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

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

G = MAT: Linking Transcription Factor Expression and DNA Binding Data

(2011) Konstantin Tretyakov et al.   PLoS One

The Human Phenotype Ontology

(2010) PN Robinson et al.   CLINICAL GENETICS

A Consensus of Core Protein Complex Compositions for Saccharomyces cerevisiae

(2010) Joris J. Benschop et al.   MOLECULAR CELL

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

(2010) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

AgBase: supporting functional modeling in agricultural organisms

(2010) Fiona M. McCarthy et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells

(2010) Marc Jung et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development

(2010) Nathalie Billon et al.   GENOME BIOLOGY

Next generation software for functional trend analysis

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

ENFIN – A European network for integrative systems biology

(2009) Pascal Kahlem et al.   COMPTES RENDUS BIOLOGIES

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

VisHiC--hierarchical functional enrichment analysis of microarray data

(2009) D. Krushevskaya et al.   NUCLEIC ACIDS RESEARCH

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes: Extending Ensembl across the taxonomic space

(2009) P. J. Kersey et al.   NUCLEIC ACIDS RESEARCH

The FunGenES Database: A Genomics Resource for Mouse Embryonic Stem Cell Differentiation

(2009) Herbert Schulz et al.   PLoS One

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

(2009) Priit Adler et al.   GENOME BIOLOGY

DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression

(2008) S. Yagi et al.   GENOME RESEARCH

MicroRNA target prediction by expression analysis of host genes

(2008) V. A. Gennarino et al.   GENOME RESEARCH

Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells

(2008) P. Hatzis et al.   MOLECULAR AND CELLULAR BIOLOGY

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance

(2008) J. Reimand et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

Fast approximate hierarchical clustering using similarity heuristics

(2008) Meelis Kull et al.   BioData Mining

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

(2008) Alexey V Antonov et al.   GENOME BIOLOGY