Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain

Neurodegenerative Disease Phenotypes in Carriers of MAPT p.A152T, A Risk Factor for Frontotemporal Dementia Spectrum Disorders and Alzheimer Disease

(2013) Suzee E. Lee et al.   ALZHEIMER DISEASE & ASSOCIATED DISORDERS

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2013) Jian Shu et al.   CELL

Gene Regulatory Networks Mediating Canonical Wnt Signal-Directed Control of Pluripotency and Differentiation in Embryo Stem Cells

(2013) Xiaoxiao Zhang et al.   STEM CELLS

Analysis of the DNA-Binding Profile and Function of TALE Homeoproteins Reveals Their Specialization and Specific Interactions with Hox Genes/Proteins

(2013) Dmitry Penkov et al.   Cell Reports

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors

(2012) E. Metzakopian et al.   DEVELOPMENT

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

(2012) K. A. Peterson et al.   GENES & DEVELOPMENT

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

Forkhead box protein p1 is a transcriptional repressor of immune signaling in the CNS: implications for transcriptional dysregulation in Huntington disease

(2012) Bin Tang et al.   HUMAN MOLECULAR GENETICS

LIM Kinase 1 (LIMK1) Interacts with Tropomyosin-related Kinase B (TrkB) and Mediates Brain-derived Neurotrophic Factor (BDNF)-induced Axonal Elongation

(2012) Qing Dong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Role for WNT/β-Catenin Signaling in the Neural Mechanisms of Behavior

(2012) Kimberly A. Maguschak et al.   Journal of Neuroimmune Pharmacology

Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity

(2012) Cecilia Ballaré et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation

(2012) Gerard L Brien et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

(2012) Susan M. Sunkin et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

(2011) Gang Wei et al.   IMMUNITY

Doublesex and mab-3-related transcription factor 5 promotes midbrain dopaminergic identity in pluripotent stem cells by enforcing a ventral-medial progenitor fate

(2011) N. Gennet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

The FoxA factors in organogenesis and differentiation

(2010) Klaus H Kaestner   CURRENT OPINION IN GENETICS & DEVELOPMENT

Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube

(2010) V. Ribes et al.   GENES & DEVELOPMENT

Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity

(2010) Yannis E. Mavromatakis et al.   MECHANISMS OF DEVELOPMENT

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Mechanisms and Molecules of Neuronal Wiring: A Primer

(2010) A. L. Kolodkin et al.   Cold Spring Harbor Perspectives in Biology

Slit2/Robo1 signaling in glioma migration and invasion

(2010) Yun Xu et al.   Neuroscience Bulletin

Sufu recruits GSK3β for efficient processing of Gli3

(2009) Yoshiaki Kise et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Analysis of Non-canonical Fibroblast Growth Factor Receptor 1 (FGFR1) Interaction Reveals Regulatory and Activating Domains of Neurofascin

(2009) Katja Kirschbaum et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network

(2009) Martine Uittenbogaard et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network

(2008) E. Dessaud et al.   DEVELOPMENT

Expression of the transcription factor GATA3 in the postnatal mouse central nervous system

(2008) Guang-Yu Zhao et al.   NEUROSCIENCE RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY