Single-cell delineation of lineage and genetic identity in the mouse brain

Molecular logic of cellular diversification in the mouse cerebral cortex

(2021) Daniela J. Di Bella et al.   NATURE

Comparative cellular analysis of motor cortex in human, marmoset and mouse

(2021) Trygve E. Bakken et al.   NATURE

Individual human cortical progenitors can produce excitatory and inhibitory neurons

(2021) Ryan N. Delgado et al.   NATURE

CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution

(2020) Wenjun Kong et al.   Nature Protocols

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

(2020) Sarah Bowling et al.   CELL

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

(2020) Omer Ali Bayraktar et al.   NATURE NEUROSCIENCE

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Temporal plasticity of apical progenitors in the developing mouse neocortex

(2019) Polina Oberst et al.   NATURE

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Cortical astrocytes develop in a plastic manner at both clonal and cellular levels

(2019) Solène Clavreul et al.   Nature Communications

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Early emergence of cortical interneuron diversity in the mouse embryo

(2018) Da Mi et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Progenitor Hyperpolarization Regulates the Sequential Generation of Neuronal Subtypes in the Developing Neocortex

(2018) Ilaria Vitali et al.   CELL

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   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

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Development and Functional Diversification of Cortical Interneurons

(2018) Lynette Lim et al.   NEURON

Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome

(2017) Gilad D. Evrony et al.   GENOME RESEARCH

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis

(2017) Taejeong Bae et al.   SCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

The Contribution of Mosaic Variants to Autism Spectrum Disorder

(2016) Donald Freed et al.   PLoS Genetics

Embryonic Origin of Postnatal Neural Stem Cells

(2015) Luis C. Fuentealba et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The neocortical circuit: themes and variations

(2015) Kenneth D Harris et al.   NATURE NEUROSCIENCE

Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries

(2015) Christian Mayer et al.   NEURON

Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons

(2015) Corey C. Harwell et al.   NEURON

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Modeling genome coverage in single-cell sequencing

(2014) Timothy Daley et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Somatic Mutation, Genomic Variation, and Neurological Disease

(2013) A. Poduri et al.   SCIENCE

Local generation of glia is a major astrocyte source in postnatal cortex

(2012) Woo-Ping Ge et al.   NATURE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

A spatial bias for the origins of interneuron subgroups within the medial ganglionic eminence

(2007) Carl P. Wonders et al.   DEVELOPMENTAL BIOLOGY