Reactivation of the Hedgehog pathway in esophageal progenitors turns on an embryonic-like program to initiate columnar metaplasia

GeneSwitches: Ordering gene-expression and functional events in single-cell experiments

(2020) Elaine Y Cao et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration

(2018) Shiro Yui et al.   Cell Stem Cell

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche

(2018) Ysbrand M. Nusse et al.   NATURE

Phenotypic Plasticity: Driver of Cancer Initiation, Progression, and Therapy Resistance

(2018) Piyush B. Gupta et al.   Cell Stem Cell

Diallyl Disulfide Suppresses the Inflammation and Apoptosis Resistance Induced by DCA Through ROS and the NF-κB Signaling Pathway in Human Barrett’s Epithelial Cells

(2017) Cheng Feng et al.   INFLAMMATION

Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte

(2017) Ziqing Liu et al.   NATURE

Transitional basal cells at the squamous–columnar junction generate Barrett’s oesophagus

(2017) Ming Jiang et al.   NATURE

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

From Reflux Esophagitis to Esophageal Adenocarcinoma

(2016) Rhonda F. Souza   DIGESTIVE DISEASES

Mid-Esophagus Columnar Metaplasia: What Is the Biopathogenic Pathway?

(2016) Inês Rolim et al.   INTERNATIONAL JOURNAL OF SURGICAL PATHOLOGY

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Molecular features of cellular reprogramming and development

(2016) Zachary D. Smith et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Adult cell plasticity in vivo: de-differentiation and transdifferentiation are back in style

(2016) Allyson J. Merrell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Genetic and Epigenetic Alterations in Barrett’s Esophagus and Esophageal Adenocarcinoma

(2015) Andrew M. Kaz et al.   GASTROENTEROLOGY CLINICS OF NORTH AMERICA

Dissection of keratin network formation, turnover and reorganization in living murine embryos

(2015) Nicole Schwarz et al.   Scientific Reports

Cox2 and β-Catenin/T-cell Factor Signaling Intestinalize Human Esophageal Keratinocytes When Cultured under Organotypic Conditions

(2015) Jianping Kong et al.   NEOPLASIA

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Hedgehog signaling regulates FOXA2 in esophageal embryogenesis and Barrett’s metaplasia

(2014) David H. Wang et al.   JOURNAL OF CLINICAL INVESTIGATION

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Global Changes in Gene Expression of Barrett's Esophagus Compared to Normal Squamous Esophagus and Gastric Cardia Tissues

(2014) Paula L. Hyland et al.   PLoS One

Cellular Heterogeneity in the Mouse Esophagus Implicates the Presence of a Nonquiescent Epithelial Stem Cell Population

(2014) Aaron D. DeWard et al.   Cell Reports

PAVIS: a tool for Peak Annotation and Visualization

(2013) Weichun Huang et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Sox9 drives columnar differentiation of esophageal squamous epithelium: a possible role in the pathogenesis of Barrett's esophagus

(2012) Nicholas J. Clemons et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Bile Acid and Inflammation Activate Gastric Cardia Stem Cells in a Mouse Model of Barrett-Like Metaplasia

(2012) Michael Quante et al.   CANCER CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Barrett's Esophagus: Is the Goblet Half Empty?

(2012) Stuart Jon Spechler   Clinical Gastroenterology and Hepatology

Hedgehog signalling stimulates precursor cell accumulation and impairs epithelial maturation in the murine oesophagus

(2012) Willemijn A van Dop et al.   GUT

Activation of Wnt signalling promotes development of dysplasia in Barrett's oesophagus

(2012) Lisa H Moyes et al.   JOURNAL OF PATHOLOGY

Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation

(2012) Khalil Kass Youssef et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evidence for a functional role of epigenetically regulated midcluster HOXB genes in the development of Barrett esophagus

(2012) M. di Pietro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Single Progenitor Population Switches Behavior to Maintain and Repair Esophageal Epithelium

(2012) D. P. Doupe et al.   SCIENCE

Residual Embryonic Cells as Precursors of a Barrett's-like Metaplasia

(2011) Xia Wang et al.   CELL

DNA methylation profiling in Barrett’s esophagus and esophageal adenocarcinoma reveals unique methylation signatures and molecular subclasses

(2011) Andrew M. Kaz et al.   Epigenetics

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif

(2011) Masato Morikawa et al.   NUCLEIC ACIDS RESEARCH

Ectopic Cdx2 Expression in Murine Esophagus Models an Intermediate Stage in the Emergence of Barrett's Esophagus

(2011) Jianping Kong et al.   PLoS One

Barx1-Mediated Inhibition of Wnt Signaling in the Mouse Thoracic Foregut Controls Tracheo-Esophageal Septation and Epithelial Differentiation

(2011) Janghee Woo et al.   PLoS One

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

BMP signaling in the development of the mouse esophagus and forestomach

(2010) P. Rodriguez et al.   DEVELOPMENT

Aberrant Epithelial–Mesenchymal Hedgehog Signaling Characterizes Barrett's Metaplasia

(2010) David H. Wang et al.   GASTROENTEROLOGY

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

Primary contribution to zebrafish heart regeneration by gata4 + cardiomyocytes

(2010) Kazu Kikuchi et al.   NATURE

Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation

(2010) Chris Jopling et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cells keep a memory of their tissue origin during axolotl limb regeneration

(2009) Martin Kragl et al.   NATURE

Notch controls embryonic Schwann cell differentiation, postnatal myelination and adult plasticity

(2009) Ashwin Woodhoo et al.   NATURE NEUROSCIENCE

Novel signals controlling embryonic Schwann cell development, myelination and dedifferentiation

(2008) Rhona Mirsky et al.   JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM

Cdx1 and c-Myc Foster the Initiation of Transdifferentiation of the Normal Esophageal Squamous Epithelium toward Barrett's Esophagus

(2008) Douglas B. Stairs et al.   PLoS One