Molecular logic of cellular diversification in the mouse cerebral cortex

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex

(2019) L. Telley et al.   SCIENCE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

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

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture

(2019) Alfredo Llorca et al.   eLife

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

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

A Translational Repression Complex in Developing Mammalian Neural Stem Cells that Regulates Neuronal Specification

(2018) Siraj K. Zahr et al.   NEURON

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing

(2017) Sarah Frazer et al.   Nature Communications

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

(2017) Scott A. Yuzwa et al.   Cell Reports

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

DMRTA2 (DMRT5) is mutated in a novel cortical brain malformation

(2016) J.E. Urquhart et al.   CLINICAL GENETICS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Generating Neuronal Diversity in the Mammalian Cerebral Cortex

(2015) Simona Lodato et al.   Annual Review of Cell and Developmental Biology

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

(2015) Philipp Angerer et al.   BIOINFORMATICS

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

DeCoN: Genome-wide Analysis of In Vivo Transcriptional Dynamics during Pyramidal Neuron Fate Selection in Neocortex

(2015) Bradley J. Molyneaux et al.   NEURON

Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function

(2015) Euiseok J. Kim et al.   NEURON

Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex

(2014) Peng Gao et al.   CELL

Neural progenitors, neurogenesis and the evolution of the neocortex

(2014) M. Florio et al.   DEVELOPMENT

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

(2014) Simona Lodato et al.   NATURE NEUROSCIENCE

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

(2014) Carol L. Thompson et al.   NEURON

Radial glia - from boring cables to stem cell stars

(2013) P. Malatesta et al.   DEVELOPMENT

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

Fezf2 Expression Identifies a Multipotent Progenitor for Neocortical Projection Neurons, Astrocytes, and Oligodendrocytes

(2013) Chao Guo et al.   NEURON

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Fate-Restricted Neural Progenitors in the Mammalian Cerebral Cortex

(2012) S. J. Franco et al.   SCIENCE

Excitatory Projection Neuron Subtypes Control the Distribution of Local Inhibitory Interneurons in the Cerebral Cortex

(2011) Simona Lodato et al.   NEURON

Cux1 and Cux2 Regulate Dendritic Branching, Spine Morphology, and Synapses of the Upper Layer Neurons of the Cortex

(2010) Beatriz Cubelos et al.   NEURON

Fast unfolding of communities in large networks

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