ORCID Profile
0000-0001-9842-9718
Current Organisations
University of Amsterdam
,
University of Manchester
,
Szent-Györgyi Albert Medical School, University of Szeged
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: The Company of Biologists
Date: 2014
DOI: 10.1242/JCS.141556
Abstract: Here we identify a role for the matrilin-2 (Matn2) extracellular matrix protein in controlling early steps of myogenic differentiation. We observed Matn2 deposition around proliferating, differentiating and fusing myoblasts in culture and during muscle regeneration in vivo. Matn2 silencing delayed expression of the Cdk inhibitor p21 and of the Nfix, MyoD, Myog myogenic genes, explaining the retarded cell cycle exit and myoblast differentiation. Matn2 expression rescue restored differentiation and the expression of p21 and of the myogenic genes. TGF-β1 inhibited myogenic differentiation at least in part by repressing Matn2 expression, which inhibited the onset of a positive feedback loop whereby Matn2 and Nfix activate each other's expression as well as myoblast differentiation. In vivo, myoblast cell cycle arrest and muscle regeneration was delayed in Matn2−/− relative to wild-type mice. Trf3 and myogenic gene expression levels robustly dropped in Matn2−/− fetal limbs and in differentiating primary myoblast cultures, establishing Matn2 as a key modulator of the regulatory cascade that initiates terminal myogenic differentiation. Our data thus identify Matn2 as a critical component of a genetic switch that modulates tissue repair onset.
Publisher: IOS Press
Date: 20-07-2022
DOI: 10.3233/DS-210053
Abstract: An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema.org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying “just enough” Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article11 o/doi/10.5281/zenodo.5146227 is archived at 0.5281/zenodo.5146227.
Publisher: Oxford University Press (OUP)
Date: 11-2019
DOI: 10.1093/GIGASCIENCE/GIZ095
Abstract: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable automation, scaling, adaptation, and provenance support. However, there are still several challenges associated with the effective sharing, publication, and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Based on best-practice recommendations identified from the literature on workflow design, sharing, and publishing, we define a hierarchical provenance framework to achieve uniformity in provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realize this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We use open source community-driven standards, interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric research objects generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. The underlying principles of the standards utilized by CWLProv enable semantically rich and executable research objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, reuse the methods for partial reruns, or reproduce the analysis to validate the published findings.
Publisher: Software Sustainability Institute: Collaborations Workshop
Date: 2021
Publisher: Center for Open Science
Date: 19-12-2022
Abstract: Status of discussions around the topic of data standard formats for plant sciences and their interoperability at the BioHackathon Europe 2022 in Paris.
Publisher: Springer Science and Business Media LLC
Date: 27-11-2014
Location: United Kingdom of Great Britain and Northern Ireland
Location: Hungary
Start Date: 2019
End Date: 2021
Funder: European Commission
View Funded Activity