Author
University of DundeeORCID 0000-0002-2198-1958Unclaimed ORCID profile · follow to get notified of new preprints
12 papers
Recent·Most cited
María Juliana Rodríguez-Cubillos, T. Zieliński, Jason R. Swedlow, T. Ian Simpson, Andrew John Millar
The paper quantifies metadata richness in three biological repositories using NLP metrics, finding differences in word count, information density, and entity consistency across repositories.
bioRxiv · Sep 10, 2026 · PreprintBioinformatics
Khaled Mohamed, William Moore, Dominik Lindner, Josh Moore, Jason R. Swedlow, Petr Walczysko, Frances Wong, Jean‐Marie Burel
The paper introduces IDR searcher, an open-source search engine for public bioimaging resources, aiming to improve dataset discovery and address disparities in accessing quality datasets.
Bioinformatics · Jul 1, 2026Peer-reviewedBioinformatics
Jimena Druker, Hao Jiang, Dilem Shakir, Fraser Child, Vanesa Álvarez, Melpomeni Platani, Andrea Corno, Constance Alabert, Adrian Thomas Saurin, Jason R. Swedlow, Sónia Rocha, Angus I. Lamond
This study identifies PHD1-dependent hydroxylation of RepoMan at P604, showing it regulates mitotic progression by modulating PP2A interaction and H3T3 phosphorylation.
bioRxiv · May 6, 2025Cell Biology
Alejandro J. Brenes, Eva Griesser, Linda V. Sinclair, Lindsay Davidson, Alan R. Prescott, François Singh, Elizabeth K. J. Hogg, Carmen Espejo-Serrano, Hao Jiang, Harunori Yoshikawa, Melpomeni Platani, Jason R. Swedlow, Greg M. Findlay, Doreen Ann Cantrell, Angus I. Lamond
This study compares the proteomes of human induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs), finding quantitative differences in protein expression affecting growth, metabolism, and secreted factors.
eLife · Oct 28, 2024Peer-reviewedSystems Biology
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M. Brown, Jean‐Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E. Diel, David Gault, Satrajit Ghosh, Ilan Gold, Yaroslav O. Halchenko, Matthew Hartley, , Jason R. Swedlow
This paper describes OME-Zarr, a cloud-optimized bioimaging file format developed through community collaboration to improve scalability and data access.
Histochemistry and Cell Biology · Jul 10, 2023Peer-reviewedBioinformatics
Xiaopeng Zhu, Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S. Belmont, Jason R. Swedlow, Jian Ma
Nucleome Browser integrates heterogeneous 4D Nucleome data into an interactive platform for visualization and exploration across biological contexts.
Nature Methods · Jul 21, 2022Peer-reviewedBioinformatics
Matthew Hartley, Gerard J. Kleywegt, Ardan Patwardhan, Uğis Sarkans, Jason R. Swedlow, Alvis Brāzma
The BioImage Archive provides a centralized repository for biological imaging data to enhance reproducibility, reuse, and development of image analysis tools.
Journal of Molecular Biology · Feb 18, 2022Peer-reviewedBioinformatics
Josh Moore, Chris Allan, Sébastien Besson, Jean‐Marie Burel, Erin E. Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
The paper introduces next-generation file formats (NGFF) to improve the FAIRness of bioimaging data by addressing limitations of translation and conversion approaches.
bioRxiv · Mar 31, 2021 · PreprintBioinformatics
Alejandra N Gonzalez-Beltran, Paola Masuzzo, Christophe Ampè, Gert‐Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca‐Serra, , Lennart Martens
This paper presents standardization efforts for cell migration data to improve data sharing and analysis.
GigaScience · May 1, 2020Peer-reviewedBioinformatics
Eleanor M. Williams, Josh Moore, Simon Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K Ferguson, Uğis Sarkans, Alvis Brāzma, Rafael E. Carazo Salas, Jason R. Swedlow
The paper introduces IDR, a platform for integrating and disseminating biological image data, enabling analysis of gene networks and functional interactions through linked data and computational resources.
Nature Methods · Jun 19, 2017Peer-reviewedBioinformatics
Roger Leigh, David Gault, Melissa Linkert, Jean‐Marie Burel, Josh Moore, Sébastien Besson, Jason R. Swedlow
The paper introduces OME Files, an open-source reference library for the OME-XML metadata model and OME-TIFF file format to standardize biological imaging data.
bioRxiv · Mar 9, 2017 · PreprintBioinformatics
Sandra C Moser, Dalila Bensaddek, Brian Ortmann, Sonia Rocha, Angus I Lamond, Jason R Swedlow
This study shows PHD2 hydroxylates CENP-N, regulating its localization and interaction with CENP-L, which affects CENP-A stability at centromeres.
bioRxiv · Nov 3, 2015 · PreprintCell Biology