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description Publicationkeyboard_double_arrow_right Other literature type , Article 2016 France, Switzerland, Brazil, Denmark, United Kingdom, GermanyPublisher:Springer Science and Business Media LLC Funded by:EC | PHARMASEAEC| PHARMASEAMingxun Wang; Jeremy Carver; Vanessa V. Phelan; Laura M. Sanchez; Neha Garg; Yao Peng; Don D. Nguyen; Jeramie D. Watrous; Clifford A. Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V. Melnik; Michael J. Meehan; Wei-Ting Liu; Max Crüsemann; Paul D. Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D. Kersten; Laura A. Pace; Robert A. Quinn; Katherine R. Duncan; Cheng-Chih Hsu; Dimitrios J. Floros; Ronnie G. Gavilan; Karin Kleigrewe; Trent R. Northen; Rachel J. Dutton; Delphine Parrot; Erin E. Carlson; Bertrand Aigle; Charlotte Frydenlund Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel A. Pevzner; Anna Edlund; Jeffrey S. McLean; Jörn Piel; Brian T. Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A. Keyzers; Amy C. Sims; Andrew R. Johnson; Ashley M. Sidebottom; Brian E. Sedio; Andreas Klitgaard; Charles B. Larson; Cristopher A. Boya P.; Daniel Torres-Mendoza; David Gonzalez; Denise Brentan Silva; Lucas Miranda Marques; Daniel P. Demarque; Egle Pociute; Ellis C. O’Neill; Enora Briand; Eric J. N. Helfrich; Eve A. Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J. Kharbush; Yi Zeng; Julia A. Vorholt; Kenji L. Kurita; Pep Charusanti; Kerry L. McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F. Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B. Vining; Ralph S. Baric; Ricardo Pianta Rodrigues da Silva; Samantha J. Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat R. Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G. Williams; Jingqui Dai; Ram P. Neupane; Joshua R. Gurr; Andrés M. C. Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M. Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Félix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E. Kyle; Thomas O. Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M. Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R. Jensen; Bernhard O. Palsson; Kit Pogliano; Roger G. Linington; Marcelino Gutiérrez; Norberto Peporine Lopes; William H. Gerwick; Bradley S. Moore; Pieter C. Dorrestein; Nuno Bandeira;International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 3K citations 2,812 popularity Top 0.01% influence Top 0.1% impulse Top 0.01% Powered by BIP!visibility 19visibility views 19 download downloads 417 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2004 Spain, France, Germany, Germany, GermanyPublisher:Oxford University Press (OUP) Güldener, U.; Münsterkötter, M.; Kastenmüller, G.; Strack, N.; van Helden, J.; Lemer, C.; Richelles, J.; Wodak, S. J.; García-Martínez, J.; Pérez-Ortín, J. E.; Michael, H.; Kaps, A.; Talla, E.; Dujon, B.; André, Bernard; Souciet, J. L.; de Montigny, J.; Bon, Elisabeth; Gaillardin, C.; Mewes, H. W.;The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.; International audience; The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 309 citations 309 popularity Top 10% influence Top 1% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2004 FrancePublisher:Oxford University Press (OUP) Authors: Suhre, K.; Sanejouand, Yves-Henri;Suhre, K.; Sanejouand, Yves-Henri;Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkh368&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 649 citations 649 popularity Top 1% influence Top 1% impulse Top 1% Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkh368&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 France, Germany EnglishPublisher:BioMed Central Funded by:EC | MECHANODEVOEC| MECHANODEVOAuthors: Erguvan, Özer; Louveaux, Marion; Hamant, Olivier; Verger, Stéphane;Erguvan, Özer; Louveaux, Marion; Hamant, Olivier; Verger, Stéphane;pmc: PMC6509810
pmid: 31072374
Background Many methods have been developed to quantify cell shape in 2D in tissues. For instance, the analysis of epithelial cells in Drosophila embryogenesis or jigsaw puzzle-shaped pavement cells in plant epidermis has led to the development of numerous quantification methods that are applied to 2D images. However, proper extraction of 2D cell contours from 3D confocal stacks for such analysis can be problematic. Results We developed a macro in ImageJ, SurfCut, with the goal to provide a user-friendly pipeline specifically designed to extract epidermal cell contour signals, segment cells in 2D and analyze cell shape. As a reference point, we compared our output to that obtained with MorphoGraphX (MGX). While both methods differ in the approach used to extract the layer of signal, they output comparable results for tissues with shallow curvature, such as pavement cell shape in cotyledon epidermis (as quantified with PaCeQuant). SurfCut was however not appropriate for cell or tissue samples with high curvature, as evidenced by a significant bias in shape and area quantification. Conclusion We provide a new ImageJ pipeline, SurfCut, that allows the extraction of cell contours from 3D confocal stacks. SurfCut and MGX have complementary advantages: MGX is well suited for curvy samples and more complex analyses, up to computational cell-based modeling on real templates; SurfCut is well suited for rather flat samples, is simple to use, and has the advantage to be easily automated for batch analysis of images in ImageJ. The combination of these two methods thus provides an ideal suite of tools for cell contour extraction in most biological samples, whether 3D precision or high-throughput analysis is the main priority. Electronic supplementary material The online version of this article (10.1186/s12915-019-0657-1) contains supplementary material, which is available to authorized users.
Heidelberger Dokumen... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6509810Data sources: PubMed CentralHAL-ENS-LYON; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYFull-Text: https://hal.science/hal-02269504/documenthttps://doi.org/10.1186/s12915...Article . Peer-reviewedData sources: European Union Open Data Portaladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6509810&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 16 citations 16 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Heidelberger Dokumen... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6509810Data sources: PubMed CentralHAL-ENS-LYON; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYFull-Text: https://hal.science/hal-02269504/documenthttps://doi.org/10.1186/s12915...Article . Peer-reviewedData sources: European Union Open Data Portaladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6509810&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Other literature type , Article 2016 France, Switzerland, Brazil, Denmark, United Kingdom, GermanyPublisher:Springer Science and Business Media LLC Funded by:EC | PHARMASEAEC| PHARMASEAMingxun Wang; Jeremy Carver; Vanessa V. Phelan; Laura M. Sanchez; Neha Garg; Yao Peng; Don D. Nguyen; Jeramie D. Watrous; Clifford A. Kapono; Tal Luzzatto-Knaan; Carla Porto; Amina Bouslimani; Alexey V. Melnik; Michael J. Meehan; Wei-Ting Liu; Max Crüsemann; Paul D. Boudreau; Eduardo Esquenazi; Mario Sandoval-Calderón; Roland D. Kersten; Laura A. Pace; Robert A. Quinn; Katherine R. Duncan; Cheng-Chih Hsu; Dimitrios J. Floros; Ronnie G. Gavilan; Karin Kleigrewe; Trent R. Northen; Rachel J. Dutton; Delphine Parrot; Erin E. Carlson; Bertrand Aigle; Charlotte Frydenlund Michelsen; Lars Jelsbak; Christian Sohlenkamp; Pavel A. Pevzner; Anna Edlund; Jeffrey S. McLean; Jörn Piel; Brian T. Murphy; Lena Gerwick; Chih-Chuang Liaw; Yu-Liang Yang; Hans-Ulrich Humpf; Maria Maansson; Robert A. Keyzers; Amy C. Sims; Andrew R. Johnson; Ashley M. Sidebottom; Brian E. Sedio; Andreas Klitgaard; Charles B. Larson; Cristopher A. Boya P.; Daniel Torres-Mendoza; David Gonzalez; Denise Brentan Silva; Lucas Miranda Marques; Daniel P. Demarque; Egle Pociute; Ellis C. O’Neill; Enora Briand; Eric J. N. Helfrich; Eve A. Granatosky; Evgenia Glukhov; Florian Ryffel; Hailey Houson; Hosein Mohimani; Jenan J. Kharbush; Yi Zeng; Julia A. Vorholt; Kenji L. Kurita; Pep Charusanti; Kerry L. McPhail; Kristian Fog Nielsen; Lisa Vuong; Maryam Elfeki; Matthew F. Traxler; Niclas Engene; Nobuhiro Koyama; Oliver B. Vining; Ralph S. Baric; Ricardo Pianta Rodrigues da Silva; Samantha J. Mascuch; Sophie Tomasi; Stefan Jenkins; Venkat R. Macherla; Thomas Hoffman; Vinayak Agarwal; Philip G. Williams; Jingqui Dai; Ram P. Neupane; Joshua R. Gurr; Andrés M. C. Rodríguez; Anne Lamsa; Chen Zhang; Kathleen Dorrestein; Brendan M. Duggan; Jehad Almaliti; Pierre-Marie Allard; Prasad Phapale; Louis-Félix Nothias; Theodore Alexandrov; Marc Litaudon; Jean-Luc Wolfender; Jennifer E. Kyle; Thomas O. Metz; Tyler Peryea; Dac-Trung Nguyen; Danielle VanLeer; Paul Shinn; Ajit Jadhav; Rolf Müller; Katrina M. Waters; Wenyuan Shi; Xueting Liu; Lixin Zhang; Rob Knight; Paul R. Jensen; Bernhard O. Palsson; Kit Pogliano; Roger G. Linington; Marcelino Gutiérrez; Norberto Peporine Lopes; William H. Gerwick; Bradley S. Moore; Pieter C. Dorrestein; Nuno Bandeira;International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 3K citations 2,812 popularity Top 0.01% influence Top 0.1% impulse Top 0.01% Powered by BIP!visibility 19visibility views 19 download downloads 417 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Oxford University Research ArchiveOther literature type . 2016Data sources: Oxford University Research ArchiveArchiMer - Institutional Archive of IfremerOther literature type . 2016Data sources: ArchiMer - Institutional Archive of IfremerOnline Research Database In TechnologyArticle . 2016Data sources: Online Research Database In TechnologyRepositório Institucional da USP (Biblioteca Digital da Produção Intelectual) - Universidade de São Paulo (USP); Nature BiotechnologyOther literature type . Article . 2016 . Peer-reviewedLicense: Springer TDMHelmholtz Zentrum für Infektionsforschung RepositoryArticle . 2016License: CC BY NC SAData sources: Helmholtz Zentrum für Infektionsforschung RepositoryHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2016add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/nbt.3597&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2004 Spain, France, Germany, Germany, GermanyPublisher:Oxford University Press (OUP) Güldener, U.; Münsterkötter, M.; Kastenmüller, G.; Strack, N.; van Helden, J.; Lemer, C.; Richelles, J.; Wodak, S. J.; García-Martínez, J.; Pérez-Ortín, J. E.; Michael, H.; Kaps, A.; Talla, E.; Dujon, B.; André, Bernard; Souciet, J. L.; de Montigny, J.; Bon, Elisabeth; Gaillardin, C.; Mewes, H. W.;The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.; International audience; The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 309 citations 309 popularity Top 10% influence Top 1% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2004Full-Text: http://europepmc.org/articles/PMC540007Data sources: PubMed CentralGöttingen Research Online PublicationsArticle . 2018Data sources: Göttingen Research Online PublicationsNucleic Acids Research; Recolector de Ciencia Abierta, RECOLECTAArticle . 2005 . 2004 . Peer-reviewedPublikationenserver der Georg-August-Universität GöttingenArticle . 2005 . Peer-reviewedPublication Server of Helmholtz Zentrum München (PuSH)Article . 2005Data sources: Publication Server of Helmholtz Zentrum München (PuSH)HAL-ENS-LYON; HAL-Pasteur; Mémoires en Sciences de l'Information et de la Communication; HAL-CEA; HAL-UPMCArticle . 2005License: CC BY NCHAL - UPEC / UPEM; HAL-Inserm; Hal-DiderotArticle . 2005License: CC BY NCFull-Text: https://hal.inria.fr/inria-00339841/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/gki053&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2004 FrancePublisher:Oxford University Press (OUP) Authors: Suhre, K.; Sanejouand, Yves-Henri;Suhre, K.; Sanejouand, Yves-Henri;Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkh368&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 649 citations 649 popularity Top 1% influence Top 1% impulse Top 1% Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/nar/gkh368&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 France, Germany EnglishPublisher:BioMed Central Funded by:EC | MECHANODEVOEC| MECHANODEVOAuthors: Erguvan, Özer; Louveaux, Marion; Hamant, Olivier; Verger, Stéphane;Erguvan, Özer; Louveaux, Marion; Hamant, Olivier; Verger, Stéphane;pmc: PMC6509810
pmid: 31072374
Background Many methods have been developed to quantify cell shape in 2D in tissues. For instance, the analysis of epithelial cells in Drosophila embryogenesis or jigsaw puzzle-shaped pavement cells in plant epidermis has led to the development of numerous quantification methods that are applied to 2D images. However, proper extraction of 2D cell contours from 3D confocal stacks for such analysis can be problematic. Results We developed a macro in ImageJ, SurfCut, with the goal to provide a user-friendly pipeline specifically designed to extract epidermal cell contour signals, segment cells in 2D and analyze cell shape. As a reference point, we compared our output to that obtained with MorphoGraphX (MGX). While both methods differ in the approach used to extract the layer of signal, they output comparable results for tissues with shallow curvature, such as pavement cell shape in cotyledon epidermis (as quantified with PaCeQuant). SurfCut was however not appropriate for cell or tissue samples with high curvature, as evidenced by a significant bias in shape and area quantification. Conclusion We provide a new ImageJ pipeline, SurfCut, that allows the extraction of cell contours from 3D confocal stacks. SurfCut and MGX have complementary advantages: MGX is well suited for curvy samples and more complex analyses, up to computational cell-based modeling on real templates; SurfCut is well suited for rather flat samples, is simple to use, and has the advantage to be easily automated for batch analysis of images in ImageJ. The combination of these two methods thus provides an ideal suite of tools for cell contour extraction in most biological samples, whether 3D precision or high-throughput analysis is the main priority. Electronic supplementary material The online version of this article (10.1186/s12915-019-0657-1) contains supplementary material, which is available to authorized users.
Heidelberger Dokumen... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6509810Data sources: PubMed CentralHAL-ENS-LYON; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYFull-Text: https://hal.science/hal-02269504/documenthttps://doi.org/10.1186/s12915...Article . Peer-reviewedData sources: European Union Open Data Portaladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6509810&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 16 citations 16 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Heidelberger Dokumen... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6509810Data sources: PubMed CentralHAL-ENS-LYON; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BYFull-Text: https://hal.science/hal-02269504/documenthttps://doi.org/10.1186/s12915...Article . Peer-reviewedData sources: European Union Open Data Portaladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6509810&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu