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description Publicationkeyboard_double_arrow_right Article 2016Publisher:Oxford University Press (OUP) Publicly fundedFunded by:SFI | BCL-2 family proteins and..., SFI | microRNA as novel therape...SFI| BCL-2 family proteins and cellular bioenergetics in the control of cell survival: Towards novel predictive and prognostic markers for disease progression and therapy responses in colorectal cancer patients ,SFI| microRNA as novel therapeutic targets and disease biomarkers in Alzheimer's Disease, Frontotemporal dementia and Amyotrophic lateral sclerosis (NEURO-MIR)Authors: Stefan J, Haunsberger; Niamh M C, Connolly; Jochen H M, Prehn;Stefan J, Haunsberger; Niamh M C, Connolly; Jochen H M, Prehn;pmid: 27797767
Abstract Summary The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter, available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results. Availability and Implementation The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor (http://bioconductor.org/packages/miRNAmeConverter). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/. The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor (http://bioconductor.org/packages/miRBaseVersions.db). Minimum R version 3.3.0 is required. Supplementary information Supplementary data are available at Bioinformatics online.
Bioinformatics arrow_drop_down BioinformaticsArticle . 2016 . Peer-reviewedLicense: OUP Terms of Use and Content Access PolicyData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btw660&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu42 citations 42 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Bioinformatics arrow_drop_down BioinformaticsArticle . 2016 . Peer-reviewedLicense: OUP Terms of Use and Content Access PolicyData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btw660&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 FrancePublisher:Public Library of Science (PLoS) Publicly fundedFunded by:SFI | Microbial Phylogeography, WTSFI| Microbial Phylogeography ,WTFabre, Laëtitia; Zhang, Jian; Guigon, Ghislaine; Le Hello, Simon; Guibert, Véronique; Accou-Demartin, Marie; de Romans, Saïana; Lim, Catherine; Roux, Chrystelle; Passet, Virginie; Diancourt, Laure; Guibourdenche, Martine; Issenhuth-Jeanjean, Sylvie; Achtman, Mark; Brisse, Sylvain; Sola, Christophe; Weill, François-Xavier;International audience; Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3356390Data sources: PubMed CentralHAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2012License: CC BYFull-Text: https://hal.science/hal-00762219/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=10.1371/journal.pone.0036995&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 211 citations 211 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 7visibility views 7 download downloads 83 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3356390Data sources: PubMed CentralHAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2012License: CC BYFull-Text: https://hal.science/hal-00762219/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=10.1371/journal.pone.0036995&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2015 IrelandPublisher:Springer Science and Business Media LLC Publicly fundedFunded by:SFI | Clustal Omega and the fut...SFI| Clustal Omega and the future of Multiple AlignmentsAuthors: Jehl, Peter; Sievers, Fabian; Higgins, Desmond G;Jehl, Peter; Sievers, Fabian; Higgins, Desmond G;Background: Multiple sequence alignments (MSA) are widely used in sequence analysis for a variety of tasks. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This paper describes a simple method for automatically detecting outliers and accompanying software called OD-seq. It is based on finding sequences whose average distance to the rest of the sequences in a dataset, is anomalous. Results: The software can take a MSA, distance matrix or set of unaligned sequences as input. Outlier sequences are found by examining the average distance of each sequence to the rest. Anomalous average distances are then found using the interquartile range of the distribution of average distances or by bootstrapping them. The complexity of any analysis of a distance matrix is normally at least O(N2 ) for N sequences. This is prohibitive for large N but is reduced here by using the mBed algorithm from Clustal Omega. This reduces the complexity to O(N log(N)) which makes even very large alignments easy to analyse on a single core. We tested the ability of OD-seq to detect outliers using artificial test cases of sequences from Pfam families, seeded with sequences from other Pfam families. Using a MSA as input, OD-seq is able to detect outliers with very high sensitivity and specificity. Conclusion: OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy. For medium sized alignments, of a few thousand sequences, it can detect outliers in a few seconds. Science Foundation Ireland
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4548304Data 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/s12859-015-0702-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 38 citations 38 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4548304Data 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/s12859-015-0702-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 IrelandPublisher:Frontiers Media SA Publicly fundedFunded by:SFI | Multi-Gene Assay Cloud Co..., EC | SAGE-CARE, IRCSFI| Multi-Gene Assay Cloud Computing Platform ,EC| SAGE-CARE ,IRCCintia C. Palu; Cintia C. Palu; Marcelo Ribeiro-Alves; Yanxin Wu; Yanxin Wu; Brendan Lawlor; Brendan Lawlor; Pavel V. Baranov; Pavel V. Baranov; Brian Kelly; Paul Walsh; Paul Walsh;One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to freely explore the data and test a new hypothesis with independence. Simplicity DiffExpress is a data-driven software platform dedicated to enabling non-bioinformaticians to take ownership of the differential expression analysis step in a transcriptomics experiment while presenting the results in a comprehensible layout, which supports an efficient results exploration, information storage, and reproducibility. Simplicity DiffExpress’ key component is the bespoke statistical model validation that guides the user through any necessary alteration in the dataset or model, tackling the challenges behind complex data analysis. The software utilizes edgeR, and it is implemented as part of the SimplicityTM platform, providing a dynamic interface, with well-organized results, easy to navigate and shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual differential expression analysis resources. Wet-lab collaborators can benefit from receiving their results in an organized interface. Simplicity DiffExpress is freely available for academic use, and it is cloud-based (https://simplicity.nsilico.com/dea).
Frontiers in Genetic... arrow_drop_down Frontiers in GeneticsArticle . 2019Full-Text: http://europepmc.org/articles/PMC6527599Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2019License: CC BYData sources: Cork Open Research Archive (CORA)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=10.3389/fgene.2019.00356&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 Frontiers in Genetic... arrow_drop_down Frontiers in GeneticsArticle . 2019Full-Text: http://europepmc.org/articles/PMC6527599Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2019License: CC BYData sources: Cork Open Research Archive (CORA)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=10.3389/fgene.2019.00356&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2013 IrelandPublisher:Oxford University Press (OUP) Publicly fundedFunded by:SFI | Development of computatio..., WT | Genome wide characterizat...SFI| Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS). ,WT| Genome wide characterization of utilization of non-standard decoding by ribosomal profiling.Michel, Audrey M.; Fox, Gearoid; Kiran, Anmol M.; De Bo, Christof; O'Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.;We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3965066Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2014License: CC BYData sources: Cork Open Research Archive (CORA)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/gkt1035&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 218 citations 218 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3965066Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2014License: CC BYData sources: Cork Open Research Archive (CORA)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/gkt1035&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017Publisher:Springer Science and Business Media LLC Publicly fundedFunded by:SFI | Irish Centre for Fetal an...SFI| Irish Centre for Fetal and Neonatal Translational Research (INFANT)Authors: Grégoire Thomas; Louise C. Kenny; Philip N. Baker; Robin Tuytten;Grégoire Thomas; Louise C. Kenny; Philip N. Baker; Robin Tuytten;Background Disease prevalence is rarely explicitly considered in the early stages of the development of novel prognostic tests. Rather, researchers use the area under the receiver operating characteristic (AUROC) as the key metric to gauge and report predictive performance ability. Because this statistic does not account for disease prevalence, proposed tests may not appropriately address clinical requirements. This ultimately impedes the translation of prognostic tests into clinical practice. Methods A method to express positive- and/or negative predictive value criteria (PPV, NPV) within the ROC space is presented. Equations are derived for so-called equi-PPV (and equi-NPV) lines. Herewith it is possible, for any given prevalence, to plot a series of sensitivity-specificity pairs which meet a specified PPV (or NPV) criterion onto the ROC space. This concept is introduced by firstly reviewing the well-established “mechanics”, strengths and limitations of the ROC analysis in the context of developing prognostic models. Then, the use of PPV (and/or) NPV criteria to augment the ROC analysis is elaborated. Additionally, an interactive web tool was also created to enable people to explore the dynamics of lines of equi-predictive value in function of prevalence. The web tool also allows to gauge what ROC curve shapes best meet specific positive and/or negative predictive value criteria (http://d4ta.link/ppvnpv/). Results To illustrate the merits and implications of this concept, an example on the prediction of pre-eclampsia risk in low-risk nulliparous pregnancies is elaborated. Conclusions In risk stratification, the clinical usefulness of a prognostic test can be expressed in positive- and negative predictive value criteria; the development of novel prognostic tests will be facilitated by the possibility to co-visualise such criteria together with ROC curves. To achieve clinically meaningful risk stratification, the development of separate tests to meet either a pre-specified positive value (rule-in) or a negative predictive value (rule-out) criteria should be considered: the characteristics of successful rule-in and rule-out tests may markedly differ. Electronic supplementary material The online version of this article (10.1186/s41512-017-0017-y) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC6460848Data 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/s41512-017-0017-y&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 14 citations 14 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC6460848Data 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/s41512-017-0017-y&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2016Publisher:Informa UK Limited Publicly fundedFunded by:SFI | Development of computatio...SFI| Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS).Authors: Audrey M, Michel; James P A, Mullan; Vimalkumar, Velayudhan; Patrick B F, O'Connor; +2 AuthorsAudrey M, Michel; James P A, Mullan; Vimalkumar, Velayudhan; Patrick B F, O'Connor; Claire A, Donohue; Pavel V, Baranov;ABSTRACT Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4829337Data 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=10.1080/15476286.2016.1141862&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 80 citations 80 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4829337Data 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=10.1080/15476286.2016.1141862&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021Publisher:Cold Spring Harbor Laboratory Publicly fundedFunded by:SFI | Precision Oncology Irelan..., Irish Cancer Society, IRC +1 projectsSFI| Precision Oncology Ireland ,Irish Cancer Society ,IRC ,SFI| Overcoming Drug Resistance in Metastatic Malignant Melanoma by Personalizing TreatmentAuthors: Luis F. Iglesias-Martinez; Barbara De Kegel; Walter Kolch;Luis F. Iglesias-Martinez; Barbara De Kegel; Walter Kolch;AbstractReconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. We have benchmarked KBoost against other high performing algorithms using three different datasets. The results show that our method compares favorably to other methods across datasets. We have also applied KBoost to a large cohort of close to 2000 breast cancer patients and 24,000 genes in less than 2 h on standard hardware. Our results show that molecularly defined breast cancer subtypes also feature differences in their GRNs. An implementation of KBoost in the form of an R package is available at: https://github.com/Luisiglm/KBoost and as a Bioconductor software package.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8322418Data 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=10.1101/2021.04.01.438059&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 7 citations 7 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/PMC8322418Data 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=10.1101/2021.04.01.438059&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Article 2016Publisher:Oxford University Press (OUP) Publicly fundedFunded by:SFI | BCL-2 family proteins and..., SFI | microRNA as novel therape...SFI| BCL-2 family proteins and cellular bioenergetics in the control of cell survival: Towards novel predictive and prognostic markers for disease progression and therapy responses in colorectal cancer patients ,SFI| microRNA as novel therapeutic targets and disease biomarkers in Alzheimer's Disease, Frontotemporal dementia and Amyotrophic lateral sclerosis (NEURO-MIR)Authors: Stefan J, Haunsberger; Niamh M C, Connolly; Jochen H M, Prehn;Stefan J, Haunsberger; Niamh M C, Connolly; Jochen H M, Prehn;pmid: 27797767
Abstract Summary The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working with only a small number of miRNAs the translation can be done manually. However, with large sets of miRNAs, the necessary correction of such inconsistencies becomes burdensome and error-prone. We developed miRNAmeConverter, available as a Bioconductor R package and web interface that addresses the challenges associated with mature miRNA name inconsistencies. The main algorithm implemented enables high-throughput automatic translation of species-independent mature miRNA names to user selected miRBase versions. The web interface enables users less familiar with R to translate miRNA names given in form of a list or embedded in text and download of the results. Availability and Implementation The miRNAmeConverter R package is open source under the Artistic-2.0 license. It is freely available from Bioconductor (http://bioconductor.org/packages/miRNAmeConverter). The web interface is based on R Shiny and can be accessed under the URL http://www.systemsmedicineireland.ie/tools/mirna-name-converter/. The database that miRNAmeConverter depends on is provided by the annotation package miRBaseVersions.db and can be downloaded from Bioconductor (http://bioconductor.org/packages/miRBaseVersions.db). Minimum R version 3.3.0 is required. Supplementary information Supplementary data are available at Bioinformatics online.
Bioinformatics arrow_drop_down BioinformaticsArticle . 2016 . Peer-reviewedLicense: OUP Terms of Use and Content Access PolicyData sources: Crossrefadd 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.eu42 citations 42 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Bioinformatics arrow_drop_down BioinformaticsArticle . 2016 . Peer-reviewedLicense: OUP Terms of Use and Content Access PolicyData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1093/bioinformatics/btw660&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2012 FrancePublisher:Public Library of Science (PLoS) Publicly fundedFunded by:SFI | Microbial Phylogeography, WTSFI| Microbial Phylogeography ,WTFabre, Laëtitia; Zhang, Jian; Guigon, Ghislaine; Le Hello, Simon; Guibert, Véronique; Accou-Demartin, Marie; de Romans, Saïana; Lim, Catherine; Roux, Chrystelle; Passet, Virginie; Diancourt, Laure; Guibourdenche, Martine; Issenhuth-Jeanjean, Sylvie; Achtman, Mark; Brisse, Sylvain; Sola, Christophe; Weill, François-Xavier;International audience; Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.
CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3356390Data sources: PubMed CentralHAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2012License: CC BYFull-Text: https://hal.science/hal-00762219/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 211 citations 211 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!visibility 7visibility views 7 download downloads 83 Powered bymore_vert CORE (RIOXX-UK Aggre... arrow_drop_down Europe PubMed CentralArticle . 2012Full-Text: http://europepmc.org/articles/PMC3356390Data sources: PubMed CentralHAL-Pasteur; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2012License: CC BYFull-Text: https://hal.science/hal-00762219/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2015 IrelandPublisher:Springer Science and Business Media LLC Publicly fundedFunded by:SFI | Clustal Omega and the fut...SFI| Clustal Omega and the future of Multiple AlignmentsAuthors: Jehl, Peter; Sievers, Fabian; Higgins, Desmond G;Jehl, Peter; Sievers, Fabian; Higgins, Desmond G;Background: Multiple sequence alignments (MSA) are widely used in sequence analysis for a variety of tasks. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This paper describes a simple method for automatically detecting outliers and accompanying software called OD-seq. It is based on finding sequences whose average distance to the rest of the sequences in a dataset, is anomalous. Results: The software can take a MSA, distance matrix or set of unaligned sequences as input. Outlier sequences are found by examining the average distance of each sequence to the rest. Anomalous average distances are then found using the interquartile range of the distribution of average distances or by bootstrapping them. The complexity of any analysis of a distance matrix is normally at least O(N2 ) for N sequences. This is prohibitive for large N but is reduced here by using the mBed algorithm from Clustal Omega. This reduces the complexity to O(N log(N)) which makes even very large alignments easy to analyse on a single core. We tested the ability of OD-seq to detect outliers using artificial test cases of sequences from Pfam families, seeded with sequences from other Pfam families. Using a MSA as input, OD-seq is able to detect outliers with very high sensitivity and specificity. Conclusion: OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy. For medium sized alignments, of a few thousand sequences, it can detect outliers in a few seconds. Science Foundation Ireland
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4548304Data 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/s12859-015-0702-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 38 citations 38 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2015Full-Text: http://europepmc.org/articles/PMC4548304Data 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/s12859-015-0702-1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 IrelandPublisher:Frontiers Media SA Publicly fundedFunded by:SFI | Multi-Gene Assay Cloud Co..., EC | SAGE-CARE, IRCSFI| Multi-Gene Assay Cloud Computing Platform ,EC| SAGE-CARE ,IRCCintia C. Palu; Cintia C. Palu; Marcelo Ribeiro-Alves; Yanxin Wu; Yanxin Wu; Brendan Lawlor; Brendan Lawlor; Pavel V. Baranov; Pavel V. Baranov; Brian Kelly; Paul Walsh; Paul Walsh;One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to freely explore the data and test a new hypothesis with independence. Simplicity DiffExpress is a data-driven software platform dedicated to enabling non-bioinformaticians to take ownership of the differential expression analysis step in a transcriptomics experiment while presenting the results in a comprehensible layout, which supports an efficient results exploration, information storage, and reproducibility. Simplicity DiffExpress’ key component is the bespoke statistical model validation that guides the user through any necessary alteration in the dataset or model, tackling the challenges behind complex data analysis. The software utilizes edgeR, and it is implemented as part of the SimplicityTM platform, providing a dynamic interface, with well-organized results, easy to navigate and shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual differential expression analysis resources. Wet-lab collaborators can benefit from receiving their results in an organized interface. Simplicity DiffExpress is freely available for academic use, and it is cloud-based (https://simplicity.nsilico.com/dea).
Frontiers in Genetic... arrow_drop_down Frontiers in GeneticsArticle . 2019Full-Text: http://europepmc.org/articles/PMC6527599Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2019License: CC BYData sources: Cork Open Research Archive (CORA)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=10.3389/fgene.2019.00356&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 Frontiers in Genetic... arrow_drop_down Frontiers in GeneticsArticle . 2019Full-Text: http://europepmc.org/articles/PMC6527599Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2019License: CC BYData sources: Cork Open Research Archive (CORA)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=10.3389/fgene.2019.00356&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2013 IrelandPublisher:Oxford University Press (OUP) Publicly fundedFunded by:SFI | Development of computatio..., WT | Genome wide characterizat...SFI| Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS). ,WT| Genome wide characterization of utilization of non-standard decoding by ribosomal profiling.Michel, Audrey M.; Fox, Gearoid; Kiran, Anmol M.; De Bo, Christof; O'Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.;We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3965066Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2014License: CC BYData sources: Cork Open Research Archive (CORA)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/gkt1035&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 218 citations 218 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2013Full-Text: http://europepmc.org/articles/PMC3965066Data sources: PubMed CentralCork Open Research Archive (CORA)Article . 2014License: CC BYData sources: Cork Open Research Archive (CORA)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/gkt1035&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017Publisher:Springer Science and Business Media LLC Publicly fundedFunded by:SFI | Irish Centre for Fetal an...SFI| Irish Centre for Fetal and Neonatal Translational Research (INFANT)Authors: Grégoire Thomas; Louise C. Kenny; Philip N. Baker; Robin Tuytten;Grégoire Thomas; Louise C. Kenny; Philip N. Baker; Robin Tuytten;Background Disease prevalence is rarely explicitly considered in the early stages of the development of novel prognostic tests. Rather, researchers use the area under the receiver operating characteristic (AUROC) as the key metric to gauge and report predictive performance ability. Because this statistic does not account for disease prevalence, proposed tests may not appropriately address clinical requirements. This ultimately impedes the translation of prognostic tests into clinical practice. Methods A method to express positive- and/or negative predictive value criteria (PPV, NPV) within the ROC space is presented. Equations are derived for so-called equi-PPV (and equi-NPV) lines. Herewith it is possible, for any given prevalence, to plot a series of sensitivity-specificity pairs which meet a specified PPV (or NPV) criterion onto the ROC space. This concept is introduced by firstly reviewing the well-established “mechanics”, strengths and limitations of the ROC analysis in the context of developing prognostic models. Then, the use of PPV (and/or) NPV criteria to augment the ROC analysis is elaborated. Additionally, an interactive web tool was also created to enable people to explore the dynamics of lines of equi-predictive value in function of prevalence. The web tool also allows to gauge what ROC curve shapes best meet specific positive and/or negative predictive value criteria (http://d4ta.link/ppvnpv/). Results To illustrate the merits and implications of this concept, an example on the prediction of pre-eclampsia risk in low-risk nulliparous pregnancies is elaborated. Conclusions In risk stratification, the clinical usefulness of a prognostic test can be expressed in positive- and negative predictive value criteria; the development of novel prognostic tests will be facilitated by the possibility to co-visualise such criteria together with ROC curves. To achieve clinically meaningful risk stratification, the development of separate tests to meet either a pre-specified positive value (rule-in) or a negative predictive value (rule-out) criteria should be considered: the characteristics of successful rule-in and rule-out tests may markedly differ. Electronic supplementary material The online version of this article (10.1186/s41512-017-0017-y) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC6460848Data 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/s41512-017-0017-y&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 14 citations 14 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2017Full-Text: http://europepmc.org/articles/PMC6460848Data 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/s41512-017-0017-y&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2016Publisher:Informa UK Limited Publicly fundedFunded by:SFI | Development of computatio...SFI| Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS).Authors: Audrey M, Michel; James P A, Mullan; Vimalkumar, Velayudhan; Patrick B F, O'Connor; +2 AuthorsAudrey M, Michel; James P A, Mullan; Vimalkumar, Velayudhan; Patrick B F, O'Connor; Claire A, Donohue; Pavel V, Baranov;ABSTRACT Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4829337Data 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=10.1080/15476286.2016.1141862&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 80 citations 80 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2016Full-Text: http://europepmc.org/articles/PMC4829337Data 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=10.1080/15476286.2016.1141862&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2021Publisher:Cold Spring Harbor Laboratory Publicly fundedFunded by:SFI | Precision Oncology Irelan..., Irish Cancer Society, IRC +1 projectsSFI| Precision Oncology Ireland ,Irish Cancer Society ,IRC ,SFI| Overcoming Drug Resistance in Metastatic Malignant Melanoma by Personalizing TreatmentAuthors: Luis F. Iglesias-Martinez; Barbara De Kegel; Walter Kolch;Luis F. Iglesias-Martinez; Barbara De Kegel; Walter Kolch;AbstractReconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. We have benchmarked KBoost against other high performing algorithms using three different datasets. The results show that our method compares favorably to other methods across datasets. We have also applied KBoost to a large cohort of close to 2000 breast cancer patients and 24,000 genes in less than 2 h on standard hardware. Our results show that molecularly defined breast cancer subtypes also feature differences in their GRNs. An implementation of KBoost in the form of an R package is available at: https://github.com/Luisiglm/KBoost and as a Bioconductor software package.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2021Full-Text: http://europepmc.org/articles/PMC8322418Data 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=10.1101/2021.04.01.438059&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 7 citations 7 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/PMC8322418Data 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=10.1101/2021.04.01.438059&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu