Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

(2022) Martin Guilliams et al.   CELL

Advances in targeting ‘undruggable’ transcription factors with small molecules

(2021) Matthew J. Henley et al.   NATURE REVIEWS DRUG DISCOVERY

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Fibroblasts: Origins, definitions, and functions in health and disease

(2021) Maksim V. Plikus et al.   CELL

Dynamic of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes

(2021) Mohamed Belhocine et al.   GENOME RESEARCH

Transcription factors: Bridge between cell signaling and gene regulation

(2021) Paula Weidemüller et al.   PROTEOMICS

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes

(2021) Tasnim H. Beacon et al.   Clinical Epigenetics

Loss of hepatocyte identity following aberrant YAP activation: A key mechanism in alcoholic hepatitis

(2021) Mohamed Bou Saleh et al.   JOURNAL OF HEPATOLOGY

Transcriptional dynamics of hepatic sinusoid‐associated cells after liver injury

(2020) Mike K. Terkelsen et al.   HEPATOLOGY

Hepatic molecular signatures highlight the sexual dimorphism of Non‐Alcoholic SteatoHepatitis (NASH)

(2020) Jimmy Vandel et al.   HEPATOLOGY

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver

(2020) Vanessa Dubois et al.   Molecular Systems Biology

Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes

(2020) Julie Dubois-Chevalier et al.   Epigenomics

Machine learning uncovers cell identity regulator by histone code

(2020) Bo Xia et al.   Nature Communications

Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis

(2020) Tatsuya Tsukui et al.   Nature Communications

Bariatric Surgery Provides Long-term Resolution of Nonalcoholic Steatohepatitis and Regression of Fibrosis

(2020) Guillaume Lassailly et al.   GASTROENTEROLOGY

The myofibroblast at a glance

(2020) Pardis Pakshir et al.   JOURNAL OF CELL SCIENCE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

HiCoP, a simple and robust method for detecting interactions of regulatory regions

(2020) Yan Zhang et al.   Epigenetics & Chromatin

Dissecting Fibroblast Heterogeneity in Health and Fibrotic Disease

(2020) Tanya J Shaw et al.   Current Rheumatology Reports

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results

(2020) Ewoud Ewing et al.   BMC BIOINFORMATICS

Fibrosis: from mechanisms to medicines

(2020) Neil C. Henderson et al.   NATURE

GIANT: galaxy-based tool for interactive analysis of transcriptomic data

(2020) Jimmy Vandel et al.   Scientific Reports

Deletion of the nuclear receptor RORα in macrophages does not modify the development of obesity, insulin resistance and NASH

(2020) Laurent L’homme et al.   Scientific Reports

Transcriptional regulation of Hepatic Stellate Cell activation in NASH

(2019) Ann-Britt Marcher et al.   Scientific Reports

Rare Variants in BNC2 Are Implicated in Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction

(2019) Caroline M. Kolvenbach et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epithelial-Mesenchymal Plasticity in Cancer Progression and Metastasis

(2019) Wei Lu et al.   DEVELOPMENTAL CELL

RASSF1A controls tissue stiffness and cancer stem‐like cells in lung adenocarcinoma

(2019) Daniela Pankova et al.   EMBO JOURNAL

Hepatic transcriptomic signatures of statin treatment are associated with impaired glucose homeostasis in severely obese patients

(2019) Daniel Margerie et al.   BMC Medical Genomics

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis

(2019) Yang Xiao et al.   GENES & DEVELOPMENT

Identifying gene function and module connections by the integration of multispecies expression compendia

(2019) Hao Li et al.   GENOME RESEARCH

Shared and distinct mechanisms of fibrosis

(2019) Jörg H. W. Distler et al.   Nature Reviews Rheumatology

MatrisomeDB: the ECM-protein knowledge database

(2019) Xinhao Shao et al.   NUCLEIC ACIDS RESEARCH

TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts

(2018) Masafumi Horie et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Extracellular matrix as a driver of progressive fibrosis

(2018) Jeremy Herrera et al.   JOURNAL OF CLINICAL INVESTIGATION

Specialized fibroblast differentiated states underlie scar formation in the infarcted mouse heart

(2018) Xing Fu et al.   JOURNAL OF CLINICAL INVESTIGATION

The Nuclear Bile Acid Receptor FXR is a PKA- and FOXA2-Sensitive Activator of Fasting Hepatic Gluconeogenesis

(2018) Maheul Ploton et al.   JOURNAL OF HEPATOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Matrix Stiffness: the Conductor of Organ Fibrosis

(2018) Alba Santos et al.   Current Rheumatology Reports

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus

(2018) Melissa A. Buckley et al.   CANCER RESEARCH

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN

(2018) Quinlan L. Sievers et al.   SCIENCE

The logic of transcriptional regulator recruitment architecture at cis -regulatory modules controlling liver functions

(2017) Julie Dubois-Chevalier et al.   GENOME RESEARCH

Main drivers of outcome differ between short term and long term in severe alcoholic hepatitis: A prospective study

(2017) Alexandre Louvet et al.   HEPATOLOGY

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis

(2017) Ji-Eun Lee et al.   Nature Communications

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype

(2017) W. A. da Silveira et al.   Scientific Reports

Pathophysiology and Mechanisms of Nonalcoholic Fatty Liver Disease

(2016) Joel T. Haas et al.   Annual Review of Physiology

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

(2016) Chan Zhou et al.   Genome Medicine

A Functional SNP in BNC2 Is Associated with Adolescent Idiopathic Scoliosis

(2015) Yoji Ogura et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Combining Data From Liver Disease Scoring Systems Better Predicts Outcomes of Patients With Alcoholic Hepatitis

(2015) Alexandre Louvet et al.   GASTROENTEROLOGY

The Hippo pathway effector YAP controls mouse hepatic stellate cell activation

(2015) Inge Mannaerts et al.   JOURNAL OF HEPATOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS

(2015) Jan Krönke et al.   NATURE

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

High-yield and high-purity isolation of hepatic stellate cells from normal and fibrotic mouse livers

(2015) Ingmar Mederacke et al.   Nature Protocols

Fibrosis — A Common Pathway to Organ Injury and Failure

(2015) Don C. Rockey et al.   NEW ENGLAND JOURNAL OF MEDICINE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts

(2015) Youichi Higuchi et al.   PLoS One

BRD4 is a novel therapeutic target for liver fibrosis

(2015) Ning Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The liver's weighty problem

(2015) M. Leslie   SCIENCE

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers

(2015) Claudia Stein et al.   PLoS Genetics

Roux-en-Y Gastric Bypass Versus Adjustable Gastric Banding to Reduce Nonalcoholic Fatty Liver Disease

(2014) Robert Caiazzo et al.   ANNALS OF SURGERY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

(2014) Julie Dubois-Chevalier et al.   NUCLEIC ACIDS RESEARCH

Origin of myofibroblasts in the fibrotic liver in mice

(2014) K. Iwaisako et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

A Vitamin D Receptor/SMAD Genomic Circuit Gates Hepatic Fibrotic Response

(2013) Ning Ding et al.   CELL

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology

(2013) Ingmar Mederacke et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

(2012) Morgane Thomas-Chollier et al.   Nature Protocols

The human hepatocyte cell lines IHH and HepaRG: models to study glucose, lipid and lipoprotein metabolism

(2012) Carolina Huaman Samanez et al.   ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY

The Matrisome:In SilicoDefinition andIn VivoCharacterization by Proteomics of Normal and Tumor Extracellular Matrices

(2011) Alexandra Naba et al.   MOLECULAR & CELLULAR PROTEOMICS

Scraping fibrosis: Expressway to the core of fibrosis

(2011) Wajahat Z Mehal et al.   NATURE MEDICINE

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

A unique H3K4me2 profile marks tissue-specific gene regulation

(2010) A. Pekowska et al.   GENOME RESEARCH

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins

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

Functional linkage of cirrhosis-predictive single nucleotide polymorphisms of toll-like receptor 4 to hepatic stellate cell responses

(2008) Jinsheng Guo et al.   HEPATOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY