g:Profiler—a web server for functional interpretation of gene lists (2016 update)

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

(2016) Richard Marcotte et al.   CELL

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

(2016) J V Sanchez-Mut et al.   Translational Psychiatry

Cytoscape.js: a graph theory library for visualisation and analysis

(2015) Max Franz et al.   BIOINFORMATICS

Human three-dimensional engineered neural tissue reveals cellular and molecular events following cytomegalovirus infection

(2015) Érika Cosset et al.   BIOMATERIALS

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

(2015) Kristian W. Pajtler et al.   CANCER CELL

Genetic subdivision and candidate genes under selection in North American grey wolves

(2015) Rena M. Schweizer et al.   MOLECULAR ECOLOGY

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

EAG2 potassium channel with evolutionarily conserved function as a brain tumor target

(2015) Xi Huang et al.   NATURE NEUROSCIENCE

Babelomics 5.0: functional interpretation for new generations of genomic data

(2015) Roberto Alonso et al.   NUCLEIC ACIDS RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu 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

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

(2015) Mona Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes

(2015) Liina Tserel et al.   Scientific Reports

Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes

(2015) Jüri Reimand et al.   PLoS Genetics

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Dissemination of scientific software with Galaxy ToolShed

(2014) Daniel Blankenberg et al.   GENOME BIOLOGY

BioJS: an open source JavaScript framework for biological data visualization

(2013) J. Gomez et al.   BIOINFORMATICS

The relationship between brain tumor cell invasion of engineered neural tissues and in vivo features of glioblastoma

(2013) Zeynab Nayernia et al.   BIOMATERIALS

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

(2013) Y.-C. Lin et al.   PLANT CELL

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

(2012) Anne K. Krug et al.   ARCHIVES OF TOXICOLOGY

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Comparative Transcriptome Analyses of Deltamethrin-Resistant and -Susceptible Anopheles gambiae Mosquitoes from Kenya by RNA-Seq

(2012) Mariangela Bonizzoni et al.   PLoS One

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods

(2009) Priit Adler et al.   GENOME BIOLOGY

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS