The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

(2018) Rafael Hernández-de-Diego et al.   NUCLEIC ACIDS RESEARCH

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Maintaining maximal metabolic flux by gene expression control

(2018) Robert Planqué et al.   PLoS Computational Biology

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

(2018) Shinya Oki et al.   EMBO REPORTS

Insulin-like growth factor-1 activates AMPK to augment mitochondrial function and correct neuronal metabolism in sensory neurons in type 1 diabetes

(2018) Mohamad-Reza Aghanoori et al.   Molecular Metabolism

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

(2018) Denis Torre et al.   Cell Systems

A data citation roadmap for scientific publishers

(2018) Helena Cousijn et al.   Scientific Data

Discovering and linking public omics data sets using the Omics Discovery Index

(2017) Yasset Perez-Riverol et al.   NATURE BIOTECHNOLOGY

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

Reactivation of androgen receptor-regulated lipid biosynthesis drives the progression of castration-resistant prostate cancer

(2017) W Han et al.   ONCOGENE

Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine

(2017) Lauren B. Becnel et al.   Science Signaling

Mitochondrial homeostasis in adipose tissue remodeling

(2017) Svetlana Altshuler-Keylin et al.   Science Signaling

Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine

(2017) Lauren B. Becnel et al.   Science Signaling

Mitochondrial homeostasis in adipose tissue remodeling

(2017) Svetlana Altshuler-Keylin et al.   Science Signaling

Lysophosphatidylcholine acyltransferase 4 is involved in chondrogenic differentiation of ATDC5 cells

(2017) Shirou Tabe et al.   Scientific Reports

Complementary Roles of Estrogen-Related Receptors in Brown Adipocyte Thermogenic Function

(2016) Marin L. Gantner et al.   ENDOCRINOLOGY

Improving the discoverability, accessibility, and citability of omics datasets: a case report

(2016) Yolanda F Darlington et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The Comparative Toxicogenomics Database: update 2017

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

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

(2016) Zichen Wang et al.   Nature Communications

High throughput microscopy identifies bisphenol AP, a bisphenol A analog, as a novel AR down-regulator

(2016) Fabio Stossi et al.   Oncotarget

mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes

(2016) Annabel Y. Minard et al.   Cell Reports

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Constitutive activities of estrogen-related receptors: Transcriptional regulation of metabolism by the ERR pathways in health and disease

(2015) Janice M. Huss et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

DSigDB: drug signatures database for gene set analysis: Fig. 1.

(2015) Minjae Yoo et al.   BIOINFORMATICS

Transcriptomic Effects of Estrogen Starvation and Induction in the MCF7 Cells. The Meta-analysis of Microarray Results

(2015) Anna Stanislawska-Sachadyn et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Insulin and Insulin-like Growth Factor 1 (IGF-1) Modulate Cytoplasmic Glucose and Glycogen Levels but Not Glucose Transport across the Membrane in Astrocytes

(2015) Marko Muhič et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

(2015) Christopher Southan et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Tissue-Specific Signals Control Reversible Program of Localization and Functional Polarization of Macrophages

(2014) Yasutaka Okabe et al.   CELL

GADD45  regulates the thermogenic capacity of brown adipose tissue

(2014) M. L. Gantner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of cell cycle transcription during G1 and S phases

(2013) Cosetta Bertoli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The AMPK  2 Subunit Is Required for Energy Homeostasis during Metabolic Stress

(2012) B. Dasgupta et al.   MOLECULAR AND CELLULAR BIOLOGY

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Transcriptomine, a web resource for nuclear receptor signaling transcriptomes

(2012) Scott A. Ochsner et al.   PHYSIOLOGICAL GENOMICS

Modeling Truncated AR Expression in a Natural Androgen Responsive Environment and Identification of RHOB as a Direct Transcriptional Target

(2012) Hui-Chi Tsai et al.   PLoS One

Estrogen-related receptor α regulates skeletal myocyte differentiation via modulation of the ERK MAP kinase pathway

(2011) Jennifer Murray et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair

(2011) Vidhya Jagannathan et al.   BMC Systems Biology

Sex differences of chondrogenic progenitor cells in late stages of osteoarthritis

(2010) Sebastian Koelling et al.   ARTHRITIS AND RHEUMATISM

Research Resource: Expression Profiling Reveals Unexpected Targets and Functions of the Human Steroid Receptor RNA Activator (SRA) Gene

(2010) Charles E. Foulds et al.   MOLECULAR ENDOCRINOLOGY

Discovering causal signaling pathways through gene-expression patterns

(2010) Jignesh R. Parikh et al.   NUCLEIC ACIDS RESEARCH

Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors

(2009) Min Zhao et al.   BMC GENOMICS

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

Discovery of a lysophospholipid acyltransferase family essential for membrane asymmetry and diversity

(2008) D. Hishikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA