iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator

(2017) Nohra Park et al.   MOLECULES AND CELLS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

(2017) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

The START App: a web-based RNAseq analysis and visualization resource

(2016) Jonathan W. Nelson et al.   BIOINFORMATICS

Dual Role of p21 in the Progression of Cancer and Its Treatment

(2016) Amna Parveen et al.   CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

(2016) Jernej Godec et al.   IMMUNITY

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database: update 2017

(2016) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Regulatory module involving FGF13, miR-504, and p53 regulates ribosomal biogenesis and supports cancer cell survival

(2016) Débora R. Bublik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

(2016) Nirav Merchant et al.   PLOS BIOLOGY

VisRseq: R-based visual framework for analysis of sequencing data

(2015) Hamid Younesy et al.   BMC BIOINFORMATICS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo

(2015) Claudia Tonelli et al.   Oncotarget

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Genetic Mutation of p53 and Suppression of the miR-17 92 Cluster Are Synthetic Lethal in Non-Small Cell Lung Cancer due to Upregulation of Vitamin D Signaling

(2014) R. Borkowski et al.   CANCER RESEARCH

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

miR-92a family and their target genes in tumorigenesis and metastasis

(2014) Molin Li et al.   EXPERIMENTAL CELL RESEARCH

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data

(2014) Sanghamitra Bandyopadhyay et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

miRDB: an online resource for microRNA target prediction and functional annotations

(2014) Nathan Wong et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

(2013) Tobias Wittkop et al.   BMC BIOINFORMATICS

miR-192, miR-194 and miR-215: a convergent microRNA network suppressing tumor progression in renal cell carcinoma

(2013) H.W.Z. Khella et al.   CARCINOGENESIS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Nano GO Consortium—A Team Science Approach to Assess Engineered Nanomaterials: Reliable Assays and Methods

(2013) Thaddeus T. Schug et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

(2013) Timothy Jewison 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

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

AraPath: a knowledgebase for pathway analysis in Arabidopsis

(2012) L. Lai et al.   BIOINFORMATICS

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

(2012) Cynthia L. Smith et al.   MAMMALIAN GENOME

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc

(2012) Miles Trupp et al.   GENOME BIOLOGY

GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis

(2012) Hiromitsu Araki et al.   FEBS Open Bio

Effects of ionizing radiation on the immune system with special emphasis on the interaction of dendritic and T cells

(2012) Katrin Manda et al.   Frontiers in Oncology

PREDA: an R-package to identify regional variations in genomic data

(2011) Francesco Ferrari et al.   BIOINFORMATICS

Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

(2011) Steven X Ge   BMC Systems Biology

NOA: a novel Network Ontology Analysis method

(2011) Jiguang Wang et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs MiR-17, MiR-20a, and MiR-106b Act in Concert to Modulate E2F Activity on Cell Cycle Arrest during Neuronal Lineage Differentiation of USSC

(2011) Hans-Ingo Trompeter et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

MicroRNA-193b Represses Cell Proliferation and Regulates Cyclin D1 in Melanoma

(2010) Jiamin Chen et al.   AMERICAN JOURNAL OF PATHOLOGY

CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse

(2010) Olivier Friard et al.   BMC BIOINFORMATICS

Negative Regulation of Tumor Suppressor p53 by MicroRNA miR-504

(2010) Wenwei Hu et al.   MOLECULAR CELL

Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data

(2010) Ahmed Essaghir et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

HOXA1 A218G Polymorphism is Associated with Smaller Cerebellar Volume in Healthy Humans

(2009) Elisa Canu et al.   JOURNAL OF NEUROIMAGING

Transcription factor Foxo3 controls the magnitude of T cell immune responses by modulating the function of dendritic cells

(2009) Anne S Dejean et al.   NATURE IMMUNOLOGY

WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

(2009) D. Glez-Pena et al.   NUCLEIC ACIDS RESEARCH

CORUM: the comprehensive resource of mammalian protein complexes—2009

(2009) Andreas Ruepp et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

MethCancerDB – aberrant DNA methylation in human cancer

(2008) M Lauss et al.   BRITISH JOURNAL OF CANCER

E2F1-Regulated MicroRNAs Impair TGFβ-Dependent Cell-Cycle Arrest and Apoptosis in Gastric Cancer

(2008) Fabio Petrocca et al.   CANCER CELL

miR-192 Regulates Dihydrofolate Reductase and Cellular Proliferation through the p53-microRNA Circuit

(2008) B. Song et al.   CLINICAL CANCER RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition

(2008) Nicole Cloonan et al.   GENOME BIOLOGY