Single-Cell RNA Sequencing Unifies Developmental Programs of Esophageal and Gastric Intestinal Metaplasia

Hallmarks of Cancer: New Dimensions

(2022) Douglas Hanahan   Cancer Discovery

Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals early structural variation and retrotransposon activity

(2022) A. C. Katz-Summercorn et al.   Nature Communications

Cells of the human intestinal tract mapped across space and time

(2021) Rasa Elmentaite et al.   NATURE

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

(2021) Karol Nowicki-Osuch et al.   SCIENCE

Clonal Transitions and Phenotypic Evolution in Barrett’s Esophagus

(2021) James A. Evans et al.   GASTROENTEROLOGY

Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer

(2021) Harshabad Singh et al.   GENES & DEVELOPMENT

Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer

(2021) Vikrant Kumar et al.   Cancer Discovery

Gastric Cancer Risk of Intestinal Metaplasia Subtypes: A Systematic Review and Meta-Analysis of Cohort Studies

(2021) Sijing Du et al.   Clinical and Translational Gastroenterology

Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment

(2020) Anuja Sathe et al.   CLINICAL CANCER RESEARCH

A panel of intestinal differentiation markers (CDX2, GPA33, and LI-cadherin) identifies gastric cancer patients with favourable prognosis

(2020) Nair Lopes et al.   Gastric Cancer

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth

(2020) Sarah Davidson et al.   Cell Reports

The Tumor Microenvironment: A Milieu Hindering and Obstructing Antitumor Immune Responses

(2020) Alireza Labani-Motlagh et al.   Frontiers in Immunology

Single Cell Transcriptional Analyses Identify Lineage-Specific Epithelial Responses to Inflammation and Metaplastic Development in the Gastric Corpus

(2020) Kevin A. Bockerstett et al.   GASTROENTEROLOGY

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

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

(2019) Xuran Wang et al.   Nature Communications

The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic

(2019) Alexander M. Frankell et al.   NATURE GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer

(2019) Peng Zhang et al.   Cell Reports

Barrett oesophagus

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

Single-cell transcriptional analyses of spasmolytic polypeptide-expressing metaplasia arising from acute drug injury and chronic inflammation in the stomach

(2019) Kevin A Bockerstett et al.   GUT

Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine

(2019) Yalong Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

(2018) Yang Liu et al.   CANCER CELL

Cardiac Metaplasia: Follow, Treat, or Ignore?

(2018) Stuart J. Spechler   DIGESTIVE DISEASES AND SCIENCES

Effects of Helicobacter pylori Treatment on Incidence of Gastric Cancer in Older Individuals

(2018) Wai K. Leung et al.   GASTROENTEROLOGY

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Helicobacter pylori Therapy for the Prevention of Metachronous Gastric Cancer

(2018) Il Ju Choi et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2018) Richard Peter Owen et al.   Nature Communications

Metaplasia in the Stomach—Precursor of Gastric Cancer?

(2017) Hiroto Kinoshita et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Genetic progression of Barrett’s oesophagus to oesophageal adenocarcinoma

(2016) Eleanor M Gregson et al.   BRITISH JOURNAL OF CANCER

Cardiac mucosa, Barrett's oesophagus and cancer of the gastro-oesophageal junction: what's in a name?

(2016) Stuart Jon Spechler   GUT

Incomplete type of intestinal metaplasia has the highest risk to progress to gastric cancer: results of the Spanish follow-up multicenter study

(2016) Carlos A. González et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

(2016) Maria Secrier et al.   NATURE GENETICS

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

ACG Clinical Guideline: Diagnosis and Management of Barrett’s Esophagus

(2015) Nicholas J Shaheen et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Diagnosis and Management of High Risk Group for Gastric Cancer

(2015) Hyuk Yoon et al.   Gut and Liver

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

(2015) et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The incidence of Barrett's oesophagus and oesophageal adenocarcinoma in the United Kingdom and the Netherlands is levelling off

(2014) G. M. C. Masclee et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Barrett oesophagus: lessons on its origins from the lesion itself

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

Barrett's Esophagus

(2014) Stuart J. Spechler et al.   NEW ENGLAND JOURNAL OF MEDICINE

Central Obesity in Asymptomatic Volunteers Is Associated With Increased Intrasphincteric Acid Reflux and Lengthening of the Cardiac Mucosa

(2013) Elaine V. Robertson et al.   GASTROENTEROLOGY

British Society of Gastroenterology guidelines on the diagnosis and management of Barrett's oesophagus

(2013) Rebecca C Fitzgerald et al.   GUT

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

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

(2012) Michael Quante et al.   CANCER CELL

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

(2011) Xia Wang et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

American Gastroenterological Association Medical Position Statement on the Management of Barrett's Esophagus

(2011)   GASTROENTEROLOGY

Risk of Malignant Progression in Barrett's Esophagus Patients: Results from a Large Population-Based Study

(2011) S. Bhat et al.   JNCI-Journal of the National Cancer Institute

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

Gastric Cancer Risk in Patients With Premalignant Gastric Lesions: A Nationwide Cohort Study in the Netherlands

(2008) Annemarie C. de Vries et al.   GASTROENTEROLOGY

Cardiac rather than intestinal-type background in endoscopic resection specimens of minute Barrett adenocarcinoma

(2008) Kaiyo Takubo et al.   HUMAN PATHOLOGY