Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases

Cell stress in cortical organoids impairs molecular subtype specification

(2020) Aparna Bhaduri et al.   NATURE

Human CNS barrier-forming organoids with cerebrospinal fluid production

(2020) Laura Pellegrini et al.   SCIENCE

Single-cell transcriptomic analysis of mouse neocortical development

(2019) Lipin Loo et al.   Nature Communications

Cerebral organoids at the air–liquid interface generate diverse nerve tracts with functional output

(2019) Stefano L. Giandomenico et al.   NATURE NEUROSCIENCE

hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids

(2019) Yangfei Xiang et al.   Cell Stem Cell

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

(2019) Alex A. Pollen et al.   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

(2019) Silvia Velasco et al.   NATURE

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation

(2019) Damon Polioudakis et al.   NEURON

Model-based understanding of single-cell CRISPR screening

(2019) Bin Duan et al.   Nature Communications

Organoid single-cell genomic atlas uncovers human-specific features of brain development

(2019) Sabina Kanton et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis

(2018) Xiaoying Fan et al.   CELL RESEARCH

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Organoids required! A new path to understanding human brain development and disease

(2018) Paola Arlotta   NATURE METHODS

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Mouse Genome Database (MGD) 2019

(2018) Carol J Bult et al.   NUCLEIC ACIDS RESEARCH

Assembly of functionally integrated human forebrain spheroids

(2017) Fikri Birey et al.   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Fused cerebral organoids model interactions between brain regions

(2017) Joshua A Bagley et al.   NATURE METHODS

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

(2016) Xuyu Qian et al.   CELL

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

(2016) Felipe Mora-Bermúdez et al.   eLife

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

(2015) Anca M Paşca et al.   NATURE METHODS

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of cerebral organoids from human pluripotent stem cells

(2014) Madeline A Lancaster et al.   Nature Protocols

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

(2014) Simone Picelli et al.   Nature Protocols

A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

(2014) Carol L. Thompson et al.   NEURON

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex

(2013) T. Kadoshima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A Targeted NKX2.1 Human Embryonic Stem Cell Reporter Line Enables Identification of Human Basal Forebrain Derivatives

(2011) Adam L. Goulburn et al.   STEM CELLS

Self-Organized Formation of Polarized Cortical Tissues from ESCs and Its Active Manipulation by Extrinsic Signals

(2008) Mototsugu Eiraku et al.   Cell Stem Cell

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT