Cis-regulatory landscapes of four cell types of the retina

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Lxr regulates lipid metabolic and visual perception pathways during zebrafish development

(2016) Caroline Lucia Pinto et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors

(2016) Jung-Woong Kim et al.   Cell Reports

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

(2015) Matthew S Wilken et al.   Epigenetics & Chromatin

Tfap2a and 2b act downstream of Ptf1a to promote amacrine cell differentiation during retinogenesis

(2015) Kangxin Jin et al.   Molecular Brain

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Intrinsically different retinal progenitor cells produce specific types of progeny

(2014) Connie Cepko   NATURE REVIEWS NEUROSCIENCE

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene Therapy for Blindness

(2013) José-Alain Sahel et al.   Annual Review of Neuroscience

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

NFIA Controls Telencephalic Progenitor Cell Differentiation through Repression of the Notch Effector Hes1

(2013) M. Piper et al.   JOURNAL OF NEUROSCIENCE

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

A Comprehensive Review of Retinal Gene Therapy

(2013) Shannon E Boye et al.   MOLECULAR THERAPY

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Designing an Enhancer Landscape

(2012) Jian Xu et al.   CELL

Transcriptional Activity of Neural Retina Leucine Zipper (Nrl) Is Regulated by c-Jun N-Terminal Kinase and Tip60 during Retina Development

(2012) J.-W. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Transcriptional code and disease map for adult retinal cell types

(2012) Sandra Siegert et al.   NATURE NEUROSCIENCE

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

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

(2011) Jason Ernst et al.   NATURE

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

Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina

(2010) Anand Swaroop et al.   NATURE REVIEWS NEUROSCIENCE

Genetic Reactivation of Cone Photoreceptors Restores Visual Responses in Retinitis Pigmentosa

(2010) V. Busskamp et al.   SCIENCE

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

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

(2009) Nathaniel D. Heintzman et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Genetic address book for retinal cell types

(2009) Sandra Siegert et al.   NATURE NEUROSCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Clinical gene therapy using recombinant adeno-associated virus vectors

(2008) C Mueller et al.   GENE THERAPY

Subretinal Delivery of Recombinant AAV Serotype 8 Vector in Dogs Results in Gene Transfer to Neurons in the Brain

(2008) Knut Stieger et al.   MOLECULAR THERAPY