Expression Atlas: gene and protein expression across multiple studies and organisms

A Golden Age for Working with Public Proteomics Data

(2017) Lennart Martens et al.   TRENDS IN BIOCHEMICAL SCIENCES

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

The human-induced pluripotent stem cell initiative—data resources for cellular genetics

(2016) Ian Streeter et al.   NUCLEIC ACIDS RESEARCH

European Nucleotide Archive in 2016

(2016) Ana Luisa Toribio et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Open Targets: a platform for therapeutic target identification and validation

(2016) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

Plant Reactome: a resource for plant pathways and comparative analysis

(2016) Sushma Naithani et al.   NUCLEIC ACIDS RESEARCH

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

(2016) Eric W. Deutsch et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

WormBase 2016: expanding to enable helminth genomic research

(2015) Kevin L. Howe et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

Gramene 2016: comparative plant genomics and pathway resources

(2015) Marcela K. Tello-Ruiz et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The complex portal - an encyclopaedia of macromolecular complexes

(2014) Birgit H.M. Meldal et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS