Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells

Nebula—a web-server for advanced ChIP-seq data analysis

(2012) Valentina Boeva et al.   BIOINFORMATICS

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages

(2012) Petri Pehkonen et al.   BMC GENOMICS

Amorfrutins are potent antidiabetic dietary natural products

(2012) C. Weidner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liver X receptor biology and pharmacology: new pathways, challenges and opportunities

(2012) Tomas Jakobsson et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Macrophages in the Pathogenesis of Atherosclerosis

(2011) Kathryn J. Moore et al.   CELL

PARP-1 Inhibition Increases Mitochondrial Metabolism through SIRT1 Activation

(2011) Péter Bai et al.   Cell Metabolism

Human Atherosclerotic Plaque Alternative Macrophages Display Low Cholesterol Handling but High Phagocytosis Because of Distinct Activities of the PPARγ and LXRα Pathways

(2011) Giulia Chinetti-Gbaguidi et al.   CIRCULATION RESEARCH

Structure and function of active chromatin and DNase I hypersensitive sites

(2011) Peter N. Cockerill   FEBS Journal

Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor   in Mouse Liver Reveals Extensive Sharing of Binding Sites

(2011) M. Boergesen et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

A computational pipeline for comparative ChIP-seq analyses

(2011) Anaïs F Bardet et al.   Nature Protocols

DistiLD Database: diseases and traits in linkage disequilibrium blocks

(2011) A. Palleja et al.   NUCLEIC ACIDS RESEARCH

Metabolic nuclear receptor signaling and the inflammatory acute phase response

(2011) Nicolas Venteclef et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The Reactome BioMart

(2011) R. A. Haw et al.   Database-The Journal of Biological Databases and Curation

Liver X Receptor Signaling Pathways and Atherosclerosis

(2010) Anna C. Calkin et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

PPARγ activates ABCA1 gene transcription but reduces the level of ABCA1 protein in HepG2 cells

(2010) Denis A. Mogilenko et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Predicting Gene-Regulation Functions: Lessons from Temperate Bacteriophages

(2010) Vladimir B. Teif   BIOPHYSICAL JOURNAL

Dynamic Changes in Genome-Wide Histone H3 Lysine 4 Methylation Patterns in Response to Dehydration Stress in Arabidopsis thaliana

(2010) Karin van Dijk et al.   BMC PLANT BIOLOGY

A Macrophage Sterol-Responsive Network Linked to Atherogenesis

(2010) Lev Becker et al.   Cell Metabolism

Orphan Nuclear Receptor DAX-1 Acts as a Novel Corepressor of Liver X Receptor α and Inhibits Hepatic Lipogenesis

(2010) Balachandar Nedumaran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Non-redundant roles for LXR  and LXR  in atherosclerosis susceptibility in low density lipoprotein receptor knockout mice

(2010) E. D. Bischoff et al.   JOURNAL OF LIPID RESEARCH

Evolution of promiscuous nuclear hormone receptors: LXR, FXR, VDR, PXR, and CAR

(2010) Matthew D. Krasowski et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

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

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

(2010) Morten Beck Rye et al.   NUCLEIC ACIDS RESEARCH

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

(2010) Ilya Kupershmidt et al.   PLoS One

Blueprint for antimicrobial hit discovery targeting metabolic networks

(2010) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

GPS2 Is Required for Cholesterol Efflux by Triggering Histone Demethylation, LXR Recruitment, and Coregulator Assembly at the ABCG1 Locus

(2009) Tomas Jakobsson et al.   MOLECULAR CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

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

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

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

The implications of human metabolic network topology for disease comorbidity

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY