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

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

(2019) Alex A. Pollen et al.   CELL

Species-specific maturation profiles of human, chimpanzee and bonobo neural cells

(2019) Maria C Marchetto et al.   eLife

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

(2019) Silvia Velasco et al.   NATURE

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Collagen VI in healthy and diseased nervous system

(2018) Ilaria Gregorio et al.   Disease Models & Mechanisms

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

(2018) Marta Florio et al.   eLife

Transcriptional fates of human-specific segmental duplications in brain

(2018) Max L. Dougherty et al.   GENOME RESEARCH

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

Detecting ancient positive selection in humans using extended lineage sorting

(2017) Stéphane Peyrégne et al.   GENOME RESEARCH

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques

(2017) Zhisong He et al.   NATURE NEUROSCIENCE

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

(2017) Steven A. Sloan et al.   NEURON

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Molecular and cellular reorganization of neural circuits in the human lineage

(2017) André M. M. Sousa et al.   SCIENCE

2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size

(2016) Tomoki Otani et al.   Cell Stem Cell

Natural Selection in the Great Apes

(2016) Alexander Cagan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive transcriptional map of primate brain development

(2016) Trygve E. Bakken et al.   NATURE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

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

(2016) Felipe Mora-Bermúdez et al.   eLife

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Comprehensive identification and analysis of human accelerated regulatory DNA

(2015) Rachel M. Gittelman et al.   GENOME RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

Targeted Gene Correction Minimally Impacts Whole-Genome Mutational Load in Human-Disease-Specific Induced Pluripotent Stem Cell Clones

(2014) Keiichiro Suzuki et al.   Cell Stem Cell

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Generation of cerebral organoids from human pluripotent stem cells

(2014) Madeline A Lancaster et al.   Nature Protocols

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation

(2014) Z. He et al.   RNA

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication

(2012) Megan Y. Dennis et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Human-Specific Transcriptional Networks in the Brain

(2012) Genevieve Konopka et al.   NEURON

An Efficient Nonviral Method to Generate Integration-Free Human-Induced Pluripotent Stem Cells from Cord Blood and Peripheral Blood Cells

(2012) Keisuke Okita et al.   STEM CELLS

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transcriptional neoteny in the human brain

(2009) M. Somel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA