- home
- Advanced Search
- ELIXIR GR
- 2017-2021
- Publications
- Research data
- Article
- FR
- Lirias
- ELIXIR GR
- 2017-2021
- Publications
- Research data
- Article
- FR
- Lirias
Loading
description Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2017 Belgium, PortugalPublisher:Cold Spring Harbor Laboratory Funded by:ANR | GWIS-AMANR| GWIS-AMKridsadakorn Chaichoompu; Fentaw Abegaz; Sissades Tongsima; Philip J. Shaw; Anavaj Sakuntabhai; Luísa Pereira; Kristel Van Steen;AbstractBackgroundResolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.ResultsThis work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.ConclusionsIPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available from bio3.giga.ulg.ac.be/ipcaps
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6427891Data sources: PubMed CentralbioRxivPreprint . 2017Repositório Aberto da Universidade do PortoArticle . 2019Data sources: Repositório Aberto da Universidade do PortoSource Code for Biology and MedicineArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/186874&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 14 citations 14 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6427891Data sources: PubMed CentralbioRxivPreprint . 2017Repositório Aberto da Universidade do PortoArticle . 2019Data sources: Repositório Aberto da Universidade do PortoSource Code for Biology and MedicineArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/186874&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
Loading
description Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2017 Belgium, PortugalPublisher:Cold Spring Harbor Laboratory Funded by:ANR | GWIS-AMANR| GWIS-AMKridsadakorn Chaichoompu; Fentaw Abegaz; Sissades Tongsima; Philip J. Shaw; Anavaj Sakuntabhai; Luísa Pereira; Kristel Van Steen;AbstractBackgroundResolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.ResultsThis work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.ConclusionsIPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available from bio3.giga.ulg.ac.be/ipcaps
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6427891Data sources: PubMed CentralbioRxivPreprint . 2017Repositório Aberto da Universidade do PortoArticle . 2019Data sources: Repositório Aberto da Universidade do PortoSource Code for Biology and MedicineArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/186874&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 14 citations 14 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6427891Data sources: PubMed CentralbioRxivPreprint . 2017Repositório Aberto da Universidade do PortoArticle . 2019Data sources: Repositório Aberto da Universidade do PortoSource Code for Biology and MedicineArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/186874&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu