Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers

Spectral identification of topological domains

(2016) Jie Chen et al.   BIOINFORMATICS

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Midbrain-like Organoids from Human Pluripotent Stem Cells Contain Functional Dopaminergic and Neuromelanin-Producing Neurons

(2016) Junghyun Jo et al.   Cell Stem Cell

Organoids: Modeling Development and the Stem Cell Niche in a Dish

(2016) Kai Kretzschmar et al.   DEVELOPMENTAL CELL

Three-Dimensional Cell Culture: A Breakthrough in Vivo

(2015) Delphine Antoni et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional organization of the human 4D Nucleome

(2015) Haiming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

(2015) Haiming Chen et al.   Nucleus

Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

(2015) Haiming Chen et al.   Nucleus

The need for complex 3D culture models to unravel novel pathways and identify accurate biomarkers in breast cancer

(2014) Britta Weigelt et al.   ADVANCED DRUG DELIVERY REVIEWS

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

Expression of Human Skin-Specific Genes Defined by Transcriptomics and Antibody-Based Profiling

(2014) Per-Henrik D. Edqvist et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

A three-dimensional human neural cell culture model of Alzheimer’s disease

(2014) Se Hoon Choi et al.   NATURE

Next-Generation Regenerative Medicine: Organogenesis from Stem Cells in 3D Culture

(2013) Yoshiki Sasai   Cell Stem Cell

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY