A fully defined 3D matrix for ex vivo expansion of human colonic organoids from biopsy tissue

Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids

(2019) Meghan M. Capeling et al.   Stem Cell Reports

Rectal Organoids Enable Personalized Treatment of Cystic Fibrosis

(2019) Gitte Berkers et al.   Cell Reports

Organoids — Preclinical Models of Human Disease

(2019) Mo Li et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Reconstruction of the Human Colon Epithelium In Vivo

(2018) Shinya Sugimoto et al.   Cell Stem Cell

A PDX/Organoid Biobank of Advanced Prostate Cancers Captures Genomic and Phenotypic Heterogeneity for Disease Modeling and Therapeutic Screening

(2018) Michael L. Beshiri et al.   CLINICAL CANCER RESEARCH

A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer

(2018) Atsushi Yamada et al.   Scientific Reports

Automated brightfield morphometry of 3D organoid populations by OrganoSeg

(2018) Michael A. Borten et al.   Scientific Reports

Growth of Epithelial Organoids in a Defined Hydrogel

(2018) Nicolas Broguiere et al.   ADVANCED MATERIALS

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Bioengineering strategies to accelerate stem cell therapeutics

(2018) Christopher M. Madl et al.   NATURE

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

(2018) Michal Shoshkes-Carmel et al.   NATURE

COX-2–PGE2 Signaling Impairs Intestinal Epithelial Regeneration and Associates with TNF Inhibitor Responsiveness in Ulcerative Colitis

(2018) Yuan Li et al.   EBioMedicine

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

(2018) Masayuki Fujii et al.   Cell Stem Cell

Copenhagen Prospective Personalized Oncology (CoPPO)—Clinical Utility of Using Molecular Profiling to Select Patients to Phase I Trials

(2018) Ida Viller Tuxen et al.   CLINICAL CANCER RESEARCH

Synthetic hydrogels for human intestinal organoid generation and colonic wound repair

(2017) Ricardo Cruz-Acuña et al.   NATURE CELL BIOLOGY

Synthesis and characterization of well-defined hydrogel matrices and their application to intestinal stem cell and organoid culture

(2017) Nikolce Gjorevski et al.   Nature Protocols

Disease Modeling in Stem Cell-Derived 3D Organoid Systems

(2017) Devanjali Dutta et al.   TRENDS IN MOLECULAR MEDICINE

Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium

(2016) Hiroyuki Miyoshi et al.   EMBO JOURNAL

Designer matrices for intestinal stem cell and organoid culture

(2016) Nikolce Gjorevski et al.   NATURE

A practical guide to hydrogels for cell culture

(2016) Steven R Caliari et al.   NATURE METHODS

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Cloning and variation of ground state intestinal stem cells

(2015) Xia Wang et al.   NATURE

Extracellular Matrix and Growth Factors Improve the Efficacy of Intramuscular Islet Transplantation

(2015) Haruyuki Tsuchiya et al.   PLoS One

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients

(2014) Seon-Kyu Kim et al.   Molecular Oncology

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Type I Collagen as an Extracellular Matrix for the In Vitro Growth of Human Small Intestinal Epithelium

(2014) Ziyad Jabaji et al.   PLoS One

3D niche microarrays for systems-level analyses of cell fate

(2014) A. Ranga et al.   Nature Communications

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5+ stem cell

(2012) Shiro Yui et al.   NATURE MEDICINE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium

(2011) Toshiro Sato et al.   GASTROENTEROLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Matrigel: A complex protein mixture required for optimal growth of cell culture

(2010) Chris S. Hughes et al.   PROTEOMICS

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

(2009) Toshiro Sato et al.   NATURE