Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

BMP restricts stemness of intestinal Lgr5+ stem cells by directly suppressing their signature genes

(2017) Zhen Qi et al.   Nature Communications

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann et al.   BIOINFORMATICS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

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

(2016) Dominic Grün et al.   Cell Stem Cell

Stomach development, stem cells and disease

(2016) Tae-Hee Kim et al.   DEVELOPMENT

Annexin A1 is involved in resistance to 5-FU in colon cancer cells

(2016) Hisashi Onozawa et al.   ONCOLOGY REPORTS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

In Vitro Expansion of Human Gastric Epithelial Stem Cells and Their Responses to Bacterial Infection

(2015) Sina Bartfeld et al.   GASTROENTEROLOGY

The use of murine-derived fundic organoids in studies of gastric physiology

(2015) Michael A. Schumacher et al.   JOURNAL OF PHYSIOLOGY-LONDON

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Generation of stomach tissue from mouse embryonic stem cells

(2015) Taka-aki K. Noguchi et al.   NATURE CELL BIOLOGY

Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments

(2015) Margaret A. Goodell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

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

(2014) S. Anders et al.   BIOINFORMATICS

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Modelling human development and disease in pluripotent stem-cell-derived gastric organoids

(2014) Kyle W. McCracken et al.   NATURE

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

(2014) Manon D. Schulz et al.   NATURE

Identification of multipotent mammary stem cells by protein C receptor expression

(2014) Daisong Wang et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

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

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

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration

(2013) Nick Barker   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules

(2013) Nicola A. Kearns et al.   Stem Cell Research

Patterning and shaping the endoderm in vivo and in culture

(2012) Marine RC Kraus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Peyer's Patch M Cells Derived from Lgr5+ Stem Cells Require SpiB and Are Induced by RankL in Cultured "Miniguts"

(2012) W. de Lau et al.   MOLECULAR AND CELLULAR BIOLOGY

Reciprocal interactions of the intestinal microbiota and immune system

(2012) Craig L. Maynard et al.   NATURE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Molecular aspects of esophageal development

(2011) Mark Rishniw et al.   Annals of the New York Academy of Sciences

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Intestinal development and differentiation

(2011) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Hedgehog signalling in gut development, physiology and cancer

(2011) Juanita L. Merchant   JOURNAL OF PHYSIOLOGY-LONDON

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

TFF2 mRNA Transcript Expression Marks a Gland Progenitor Cell of the Gastric Oxyntic Mucosa

(2010) Michael Quante et al.   GASTROENTEROLOGY

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Vertebrate Endoderm Development and Organ Formation

(2009) Aaron M. Zorn et al.   Annual Review of Cell and Developmental Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

New Insights into the Role of Hedgehog Signaling in Gastrointestinal Development and Cancer

(2009) Byeong–Moo Kim et al.   GASTROENTEROLOGY

Transcriptional dynamics of endodermal organ formation

(2008) Richard I. Sherwood et al.   DEVELOPMENTAL DYNAMICS