Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver

Intracellular XBP1-IL-24 axis dismantles cytotoxic unfolded protein response in the liver

(2020) Jianye Wang et al.   Cell Death & Disease

Hepatic PPARα is critical in the metabolic adaptation to sepsis

(2019) Réjane Paumelle et al.   JOURNAL OF HEPATOLOGY

Understanding the marvels behind liver regeneration

(2019) Anan Abu Rmilah et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver

(2019) Avinash Thakur et al.   HEPATOLOGY

The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding

(2018) Giorgia Benegiamo et al.   Cell Metabolism

Liver function and dysfunction - a unique window into the physiological reach of ER stress and the unfolded protein response

(2018) D. Thomas Rutkowski   FEBS Journal

Endoplasmic Reticulum Stress signalling - from basic mechanisms to clinical applications

(2018) Aitor Almanza et al.   FEBS Journal

The molecular functions of hepatocyte nuclear factors – In and beyond the liver

(2018) Hwee Hui Lau et al.   JOURNAL OF HEPATOLOGY

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

Molecular mechanisms driving transcriptional stress responses

(2018) Anniina Vihervaara et al.   NATURE REVIEWS GENETICS

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

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Endoplasmic reticulum stress activates SRC, relocating chaperones to the cell surface where GRP78/CD109 blocks TGF-β signaling

(2018) Yuan-Li Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription

(2018) Yong Hoon Kim et al.   SCIENCE

Liver dysfunction in sepsis

(2018) Ewa Woźnica et al.   Advances in Clinical and Experimental Medicine

Cycles of gene expression and genome response during mammalian tissue regeneration

(2018) Leonor Rib et al.   Epigenetics & Chromatin

HRD1‐ERAD controls production of the hepatokine FGF21 through CREBH polyubiquitination

(2018) Juncheng Wei et al.   EMBO JOURNAL

Hepatocyte Nuclear Factor 4 alpha (HNF4α) Activation is Essential for Termination of Liver Regeneration

(2018) Ian Huck et al.   HEPATOLOGY

Defining the Transcriptional Ecosystem

(2018) Maruhen A.D. Silveira et al.   MOLECULAR CELL

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

XBP1-KLF9 Axis Acts as a Molecular Rheostat to Control the Transition from Adaptive to Cytotoxic Unfolded Protein Response

(2018) Emily E. Fink et al.   Cell Reports

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver

(2018) Adrija Kalvisa et al.   PLOS BIOLOGY

X-box Binding Protein 1 Regulates Unfolded Protein, Acute-Phase, and DNA Damage Responses During Regeneration of Mouse Liver

(2017) Josepmaria Argemí et al.   GASTROENTEROLOGY

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

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

A single-cell transcriptomic analysis reveals precise pathways and regulatory mechanisms underlying hepatoblast differentiation

(2017) Li Yang et al.   HEPATOLOGY

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

(2017) Michal Levo et al.   MOLECULAR CELL

A mouse tissue transcription factor atlas

(2017) Quan Zhou et al.   Nature Communications

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

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

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

FOXA2 alleviates CCl4-induced liver fibrosis by protecting hepatocytes in mice

(2017) Wei Wang et al.   Scientific Reports

Use of a Central Venous Line for Fluids, Drugs and Nutrient Administration in a Mouse Model of Critical Illness

(2017) Sarah Derde et al.   Jove-Journal of Visualized Experiments

Clock Gene Dysregulation Induced by Chronic ER Stress Disrupts β-cell Function

(2017) Yasuharu Ohta et al.   EBioMedicine

Cofactor squelching: Artifact or fact?

(2016) Søren Fisker Schmidt et al.   BIOESSAYS

Integrated genome browser: visual analytics platform for genomics

(2016) Nowlan H. Freese et al.   BIOINFORMATICS

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4

(2015) Michael Zengerle et al.   ACS Chemical Biology

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses

(2015) Lionel Spinelli et al.   BMC GENOMICS

Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers

(2015) Søren Fisker Schmidt et al.   GENOME RESEARCH

Role for the endoplasmic reticulum stress sensor IRE1α in liver regenerative responses

(2015) Yang Liu et al.   JOURNAL OF HEPATOLOGY

BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia

(2015) Jae-Seok Roe et al.   MOLECULAR CELL

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

(2015) Kaifu Chen et al.   NATURE GENETICS

Pervasive robustness in biological systems

(2015) Marie-Anne Félix et al.   NATURE REVIEWS GENETICS

BioGPS: building your own mash-up of gene annotations and expression profiles

(2015) Chunlei Wu et al.   NUCLEIC ACIDS RESEARCH

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Genetic Deletion of the Transcriptional Repressor NFIL3 Enhances Axon Growth In Vitro but Not Axonal Repair In Vivo

(2015) Loek R. van der Kallen et al.   PLoS One

ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation

(2015) Amruta Bhate et al.   Nature Communications

Treatment of Liver Cancer

(2015) Chun-Yu Liu et al.   Cold Spring Harbor Perspectives in Medicine

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Cdkn2a/p16Ink4a Regulates Fasting-Induced Hepatic Gluconeogenesis Through the PKA-CREB-PGC1  Pathway

(2014) K. Bantubungi et al.   DIABETES

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

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

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

Control of Embryonic Stem Cell Identity by BRD4-Dependent Transcriptional Elongation of Super-Enhancer-Associated Pluripotency Genes

(2014) Raffaella Di Micco et al.   Cell Reports

Mechanisms of Cardiac and Renal Dysfunction in Patients Dying of Sepsis

(2013) Osamu Takasu et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

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

(2013) Warren A. Whyte et al.   CELL

Glucagon-Induced Acetylation of Foxa2 Regulates Hepatic Lipid Metabolism

(2013) Ferdinand von Meyenn et al.   Cell Metabolism

Regulatory crosstalk within the mammalian unfolded protein response

(2013) Joseph W. Brewer   CELLULAR AND MOLECULAR LIFE SCIENCES

C/EBP Homologous Protein (CHOP) Contributes to Suppression of Metabolic Genes during Endoplasmic Reticulum Stress in the Liver

(2013) Madhusudana R. Chikka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Temporal clustering of gene expression links the metabolic transcription factor HNF4α to the ER stress-dependent gene regulatory network

(2013) Angela M. Arensdorf et al.   Frontiers in Genetics

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The unfolded protein response: controlling cell fate decisions under ER stress and beyond

(2012) Claudio Hetz   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Src tyrosine kinase phosphorylation of nuclear receptor HNF4  correlates with isoform-specific loss of HNF4  in human colon cancer

(2012) K. Chellappa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of glucose homeostasis through a XBP-1–FoxO1 interaction

(2011) Yingjiang Zhou et al.   NATURE MEDICINE

The UCSC Genome Browser database: extensions and updates 2011

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

bioDBnet: the biological database network

(2009) Uma Mudunuri et al.   BIOINFORMATICS

FXR Acetylation Is Normally Dynamically Regulated by p300 and SIRT1 but Constitutively Elevated in Metabolic Disease States

(2009) Jongsook Kim Kemper et al.   Cell Metabolism

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development

(2008) Tingting Li et al.   GENOMICS