Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons

Long non-coding RNA repertoire and open chromatin regions constitute midbrain dopaminergic neuron - specific molecular signatures

(2019) J. Gendron et al.   Scientific Reports

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

(2019) Mike A Nalls et al.   LANCET NEUROLOGY

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

Parkinson's disease genetic risk in a midbrain neuronal cell line

(2018) Steven E. Pierce et al.   NEUROBIOLOGY OF DISEASE

Gene Therapy for Parkinson’s Disease, An Update

(2018) Tobias M. Axelsen et al.   Journal of Parkinsons Disease

Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency

(2018) Kenjiro Adachi et al.   Cell Stem Cell

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Hoxa9 and EGFP reporter expression in human Embryonic Stem Cells (hESC) as useful tools for studying human development

(2017) Joan Domingo-Reines et al.   Stem Cell Research

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury

(2017) Raquel Cuevas-Diaz Duran et al.   Scientific Reports

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Semaphorin 3C Released from a Biocompatible Hydrogel Guides and Promotes Axonal Growth of Rodent and Human Dopaminergic Neurons

(2016) Oscar A. Carballo-Molina et al.   TISSUE ENGINEERING PART A

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

(2015) Michael W. Linhoff et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

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

(2012) A. Natarajan et al.   GENOME RESEARCH

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

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A practical guide to evaluating colocalization in biological microscopy

(2011) Kenneth W. Dunn et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Lmx1a and Lmx1b Function Cooperatively to Regulate Proliferation, Specification, and Differentiation of Midbrain Dopaminergic Progenitors

(2011) C. H. Yan et al.   JOURNAL OF NEUROSCIENCE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson’s disease

(2011) Sonja Kriks et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin

(2010) Thomas Treiber et al.   IMMUNITY

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

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Pathogenesis of familial Parkinson’s disease: new insights based on monogenic forms of Parkinson’s disease

(2009) Taku Hatano et al.   JOURNAL OF NEUROCHEMISTRY

Expression Profiling of Nuclear Receptors in Human and Mouse Embryonic Stem Cells

(2009) Chang-Qing Xie et al.   MOLECULAR ENDOCRINOLOGY

MicroRNA-mediated switching of chromatin-remodelling complexes in neural development

(2009) Andrew S. Yoo et al.   NATURE

Chd1 regulates open chromatin and pluripotency of embryonic stem cells

(2009) Alexandre Gaspar-Maia et al.   NATURE

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

(2009) Bo Feng et al.   NATURE CELL BIOLOGY

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY