LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA

(2019) Unmesh Jadhav et al.   MOLECULAR CELL

Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell

(2019) Arshad Ayyaz et al.   NATURE

Tracing the origin of adult intestinal stem cells

(2019) Jordi Guiu et al.   NATURE

LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors

(2019) Shaun Egolf et al.   Cell Reports

Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation

(2019) Jesse R. Raab et al.   DEVELOPMENT

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

(2019) Johan H. van Es et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Shiro Yui et al.   Cell Stem Cell

Enhancer Activation by Pharmacologic Displacement of LSD1 from GFI1 Induces Differentiation in Acute Myeloid Leukemia

(2018) Alba Maiques-Diaz et al.   Cell Reports

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

(2018) Ysbrand M. Nusse et al.   NATURE

Subepithelial telocytes are an important source of Wnts that supports intestinal crypts

(2018) Michal Shoshkes-Carmel et al.   NATURE

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition

(2018) Masayuki Fujii et al.   Cell Stem Cell

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

A chemical biology toolbox to study protein methyltransferases and epigenetic signaling

(2018) Sebastian Scheer et al.   Nature Communications

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells

(2017) Juri Kazakevych et al.   NUCLEIC ACIDS RESEARCH

PRC2 preserves intestinal progenitors and restricts secretory lineage commitment

(2016) Fulvio Chiacchiera et al.   EMBO JOURNAL

Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells

(2016) Martijn A.J. Koppens et al.   GASTROENTEROLOGY

Nuclear GSK3β promotes tumorigenesis by phosphorylating KDM1A and inducing its deubiquitylation by USP22

(2016) Aidong Zhou et al.   NATURE CELL BIOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A DNA Hypomethylation Signature Predicts Antitumor Activity of LSD1 Inhibitors in SCLC

(2015) Helai P. Mohammad et al.   CANCER CELL

Yap-dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

(2015) Alex Gregorieff et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

YAP/TAZ Incorporation in the β-Catenin Destruction Complex Orchestrates the Wnt Response

(2014) Luca Azzolin et al.   CELL

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

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

(2013) Y. Liao et al.   BIOINFORMATICS

Transplantation of Expanded Fetal Intestinal Progenitors Contributes to Colon Regeneration after Injury

(2013) Robert P. Fordham et al.   Cell Stem Cell

Intestinal label-retaining cells are secretory precursors expressing Lgr5

(2013) Simon J. A. Buczacki et al.   NATURE

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

(2013) Xiaolei Yin et al.   NATURE METHODS

Identification of Lgr5-Independent Spheroid-Generating Progenitors of the Mouse Fetal Intestinal Epithelium

(2013) Roxana C. Mustata et al.   Cell Reports

Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation

(2013) Marc A Kerenyi et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

(2012) Javier Muñoz et al.   EMBO JOURNAL

Redundant Sources of Wnt Regulate Intestinal Stem Cells and Promote Formation of Paneth Cells

(2012) Henner F. Farin et al.   GASTROENTEROLOGY

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

(2012) Johan H. van Es et al.   NATURE CELL BIOLOGY

Functional intestinal stem cells after Paneth cell ablation induced by the loss of transcription factor Math1 (Atoh1)

(2012) A. Durand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intact function of Lgr5 receptor-expressing intestinal stem cells in the absence of Paneth cells

(2012) T.-H. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sortase A as a tool for high-yield histatin cyclization

(2011) Jan G. M. Bolscher et al.   FASEB JOURNAL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

DNA Demethylase Activity Maintains Intestinal Cells in an Undifferentiated State Following Loss of APC

(2010) Kunal Rai et al.   CELL

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

(2010) Toshiro Sato et al.   NATURE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

A rapid micro chromatin immunoprecipitation assay (ChIP)

(2008) John Arne Dahl et al.   Nature Protocols

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY