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

Dynamic transcriptional and epigenetic changes drive cellular plasticity in the liver

(2021) Allyson J Merrell et al.   HEPATOLOGY

Mechanisms of Fibrosis Development in NASH

(2020) Robert F. Schwabe et al.   GASTROENTEROLOGY

Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis

(2020) Helene M. Ægidius et al.   Scientific Reports

Cholesterol Stabilizes TAZ in Hepatocytes to Promote Experimental Non-alcoholic Steatohepatitis

(2020) Xiaobo Wang et al.   Cell Metabolism

Transcriptional dynamics of hepatic sinusoid‐associated cells after liver injury

(2020) Mike K. Terkelsen et al.   HEPATOLOGY

Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis

(2020) Jason S. Seidman et al.   IMMUNITY

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver

(2020) Vanessa Dubois et al.   Molecular Systems Biology

Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis

(2020) Prakash Ramachandran et al.   Nature Reviews Gastroenterology & Hepatology

Plasma proteome profiles treatment efficacy of incretin dual agonism in diet‐induced obese female and male mice

(2020) Stephan Sachs et al.   DIABETES OBESITY & METABOLISM

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver

(2020) Anneleen Remmerie et al.   IMMUNITY

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

Protein aggregation capture on microparticles enables multi-purpose proteomics sample preparation.

(2019) Tanveer Singh Batth et al.   MOLECULAR & CELLULAR PROTEOMICS

Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis

(2019) Oliver Krenkel et al.   GUT

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

(2019) Xuelian Xiong et al.   MOLECULAR CELL

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis

(2019) Ross Dobie et al.   Cell Reports

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

A simple diet- and chemical-induced murine NASH model with rapid progression of steatohepatitis, fibrosis and liver cancer

(2018) Takuma Tsuchida et al.   JOURNAL OF HEPATOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Mechanisms of NAFLD development and therapeutic strategies

(2018) Scott L. Friedman et al.   NATURE MEDICINE

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

(2018) Ryan M Layer et al.   NATURE METHODS

ELF3 promotes epithelial–mesenchymal transition by protecting ZEB1 from miR-141-3p-mediated silencing in hepatocellular carcinoma

(2018) Longbo Zheng et al.   Cell Death & Disease

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Hepatocyte Notch activation induces liver fibrosis in nonalcoholic steatohepatitis

(2018) Changyu Zhu et al.   Science Translational Medicine

Mapping the molecular signatures of diet-induced NASH and its regulation by the hepatokine Tsukushi

(2018) Xuelian Xiong et al.   Molecular Metabolism

Liver Cancer Cell of Origin, Molecular Class, and Effects on Patient Prognosis

(2017) Daniela Sia et al.   GASTROENTEROLOGY

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

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

Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor

(2017) Virginia Sanchez-Quiles et al.   MOLECULAR & CELLULAR PROTEOMICS

Hepatokines: linking nonalcoholic fatty liver disease and insulin resistance

(2017) Ruth C. R. Meex et al.   Nature Reviews Endocrinology

Global burden of NAFLD and NASH: trends, predictions, risk factors and prevention

(2017) Zobair Younossi et al.   Nature Reviews Gastroenterology & Hepatology

Genome-Wide Insights into the Development and Function of Thermogenic Adipocytes

(2017) Anne Loft et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss

(2017) Majken Siersbæk et al.   Scientific Reports

Hepatocyte TAZ/WWTR1 Promotes Inflammation and Fibrosis in Nonalcoholic Steatohepatitis

(2016) Xiaobo Wang et al.   Cell Metabolism

Signalling via the osteopontin and high mobility group box-1 axis drives the fibrogenic response to liver injury

(2016) Elena Arriazu et al.   GUT

Osteopontin promotes epithelial-mesenchymal transition of hepatocellular carcinoma through regulating vimentin

(2016) Qiongzhu Dong et al.   Oncotarget

Liver Fibrosis, but No Other Histologic Features, Is Associated With Long-term Outcomes of Patients With Nonalcoholic Fatty Liver Disease

(2015) Paul Angulo et al.   GASTROENTEROLOGY

Association of Adipose Tissue Inflammation With Histologic Severity of Nonalcoholic Fatty Liver Disease

(2015) Johannie du Plessis et al.   GASTROENTEROLOGY

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

Integrative Genomic Signatures Of Hepatocellular Carcinoma Derived from Nonalcoholic Fatty Liver Disease

(2015) Itziar Frades et al.   PLoS One

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Regulation of Steatohepatitis and PPARγ Signaling by Distinct AP-1 Dimers

(2014) Sebastian C. Hasenfuss et al.   Cell Metabolism

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

Image analysis of immunohistochemistry is superior to visual scoring as shown for patient outcome of esophageal adenocarcinoma

(2014) Annette Feuchtinger et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Transcriptome Analysis on the Inflammatory Cell Infiltration of Nonalcoholic Steatohepatitis in Bama Minipigs Induced by a Long-Term High-Fat, High-Sucrose Diet

(2014) Jihan Xia et al.   PLoS One

Diet-induced mouse model of fatty liver disease and nonalcoholic steatohepatitis reflecting clinical disease progression and methods of assessment

(2013) Jason R. Clapper et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

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

(2013) Warren A. Whyte et al.   CELL

DNA Methylation Analysis in Nonalcoholic Fatty Liver Disease Suggests Distinct Disease-Specific and Remodeling Signatures after Bariatric Surgery

(2013) Markus Ahrens et al.   Cell Metabolism

TSC22D4 is a molecular output of hepatic wasting metabolism

(2013) Allan Jones et al.   EMBO Molecular Medicine

Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease

(2013) Cynthia A. Moylan et al.   HEPATOLOGY

An improved mouse model that rapidly develops fibrosis in non-alcoholic steatohepatitis

(2013) Masahiko Matsumoto et al.   INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY

A murine model for non-alcoholic steatohepatitis showing evidence of association between diabetes and hepatocellular carcinoma

(2013) Masato Fujii et al.   Medical Molecular Morphology

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

The role of hepatokines in metabolism

(2013) Norbert Stefan et al.   Nature Reviews Endocrinology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

Metformin Prevents and Reverses Inflammation in a Non-Diabetic Mouse Model of Nonalcoholic Steatohepatitis

(2012) Yuki Kita et al.   PLoS One

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

Pharmacological inhibition of the chemokine CCL2 (MCP-1) diminishes liver macrophage infiltration and steatohepatitis in chronic hepatic injury

(2011) Christer Baeck et al.   GUT

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

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

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

Organogenesis and Development of the Liver

(2010) Karim Si-Tayeb 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

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

Kruppel-Like Zinc Finger Protein Glis2 Is Essential for the Maintenance of Normal Renal Functions

(2008) Y.-S. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY