The minimum information about a proteomics experiment (MIAPE)

CF Taylor, NW Paton, KS Lilley, PA Binz… - Nature …, 2007 - nature.com
Both the generation and the analysis of proteomics data are now widespread, and high-
throughput approaches are commonplace. Protocols continue to increase in complexity as …

An overview of Ensembl

E Birney, TD Andrews, P Bevan, M Caccamo… - Genome …, 2004 - genome.cshlp.org
Ensembl (http://www. ensembl. org/) is a bioinformatics project to organize biological
information around the sequences of large genomes. It is a comprehensive source of stable …

The BioMart community portal: an innovative alternative to large, centralized data repositories

D Smedley, S Haider, S Durinck, L Pandini… - Nucleic acids …, 2015 - academic.oup.com
Abstract The BioMart Community Portal (www. biomart. org) is a community-driven effort to
provide a unified interface to biomedical databases that are distributed worldwide. The …

Map** identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

S Durinck, PT Spellman, E Birney, W Huber - Nature protocols, 2009 - nature.com
Genomic experiments produce multiple views of biological systems, among them are DNA
sequence and copy number variation, and mRNA and protein abundance. Understanding …

A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment

AJ Schork, H Won, V Appadurai, R Nudel… - Nature …, 2019 - nature.com
There is mounting evidence that seemingly diverse psychiatric disorders share genetic
etiology, but the biological substrates mediating this overlap are not well characterized. Here …

Human microRNA targets

B John, AJ Enright, A Aravin, T Tuschl, C Sander… - PLoS …, 2004 - journals.plos.org
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the
message or inhibit translation. The specific function of most mammalian miRNAs is …

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

S Durinck, Y Moreau, A Kasprzyk, S Davis… - …, 2005 - academic.oup.com
biomaRt is a new Bioconductor package that integrates BioMart data resources with data
analysis software in Bioconductor. It can annotate a wide range of gene or gene product …

International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data

J Zhang, J Baran, A Cros, JM Guberman, S Haider… - Database, 2011 - academic.oup.com
Abstract The International Cancer Genome Consortium (ICGC) is a collaborative effort to
characterize genomic abnormalities in 50 different cancer types. To make this data …

g: Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments

J Reimand, M Kull, H Peterson, J Hansen… - Nucleic acids …, 2007 - academic.oup.com
Abstract g: Profiler (http://biit. cs. ut. ee/gprofiler/) is a public web server for characterising
and manipulating gene lists resulting from mining high-throughput genomic data. g: Profiler …

WebGestalt: an integrated system for exploring gene sets in various biological contexts

B Zhang, S Kirov, J Snoddy - Nucleic acids research, 2005 - academic.oup.com
High-throughput technologies have led to the rapid generation of large-scale datasets about
genes and gene products. These technologies have also shifted our research focus from …