Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition

Identification of Subtypes of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data

(2020) SriGanesh Jammula et al.   GASTROENTEROLOGY

TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions

(2020) Clémentine Leporcq et al.   NUCLEIC ACIDS RESEARCH

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

High-fat Diet Accelerates Carcinogenesis in a Mouse Model of Barrett’s Esophagus via IL8 and Alterations to the Gut Microbiome

(2019) Natasha Stephens Münch et al.   GASTROENTEROLOGY

Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state

(2019) Connor Rogerson et al.   GENOME RESEARCH

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

Barrett oesophagus

(2019) Yonne Peters et al.   Nature Reviews Disease Primers

Progress in cancer survival, mortality, and incidence in seven high-income countries 1995–2014 (ICBP SURVMARK-2): a population-based study

(2019) Melina Arnold et al.   LANCET ONCOLOGY

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Low Prevalence of Suspected Barrett’s Esophagus in Gastroesophageal Reflux Disease Without Alarm Symptoms

(2018) Emery C. Lin et al.   Clinical Gastroenterology and Hepatology

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

Identification of Prognostic Phenotypes of Esophageal Adenocarcinoma in 2 Independent Cohorts

(2018) Tarek Sawas et al.   GASTROENTEROLOGY

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Single cell RNA-seq reveals profound transcriptional similarity between Barrett’s oesophagus and oesophageal submucosal glands

(2018) Richard Peter Owen et al.   Nature Communications

Integrated genomic characterization of oesophageal carcinoma

(2017)   NATURE

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

(2017) Ming Jiang et al.   NATURE

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

(2017) Young Seok Ju et al.   NATURE

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

(2017) M Ryan Corces et al.   NATURE METHODS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Principles of Reconstructing the Subclonal Architecture of Cancers

(2017) Stefan C. Dentro et al.   Cold Spring Harbor Perspectives in Medicine

Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma

(2017) Edward Britton et al.   PLoS Genetics

Oesophageal cancer

(2017) Elizabeth C. Smyth et al.   Nature Reviews Disease Primers

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Characterization of oncocytes in deep esophageal glands

(2015) G. Gonzalez et al.   DISEASES OF THE ESOPHAGUS

Ductal metaplasia in oesophageal submucosal glands is associated with inflammation and oesophageal adenocarcinoma

(2015) Katherine S Garman et al.   HISTOPATHOLOGY

Sequential cancer mutations in cultured human intestinal stem cells

(2015) Jarno Drost et al.   NATURE

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

(2015) Caryn S Ross-Innes et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Barrett oesophagus: lessons on its origins from the lesion itself

(2014) Stuart A. C. McDonald et al.   Nature Reviews Gastroenterology & Hepatology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The relevance of the Siewert classification in the era of multimodal therapy for adenocarcinoma of the gastro-oesophageal junction

(2013) Nathan J. Curtis et al.   JOURNAL OF SURGICAL ONCOLOGY

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

(2012) Michael Quante et al.   CANCER CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The intestinal epithelium tuft cells: specification and function

(2012) François Gerbe et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A discrete population of squamocolumnar junction cells implicated in the pathogenesis of cervical cancer

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

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

(2011) Xia Wang et al.   CELL

The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo

(2011) Kristen L. Meerbrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Human Barrett's Adenocarcinoma of the Esophagus, Associated Myofibroblasts, and Endothelium Can Arise from Bone Marrow-Derived Cells After Allogeneic Stem Cell Transplant

(2010) Lloyd Hutchinson et al.   STEM CELLS AND DEVELOPMENT

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Individual crypt genetic heterogeneity and the origin of metaplastic glandular epithelium in human Barrett's oesophagus

(2008) S J Leedham et al.   GUT

HCO3−Secretion by Murine Nasal Submucosal Gland Serous Acinar Cells during Ca2+-stimulated Fluid Secretion

(2008) Robert J. Lee et al.   JOURNAL OF GENERAL PHYSIOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY