Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1

Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation

(2017) Svetlana Petruk et al.   MOLECULAR CELL

A UTX-MLL4-p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription

(2017) Shu-Ping Wang et al.   MOLECULAR CELL

Physiological functions of programmed DNA breaks in signal-induced transcription

(2017) Janusz Puc et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis

(2017) Issam Aldiri et al.   NEURON

UTX-guided neural crest function underlies craniofacial features of Kabuki syndrome

(2017) Karl B. Shpargel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

(2016) Pei-Chi Wei et al.   CELL

53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms

(2016) Raquel Cuella-Martin et al.   MOLECULAR CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

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

Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells

(2016) Bjoern Schwer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Transcriptional elongation requires DNA break-induced signalling

(2015) Heeyoun Bunch et al.   Nature Communications

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

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

(2014) S. Anders et al.   BIOINFORMATICS

JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

(2014) Xusheng Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Generation of cerebral organoids from human pluripotent stem cells

(2014) Madeline A Lancaster et al.   Nature Protocols

Activation of Neuronal Gene Expression by the JMJD3 Demethylase Is Required for Postnatal and Adult Brain Neurogenesis

(2014) Dae Hwi Park et al.   Cell Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Double-strand break repair: 53BP1 comes into focus

(2013) Stephanie Panier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Neural Stem Cells: Generating and Regenerating the Brain

(2013) Fred H. Gage et al.   NEURON

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex

(2013) T. Kadoshima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

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

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Histone Demethylase UTX and Chromatin Remodeler BRM Bind Directly to CBP and Modulate Acetylation of Histone H3 Lysine 27

(2012) F. Tie et al.   MOLECULAR AND CELLULAR BIOLOGY

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity

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

X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner

(2012) G. G. Welstead et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global identification of MLL2-targeted loci reveals MLL2's role in diverse signaling pathways

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

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

The C. elegans H3K27 Demethylase UTX-1 Is Essential for Normal Development, Independent of Its Enzymatic Activity

(2012) Julien Vandamme et al.   PLoS Genetics

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Jmjd3 and UTX Play a Demethylase-Independent Role in Chromatin Remodeling to Regulate T-Box Family Member-Dependent Gene Expression

(2010) Sara A. Miller et al.   MOLECULAR CELL

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq

(2008) Yong Zhang et al.   BMC GENOMICS

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

The Histone H3 Lysine 27-Specific Demethylase Jmjd3 Is Required for Neural Commitment

(2008) Thomas Burgold et al.   PLoS One