Massively parallel cis -regulatory analysis in the mammalian central nervous system

Genetic Changes Shaping the Human Brain

(2015) Byoung-Il Bae et al.   DEVELOPMENTAL CELL

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Human Promoters Are Intrinsically Directional

(2015) Sascha H.C. Duttke et al.   MOLECULAR CELL

Roadmap for regulation

(2015) Casey E. Romanoski et al.   NATURE

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genomic Perspectives of Transcriptional Regulation in Forebrain Development

(2015) Alex S. Nord et al.   NEURON

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

(2015) Charles Blatti et al.   NUCLEIC ACIDS RESEARCH

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

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

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Mechanisms Underlying Nucleosome Positioning In Vivo

(2014) Amanda L. Hughes et al.   Annual Review of Biophysics

High-throughput functional testing of ENCODE segmentation predictions

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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

In search of the determinants of enhancer–promoter interaction specificity

(2014) Joris van Arensbergen et al.   TRENDS IN CELL BIOLOGY

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Transcriptional repressors: multifaceted regulators of gene expression

(2013) N. Reynolds et al.   DEVELOPMENT

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

(2013) Stephen S Gisselbrecht et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Analysis of Transduction Efficiency, Tropism and Axonal Transport of AAV Serotypes 1, 2, 5, 6, 8 and 9 in the Mouse Brain

(2013) Dominik F. Aschauer et al.   PLoS One

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

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The retina as a window to the brain—from eye research to CNS disorders

(2012) Anat London et al.   Nature Reviews Neurology

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

Universal Real-Time PCR for the Detection and Quantification of Adeno-Associated Virus Serotype 2-Derived Inverted Terminal Repeat Sequences

(2012) Christine Aurnhammer et al.   Human Gene Therapy Methods

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9

(2011) D Dalkara et al.   GENE THERAPY

Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper GeneNrl, Revealed byin VivoPromoter Analysis

(2011) Marie-Audrey I. Kautzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional Regulation of Neural Retina Leucine Zipper (Nrl), a Photoreceptor Cell Fate Determinant

(2011) Cynthia L. Montana et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cell Type-Specific Transcriptomics in the Brain

(2011) B. W. Okaty et al.   JOURNAL OF NEUROSCIENCE

Microarrays, megasynthesis

(2011) Monya Baker   NATURE METHODS

Therapeutic in vivo gene transfer for genetic disease using AAV: progress and challenges

(2011) Federico Mingozzi et al.   NATURE REVIEWS GENETICS

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains

(2011) Wenjie Shu et al.   NUCLEIC ACIDS RESEARCH

Sleep Loss Reduces the DNA-Binding of BMAL1, CLOCK, and NPAS2 to Specific Clock Genes in the Mouse Cerebral Cortex

(2011) Valérie Mongrain et al.   PLoS One

Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

(2011) Cynthia L. Montana et al.   Jove-Journal of Visualized Experiments

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing

(2010) Hane Lee et al.   BMC GENOMICS

Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites

(2010) J Lee et al.   GENE THERAPY

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

(2010) J. C. Corbo et al.   GENOME RESEARCH

Transfection Techniques for Neuronal Cells

(2010) D. Karra et al.   JOURNAL OF NEUROSCIENCE

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait

(2010) Alan F. Wright et al.   NATURE REVIEWS GENETICS

Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina

(2010) Anand Swaroop et al.   NATURE REVIEWS NEUROSCIENCE

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Effect of Genome Size on AAV Vector Packaging

(2009) Zhijian Wu et al.   MOLECULAR THERAPY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Gene Therapy Using Adeno-Associated Virus Vectors

(2008) S. Daya et al.   CLINICAL MICROBIOLOGY REVIEWS

Adeno-Associated Virus Vector Genomes Persist as Episomal Chromatin in Primate Muscle

(2008) M. Penaud-Budloo et al.   JOURNAL OF VIROLOGY

Ascl1 (Mash1) lineage cells contribute to discrete cell populations in CNS architecture

(2008) Euiseok J. Kim et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Self-complementary AAV Vectors; Advances and Applications

(2008) Douglas M McCarty   MOLECULAR THERAPY

Analysis of AAV Serotypes 1–9 Mediated Gene Expression and Tropism in Mice After Systemic Injection

(2008) Carmela Zincarelli et al.   MOLECULAR THERAPY

Next generation of adeno-associated virus 2 vectors: Point mutations in tyrosines lead to high-efficiency transduction at lower doses

(2008) L. Zhong 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