Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Control of amino-acid transport by antigen receptors coordinates the metabolic reprogramming essential for T cell differentiation

(2013) Linda V Sinclair et al.   NATURE IMMUNOLOGY

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

(2013) Radmila Feldmann et al.   NUCLEIC ACIDS RESEARCH

Transient Infantile Hypertriglyceridemia, Fatty Liver, and Hepatic Fibrosis Caused by Mutated GPD1, Encoding Glycerol-3-Phosphate Dehydrogenase 1

(2012) Lina Basel-Vanagaite et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells

(2012) Lea H Gregersen et al.   BMC CANCER

Interplay between Lipids and Branched-Chain Amino Acids in Development of Insulin Resistance

(2012) Christopher B. Newgard   Cell Metabolism

Current concept of reverse cholesterol transport and novel strategy for atheroprotection

(2012) Koh Ono   Journal of Cardiology

Metabolism in the age of 'omes'

(2012) R. K. Suarez et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

MicroRNA-29a-c decrease fasting blood glucose levels by negatively regulating hepatic gluconeogenesis

(2012) Jichao Liang et al.   JOURNAL OF HEPATOLOGY

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

MicroRNAs in metabolism and metabolic disorders

(2012) Veerle Rottiers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes

(2012) Elisabeth John et al.   NUCLEIC ACIDS RESEARCH

Choline Kinase Alpha and Hexokinase-2 Protein Expression in Hepatocellular Carcinoma: Association with Survival

(2012) Sandi A. Kwee et al.   PLoS One

MiR-27 as a Prognostic Marker for Breast Cancer Progression and Patient Survival

(2012) Wei Tang et al.   PLoS One

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Farnesyl pyrophosphate regulates adipocyte functions as an endogenous PPARγ agonist

(2011) Tsuyoshi Goto et al.   BIOCHEMICAL JOURNAL

Acyl-CoA synthetase 1 is required for oleate and linoleate mediated inhibition of cholesterol efflux through ATP-binding cassette transporter A1 in macrophages

(2011) Jenny E. Kanter et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

(2011) Søren F Schmidt et al.   BMC GENOMICS

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

(2011) Ottar Rolfsson et al.   BMC Systems Biology

Integration of Metabolomics and Expression of Glycerol-3-phosphate Acyltransferase (GPAM) in Breast Cancer—Link to Patient Survival, Hormone Receptor Status, and Metabolic Profiling

(2011) Scarlet F. Brockmöller et al.   JOURNAL OF PROTEOME RESEARCH

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

Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors

(2011) Raymond E. Soccio et al.   MOLECULAR ENDOCRINOLOGY

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs

(2011) F. Wessely et al.   Molecular Systems Biology

miR-27a is a negative regulator of adipocyte differentiation via suppressing PPARγ expression

(2010) Sang Yun Kim et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene–disease networks

(2010) Anna Bauer-Mehren et al.   BIOINFORMATICS

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

(2010) Aaron M Newman et al.   BMC BIOINFORMATICS

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

MicroRNA Activity Is Suppressed in Mouse Oocytes

(2010) Jun Ma et al.   CURRENT BIOLOGY

Global microRNA expression profiles in insulin target tissues in a spontaneous rat model of type 2 diabetes

(2010) B. M. Herrera et al.   DIABETOLOGIA

Adipose Tissue Branched Chain Amino Acid (BCAA) Metabolism Modulates Circulating BCAA Levels

(2010) Mark A. Herman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An essential role for Dicer in adipocyte differentiation

(2010) Rajini Mudhasani et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor   Function in Adipocytes and Macrophages

(2010) M. I. Lefterova et al.   MOLECULAR AND CELLULAR BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

EpiChIP: gene-by-gene quantification of epigenetic modification levels

(2010) Daniel Hebenstreit et al.   NUCLEIC ACIDS RESEARCH

microRNA miR-27b impairs human adipocyte differentiation and targets PPARγ

(2009) Michael Karbiener et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A role ofmiR-27in the regulation of adipogenesis

(2009) Qun Lin et al.   FEBS Journal

MicroRNAlet-7Regulates 3T3-L1 Adipogenesis

(2009) Tingwan Sun et al.   MOLECULAR ENDOCRINOLOGY

LXR Regulates Cholesterol Uptake Through Idol-Dependent Ubiquitination of the LDL Receptor

(2009) Noam Zelcer et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Regulation of hepatic fatty acid elongase 5 by LXRα–SREBP-1c

(2008) Yan Qin et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Peroxisome Proliferator-Activated Receptor γ Agonists as Insulin Sensitizers: From the Discovery to Recent Progress

(2008) Nobuo Cho et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

The Selective Alzheimer's Disease Indicator-1 Gene (Seladin-1/DHCR24) Is a Liver X Receptor Target Gene

(2008) Y. Wang et al.   MOLECULAR PHARMACOLOGY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes

(2008) Mirco Castoldi et al.   Nature Protocols

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells

(2008) Lasse Sinkkonen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Microarray analyses of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle

(2008) Sophie Rome et al.   PHYSIOLOGICAL GENOMICS

miR-17-92 cluster accelerates adipocyte differentiation by negatively regulating tumor-suppressor Rb2/p130

(2008) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational analysis of small RNA cloning data

(2007) Philipp Berninger et al.   METHODS