OMERO: flexible, model-driven data management for experimental biology
C Allan, JM Burel, J Moore, C Blackburn, M Linkert… - Nature …, 2012 - nature.com
Data-intensive research depends on tools that manage multidimensional, heterogeneous
datasets. We built OME Remote Objects (OMERO), a software platform that enables access to …
datasets. We built OME Remote Objects (OMERO), a software platform that enables access to …
[HTML][HTML] Amyotrophic lateral sclerosis
Amyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disease of the
human motor system. In this Seminar, we summarise current concepts about the origin of the …
human motor system. In this Seminar, we summarise current concepts about the origin of the …
Metadata matters: access to image data in the real world
M Linkert, CT Rueden, C Allan, JM Burel… - Journal of Cell …, 2010 - rupress.org
Data sharing is important in the biological sciences to prevent duplication of effort, to promote
scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires …
scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires …
The society of algorithms
J Burrell, M Fourcade - Annual Review of Sociology, 2021 - annualreviews.org
The pairing of massive data sets with processes—or algorithms—written in computer code to
sort through, organize, extract, or mine them has made inroads in almost every major social …
sort through, organize, extract, or mine them has made inroads in almost every major social …
[HTML][HTML] The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
IG Goldberg, C Allan, JM Burel, D Creager, A Falconi… - Genome biology, 2005 - Springer
The Open Microscopy Environment (OME) defines a data model and a software implementation
to serve as an informatics framework for imaging in biological microscopy experiments, …
to serve as an informatics framework for imaging in biological microscopy experiments, …
[HTML][HTML] Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
The expression of CD45RA is generally associated with naive T cells. However, a subset of
effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation …
effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation …
[HTML][HTML] OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies
The rapid pace of innovation in biological imaging and the diversity of its applications have
prevented the establishment of a community-agreed standardized data format. We propose …
prevented the establishment of a community-agreed standardized data format. We propose …
[HTML][HTML] OME-Zarr: a cloud-optimized bioimaging file format with international community support
A growing community is constructing a next-generation file format (NGFF) for bioimaging to
overcome problems of scalability and heterogeneity. Organized by the Open Microscopy …
overcome problems of scalability and heterogeneity. Organized by the Open Microscopy …
How the machine 'thinks': Understanding opacity in machine learning algorithms
J Burrell - Big data & society, 2016 - journals.sagepub.com
This article considers the issue of opacity as a problem for socially consequential mechanisms
of classification and ranking, such as spam filters, credit card fraud detection, search …
of classification and ranking, such as spam filters, credit card fraud detection, search …
[PDF][PDF] Type I interferons regulate immune responses in humans with blood-stage Plasmodium falciparum infection
The development of immunoregulatory networks is important to prevent disease. However,
these same networks allow pathogens to persist and reduce vaccine efficacy. Here, we …
these same networks allow pathogens to persist and reduce vaccine efficacy. Here, we …