3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

Chromatin features constrain structural variation across evolutionary timescales

(2019) Geoff Fudenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development

(2019) Lei Shi et al.   National Science Review

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

(2019) Jelena Petrovic et al.   MOLECULAR CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Chromatin Decondensation by FOXP2 Promotes Human Neuron Maturation and Expression of Neurodevelopmental Disease Genes

(2019) Stephanie L. Hickey et al.   Cell Reports

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

(2019) Maria C Marchetto et al.   eLife

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

(2019) Michael Song et al.   NATURE GENETICS

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

(2019) Damon Polioudakis et al.   NEURON

Human evolved regulatory elements modulate genes involved in cortical expansion and neurodevelopmental disease susceptibility

(2019) Hyejung Won et al.   Nature Communications

The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse

(2019) Lucas J.T. Kaaij et al.   CELL

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

(2019) Yaoxi He et al.   Nature Communications

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

hPSC Modeling Reveals that Fate Selection of Cortical Deep Projection Neurons Occurs in the Subplate

(2018) M. Zeeshan Ozair et al.   Cell Stem Cell

Understanding axon guidance: are we nearly there yet?

(2018) Esther T. Stoeckli   DEVELOPMENT

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

(2018) Nathan H. Lazar et al.   GENOME RESEARCH

Human-specific features of spatial gene expression and regulation in eight brain regions

(2018) Chuan Xu et al.   GENOME RESEARCH

Canonical TGF-β Signaling Negatively Regulates Neuronal Morphogenesis through TGIF/Smad Complex-Mediated CRMP2 Suppression

(2018) Hideyuki Nakashima et al.   JOURNAL OF NEUROSCIENCE

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

Fast-Evolving Human-Specific Neural Enhancers Are Associated with Aging-Related Diseases

(2018) Han Chen et al.   Cell Systems

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

A simplified protocol for differentiation of electrophysiologically mature neuronal networks from human induced pluripotent stem cells

(2017) N Gunhanlar et al.   MOLECULAR PSYCHIATRY

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

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

The evolution and population diversity of human-specific segmental duplications

(2017) Megan Y. Dennis et al.   Nature Ecology & Evolution

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

Neocortex expansion in development and evolution — from cell biology to single genes

(2016) Michaela Wilsch-Bräuninger et al.   CURRENT OPINION IN NEUROBIOLOGY

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Comprehensive identification and analysis of human accelerated regulatory DNA

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

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Development, evolution and pathology of neocortical subplate neurons

(2015) Anna Hoerder-Suabedissen et al.   NATURE REVIEWS NEUROSCIENCE

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

(2015) Axel Cournac et al.   NUCLEIC ACIDS RESEARCH

MIR retrotransposon sequences provide insulators to the human genome

(2015) Jianrong Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons

(2014) Ying Zhu et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Nuclear factor one transcription factors: Divergent functions in developmental versus adult stem cell populations

(2014) Lachlan Harris et al.   DEVELOPMENTAL DYNAMICS

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing

(2014) Dirk Heckl et al.   NATURE BIOTECHNOLOGY

Neuronal Ig/Caspr Recognition Promotes the Formation of Axoaxonic Synapses in Mouse Spinal Cord

(2014) Soha Ashrafi et al.   NEURON

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

EphA7 signaling guides cortical dendritic development and spine maturation

(2014) Meredith A. Clifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Neelroop N. Parikshak et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

The significance of the subplate for evolution and developmental plasticity of the human brain

(2013) Miloš Judaš et al.   Frontiers in Human Neuroscience

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

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

(2011) Cory Y. McLean et al.   NATURE

Social responsiveness scale-aided analysis of the clinical impact of copy number variations in autism

(2011) Emma van Daalen et al.   NEUROGENETICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Deficiency of neural recognition molecule NB-2 affects the development of glutamatergic auditory pathways from the ventral cochlear nucleus to the superior olivary complex in mouse

(2009) Manabu Toyoshima et al.   DEVELOPMENTAL BIOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A genome-wide screen for noncoding elements important in primate evolution

(2008) Eliot C Bush et al.   BMC EVOLUTIONARY BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY