Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

(2015) Nicolas Léveillé et al.   Nature Communications

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

(2014) S. Anders et al.   BIOINFORMATICS

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation

(2014) S. Rashi-Elkeles et al.   Science Signaling

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho et al.   NATURE BIOTECHNOLOGY

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Distinct p53 genomic binding patterns in normal and cancer-derived human cells

(2012) Krassimira Botcheva et al.   CELL CYCLE

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

p53 mutations in cancer

(2012) Patricia A. J. Muller et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Can predictive biomarkers in breast cancer guide adjuvant endocrine therapy?

(2012) Karin Beelen et al.   Nature Reviews Clinical Oncology

A public genome-scale lentiviral expression library of human ORFs

(2011) Xiaoping Yang et al.   NATURE METHODS

Vigilance and Validation: Keys to Success in RNAi Screening

(2010) Frederic D. Sigoillot et al.   ACS Chemical Biology

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

BRD7 is a candidate tumour suppressor gene required for p53 function

(2010) Jarno Drost et al.   NATURE CELL BIOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Characterization of genome-wide p53-binding sites upon stress response

(2008) Leonie Smeenk et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY