A macrophage-hepatocyte glucocorticoid receptor axis coordinates fasting ketogenesis

Dietary Intervention Impacts Immune Cell Functions and Dynamics by Inducing Metabolic Rewiring

(2021) Takuma Okawa et al.   Frontiers in Immunology

Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication

(2021) Anne Loft et al.   Cell Metabolism

Hepatic PPARα function and lipid metabolic pathways are dysregulated in polymicrobial sepsis

(2020) Lise Van Wyngene et al.   EMBO Molecular Medicine

Hepatic PPARα is critical in the metabolic adaptation to sepsis

(2019) Réjane Paumelle et al.   JOURNAL OF HEPATOLOGY

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis

(2019) Alexander Rauch et al.   NATURE GENETICS

Energetic Trade-Offs and Hypometabolic States Promote Disease Tolerance

(2019) Kirthana Ganeshan et al.   CELL

TNF-α inhibits glucocorticoid receptor-induced gene expression by reshaping the GR nuclear cofactor profile

(2019) Karen Dendoncker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dietary Intake Regulates the Circulating Inflammatory Monocyte Pool

(2019) Stefan Jordan et al.   CELL

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

(2019) Xuelian Xiong et al.   MOLECULAR CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity

(2019) Mashito Sakai et al.   IMMUNITY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

Inflammatory Cytokine TNFα Promotes the Long-Term Expansion of Primary Hepatocytes in 3D Culture

(2018) Weng Chuan Peng et al.   CELL

Hepatocyte-Macrophage Acetoacetate Shuttle Protects against Tissue Fibrosis

(2018) Patrycja Puchalska et al.   Cell Metabolism

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Integrated analysis of motif activity and gene expression changes of transcription factors

(2017) Jesper Grud Skat Madsen et al.   GENOME RESEARCH

Cofactor squelching: Artifact or fact?

(2016) Søren Fisker Schmidt et al.   BIOESSAYS

Opposing Effects of Fasting Metabolism on Tissue Tolerance in Bacterial and Viral Inflammation

(2016) Andrew Wang et al.   CELL

Adipocyte Glucocorticoid Receptor Deficiency Attenuates Aging- and HFD-Induced Obesity and Impairs the Feeding-Fasting Transition

(2016) Kristina M. Mueller et al.   DIABETES

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

(2016) Ido Goldstein et al.   GENOME RESEARCH

Liver PPARα is crucial for whole-body fatty acid homeostasis and is protective against NAFLD

(2016) Alexandra Montagner et al.   GUT

Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα

(2016) Dariusz Ratman et al.   NUCLEIC ACIDS RESEARCH

Immune Dysfunction as a Cause and Consequence of Malnutrition

(2016) Claire D. Bourke et al.   TRENDS IN IMMUNOLOGY

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

(2016) Charlotte L. Scott et al.   Nature Communications

Human Glucocorticoid Receptor β Regulates Gluconeogenesis and Inflammation in Mouse Liver

(2015) Bo He et al.   MOLECULAR AND CELLULAR BIOLOGY

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

(2015) Jesper Grud Skat Madsen et al.   NUCLEIC ACIDS RESEARCH

Transcriptional and Chromatin Regulation during Fasting – The Genomic Era

(2015) Ido Goldstein et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

(2013) Patricio Godoy et al.   ARCHIVES OF TOXICOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Hepatic Deficiency in Transcriptional Cofactor TBL1 Promotes Liver Steatosis and Hypertriglyceridemia

(2011) Philipp Kulozik et al.   Cell Metabolism

Molecular Control of Systemic Bile Acid Homeostasis by the Liver Glucocorticoid Receptor

(2011) Adam J. Rose et al.   Cell Metabolism

Glucocorticoid receptor dimerization is required for survival in septic shock via suppression of interleukin-1 in macrophages

(2011) Anna Kleiman et al.   FASEB JOURNAL

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Kupffer cell activation is a causal factor for hepatic insulin resistance

(2009) Nicolas Lanthier et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Depletion of Liver Kupffer Cells Prevents the Development of Diet-Induced Hepatic Steatosis and Insulin Resistance

(2009) W. Huang et al.   DIABETES

Kupffer cells promote hepatic steatosis via interleukin-1β-dependent suppression of peroxisome proliferator-activated receptor α activity

(2009) Rinke Stienstra et al.   HEPATOLOGY