- home
- Advanced Search
- ELIXIR GR
- Publications
- Research software
- AT
- IL
- Hal-Diderot
- ELIXIR GR
- Publications
- Research software
- AT
- IL
- Hal-Diderot
Loading
description Publicationkeyboard_double_arrow_right Article , Other literature type , Conference object , Preprint 2019 Austria, FrancePublisher:Springer Science and Business Media LLC Funded by:ANR | RNALands, EC | RIBONETSANR| RNALands ,EC| RIBONETSAuthors: Stefan Hammer; Wei Wang; Sebastian Will; Yann Ponty;Stefan Hammer; Wei Wang; Sebastian Will; Yann Ponty;Background The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which substantially reduce the need for costly wet-lab experiments. Results We devise a novel approach to a central ingredient of most in-silico design methods: the generation of sequences that fold well into multiple target structures. Based on constraint networks, our approach supports generic Boltzmann-weighted sampling, which enables the positive design of RNA sequences with specific free energies (for each of multiple, possibly pseudoknotted, target structures) and GC-content. Moreover, we study general properties of our approach empirically and generate biologically relevant multi-target Boltzmann-weighted designs for an established design benchmark. Our results demonstrate the efficacy and feasibility of the method in practice as well as the benefits of Boltzmann sampling over the previously best multi-target sampling strategy—even for the case of negative design of multi-stable RNAs. Besides empirically studies, we finally justify the algorithmic details due to a fundamental theoretic result about multi-stable RNA design, namely the #P-hardness of the counting of designs. Conclusion introduces a novel, flexible, and effective approach to multi-target RNA design, which promises broad applicability and extensibility. Our free software is available at: https://github.com/yannponty/RNARedPrint Supplementary data are available online. Electronic supplementary material The online version of this article (10.1186/s12859-019-2784-7) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6482512Data sources: PubMed CentralPermanent Hosting, Archiving and Indexing of Digital Resources and AssetsOther literature type . 2019License: CC BYMémoires en Sciences de l'Information et de la CommunicationArticle . 2019Mémoires en Sciences de l'Information et de la CommunicationConference object . 2018Hal-DiderotArticle . 2019Full-Text: https://hal.inria.fr/hal-02112888/documentData sources: Hal-DiderotHal-DiderotConference object . 2018Full-Text: https://hal.inria.fr/hal-01631277v2/documentData sources: Hal-Diderothttps://doi.org/10.48550/arxiv...Article . 2018License: 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=10.1186/s12859-019-2784-7&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 . 2019Full-Text: http://europepmc.org/articles/PMC6482512Data sources: PubMed CentralPermanent Hosting, Archiving and Indexing of Digital Resources and AssetsOther literature type . 2019License: CC BYMémoires en Sciences de l'Information et de la CommunicationArticle . 2019Mémoires en Sciences de l'Information et de la CommunicationConference object . 2018Hal-DiderotArticle . 2019Full-Text: https://hal.inria.fr/hal-02112888/documentData sources: Hal-DiderotHal-DiderotConference object . 2018Full-Text: https://hal.inria.fr/hal-01631277v2/documentData sources: Hal-Diderothttps://doi.org/10.48550/arxiv...Article . 2018License: 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=10.1186/s12859-019-2784-7&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | CY-BIOBANKEC| CY-BIOBANKAuthors: Apostolos Malatras; Stephanie Duguez; William Duddy;Apostolos Malatras; Stephanie Duguez; William Duddy;Background The approach of building large collections of gene sets and then systematically testing hypotheses across these collections is a powerful tool in functional genomics, both in the pathway analysis of omics data and to uncover the polygenic effects associated with complex diseases in genome-wide association study. The Molecular Signatures Database includes collections of oncogenic and immunologic signatures enabling researchers to compare transcriptional datasets across hundreds of previous studies and leading to important insights in these fields, but such a resource does not currently exist for neuromuscular research. In previous work, we have shown the utility of gene set approaches to understand muscle cell physiology and pathology. Methods Following a systematic survey of public muscle data, we passed gene expression profiles from 4305 samples through a robust pre-processing and standardized data analysis pipeline. Two hundred eighty-two samples were discarded based on a battery of rigorous global quality controls. From among the remaining studies, 578 comparisons of interest were identified by a combination of text mining and manual curation of the study meta-data. For each comparison, significantly dysregulated genes (FDR adjusted p < 0.05) were identified. Results Lists of dysregulated genes were divided between upregulated and downregulated to give 1156 Muscle Gene Sets (MGS). This resource is available for download (www.sys-myo.com/muscle_gene_sets) and is accessible through three commonly used functional genomics platforms (GSEA, EnrichR, and WebGestalt). Basic guidance and recommendations are provided for the use of MGS through these platforms. In addition, consensus muscle gene sets were created to capture the overlap between the results of similar studies, and analysis of these highlighted the potential for novel disease-relevant findings. Conclusions The MGS resource can be used to investigate the behaviour of any list of genes across previous comparisons of muscle conditions, to compare previous studies to one another, and to explore the functional relationship of muscle dysregulation to the Gene Ontology. Its major intended use is in enrichment testing for functional genomics analysis. Electronic supplementary material The online version of this article (10.1186/s13395-019-0196-z) contains supplementary material, which is available to authorized users.
Skeletal Muscle arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6498474Data sources: PubMed Centraladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13395-019-0196-z&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Skeletal Muscle arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6498474Data sources: PubMed Centraladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13395-019-0196-z&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Conference object , Preprint 2014 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | SISYPHE, EC | ALMONDEC| SISYPHE ,EC| ALMONDAuthors: Kamil Salikhov; Gustavo Sacomoto; Gregory Kucherov;Kamil Salikhov; Gustavo Sacomoto; Gregory Kucherov;De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs. 12 pages, submitted
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2014Full-Text: http://europepmc.org/articles/PMC3974045Data sources: PubMed CentralAlgorithms for Molecular BiologyOther literature type . Article . 2014 . Peer-reviewedHyper Article en Ligne; INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationOther literature type . Conference object . 2013add 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=10.1186/1748-7188-9-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 66 citations 66 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2014Full-Text: http://europepmc.org/articles/PMC3974045Data sources: PubMed CentralAlgorithms for Molecular BiologyOther literature type . Article . 2014 . Peer-reviewedHyper Article en Ligne; INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationOther literature type . Conference object . 2013add 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=10.1186/1748-7188-9-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
Loading
description Publicationkeyboard_double_arrow_right Article , Other literature type , Conference object , Preprint 2019 Austria, FrancePublisher:Springer Science and Business Media LLC Funded by:ANR | RNALands, EC | RIBONETSANR| RNALands ,EC| RIBONETSAuthors: Stefan Hammer; Wei Wang; Sebastian Will; Yann Ponty;Stefan Hammer; Wei Wang; Sebastian Will; Yann Ponty;Background The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which substantially reduce the need for costly wet-lab experiments. Results We devise a novel approach to a central ingredient of most in-silico design methods: the generation of sequences that fold well into multiple target structures. Based on constraint networks, our approach supports generic Boltzmann-weighted sampling, which enables the positive design of RNA sequences with specific free energies (for each of multiple, possibly pseudoknotted, target structures) and GC-content. Moreover, we study general properties of our approach empirically and generate biologically relevant multi-target Boltzmann-weighted designs for an established design benchmark. Our results demonstrate the efficacy and feasibility of the method in practice as well as the benefits of Boltzmann sampling over the previously best multi-target sampling strategy—even for the case of negative design of multi-stable RNAs. Besides empirically studies, we finally justify the algorithmic details due to a fundamental theoretic result about multi-stable RNA design, namely the #P-hardness of the counting of designs. Conclusion introduces a novel, flexible, and effective approach to multi-target RNA design, which promises broad applicability and extensibility. Our free software is available at: https://github.com/yannponty/RNARedPrint Supplementary data are available online. Electronic supplementary material The online version of this article (10.1186/s12859-019-2784-7) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6482512Data sources: PubMed CentralPermanent Hosting, Archiving and Indexing of Digital Resources and AssetsOther literature type . 2019License: CC BYMémoires en Sciences de l'Information et de la CommunicationArticle . 2019Mémoires en Sciences de l'Information et de la CommunicationConference object . 2018Hal-DiderotArticle . 2019Full-Text: https://hal.inria.fr/hal-02112888/documentData sources: Hal-DiderotHal-DiderotConference object . 2018Full-Text: https://hal.inria.fr/hal-01631277v2/documentData sources: Hal-Diderothttps://doi.org/10.48550/arxiv...Article . 2018License: 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=10.1186/s12859-019-2784-7&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 . 2019Full-Text: http://europepmc.org/articles/PMC6482512Data sources: PubMed CentralPermanent Hosting, Archiving and Indexing of Digital Resources and AssetsOther literature type . 2019License: CC BYMémoires en Sciences de l'Information et de la CommunicationArticle . 2019Mémoires en Sciences de l'Information et de la CommunicationConference object . 2018Hal-DiderotArticle . 2019Full-Text: https://hal.inria.fr/hal-02112888/documentData sources: Hal-DiderotHal-DiderotConference object . 2018Full-Text: https://hal.inria.fr/hal-01631277v2/documentData sources: Hal-Diderothttps://doi.org/10.48550/arxiv...Article . 2018License: 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=10.1186/s12859-019-2784-7&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | CY-BIOBANKEC| CY-BIOBANKAuthors: Apostolos Malatras; Stephanie Duguez; William Duddy;Apostolos Malatras; Stephanie Duguez; William Duddy;Background The approach of building large collections of gene sets and then systematically testing hypotheses across these collections is a powerful tool in functional genomics, both in the pathway analysis of omics data and to uncover the polygenic effects associated with complex diseases in genome-wide association study. The Molecular Signatures Database includes collections of oncogenic and immunologic signatures enabling researchers to compare transcriptional datasets across hundreds of previous studies and leading to important insights in these fields, but such a resource does not currently exist for neuromuscular research. In previous work, we have shown the utility of gene set approaches to understand muscle cell physiology and pathology. Methods Following a systematic survey of public muscle data, we passed gene expression profiles from 4305 samples through a robust pre-processing and standardized data analysis pipeline. Two hundred eighty-two samples were discarded based on a battery of rigorous global quality controls. From among the remaining studies, 578 comparisons of interest were identified by a combination of text mining and manual curation of the study meta-data. For each comparison, significantly dysregulated genes (FDR adjusted p < 0.05) were identified. Results Lists of dysregulated genes were divided between upregulated and downregulated to give 1156 Muscle Gene Sets (MGS). This resource is available for download (www.sys-myo.com/muscle_gene_sets) and is accessible through three commonly used functional genomics platforms (GSEA, EnrichR, and WebGestalt). Basic guidance and recommendations are provided for the use of MGS through these platforms. In addition, consensus muscle gene sets were created to capture the overlap between the results of similar studies, and analysis of these highlighted the potential for novel disease-relevant findings. Conclusions The MGS resource can be used to investigate the behaviour of any list of genes across previous comparisons of muscle conditions, to compare previous studies to one another, and to explore the functional relationship of muscle dysregulation to the Gene Ontology. Its major intended use is in enrichment testing for functional genomics analysis. Electronic supplementary material The online version of this article (10.1186/s13395-019-0196-z) contains supplementary material, which is available to authorized users.
Skeletal Muscle arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6498474Data sources: PubMed Centraladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13395-019-0196-z&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Skeletal Muscle arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6498474Data sources: PubMed Centraladd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13395-019-0196-z&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Conference object , Preprint 2014 FrancePublisher:Springer Science and Business Media LLC Funded by:EC | SISYPHE, EC | ALMONDEC| SISYPHE ,EC| ALMONDAuthors: Kamil Salikhov; Gustavo Sacomoto; Gregory Kucherov;Kamil Salikhov; Gustavo Sacomoto; Gregory Kucherov;De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs. 12 pages, submitted
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2014Full-Text: http://europepmc.org/articles/PMC3974045Data sources: PubMed CentralAlgorithms for Molecular BiologyOther literature type . Article . 2014 . Peer-reviewedHyper Article en Ligne; INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationOther literature type . Conference object . 2013add 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=10.1186/1748-7188-9-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 66 citations 66 popularity Top 10% influence Top 10% impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2014Full-Text: http://europepmc.org/articles/PMC3974045Data sources: PubMed CentralAlgorithms for Molecular BiologyOther literature type . Article . 2014 . Peer-reviewedHyper Article en Ligne; INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationOther literature type . Conference object . 2013add 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=10.1186/1748-7188-9-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu