Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

(2021) Andreas Tjärnberg et al.   PLoS Computational Biology

Cell stress in cortical organoids impairs molecular subtype specification

(2020) Aparna Bhaduri et al.   NATURE

Chromatin accessibility dynamics in a model of human forebrain development

(2020) Alexandro E. Trevino et al.   SCIENCE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

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

Cell-type-specific 3D epigenomes in the developing human cortex

(2020) Michael Song et al.   NATURE

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

(2020) Mette Bentsen et al.   Nature Communications

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

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

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

(2019) Damon Polioudakis et al.   NEURON

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Nuclear Respiratory Factor 1 (NRF-1) Controls the Activity Dependent Transcription of the GABA-A Receptor Beta 1 Subunit Gene in Neurons

(2018) Zhuting Li et al.   Frontiers in Molecular Neuroscience

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

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

(2017) Alicia N Schep et al.   NATURE METHODS

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

(2017) Steven A. Sloan et al.   NEURON

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development

(2016) Tomasz J. Nowakowski et al.   NEURON

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

(2013) A. Jeremy Willsey et al.   CELL

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

(2013) Neelroop N. Parikshak et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Molecular logic of neocortical projection neuron specification, development and diversity

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

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oscillatory Control of Factors Determining Multipotency and Fate in Mouse Neural Progenitors

(2013) I. Imayoshi et al.   SCIENCE

SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs)

(2013) Brett S Abrahams et al.   Molecular Autism

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

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

Astrocytes as a Source for Extracellular Matrix Molecules and Cytokines

(2012) Stefan Wiese et al.   Frontiers in Pharmacology

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Annual Research Review: Development of the cerebral cortex: implications for neurodevelopmental disorders

(2010) John L.R. Rubenstein   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

Neurogenic radial glia in the outer subventricular zone of human neocortex

(2010) David V. Hansen et al.   NATURE

OSVZ progenitors of human and ferret neocortex are epithelial-like and expand by integrin signaling

(2010) Simone A Fietz et al.   NATURE NEUROSCIENCE

FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain

(2009) B. V. Jacquet et al.   DEVELOPMENT

Uniquely Hominid Features of Adult Human Astrocytes

(2009) N. A. Oberheim et al.   JOURNAL OF NEUROSCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY