Responsible, practical genomic data sharing that accelerates research

JB Byrd, AC Greene, DV Prasad, X Jiang… - Nature Reviews …, 2020 - nature.com
Data sharing anchors reproducible science, but expectations and best practices are often
nebulous. Communities of funders, researchers and publishers continue to grapple with …

Big data application in biomedical research and health care: a literature review

J Luo, M Wu, D Gopukumar… - Biomedical informatics …, 2016 - journals.sagepub.com
Big data technologies are increasingly used for biomedical and health-care informatics
research. Large amounts of biological and clinical data have been generated and collected …

[HTML][HTML] The molecular signatures database hallmark gene set collection

A Liberzon, C Birger, H Thorvaldsdóttir, M Ghandi… - Cell systems, 2015 - cell.com
Summary The Molecular Signatures Database (MSigDB) is one of the most widely used and
comprehensive databases of gene sets for performing gene set enrichment analysis. Since …

Inferring tumour purity and stromal and immune cell admixture from expression data

K Yoshihara, M Shahmoradgoli, E Martínez… - Nature …, 2013 - nature.com
Infiltrating stromal and immune cells form the major fraction of normal cells in tumour tissue
and not only perturb the tumour signal in molecular studies but also have an important role …

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

R Petryszak, M Keays, YA Tang… - Nucleic acids …, 2016 - academic.oup.com
Abstract Expression Atlas (http://www. ebi. ac. uk/gxa) provides information about gene and
protein expression in animal and plant samples of different cell types, organism parts …

The Database of Genomic Variants: a curated collection of structural variation in the human genome

JR MacDonald, R Ziman, RKC Yuen… - Nucleic acids …, 2014 - academic.oup.com
Over the past decade, the Database of Genomic Variants (DGV; http://dgv. tcag. ca/) has
provided a publicly accessible, comprehensive curated catalogue of structural variation (SV) …

ArrayExpress update—simplifying data submissions

N Kolesnikov, E Hastings, M Keays… - Nucleic acids …, 2015 - academic.oup.com
Abstract The ArrayExpress Archive of Functional Genomics Data (http://www. ebi. ac.
uk/arrayexpress) is an international functional genomics database at the European …

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

WA Kibbe, C Arze, V Felix, E Mitraka… - Nucleic acids …, 2015 - academic.oup.com
The current version of the Human Disease Ontology (DO)(http://www. disease-ontology. org)
database expands the utility of the ontology for the examination and comparison of genetic …

The ontology for biomedical investigations

A Bandrowski, R Brinkman, M Brochhausen, MH Brush… - PloS one, 2016 - journals.plos.org
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with
precisely defined meanings to describe all aspects of how investigations in the biological …

Gateways to the FANTOM5 promoter level mammalian expression atlas

M Lizio, J Harshbarger, H Shimoji, J Severin… - Genome biology, 2015 - Springer
The FANTOM5 project investigates transcription initiation activities in more than 1,000
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …