The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

PRISM offers a comprehensive genomic approach to transcription factor function prediction

(2013) A. M. Wenger et al.   GENOME RESEARCH

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Neurog2 Simultaneously Activates and Represses Alternative Gene Expression Programs in the Developing Neocortex

(2012) Christopher Kovach et al.   CEREBRAL CORTEX

Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex

(2012) K. Y. Kwan et al.   DEVELOPMENT

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

A network of genetic repression and derepression specifies projection fates in the developing neocortex

(2012) K. Srinivasan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Developmental Enhancers Conserved between Deuterostomes and Protostomes

(2012) Shoa L. Clarke et al.   PLoS Genetics

Evolution of Cerebral Cortical Development

(2011) Zoltán Molnár   BRAIN BEHAVIOR AND EVOLUTION

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

Tbr1 and Fezf2 Regulate Alternate Corticofugal Neuronal Identities during Neocortical Development

(2011) W. L. McKenna et al.   JOURNAL OF NEUROSCIENCE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

(2011) Kensuke Tashiro et al.   PLoS One

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing

(2011) A. E. Ayoub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract

(2011) W. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De Novo Genesis of Enhancers in Vertebrates

(2011) Michael P. Eichenlaub et al.   PLOS BIOLOGY

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

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

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

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

The mouse Gene Expression Database (GXD): 2011 update

(2010) J. H. Finger et al.   NUCLEIC ACIDS RESEARCH

Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex

(2010) F. Bedogni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systematic approach to identify functional motifs within vertebrate developmental enhancers

(2009) Qiang Li et al.   DEVELOPMENTAL BIOLOGY

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

(2009) A. A. Sharov et al.   DNA RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

(2009) Linda Z. Holland   NATURE REVIEWS NEUROSCIENCE

Multiple non-cell-autonomous defects underlie neocortical callosal dysgenesis in Nfib-deficient mice

(2009) Michael Piper et al.   Neural Development

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

(2009) Yonit Halperin et al.   NUCLEIC ACIDS RESEARCH

Discovery of Regulatory Elements is Improved by a Discriminatory Approach

(2009) Eivind Valen et al.   PLoS Computational Biology

cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation

(2008) J. Persampieri et al.   BIOINFORMATICS

NestedMICA as an ab initio protein motif discovery tool

(2008) Mutlu Doğruel et al.   BMC BIOINFORMATICS

MN1 affects expression of genes involved in hematopoiesis and can enhance as well as inhibit RAR/RXR-induced gene expression

(2008) Magda A. Meester-Smoor et al.   CARCINOGENESIS

Bhlhb5 Regulates the Postmitotic Acquisition of Area Identities in Layers II-V of the Developing Neocortex

(2008) Pushkar S. Joshi et al.   NEURON

Possible involvement of SINEs in mammalian-specific brain formation

(2008) T. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY