMadd 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=10.1016/j.csbj.2021.01.004&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 15 citations 15 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Computational and St... arrow_drop_down Computational and Structural Biotechnology JournalArticle . 2021Full-Text: http://europepmc.org/articles/PMC7890092Data sources: PubMed CentralComputational and Structural Biotechnology JournalArticle . 2020Data sources: Europe PubMed CentralGhent University Academic BibliographyArticle . 2021Data sources: Ghent University Academic BibliographyComputational and Structural Biotechnology JournalOther literature type . Article . 2021 . Peer-reviewedLicense: Elsevier TDMadd 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=10.1016/j.csbj.2021.01.004&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France, Italy, France, FrancePublisher:Rockefeller University Press Funded by:INCa, EC | INSPIREDINCa ,EC| INSPIREDAuthors: Sicari, Daria; Chatziioannou, Aristotelis; Koutsandreas, Theodoros; Sitia, Roberto; +1 AuthorsSicari, Daria; Chatziioannou, Aristotelis; Koutsandreas, Theodoros; Sitia, Roberto; Chevet, Eric;pmc: PMC7480093 , PMC7480111
handle: 20.500.11768/101728 , 20.500.11768/101727
Similar to other RNA viruses, SARS-CoV-2 must (1) enter a target/host cell, (2) reprogram it to ensure its replication, (3) exit the host cell, and (4) repeat this cycle for exponential growth. During the exit step, the virus hijacks the sophisticated machineries that host cells employ to correctly fold, assemble, and transport proteins along the exocytic pathway. Therefore, secretory pathway–mediated assemblage and excretion of infective particles represent appealing targets to reduce the efficacy of virus biogenesis, if not to block it completely. Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications. Sicari et al. discuss the early secretory pathway in the SARS-CoV-2 infection cycle and provide a perspective on potential therapeutic implications.
The Journal of Cell ... arrow_drop_down The Journal of Cell BiologyArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480093Data sources: PubMed CentralThe Journal of Cell Biology; Hal-DiderotArticle . 2020Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480111Data sources: PubMed CentralThe Journal of Cell BiologyOther literature type . Article . 2020 . Peer-reviewedLicense: CC BY NC SAArchivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele; The Journal of Cell BiologyArticle . 2020 . Peer-reviewedLicense: 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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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=10.1083/jcb.202006005&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 63 citations 63 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert The Journal of Cell ... arrow_drop_down The Journal of Cell BiologyArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480093Data sources: PubMed CentralThe Journal of Cell Biology; Hal-DiderotArticle . 2020Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480111Data sources: PubMed CentralThe Journal of Cell BiologyOther literature type . Article . 2020 . Peer-reviewedLicense: CC BY NC SAArchivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele; The Journal of Cell BiologyArticle . 2020 . Peer-reviewedLicense: 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=10.1083/jcb.202006005&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATE, ANR | IFB (ex Renabi-IFB)EC| ELIXIR-EXCELERATE ,ANR| IFB (ex Renabi-IFB)Chennen, Kirsley; Weber, Thomas; Lornage, Xavière; Kress, Arnaud; Böhm, Johann; Thompson, Julie; Laporte, Jocelyn; Poch, Olivier;pmc: PMC7394404
pmid: 32735577
International audience; The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add 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=PMC7394404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add 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 2020 FrancePublisher:Oxford University Press (OUP) Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAllain, Fabrice; Mareuil, Fabien; Ménager, Hervé; Nilges, Michael; Bardiaux, Benjamin;Abstract Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France, Cyprus, Italy EnglishPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | chemREPEATEC| IDPfun ,EC| chemREPEATMier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.; Mier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.;Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 67 citations 67 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | IGNITE, EC | SynarchiCEC| IGNITE ,EC| SynarchiCCyril Matthey-Doret; Lyam Baudry; Axel Breuer; Rémi Montagne; Nadège Guiglielmoni; Vittore F. Scolari; Etienne Jean; Arnaud Campeas; Philippe Henri Chanut; Edgar Oriol; Adrien Meot; Laurent Politis; Antoine Vigouroux; Pierrick Moreau; Romain Koszul; Axel Cournac;Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols. Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 60 citations 60 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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description 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 , 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 France EnglishPublisher:Nature Publishing Group UK Funded by:EC | CaReSyAnEC| CaReSyAnBoizard, Franck; Buffin-Meyer, Bénédicte; Aligon, Julien; Teste, Olivier; Schanstra, Joost; Klein, Julie;pmc: PMC7952700
pmid: 33707596
International audience; Abstract The urinary proteome is a promising pool of biomarkers of kidney disease. However, the protein changes observed in urine only partially reflect the deregulated mechanisms within kidney tissue. In order to improve on the mechanistic insight based on the urinary protein changes, we developed a new prioritization strategy called PRYNT (PRioritization bY protein NeTwork) that employs a combination of two closeness-based algorithms, shortest-path and random walk, and a contextualized protein–protein interaction (PPI) network, mainly based on clique consolidation of STRING network. To assess the performance of our approach, we evaluated both precision and specificity of PRYNT in prioritizing kidney disease candidates. Using four urinary proteome datasets, PRYNT prioritization performed better than other prioritization methods and tools available in the literature. Moreover, PRYNT performed to a similar, but complementary, extent compared to the upstream regulator analysis from the commercial Ingenuity Pathway Analysis software. In conclusion, PRYNT appears to be a valuable freely accessible tool to predict key proteins indirectly from urinary proteome data. In the future, PRYNT approach could be applied to other biofluids, molecular traits and diseases. The source code is freely available on GitHub at: https://github.com/Boizard/PRYNT and has been integrated as an interactive web apps to improved accessibility ( https://github.com/Boizard/PRYNT/tree/master/AppPRYNT ).
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC7952700Data 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.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC7952700Data 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=PMC7952700&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2021 France, BelgiumPublisher:Elsevier BV Funded by:FCT | MS3, EC | POPMETFCT| MS3 ,EC| POPMETSandrien Desmet; Yvan Saeys; Kevin Verstaen; Rebecca Dauwe; Hoon Kim; Claudiu Niculaes; Atsushi Fukushima; Geert Goeminne; Ruben Vanholme; John Ralph; Wout Boerjan; Kris Morreel;Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/). Graphical abstract
Computational and St... arrow_drop_down Computational and Structural Biotechnology JournalArticle . 2021Full-Text: http://europepmc.org/articles/PMC7890092Data sources: PubMed CentralComputational and Structural Biotechnology JournalArticle . 2020Data sources: Europe PubMed CentralGhent University Academic BibliographyArticle . 2021Data sources: Ghent University Academic BibliographyComputational and Structural Biotechnology JournalOther literature type . Article . 2021 . Peer-reviewedLicense: Elsevier TDMadd 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 15 citations 15 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Computational and St... arrow_drop_down Computational and Structural Biotechnology JournalArticle . 2021Full-Text: http://europepmc.org/articles/PMC7890092Data sources: PubMed CentralComputational and Structural Biotechnology JournalArticle . 2020Data sources: Europe PubMed CentralGhent University Academic BibliographyArticle . 2021Data sources: Ghent University Academic BibliographyComputational and Structural Biotechnology JournalOther literature type . Article . 2021 . Peer-reviewedLicense: Elsevier TDMadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France, Italy, France, FrancePublisher:Rockefeller University Press Funded by:INCa, EC | INSPIREDINCa ,EC| INSPIREDAuthors: Sicari, Daria; Chatziioannou, Aristotelis; Koutsandreas, Theodoros; Sitia, Roberto; +1 AuthorsSicari, Daria; Chatziioannou, Aristotelis; Koutsandreas, Theodoros; Sitia, Roberto; Chevet, Eric;pmc: PMC7480093 , PMC7480111
handle: 20.500.11768/101728 , 20.500.11768/101727
Similar to other RNA viruses, SARS-CoV-2 must (1) enter a target/host cell, (2) reprogram it to ensure its replication, (3) exit the host cell, and (4) repeat this cycle for exponential growth. During the exit step, the virus hijacks the sophisticated machineries that host cells employ to correctly fold, assemble, and transport proteins along the exocytic pathway. Therefore, secretory pathway–mediated assemblage and excretion of infective particles represent appealing targets to reduce the efficacy of virus biogenesis, if not to block it completely. Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications. Sicari et al. discuss the early secretory pathway in the SARS-CoV-2 infection cycle and provide a perspective on potential therapeutic implications.
The Journal of Cell ... arrow_drop_down The Journal of Cell BiologyArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480093Data sources: PubMed CentralThe Journal of Cell Biology; Hal-DiderotArticle . 2020Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480111Data sources: PubMed CentralThe Journal of Cell BiologyOther literature type . Article . 2020 . Peer-reviewedLicense: CC BY NC SAArchivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele; The Journal of Cell BiologyArticle . 2020 . Peer-reviewedLicense: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 63 citations 63 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert The Journal of Cell ... arrow_drop_down The Journal of Cell BiologyArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480093Data sources: PubMed CentralThe Journal of Cell Biology; Hal-DiderotArticle . 2020Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7480111Data sources: PubMed CentralThe Journal of Cell BiologyOther literature type . Article . 2020 . Peer-reviewedLicense: CC BY NC SAArchivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele; The Journal of Cell BiologyArticle . 2020 . Peer-reviewedLicense: 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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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=10.1083/jcb.202006005&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATE, ANR | IFB (ex Renabi-IFB)EC| ELIXIR-EXCELERATE ,ANR| IFB (ex Renabi-IFB)Chennen, Kirsley; Weber, Thomas; Lornage, Xavière; Kress, Arnaud; Böhm, Johann; Thompson, Julie; Laporte, Jocelyn; Poch, Olivier;pmc: PMC7394404
pmid: 32735577
International audience; The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add 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=PMC7394404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add 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=PMC7394404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 FrancePublisher:Oxford University Press (OUP) Funded by:EC | BAYCELLS, ANR | INCEPTIONEC| BAYCELLS ,ANR| INCEPTIONAllain, Fabrice; Mareuil, Fabien; Ménager, Hervé; Nilges, Michael; Bardiaux, Benjamin;Abstract Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7319541Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkaa362&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France, Cyprus, Italy EnglishPublisher:Oxford University Press (OUP) Funded by:EC | IDPfun, EC | chemREPEATEC| IDPfun ,EC| chemREPEATMier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.; Mier, Pablo; Paladin, Lisanna; Tamana, Stella; Petrosian, Sophia; Hajdu-Soltész, Borbála; Urbanek, Annika; Gruca, Aleksandra; Plewczynski, Dariusz; Grynberg, Marcin; Bernadó, Pau; Gáspári, Zoltán; Ouzounis, Christos A.; Promponas, Vasilis J.; Kajava, Andrey V.; Hancock, John M.; Tosatto, Silvio C. E.; Dosztanyi, Zsuzsanna; Andrade-Navarro, Miguel A.;Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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/bbz007&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 67 citations 67 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7299295Data sources: PubMed CentralArchivio istituzionale della ricerca - Università di Padova; Briefings in BioinformaticsOther literature type . Article . 2020 . 2019 . Peer-reviewedLicense: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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/bbz007&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | IGNITE, EC | SynarchiCEC| IGNITE ,EC| SynarchiCCyril Matthey-Doret; Lyam Baudry; Axel Breuer; Rémi Montagne; Nadège Guiglielmoni; Vittore F. Scolari; Etienne Jean; Arnaud Campeas; Philippe Henri Chanut; Edgar Oriol; Adrien Meot; Laurent Politis; Antoine Vigouroux; Pierrick Moreau; Romain Koszul; Axel Cournac;Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols. Chromatin loops bridging distant loci within chromosomes can be detected by a variety of techniques such as Hi-C. Here the authors present Chromosight, an algorithm applied on mammalian, bacterial, viral and yeast genomes, able to detect various types of pattern in chromosome contact maps, including chromosomal loops.
Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 60 citations 60 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Nature Communication... arrow_drop_down Europe PubMed CentralArticle . 2020 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC7670471Data sources: PubMed CentralHAL Descartes; HAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2020License: CC BYadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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=10.1101/2020.03.08.981910&type=result"></script>'); --> </script>
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