Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

(2014) J. Gray Camp et al.   GENOME RESEARCH

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity

(2014) Tae-Hee Kim et al.   NATURE

Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex

(2014) Kartik Pattabiraman et al.   NEURON

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Temporal Regulation of Nuclear Factor One Occupancy by Calcineurin/NFAT Governs a Voltage-Sensitive Developmental Switch in Late Maturing Neurons

(2013) B. Ding et al.   JOURNAL OF NEUROSCIENCE

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

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

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

Homozygous SALL1 Mutation Causes a Novel Multiple Congenital Anomaly—Mental Retardation Syndrome

(2012) Julia Vodopiutz et al.   JOURNAL OF PEDIATRICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

(2011) A. E. West et al.   Cold Spring Harbor Perspectives in Biology

Differential Modulation of Sonic-Hedgehog-Induced Cerebellar Granule Cell Precursor Proliferation by the IGF Signaling Network

(2010) Carla Fernandez et al.   DEVELOPMENTAL NEUROSCIENCE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Gabapentin Receptor α2δ-1 Is a Neuronal Thrombospondin Receptor Responsible for Excitatory CNS Synaptogenesis

(2009) Çagla Eroglu et al.   CELL

BDNF-Mediated Cerebellar Granule Cell Development Is Impaired in Mice Null for CaMKK2 or CaMKIV

(2009) M. Kokubo et al.   JOURNAL OF NEUROSCIENCE

AUF1 and Hu proteins in the developing rat brain: Implication in the proliferation and differentiation of neural progenitors

(2009) Dolores Hambardzumyan et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Deletion of Atoh1 Disrupts Sonic Hedgehog Signaling in the Developing Cerebellum and Prevents Medulloblastoma

(2009) A. Flora et al.   SCIENCE

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Regulation of NMDA receptor subunit expression and its implications for LTD, LTP, and metaplasticity

(2008) Koji Yashiro et al.   NEUROPHARMACOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY