Identification ofin vivoDNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development

What are super-enhancers?

(2015) Sebastian Pott et al.   NATURE GENETICS

The cellular and molecular mechanisms of vertebrate lens development

(2014) A. Cvekl et al.   DEVELOPMENT

Pax genes: regulators of lineage specification and progenitor cell maintenance

(2014) J. A. Blake et al.   DEVELOPMENT

Hmga2 regulates self-renewal of retinal progenitors

(2014) S. Parameswaran et al.   DEVELOPMENT

Pax6-dependent, but β-catenin-independent, function of Bcl9 proteins in mouse lens development

(2014) Claudio Cantù et al.   GENES & DEVELOPMENT

Pax6 Regulates the Expression of Dkk3 in Murine and Human Cell Lines, and Altered Responses to Wnt Signaling Are Shown in FlpIn-3T3 Cells Stably Expressing Either the Pax6 or the Pax6(5a) Isoform

(2014) Siri Forsdahl et al.   PLoS One

The transcription factor Fezf2 directs the differentiation of neural stem cells in the subventricular zone toward a cortical phenotype

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

PAX6 Regulates Melanogenesis in the Retinal Pigmented Epithelium through Feed-Forward Regulatory Interactions with MITF

(2014) Shaul Raviv et al.   PLoS Genetics

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

(2013) Warren A. Whyte et al.   CELL

Functional dissection of the paired domain of Pax6 reveals molecular mechanisms of coordinating neurogenesis and proliferation

(2013) T. Walcher et al.   DEVELOPMENT

Dmrta1 regulates proneural gene expression downstream of Pax6 in the mammalian telencephalon

(2013) Takako Kikkawa et al.   GENES TO CELLS

FoxP2 Regulates Neurogenesis during Embryonic Cortical Development

(2013) D. Tsui et al.   JOURNAL OF NEUROSCIENCE

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Pax6 Exerts Regional Control of Cortical Progenitor Proliferation via Direct Repression of Cdk6 and Hypophosphorylation of pRb

(2013) Da Mi et al.   NEURON

Histone posttranslational modifications and cell fate determination: lens induction requires the lysine acetyltransferases CBP and p300

(2013) Louise Wolf et al.   NUCLEIC ACIDS RESEARCH

Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain

(2013) Qing Xie et al.   PLoS One

Pax6 Regulates Gene Expression in the Vertebrate Lens through miR-204

(2013) Ohad Shaham et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs

(2012) Vahab D. Soleimani et al.   DEVELOPMENTAL CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The Wasp System: An open source environment for managing and analyzing genomic data

(2012) Andrew S. McLellan et al.   GENOMICS

A balance of FGF and BMP signals regulates cell cycle exit and Equarin expression in lens cells

(2012) Miguel Jarrin et al.   MOLECULAR BIOLOGY OF THE CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

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

Molecular Control of Neurogenesis: A View from the Mammalian Cerebral Cortex

(2012) B. Martynoga et al.   Cold Spring Harbor Perspectives in Biology

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

The mechanism of lens placode formation: A case of matrix-mediated morphogenesis

(2011) Jie Huang et al.   DEVELOPMENTAL BIOLOGY

The role of Pax6 in forebrain development

(2011) Petrina A. Georgala et al.   Developmental Neurobiology

Restrictions in time and space - new insights into generation of specific neuronal subtypes in the adult mammalian brain

(2011) Franziska Weinandy et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets

(2011) D. S. Castro et al.   GENES & DEVELOPMENT

Discovery and assessment of conserved Pax6 target genes and enhancers

(2011) Pedro Coutinho et al.   GENOME RESEARCH

The Orchestration of Mammalian Tissue Morphogenesis through a Series of Coherent Feed-forward Loops

(2011) Qing Xie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pax6 Is Required at the Telencephalic Pallial-Subpallial Boundary for the Generation of Neuronal Diversity in the Postnatal Limbic System

(2011) L. A. Cocas et al.   JOURNAL OF NEUROSCIENCE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulatory mechanisms in vertebrate eye development and disease

(2010) A Cvekl et al.   HEREDITY

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Pax6 is essential for lens fiber cell differentiation

(2009) O. Shaham et al.   DEVELOPMENT

Pax6 dosage requirements in iris and ciliary body differentiation

(2009) Noa Davis et al.   DEVELOPMENTAL BIOLOGY

Secreted frizzled-related protein disrupts PCP in eye lens fiber cells that have polarised primary cilia

(2009) Yuki Sugiyama et al.   DEVELOPMENTAL BIOLOGY

Pitx3 controls multiple aspects of lens development

(2009) Olga Medina-Martinez et al.   DEVELOPMENTAL DYNAMICS

Transcription factor GATA-3 is essential for lens development

(2009) Atsuko Maeda et al.   DEVELOPMENTAL DYNAMICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis

(2009) Stephen N. Sansom et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Er81 is a downstream target of Pax6 in cortical progenitors

(2008) Tran Tuoc et al.   BMC DEVELOPMENTAL BIOLOGY

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Notch signaling regulates growth and differentiation in the mammalian lens

(2008) Sheldon Rowan et al.   DEVELOPMENTAL BIOLOGY

Fibroblast growth factor receptor signaling is essential for lens fiber cell differentiation

(2008) Haotian Zhao et al.   DEVELOPMENTAL BIOLOGY

Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells

(2008) G. W. Yeo et al.   HUMAN MOLECULAR GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY