Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration

Atoh1 Controls Primary Cilia Formation to Allow for SHH-Triggered Granule Neuron Progenitor Proliferation

(2019) Chia-Hsiang Chang et al.   DEVELOPMENTAL CELL

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Epigenetic Compensation Promotes Liver Regeneration

(2019) Shuang Wang et al.   DEVELOPMENTAL CELL

Peribiliary gland niche participates in biliary tree regeneration in mouse and in human primary sclerosing cholangitis

(2019) Guido Carpino et al.   HEPATOLOGY

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

YAP integrates the regulatory Snail/HNF4α circuitry controlling epithelial/hepatocyte differentiation

(2019) Valeria Noce et al.   Cell Death & Disease

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Transcription factor GATA6: a novel marker and putative inducer of ductal metaplasia in biliary atresia

(2018) Tea Soini et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Targeting hepatic glutaminase activity to ameliorate hyperglycemia

(2018) Russell A Miller et al.   NATURE MEDICINE

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Dual Regulatory Functions of SUFU and Targetome of GLI2 in SHH Subgroup Medulloblastoma

(2018) Wen-Chi Yin et al.   DEVELOPMENTAL CELL

Hippo–YAP/TAZ signalling in organ regeneration and regenerative medicine

(2018) Iván M. Moya et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Dynamic Metabolic Zonation of the Hepatic Glucose Metabolism Is Accomplished by Sinusoidal Plasma Gradients of Nutrients and Hormones

(2018) Nikolaus Berndt et al.   Frontiers in Physiology

Hepatostat: Liver regeneration and normal liver tissue maintenance

(2017) George K. Michalopoulos   HEPATOLOGY

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Molecular mechanisms of Sox transcription factors during the development of liver, bile duct, and pancreas

(2017) Chunyue Yin   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Erratum: Corrigendum: The RSPO–LGR4/5–ZNRF3/RNF43 module controls liver zonation and size

(2016) Lara Planas-Paz et al.   NATURE CELL BIOLOGY

Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6

(2016) Patrick Guye et al.   Nature Communications

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

(2015) Bruce Wang et al.   NATURE

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

(2015) Amruta Bhate et al.   Nature Communications

Hippo Pathway Activity Influences Liver Cell Fate

(2014) Dean Yimlamai et al.   CELL

Bipotential Adult Liver Progenitors Are Derived from Chronically Injured Mature Hepatocytes

(2014) Branden D. Tarlow et al.   Cell Stem Cell

TWEAK/Fn14 Signaling Is Required for Liver Regeneration after Partial Hepatectomy in Mice

(2014) Gamze Karaca et al.   PLoS One

Myofibroblastic cells function as progenitors to regenerate murine livers after partial hepatectomy

(2013) M Swiderska-Syn et al.   GUT

Smoothened is a master regulator of adult liver repair

(2013) Gregory A. Michelotti et al.   JOURNAL OF CLINICAL INVESTIGATION

The intrahepatic signalling niche of hedgehog is defined by primary cilia positive cells during chronic liver injury

(2013) Candice Alexandra Grzelak et al.   JOURNAL OF HEPATOLOGY

Macrophage-derived Wnt opposes Notch signaling to specify hepatic progenitor cell fate in chronic liver disease

(2012) Luke Boulter et al.   NATURE MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The stable repression of mesenchymal program is required for hepatocyte identity: A novel role for hepatocyte nuclear factor 4α

(2011) Laura Santangelo et al.   HEPATOLOGY

The existence of multipotent stem cells with epithelial–mesenchymal transition features in the human liver bud

(2010) Juan Su et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Intrahepatic Bile Ducts Develop According to a New Mode of Tubulogenesis Regulated by the Transcription Factor SOX9

(2009) Aline Antoniou et al.   GASTROENTEROLOGY

Integrated approach for the identification of human hepatocyte nuclear factor 4α target genes using protein binding microarrays

(2009) Eugene Bolotin et al.   HEPATOLOGY

Hepatocytes do not undergo epithelial-mesenchymal transition in liver fibrosis in mice

(2009) Kojiro Taura et al.   HEPATOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Pancreatic transcription factors and their role in the birth, life and survival of the pancreatic β cell

(2008) Andreia S. Bernardo et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY